diff --git a/annotation/src/main/resources/applicationContext-annotation.xml b/annotation/src/main/resources/applicationContext-annotation.xml
index 98f2dfa11b16fdfdadf6b00de1e573903206e7d9..8d26b7a2b64972c73d6972a21d2f223b55c0f295 100644
--- a/annotation/src/main/resources/applicationContext-annotation.xml
+++ b/annotation/src/main/resources/applicationContext-annotation.xml
@@ -1,46 +1,46 @@
-<beans xmlns="http://www.springframework.org/schema/beans"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:tx="http://www.springframework.org/schema/tx"
- xmlns:context="http://www.springframework.org/schema/context"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans-4.0.xsd
- http://www.springframework.org/schema/tx
- http://www.springframework.org/schema/tx/spring-tx-4.0.xsd
- http://www.springframework.org/schema/context
- http://www.springframework.org/schema/context/spring-context.xsd">
-
-
- <!-- Annotation services -->
-
- <!-- Annotators -->
- <bean id="BiocompendiumAnnotator" class="lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator"/>
- <bean id="ChebiAnnotator" class="lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator"/>
- <bean id="EnsemblAnnotator" class="lcsb.mapviewer.annotation.services.annotators.EnsemblAnnotator"/>
- <bean id="EntrezAnnotator" class="lcsb.mapviewer.annotation.services.annotators.EntrezAnnotator"/>
- <bean id="GoAnnotator" class="lcsb.mapviewer.annotation.services.annotators.GoAnnotator"/>
- <bean id="HgncAnnotator" class="lcsb.mapviewer.annotation.services.annotators.HgncAnnotator"/>
- <bean id="ReconAnnotator" class="lcsb.mapviewer.annotation.services.annotators.ReconAnnotator"/>
- <bean id="UniprotAnnotator" class="lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator"/>
-
- <bean id="ChEMBLParser" class="lcsb.mapviewer.annotation.services.ChEMBLParser"/>
- <bean id="ChemicalParser" class="lcsb.mapviewer.annotation.services.ChemicalParser"/>
- <bean id="DrugbankHTMLParser" class="lcsb.mapviewer.annotation.services.DrugbankHTMLParser"/>
- <bean id="MiriamConnector" class="lcsb.mapviewer.annotation.services.MiriamConnector"/>
- <bean id="ModelAnnotator" class="lcsb.mapviewer.annotation.services.ModelAnnotator"/>
- <bean id="MeSHParser" class="lcsb.mapviewer.annotation.services.MeSHParser"/>
- <bean id="PubmedParser" class="lcsb.mapviewer.annotation.services.PubmedParser"/>
- <bean id="TaxonomyBackend" class="lcsb.mapviewer.annotation.services.TaxonomyBackend"/>
- <bean id="MiRNAParser" class="lcsb.mapviewer.annotation.services.MiRNAParser"/>
-
- <!-- Reference Genome services -->
-
- <bean id="UcscReferenceGenomeConnector" class="lcsb.mapviewer.annotation.services.genome.UcscReferenceGenomeConnector"/>
-
- <!-- Cache services -->
-
- <bean id="GeneralCache" class="lcsb.mapviewer.annotation.cache.GeneralCache"/>
- <bean id="PermanentDatabaseLevelCache" class="lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache"/>
- <bean id="BigFileCache" class="lcsb.mapviewer.annotation.cache.BigFileCache"/>
-
-
+<beans xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:tx="http://www.springframework.org/schema/tx"
+ xmlns:context="http://www.springframework.org/schema/context"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-4.0.xsd
+ http://www.springframework.org/schema/tx
+ http://www.springframework.org/schema/tx/spring-tx-4.0.xsd
+ http://www.springframework.org/schema/context
+ http://www.springframework.org/schema/context/spring-context.xsd">
+
+
+ <!-- Annotation services -->
+
+ <!-- Annotators -->
+ <bean id="BiocompendiumAnnotator" class="lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator"/>
+ <bean id="ChebiAnnotator" class="lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator"/>
+ <bean id="EnsemblAnnotator" class="lcsb.mapviewer.annotation.services.annotators.EnsemblAnnotator"/>
+ <bean id="EntrezAnnotator" class="lcsb.mapviewer.annotation.services.annotators.EntrezAnnotator"/>
+ <bean id="GoAnnotator" class="lcsb.mapviewer.annotation.services.annotators.GoAnnotator"/>
+ <bean id="HgncAnnotator" class="lcsb.mapviewer.annotation.services.annotators.HgncAnnotator"/>
+ <bean id="ReconAnnotator" class="lcsb.mapviewer.annotation.services.annotators.ReconAnnotator"/>
+ <bean id="UniprotAnnotator" class="lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator"/>
+
+ <bean id="ChEMBLParser" class="lcsb.mapviewer.annotation.services.ChEMBLParser"/>
+ <bean id="ChemicalParser" class="lcsb.mapviewer.annotation.services.ChemicalParser"/>
+ <bean id="DrugbankHTMLParser" class="lcsb.mapviewer.annotation.services.DrugbankHTMLParser"/>
+ <bean id="MiriamConnector" class="lcsb.mapviewer.annotation.services.MiriamConnector"/>
+ <bean id="ModelAnnotator" class="lcsb.mapviewer.annotation.services.ModelAnnotator"/>
+ <bean id="MeSHParser" class="lcsb.mapviewer.annotation.services.MeSHParser"/>
+ <bean id="PubmedParser" class="lcsb.mapviewer.annotation.services.PubmedParser"/>
+ <bean id="TaxonomyBackend" class="lcsb.mapviewer.annotation.services.TaxonomyBackend"/>
+ <bean id="MiRNAParser" class="lcsb.mapviewer.annotation.services.MiRNAParser"/>
+
+ <!-- Reference Genome services -->
+
+ <bean id="UcscReferenceGenomeConnector" class="lcsb.mapviewer.annotation.services.genome.UcscReferenceGenomeConnector"/>
+
+ <!-- Cache services -->
+
+ <bean id="GeneralCache" class="lcsb.mapviewer.annotation.cache.GeneralCache"/>
+ <bean id="PermanentDatabaseLevelCache" class="lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache"/>
+ <bean id="BigFileCache" class="lcsb.mapviewer.annotation.cache.BigFileCache"/>
+
+
</beans>
\ No newline at end of file
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java
index 4a05c389f60b7d6bf921fe336758e4bb0242712d..f14e65dd4ed3067674b4c3030db665d3a174f83f 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java
@@ -1,18 +1,18 @@
-package lcsb.mapviewer.annotation;
-
-import lcsb.mapviewer.annotation.cache.AllCacheTests;
-import lcsb.mapviewer.annotation.data.AllDataTests;
-import lcsb.mapviewer.annotation.services.AllServicesTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllCacheTests.class, //
- AllDataTests.class, //
- AllServicesTests.class, //
-})
-
-public class AllAnnotationTests {
-}
+package lcsb.mapviewer.annotation;
+
+import lcsb.mapviewer.annotation.cache.AllCacheTests;
+import lcsb.mapviewer.annotation.data.AllDataTests;
+import lcsb.mapviewer.annotation.services.AllServicesTests;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllCacheTests.class, //
+ AllDataTests.class, //
+ AllServicesTests.class, //
+})
+
+public class AllAnnotationTests {
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
index 829ed417edf2fb9a3cf6ad32dab426968630a623..2064bb94437eab2e04d2d4805c98833e8e6d50f4 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
@@ -1,297 +1,297 @@
-package lcsb.mapviewer.annotation;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.io.UnsupportedEncodingException;
-import java.net.HttpURLConnection;
-import java.net.URL;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.test.annotation.Rollback;
-import org.springframework.test.context.ContextConfiguration;
-import org.springframework.test.context.junit4.AbstractTransactionalJUnit4SpringContextTests;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-import org.springframework.transaction.annotation.Transactional;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-
-import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
-
-@Transactional(value = "txManager")
-@Rollback(false)
-@ContextConfiguration(locations = { //
- "/applicationContext-annotation.xml", //
- "/applicationContext-persist.xml", //
- "/test-applicationContext.xml", //
-})
-@RunWith(SpringJUnit4ClassRunner.class)
-public abstract class AnnotationTestFunctions extends AbstractTransactionalJUnit4SpringContextTests {
-
- @Autowired
- protected PermanentDatabaseLevelCacheInterface cache;
-
- @Autowired
- protected CacheTypeDao cacheTypeDao;
-
- @Autowired
- protected DbUtils dbUtils;
-
- private Logger logger = Logger.getLogger(AnnotationTestFunctions.class);
-
- private EventStorageLoggerAppender appender;
-
- @Before
- public final void _setUp() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- appender = new EventStorageLoggerAppender(false);
- Logger.getRootLogger().addAppender(appender);
- }
-
- @After
- public final void _tearDown() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- }
-
- protected List<LoggingEvent> getWarnings() {
- return appender.getWarnings();
- }
-
- protected List<LoggingEvent> getErrors() {
- return appender.getErrors();
- }
-
- protected List<LoggingEvent> getFatals() {
- return appender.getFatals();
- }
-
- protected String readFile(String file) throws IOException {
- StringBuilder stringBuilder = new StringBuilder();
- BufferedReader reader = new BufferedReader(new FileReader(file));
- try {
- String line = null;
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- } finally {
- reader.close();
- }
-
- return stringBuilder.toString();
- }
-
- protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
- }
-
- protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
- File file = new File(fileName);
- InputStream inputStream = new FileInputStream(file);
- Reader reader = null;
- try {
- reader = new InputStreamReader(inputStream, "UTF-8");
- InputSource is = new InputSource(reader);
-
- Document result = getXmlDocumentFromInputSource(is);
- inputStream.close();
- return result;
- } catch (UnsupportedEncodingException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-
- protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
- DocumentBuilder db;
- try {
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser");
- }
- Document doc = null;
- try {
- doc = db.parse(stream);
- } catch (SAXException e) {
- logger.error(e);
- } catch (IOException e) {
- logger.error(e);
- }
- return doc;
- }
-
- private static Map<String, Model> models = new HashMap<String, Model>();
-
- protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
- if (!fromCache) {
- logger.debug("File without cache: " + fileName);
- return new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
- }
- Model result = AnnotationTestFunctions.models.get(fileName);
- if (result == null) {
- logger.debug("File to cache: " + fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
- AnnotationTestFunctions.models.put(fileName, result);
- }
- return result;
- }
-
- protected String createTmpFileName() {
- try {
- File f = File.createTempFile("prefix", ".txt");
- String filename = f.getName();
- f.delete();
- return filename;
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
-
- protected String nodeToString(Node node) {
- return nodeToString(node, false);
- }
-
- protected String nodeToString(Node node, boolean includeHeadNode) {
- if (node == null)
- return null;
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
-
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
-
- protected boolean equalFiles(String fileA, String fileB) throws IOException {
- int BLOCK_SIZE = 65536;
- FileInputStream inputStreamA = new FileInputStream(fileA);
- FileInputStream inputStreamB = new FileInputStream(fileB);
- // vary BLOCK_SIZE to suit yourself.
- // it should probably a factor or multiple of the size of a disk
- // sector/cluster.
- // Note that your max heap size may need to be adjused
- // if you have a very big block size or lots of these comparators.
-
- // assume inputStreamA and inputStreamB are streams from your two files.
- byte[] streamABlock = new byte[BLOCK_SIZE];
- byte[] streamBBlock = new byte[BLOCK_SIZE];
- boolean match = true;
- int bytesReadA = 0;
- int bytesReadB = 0;
- do {
- bytesReadA = inputStreamA.read(streamABlock);
- bytesReadB = inputStreamB.read(streamBBlock);
- match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
- } while (match && (bytesReadA > -1));
- inputStreamA.close();
- inputStreamB.close();
- return match;
- }
-
- public File createTempDirectory() throws IOException {
- final File temp;
-
- temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
-
- if (!(temp.delete())) {
- throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
- }
-
- if (!(temp.mkdir())) {
- throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
- }
-
- return (temp);
- }
-
- protected String getWebpage(String accessUrl) throws IOException {
- String inputLine;
- IOException exception = null;
- for (int i = 0; i < 3; i++) {
- try {
- StringBuilder tmp = new StringBuilder();
- URL url = new URL(accessUrl);
- HttpURLConnection urlConn = (HttpURLConnection) url.openConnection();
- urlConn.setRequestMethod("GET");
- urlConn.connect();
- BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
-
- while ((inputLine = in.readLine()) != null) {
- tmp.append(inputLine);
- }
- in.close();
- return tmp.toString();
- } catch (IOException e) {
- exception = e;
- }
- }
- throw exception;
- }
-
- protected void waitForRefreshCacheQueueToEmpty() throws InterruptedException {
- while (cache.refreshIsBusy()) {
- logger.debug(
- "Waiting for refresh queue to empty. " + cache.getRefreshPendingQueueSize() + " pending. " + cache.getRefreshExecutingTasksSize()
- + " tasks are executed.");
- Thread.sleep(300);
- }
- }
-
-}
+package lcsb.mapviewer.annotation;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.io.UnsupportedEncodingException;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.AbstractTransactionalJUnit4SpringContextTests;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.transaction.annotation.Transactional;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
+
+@Transactional(value = "txManager")
+@Rollback(false)
+@ContextConfiguration(locations = { //
+ "/applicationContext-annotation.xml", //
+ "/applicationContext-persist.xml", //
+ "/test-applicationContext.xml", //
+})
+@RunWith(SpringJUnit4ClassRunner.class)
+public abstract class AnnotationTestFunctions extends AbstractTransactionalJUnit4SpringContextTests {
+
+ @Autowired
+ protected PermanentDatabaseLevelCacheInterface cache;
+
+ @Autowired
+ protected CacheTypeDao cacheTypeDao;
+
+ @Autowired
+ protected DbUtils dbUtils;
+
+ private Logger logger = Logger.getLogger(AnnotationTestFunctions.class);
+
+ private EventStorageLoggerAppender appender;
+
+ @Before
+ public final void _setUp() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ appender = new EventStorageLoggerAppender(false);
+ Logger.getRootLogger().addAppender(appender);
+ }
+
+ @After
+ public final void _tearDown() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+
+ protected List<LoggingEvent> getWarnings() {
+ return appender.getWarnings();
+ }
+
+ protected List<LoggingEvent> getErrors() {
+ return appender.getErrors();
+ }
+
+ protected List<LoggingEvent> getFatals() {
+ return appender.getFatals();
+ }
+
+ protected String readFile(String file) throws IOException {
+ StringBuilder stringBuilder = new StringBuilder();
+ BufferedReader reader = new BufferedReader(new FileReader(file));
+ try {
+ String line = null;
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ } finally {
+ reader.close();
+ }
+
+ return stringBuilder.toString();
+ }
+
+ protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
+ InputSource is = new InputSource();
+ is.setCharacterStream(new StringReader(text));
+ return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
+ }
+
+ protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
+ File file = new File(fileName);
+ InputStream inputStream = new FileInputStream(file);
+ Reader reader = null;
+ try {
+ reader = new InputStreamReader(inputStream, "UTF-8");
+ InputSource is = new InputSource(reader);
+
+ Document result = getXmlDocumentFromInputSource(is);
+ inputStream.close();
+ return result;
+ } catch (UnsupportedEncodingException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
+ DocumentBuilder db;
+ try {
+ db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser");
+ }
+ Document doc = null;
+ try {
+ doc = db.parse(stream);
+ } catch (SAXException e) {
+ logger.error(e);
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ return doc;
+ }
+
+ private static Map<String, Model> models = new HashMap<String, Model>();
+
+ protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
+ if (!fromCache) {
+ logger.debug("File without cache: " + fileName);
+ return new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
+ }
+ Model result = AnnotationTestFunctions.models.get(fileName);
+ if (result == null) {
+ logger.debug("File to cache: " + fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
+ AnnotationTestFunctions.models.put(fileName, result);
+ }
+ return result;
+ }
+
+ protected String createTmpFileName() {
+ try {
+ File f = File.createTempFile("prefix", ".txt");
+ String filename = f.getName();
+ f.delete();
+ return filename;
+ } catch (IOException e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
+
+ protected String nodeToString(Node node) {
+ return nodeToString(node, false);
+ }
+
+ protected String nodeToString(Node node, boolean includeHeadNode) {
+ if (node == null)
+ return null;
+ StringWriter sw = new StringWriter();
+ try {
+ Transformer t = TransformerFactory.newInstance().newTransformer();
+ t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ t.setOutputProperty(OutputKeys.INDENT, "yes");
+ t.setOutputProperty(OutputKeys.METHOD, "xml");
+
+ NodeList list = node.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node element = list.item(i);
+ t.transform(new DOMSource(element), new StreamResult(sw));
+ }
+ } catch (TransformerException te) {
+ logger.debug("nodeToString Transformer Exception");
+ }
+ if (includeHeadNode) {
+ return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+ }
+ return sw.toString();
+ }
+
+ protected boolean equalFiles(String fileA, String fileB) throws IOException {
+ int BLOCK_SIZE = 65536;
+ FileInputStream inputStreamA = new FileInputStream(fileA);
+ FileInputStream inputStreamB = new FileInputStream(fileB);
+ // vary BLOCK_SIZE to suit yourself.
+ // it should probably a factor or multiple of the size of a disk
+ // sector/cluster.
+ // Note that your max heap size may need to be adjused
+ // if you have a very big block size or lots of these comparators.
+
+ // assume inputStreamA and inputStreamB are streams from your two files.
+ byte[] streamABlock = new byte[BLOCK_SIZE];
+ byte[] streamBBlock = new byte[BLOCK_SIZE];
+ boolean match = true;
+ int bytesReadA = 0;
+ int bytesReadB = 0;
+ do {
+ bytesReadA = inputStreamA.read(streamABlock);
+ bytesReadB = inputStreamB.read(streamBBlock);
+ match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
+ } while (match && (bytesReadA > -1));
+ inputStreamA.close();
+ inputStreamB.close();
+ return match;
+ }
+
+ public File createTempDirectory() throws IOException {
+ final File temp;
+
+ temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
+
+ if (!(temp.delete())) {
+ throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
+ }
+
+ if (!(temp.mkdir())) {
+ throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
+ }
+
+ return (temp);
+ }
+
+ protected String getWebpage(String accessUrl) throws IOException {
+ String inputLine;
+ IOException exception = null;
+ for (int i = 0; i < 3; i++) {
+ try {
+ StringBuilder tmp = new StringBuilder();
+ URL url = new URL(accessUrl);
+ HttpURLConnection urlConn = (HttpURLConnection) url.openConnection();
+ urlConn.setRequestMethod("GET");
+ urlConn.connect();
+ BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
+
+ while ((inputLine = in.readLine()) != null) {
+ tmp.append(inputLine);
+ }
+ in.close();
+ return tmp.toString();
+ } catch (IOException e) {
+ exception = e;
+ }
+ }
+ throw exception;
+ }
+
+ protected void waitForRefreshCacheQueueToEmpty() throws InterruptedException {
+ while (cache.refreshIsBusy()) {
+ logger.debug(
+ "Waiting for refresh queue to empty. " + cache.getRefreshPendingQueueSize() + " pending. " + cache.getRefreshExecutingTasksSize()
+ + " tasks are executed.");
+ Thread.sleep(300);
+ }
+ }
+
+}
diff --git a/annotation/src/test/resources/log4j.properties b/annotation/src/test/resources/log4j.properties
index e550f09e6024552efd54a1b953c6608f18d0a115..473855faa6b70690575e254c92710b3c8e06fe32 100644
--- a/annotation/src/test/resources/log4j.properties
+++ b/annotation/src/test/resources/log4j.properties
@@ -1,23 +1,23 @@
-#Set root logger 's level and its appender to an appender called CONSOLE which is defined below.
-log4j.rootLogger=info, CONSOLE
-
-#Set the behavior of the CONSOLE appender
-log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
-log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
-log4j.appender.CONSOLE.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
-#log4j.appender.CONSOLE.layout.ConversionPattern=%m%n
-
-
-#Set the behavior of the FILE appender
-log4j.appender.R=org.apache.log4j.FileAppender
-log4j.appender.R.File=${catalina.home}/logs/MapViewer.log
-log4j.appender.R.layout=org.apache.log4j.PatternLayout
-log4j.appender.R.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
-
-
-log4j.logger.org.springframework=warn
-log4j.logger.org.hibernate=warn
-log4j.logger.lcsb=debug
-log4j.logger.lcsb.mapviewer.persist.DbUtils=info
-log4j.logger.lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache=info
+#Set root logger 's level and its appender to an appender called CONSOLE which is defined below.
+log4j.rootLogger=info, CONSOLE
+
+#Set the behavior of the CONSOLE appender
+log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
+log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
+log4j.appender.CONSOLE.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
+#log4j.appender.CONSOLE.layout.ConversionPattern=%m%n
+
+
+#Set the behavior of the FILE appender
+log4j.appender.R=org.apache.log4j.FileAppender
+log4j.appender.R.File=${catalina.home}/logs/MapViewer.log
+log4j.appender.R.layout=org.apache.log4j.PatternLayout
+log4j.appender.R.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
+
+
+log4j.logger.org.springframework=warn
+log4j.logger.org.hibernate=warn
+log4j.logger.lcsb=debug
+log4j.logger.lcsb.mapviewer.persist.DbUtils=info
+log4j.logger.lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache=info
log4j.logger.lcsb.mapviewer.annotation.cache.CachableInterface=info
\ No newline at end of file
diff --git a/annotation/src/test/resources/test-applicationContext.xml b/annotation/src/test/resources/test-applicationContext.xml
index cf221aca42024acd75dd281a0ae6dd47300d8c17..47dc97e5d9d6e44597f34645f8cacfc05eaa9002 100644
--- a/annotation/src/test/resources/test-applicationContext.xml
+++ b/annotation/src/test/resources/test-applicationContext.xml
@@ -1,17 +1,17 @@
-<beans xmlns="http://www.springframework.org/schema/beans"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:tx="http://www.springframework.org/schema/tx"
- xmlns:context="http://www.springframework.org/schema/context"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans-4.0.xsd
- http://www.springframework.org/schema/tx
- http://www.springframework.org/schema/tx/spring-tx-4.0.xsd
- http://www.springframework.org/schema/context
- http://www.springframework.org/schema/context/spring-context-4.0.xsd">
-
- <!-- Testing Password Encoder used for hashing passwords -->
- <bean id="PasswordEncoder" class="org.springframework.security.crypto.password.NoOpPasswordEncoder"/>
-
- <bean id="MockCacheInterface" class="lcsb.mapviewer.annotation.cache.MockCacheInterface"/>
-
-</beans>
+<beans xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:tx="http://www.springframework.org/schema/tx"
+ xmlns:context="http://www.springframework.org/schema/context"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-4.0.xsd
+ http://www.springframework.org/schema/tx
+ http://www.springframework.org/schema/tx/spring-tx-4.0.xsd
+ http://www.springframework.org/schema/context
+ http://www.springframework.org/schema/context/spring-context-4.0.xsd">
+
+ <!-- Testing Password Encoder used for hashing passwords -->
+ <bean id="PasswordEncoder" class="org.springframework.security.crypto.password.NoOpPasswordEncoder"/>
+
+ <bean id="MockCacheInterface" class="lcsb.mapviewer.annotation.cache.MockCacheInterface"/>
+
+</beans>
diff --git a/commons/src/main/java/lcsb/mapviewer/common/EventStorageLoggerAppender.java b/commons/src/main/java/lcsb/mapviewer/common/EventStorageLoggerAppender.java
index 705c545a5dd1db3c6c43223bbbbaa15fd4450d03..402e0437f505d75c6b34b3c0f00daf4462228aa9 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/EventStorageLoggerAppender.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/EventStorageLoggerAppender.java
@@ -1,140 +1,140 @@
-package lcsb.mapviewer.common;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Appender;
-import org.apache.log4j.AppenderSkeleton;
-import org.apache.log4j.Level;
-import org.apache.log4j.lf5.LogLevel;
-import org.apache.log4j.spi.LoggingEvent;
-
-/**
- * Custom log4j {@link Appender}. This class is used to store logs in the
- * memory. Such logs should be stored for short period of time. Only logs for
- * the {@link Thread} that created the object will be stored.
- *
- * @author Piotr Gawron
- *
- */
-public class EventStorageLoggerAppender extends AppenderSkeleton {
-
- /**
- * List of {@link LogLevel#DEBUG} logs.
- */
- private List<LoggingEvent> debugEvents = new ArrayList<>();
-
- /**
- * List of {@link LogLevel#INFO} logs.
- */
- private List<LoggingEvent> infoEvents = new ArrayList<>();
-
- /**
- * List of {@link LogLevel#WARN} logs.
- */
- private List<LoggingEvent> warnEvents = new ArrayList<>();
-
- /**
- * List of {@link LogLevel#ERROR} logs.
- */
- private List<LoggingEvent> errorEvents = new ArrayList<>();
-
- /**
- * List of {@link LogLevel#FATAL} logs.
- */
- private List<LoggingEvent> fatalEvents = new ArrayList<>();
-
- /**
- * List of logs with unknown log level.
- */
- private List<LoggingEvent> otherEvents = new ArrayList<>();
-
- /**
- * Identifier of {@link Thread} that created this object.
- */
- private long threadId;
-
- /**
- * Flag that describe if we log only entries for current thread (
- * <code>true</code>) or for all threads (<code>false</code>).
- */
- private boolean currentThreadLogOnly = true;
-
- /**
- * Default constructor.
- */
- public EventStorageLoggerAppender() {
- this(true);
- }
-
- /**
- * Default constructor.
- *
- * @param currentThreadLogOnly
- * if <code>true</code> logs should be taken only from thread that
- * created object, if <code>false</code> all logs will be stored
- */
- public EventStorageLoggerAppender(boolean currentThreadLogOnly) {
- this.threadId = Thread.currentThread().getId();
- this.currentThreadLogOnly = currentThreadLogOnly;
- }
-
- @Override
- protected void append(LoggingEvent event) {
-
- // store information for all thread only if it is flagged by
- // currentThreadLogOnly, if not only logs from current thread should be
- // stored
- if (!currentThreadLogOnly || threadId == Thread.currentThread().getId()) {
- if (event.getLevel().equals(Level.DEBUG)) {
- debugEvents.add(event);
- } else if (event.getLevel().equals(Level.INFO)) {
- infoEvents.add(event);
- } else if (event.getLevel().equals(Level.WARN)) {
- warnEvents.add(event);
- } else if (event.getLevel().equals(Level.ERROR)) {
- errorEvents.add(event);
- } else if (event.getLevel().equals(Level.FATAL)) {
- fatalEvents.add(event);
- } else {
- otherEvents.add(event);
- }
- }
- }
-
- @Override
- public void close() {
- }
-
- @Override
- public boolean requiresLayout() {
- return false;
- }
-
- /**
- * Returns list of warning logs.
- *
- * @return list of warning logs
- */
- public List<LoggingEvent> getWarnings() {
- return warnEvents;
- }
-
- /**
- * Returns list of error logs.
- *
- * @return list of error logs
- */
- public List<LoggingEvent> getErrors() {
- return errorEvents;
- }
-
- /**
- * Returns list of fatal logs.
- *
- * @return list of fatal logs
- */
- public List<LoggingEvent> getFatals() {
- return fatalEvents;
- }
-}
+package lcsb.mapviewer.common;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Appender;
+import org.apache.log4j.AppenderSkeleton;
+import org.apache.log4j.Level;
+import org.apache.log4j.lf5.LogLevel;
+import org.apache.log4j.spi.LoggingEvent;
+
+/**
+ * Custom log4j {@link Appender}. This class is used to store logs in the
+ * memory. Such logs should be stored for short period of time. Only logs for
+ * the {@link Thread} that created the object will be stored.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class EventStorageLoggerAppender extends AppenderSkeleton {
+
+ /**
+ * List of {@link LogLevel#DEBUG} logs.
+ */
+ private List<LoggingEvent> debugEvents = new ArrayList<>();
+
+ /**
+ * List of {@link LogLevel#INFO} logs.
+ */
+ private List<LoggingEvent> infoEvents = new ArrayList<>();
+
+ /**
+ * List of {@link LogLevel#WARN} logs.
+ */
+ private List<LoggingEvent> warnEvents = new ArrayList<>();
+
+ /**
+ * List of {@link LogLevel#ERROR} logs.
+ */
+ private List<LoggingEvent> errorEvents = new ArrayList<>();
+
+ /**
+ * List of {@link LogLevel#FATAL} logs.
+ */
+ private List<LoggingEvent> fatalEvents = new ArrayList<>();
+
+ /**
+ * List of logs with unknown log level.
+ */
+ private List<LoggingEvent> otherEvents = new ArrayList<>();
+
+ /**
+ * Identifier of {@link Thread} that created this object.
+ */
+ private long threadId;
+
+ /**
+ * Flag that describe if we log only entries for current thread (
+ * <code>true</code>) or for all threads (<code>false</code>).
+ */
+ private boolean currentThreadLogOnly = true;
+
+ /**
+ * Default constructor.
+ */
+ public EventStorageLoggerAppender() {
+ this(true);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param currentThreadLogOnly
+ * if <code>true</code> logs should be taken only from thread that
+ * created object, if <code>false</code> all logs will be stored
+ */
+ public EventStorageLoggerAppender(boolean currentThreadLogOnly) {
+ this.threadId = Thread.currentThread().getId();
+ this.currentThreadLogOnly = currentThreadLogOnly;
+ }
+
+ @Override
+ protected void append(LoggingEvent event) {
+
+ // store information for all thread only if it is flagged by
+ // currentThreadLogOnly, if not only logs from current thread should be
+ // stored
+ if (!currentThreadLogOnly || threadId == Thread.currentThread().getId()) {
+ if (event.getLevel().equals(Level.DEBUG)) {
+ debugEvents.add(event);
+ } else if (event.getLevel().equals(Level.INFO)) {
+ infoEvents.add(event);
+ } else if (event.getLevel().equals(Level.WARN)) {
+ warnEvents.add(event);
+ } else if (event.getLevel().equals(Level.ERROR)) {
+ errorEvents.add(event);
+ } else if (event.getLevel().equals(Level.FATAL)) {
+ fatalEvents.add(event);
+ } else {
+ otherEvents.add(event);
+ }
+ }
+ }
+
+ @Override
+ public void close() {
+ }
+
+ @Override
+ public boolean requiresLayout() {
+ return false;
+ }
+
+ /**
+ * Returns list of warning logs.
+ *
+ * @return list of warning logs
+ */
+ public List<LoggingEvent> getWarnings() {
+ return warnEvents;
+ }
+
+ /**
+ * Returns list of error logs.
+ *
+ * @return list of error logs
+ */
+ public List<LoggingEvent> getErrors() {
+ return errorEvents;
+ }
+
+ /**
+ * Returns list of fatal logs.
+ *
+ * @return list of fatal logs
+ */
+ public List<LoggingEvent> getFatals() {
+ return fatalEvents;
+ }
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java b/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java
index 78ed3bbf2c1582c47a2400d9c2a35bb5547ff5ff..8d5f0c432268a4361c6614a87b4276e07bf43a85 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java
@@ -1,20 +1,20 @@
-package lcsb.mapviewer.common;
-
-/**
- * Defines type of http connection method.
- *
- * @author Piotr Gawron
- *
- */
-public enum HttpConnectionMethodType {
-
- /**
- * GET method.
- */
- GET, //
-
- /**
- * POST method.
- */
- POST;
-}
+package lcsb.mapviewer.common;
+
+/**
+ * Defines type of http connection method.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum HttpConnectionMethodType {
+
+ /**
+ * GET method.
+ */
+ GET, //
+
+ /**
+ * POST method.
+ */
+ POST;
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/MimeType.java b/commons/src/main/java/lcsb/mapviewer/common/MimeType.java
index c52311b48e7d52f04018dc2b5f7030bd7e0685de..54c7c29e1bb62b8b1ed56bfcc502b6833dc7acd2 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/MimeType.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/MimeType.java
@@ -1,86 +1,86 @@
-package lcsb.mapviewer.common;
-
-/**
- * Mime content types of data used in the system. If there is publically
- * available class with all posible types then we should use it, but I couldn't
- * quickly find it. For the full list see <a
- * href="http://www.iana.org/assignments/media-types/media-types.xhtml">IANA
- * MIME media types list</a>
- *
- * @author Piotr Gawron
- *
- */
-public enum MimeType {
- /**
- * SBML type of file.
- */
- SBML("application/sbml+xml"), //
-
- /**
- * Standard text file.
- */
- TEXT("text/plain"), //
-
- /**
- * Standard XML file.
- */
- XML("application/xml"),
-
- /**
- * <a href="http://www.w3.org/TR/SVG11/mimereg.html">SVG</a> file type.
- */
- SVG("image/svg+xml"),
-
- /**
- * JPG image file type.
- */
- JPG("image/jpeg"),
-
- /**
- * PNG image file type.
- */
- PNG("image/png"),
-
- /**
- * PDF files (see <a href="http://www.rfc-editor.org/rfc/rfc3778.txt"> RFC
- * 3778, The application/pdf Media Type</a>).
- */
- PDF("application/pdf"), //
-
- /**
- * CSS files.
- */
- CSS("text/css"), //
-
- /**
- * Javascript files.
- */
- JS("text/javascript"),
-
- /**
- * Zip files.
- */
- ZIP("application/zip"); //
-
- /**
- * String representation of the MIME content.
- */
- private String textRepresentation;
-
- /**
- * Default constructor with string definition.
- *
- * @param textRepresentation
- * text representation for MIME type
- */
- MimeType(String textRepresentation) {
- this.textRepresentation = textRepresentation;
- }
-
- /**
- * @return the textRepresentation
- */
- public String getTextRepresentation() {
- return textRepresentation;
- }
-}
+package lcsb.mapviewer.common;
+
+/**
+ * Mime content types of data used in the system. If there is publically
+ * available class with all posible types then we should use it, but I couldn't
+ * quickly find it. For the full list see <a
+ * href="http://www.iana.org/assignments/media-types/media-types.xhtml">IANA
+ * MIME media types list</a>
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum MimeType {
+ /**
+ * SBML type of file.
+ */
+ SBML("application/sbml+xml"), //
+
+ /**
+ * Standard text file.
+ */
+ TEXT("text/plain"), //
+
+ /**
+ * Standard XML file.
+ */
+ XML("application/xml"),
+
+ /**
+ * <a href="http://www.w3.org/TR/SVG11/mimereg.html">SVG</a> file type.
+ */
+ SVG("image/svg+xml"),
+
+ /**
+ * JPG image file type.
+ */
+ JPG("image/jpeg"),
+
+ /**
+ * PNG image file type.
+ */
+ PNG("image/png"),
+
+ /**
+ * PDF files (see <a href="http://www.rfc-editor.org/rfc/rfc3778.txt"> RFC
+ * 3778, The application/pdf Media Type</a>).
+ */
+ PDF("application/pdf"), //
+
+ /**
+ * CSS files.
+ */
+ CSS("text/css"), //
+
+ /**
+ * Javascript files.
+ */
+ JS("text/javascript"),
+
+ /**
+ * Zip files.
+ */
+ ZIP("application/zip"); //
+
+ /**
+ * String representation of the MIME content.
+ */
+ private String textRepresentation;
+
+ /**
+ * Default constructor with string definition.
+ *
+ * @param textRepresentation
+ * text representation for MIME type
+ */
+ MimeType(String textRepresentation) {
+ this.textRepresentation = textRepresentation;
+ }
+
+ /**
+ * @return the textRepresentation
+ */
+ public String getTextRepresentation() {
+ return textRepresentation;
+ }
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java b/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java
index b5fd056b5e761d01b7161ed501910f69580a87b1..145a9790da73157efaef02c1876029f79059c410 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java
@@ -1,52 +1,52 @@
-package lcsb.mapviewer.common;
-
-import java.lang.reflect.Method;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-/**
- * Util class that performs primitive operations on the object.
- *
- * @author Piotr Gawron
- *
- */
-public final class ObjectUtils {
-
- /**
- * Default constructor. Prevents instatiation.
- */
- private ObjectUtils() {
- }
-
- /**
- * Returns object identifier. It assumes that object contains getId method
- * that returns Integer.
- *
- * @param object
- * object for which identifier is looked for
- * @return object identifier
- */
- public static Integer getIdOfObject(Object object) {
- Integer id = (Integer) getParamByGetter(object, "getId");
- return id;
- }
-
- /**
- * Returns object param using string getter function.
- *
- * @param object
- * object from which parameter will be taken
- * @param getterName
- * string with name of the getter function
- * @return object field
- */
- public static Object getParamByGetter(Object object, String getterName) {
- try {
- Method method = object.getClass().getMethod(getterName);
- Object result = method.invoke(object);
- return result;
- } catch (Exception e) {
- throw new InvalidArgumentException(e.getMessage());
- }
- }
-}
+package lcsb.mapviewer.common;
+
+import java.lang.reflect.Method;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+/**
+ * Util class that performs primitive operations on the object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class ObjectUtils {
+
+ /**
+ * Default constructor. Prevents instatiation.
+ */
+ private ObjectUtils() {
+ }
+
+ /**
+ * Returns object identifier. It assumes that object contains getId method
+ * that returns Integer.
+ *
+ * @param object
+ * object for which identifier is looked for
+ * @return object identifier
+ */
+ public static Integer getIdOfObject(Object object) {
+ Integer id = (Integer) getParamByGetter(object, "getId");
+ return id;
+ }
+
+ /**
+ * Returns object param using string getter function.
+ *
+ * @param object
+ * object from which parameter will be taken
+ * @param getterName
+ * string with name of the getter function
+ * @return object field
+ */
+ public static Object getParamByGetter(Object object, String getterName) {
+ try {
+ Method method = object.getClass().getMethod(getterName);
+ Object result = method.invoke(object);
+ return result;
+ } catch (Exception e) {
+ throw new InvalidArgumentException(e.getMessage());
+ }
+ }
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/Pair.java b/commons/src/main/java/lcsb/mapviewer/common/Pair.java
index 32fb0263a83cd1cdbc7600571f20b16d807f996e..8d8573c0c476b086bb7943b02de6c397b4896c85 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/Pair.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/Pair.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.common;
-
-import java.io.Serializable;
-
-/**
- * Represents pair of two objects. It's immutable as long as param classes are
- * immutable.
- *
- * @author Piotr Gawron
- *
- * @param <L>
- * class type of the first object
- * @param <R>
- * class type of the second object
- */
-public class Pair<L, R> implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * First object.
- */
- private final L left;
-
- /**
- * Second object.
- */
- private final R right;
-
- /**
- * Default constructor.
- *
- * @param left
- * {@link #left}
- * @param right
- * {@link #right}
- */
- public Pair(L left, R right) {
- this.left = left;
- this.right = right;
- }
-
- /**
- *
- * @return {@link #left}
- */
- public L getLeft() {
- return left;
- }
-
- /**
- *
- * @return {@link #right}
- */
- public R getRight() {
- return right;
- }
-
- @Override
- public int hashCode() {
- return left.hashCode() ^ right.hashCode();
- }
-
- @Override
- public boolean equals(Object o) {
- if (o == null) {
- return false;
- }
- if (!(o instanceof Pair)) {
- return false;
- }
- Pair<?, ?> pairo = (Pair<?, ?>) o;
- return this.left.equals(pairo.getLeft()) && this.right.equals(pairo.getRight());
- }
-
- @Override
- public String toString() {
- return "Pair: " + getLeft().toString() + ", " + getRight().toString();
- }
-
+package lcsb.mapviewer.common;
+
+import java.io.Serializable;
+
+/**
+ * Represents pair of two objects. It's immutable as long as param classes are
+ * immutable.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <L>
+ * class type of the first object
+ * @param <R>
+ * class type of the second object
+ */
+public class Pair<L, R> implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * First object.
+ */
+ private final L left;
+
+ /**
+ * Second object.
+ */
+ private final R right;
+
+ /**
+ * Default constructor.
+ *
+ * @param left
+ * {@link #left}
+ * @param right
+ * {@link #right}
+ */
+ public Pair(L left, R right) {
+ this.left = left;
+ this.right = right;
+ }
+
+ /**
+ *
+ * @return {@link #left}
+ */
+ public L getLeft() {
+ return left;
+ }
+
+ /**
+ *
+ * @return {@link #right}
+ */
+ public R getRight() {
+ return right;
+ }
+
+ @Override
+ public int hashCode() {
+ return left.hashCode() ^ right.hashCode();
+ }
+
+ @Override
+ public boolean equals(Object o) {
+ if (o == null) {
+ return false;
+ }
+ if (!(o instanceof Pair)) {
+ return false;
+ }
+ Pair<?, ?> pairo = (Pair<?, ?>) o;
+ return this.left.equals(pairo.getLeft()) && this.right.equals(pairo.getRight());
+ }
+
+ @Override
+ public String toString() {
+ return "Pair: " + getLeft().toString() + ", " + getRight().toString();
+ }
+
}
\ No newline at end of file
diff --git a/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java b/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java
index f69c4c2cb6aa07fd21e67d33a30435d3cdedc096..16585aa4ef4f142ee7ef218c7d8e1e90a91af443 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java
@@ -1,63 +1,63 @@
-package lcsb.mapviewer.common;
-
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.ClipboardOwner;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class allowing access to system clipboard.
- *
- * @author Piotr Gawron
- *
- */
-public class SystemClipboard implements ClipboardOwner {
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(SystemClipboard.class);
-
- @Override
- public void lostOwnership(Clipboard clipboard, Transferable contents) {
- }
-
- /**
- * Place a String on the clipboard, and make this class the owner of the
- * Clipboard's contents.
- *
- * @param aString
- * what we want to put into clipboard
- */
- public void setClipboardContents(String aString) {
- StringSelection stringSelection = new StringSelection(aString);
- Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
- clipboard.setContents(stringSelection, this);
- }
-
- /**
- * Get the String residing on the clipboard.
- *
- * @return any text found on the Clipboard; if none found, return an empty
- * String.
- */
- public String getClipboardContents() {
- String result = null;
- Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
- // odd: the Object param of getContents is not currently used
- Transferable contents = clipboard.getContents(null);
- boolean hasTransferableText = contents.isDataFlavorSupported(DataFlavor.stringFlavor);
- if (hasTransferableText) {
- try {
- result = (String) contents.getTransferData(DataFlavor.stringFlavor);
- } catch (Exception ex) {
- logger.error(ex, ex);
- }
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.common;
+
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.ClipboardOwner;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class allowing access to system clipboard.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SystemClipboard implements ClipboardOwner {
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(SystemClipboard.class);
+
+ @Override
+ public void lostOwnership(Clipboard clipboard, Transferable contents) {
+ }
+
+ /**
+ * Place a String on the clipboard, and make this class the owner of the
+ * Clipboard's contents.
+ *
+ * @param aString
+ * what we want to put into clipboard
+ */
+ public void setClipboardContents(String aString) {
+ StringSelection stringSelection = new StringSelection(aString);
+ Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+ clipboard.setContents(stringSelection, this);
+ }
+
+ /**
+ * Get the String residing on the clipboard.
+ *
+ * @return any text found on the Clipboard; if none found, return an empty
+ * String.
+ */
+ public String getClipboardContents() {
+ String result = null;
+ Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+ // odd: the Object param of getContents is not currently used
+ Transferable contents = clipboard.getContents(null);
+ boolean hasTransferableText = contents.isDataFlavorSupported(DataFlavor.stringFlavor);
+ if (hasTransferableText) {
+ try {
+ result = (String) contents.getTransferData(DataFlavor.stringFlavor);
+ } catch (Exception ex) {
+ logger.error(ex, ex);
+ }
+ }
+ return result;
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java b/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
index 6ae08f616915e7fcab010fb42a2d4636daee2c1c..12d74903987973302b398f8702dd6a5ba104cb6f 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
@@ -1,56 +1,56 @@
-package lcsb.mapviewer.common;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.HashMap;
-import java.util.Map;
-
-/**
- * Class with util function to operate on text files.
- *
- * @author Piotr Gawron
- *
- */
-public final class TextFileUtils {
-
- /**
- * Default constructor that prevents instatiation.
- */
- private TextFileUtils() {
-
- }
-
- /**
- * Parses input stream to get parameters from header. {@link InputStream}
- * should be a text file. Header parameters are lines at the beginning of the
- * file starting with '#' character.
- *
- * @param is
- * input stream for a file to process
- * @return map with paramteres parsed from input stream
- * @throws IOException
- * thrown when there is a problem with accessing input stream
- */
- public static Map<String, String> getHeaderParametersFromFile(InputStream is) throws IOException {
- Map<String, String> result = new HashMap<String, String>();
- BufferedReader in = new BufferedReader(new InputStreamReader(is));
- String line = null;
- while ((line = in.readLine()) != null) {
- if (line.startsWith("#")) {
- String tmp = line.substring(1);
- if (tmp.indexOf("=") > 0) {
- String key = tmp.substring(0, tmp.indexOf("=")).trim();
- String value = tmp.substring(tmp.indexOf("=") + 1).trim();
- result.put(key, value);
- }
- } else {
- break;
- }
- }
- is.close();
- return result;
- }
-
-}
+package lcsb.mapviewer.common;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Class with util function to operate on text files.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class TextFileUtils {
+
+ /**
+ * Default constructor that prevents instatiation.
+ */
+ private TextFileUtils() {
+
+ }
+
+ /**
+ * Parses input stream to get parameters from header. {@link InputStream}
+ * should be a text file. Header parameters are lines at the beginning of the
+ * file starting with '#' character.
+ *
+ * @param is
+ * input stream for a file to process
+ * @return map with paramteres parsed from input stream
+ * @throws IOException
+ * thrown when there is a problem with accessing input stream
+ */
+ public static Map<String, String> getHeaderParametersFromFile(InputStream is) throws IOException {
+ Map<String, String> result = new HashMap<String, String>();
+ BufferedReader in = new BufferedReader(new InputStreamReader(is));
+ String line = null;
+ while ((line = in.readLine()) != null) {
+ if (line.startsWith("#")) {
+ String tmp = line.substring(1);
+ if (tmp.indexOf("=") > 0) {
+ String key = tmp.substring(0, tmp.indexOf("=")).trim();
+ String value = tmp.substring(tmp.indexOf("=") + 1).trim();
+ result.put(key, value);
+ }
+ } else {
+ break;
+ }
+ }
+ is.close();
+ return result;
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
index 82797927119b7c04f7e9e39767460eb6cd8537f5..0f0530880c2579459a31ce4729ed8ddf943dad6d 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
@@ -1,357 +1,357 @@
-package lcsb.mapviewer.common;
-
-import java.awt.Color;
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringEscapeUtils;
-import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
-import org.w3c.dom.NamedNodeMap;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-
-/**
- * Abstract class with methods which help in parsing xml using DOM.
- *
- * @author Piotr Gawron
- *
- */
-public class XmlParser {
- /**
- * Base of the hex representation.
- */
- private static final int HEX_BASE = 16;
-
- /**
- * {@link DocumentBuilderFactory} used to create {@link DocumentBuilder}
- * objects that will manipulate xml nodes.
- */
- private static DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(XmlParser.class.getName());
-
- /**
- * DOM document builder used for xml transformations.
- */
- private DocumentBuilder db;
-
- /**
- * Default constructor that prevents from instatiation of the class and
- * initializes fields.
- */
- protected XmlParser() {
- try {
- db = documentBuilderFactory.newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidStateException("Problem with xml parser");
- }
-
- }
-
- /**
- * Method returns the node of xml nodelist 'nodes' with 'tagName' name. If
- * node could not be found then null is returned.
- *
- * @param tagName
- * name of node to look for
- * @param nodes
- * list of nodes
- * @return node from nodes list with the tagName name, <b>null</b> if such
- * node doesn't exist
- */
- protected Node getNode(final String tagName, final NodeList nodes) {
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase(tagName)) {
- return node;
- }
- }
- }
- return null;
- }
-
- /**
- * Method returns the child node of xml 'parentNode' with 'tagName' name. If
- * node could not be found then null is returned.
- *
- * @param tagName
- * name of node to look for
- * @param parentNode
- * parent node
- * @return node from nodes list with the tagName name, <b>null</b> if such
- * node doesn't exist
- */
- protected Node getNode(final String tagName, final Node parentNode) {
- return getNode(tagName, parentNode.getChildNodes());
- }
-
- /**
- * Method returns list of nodes with 'tagName' name. If node could not be
- * found then empty list is returned.
- *
- * @param tagName
- * name of node to look for
- * @param nodes
- * list of input nodes
- * @return list of nodes with 'tagName' name
- */
- protected List<Node> getNodes(final String tagName, final NodeList nodes) {
- List<Node> result = new ArrayList<Node>();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeName().equalsIgnoreCase(tagName)) {
- result.add(node);
- }
- }
- return result;
- }
-
- /**
- * Method returns the value of node attribute. If attribute could not be found
- * then "" is returned.
- *
- * @param attrName
- * name of the attribute to look for
- * @param node
- * a node
- * @return the value of node attribute, empty string("") if attribute doesn't
- * exist
- */
- protected String getNodeAttr(final String attrName, final Node node) {
- NamedNodeMap attrs = node.getAttributes();
- for (int y = 0; y < attrs.getLength(); y++) {
- Node attr = attrs.item(y);
- if (attr.getNodeName().equalsIgnoreCase(attrName)) {
- return attr.getNodeValue();
- }
- }
- return "";
- }
-
- /**
- * Method returns the text value of node. If text could not be found then ""
- * is returned.
- *
- * @param node
- * a node
- * @return the text value of node or empty string ("") if the text could be
- * found.
- */
- protected String getNodeValue(final Node node) {
- if (node == null) {
- return "";
- }
- NodeList childNodes = node.getChildNodes();
- for (int x = 0; x < childNodes.getLength(); x++) {
- Node data = childNodes.item(x);
- if (data.getNodeType() == Node.TEXT_NODE) {
- return data.getNodeValue();
- }
- }
- return "";
- }
-
- /**
- * Method returns the xml Document from input source given as a parameter.
- *
- * @param stream
- * input stream with xml document
- * @return Document node for the input stream
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- protected Document getXmlDocumentFromInputSource(final InputSource stream) throws InvalidXmlSchemaException {
- try {
- return db.parse(stream);
- } catch (SAXException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser", e);
- } catch (IOException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser", e);
- }
- }
-
- /**
- * Method returns the xml Document from text given as a source.
- *
- * @param text
- * string representing xml document
- * @return Document for the xml document given in the input
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- protected Document getXmlDocumentFromString(final String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is);
- }
-
- /**
- * Transforms node into string xml format.
- *
- * @param node
- * node that should be transformed into xml string
- * @return string representation of the xml node
- */
- protected String nodeToString(final Node node) {
- return nodeToString(node, false);
- }
-
- /**
- * Transforms node into string xml format.
- *
- * @param node
- * node that should be transformed into xml string
- * @param includeHeadNode
- * should the top level node exist in the output
- * @return string representation of the xml node
- */
- protected String nodeToString(final Node node, final boolean includeHeadNode) {
- if (node == null) {
- return null;
- }
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
-
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
-
- /**
- * This method transform color encoded in string (CellDesigner format) into
- * Color.
- *
- * @param color
- * string representing color
- * @return Color object for the fiven string
- */
- protected Color stringToColor(final String color) {
- try {
- String alpha = color.substring(0, 2);
- Color tmp = new Color(hexToInteger(color.substring(2)));
- return new Color(tmp.getRed(), tmp.getGreen(), tmp.getBlue(), hexToInteger(alpha));
- } catch (Exception e) {
- throw new InvalidArgumentException("Invalid color string: " + color);
- }
- }
-
- /**
- * Transforms hex string into Integer.
- *
- * @param hexString
- * string representation in hex base
- * @return Integer value of the hex string
- */
- private Integer hexToInteger(String hexString) {
- return Integer.valueOf(hexString, HEX_BASE);
- }
-
- /**
- * Transforms Color object into string representing this color in RGB.
- *
- * @param color
- * color that should be converted into string
- * @return hex string representation of the color
- */
- protected String colorToString(final Color color) {
- return String.format("%08X", color.getRGB());
- }
-
- /**
- * Method that reads file and transforms it into a string.
- *
- * @param fileName
- * path to a file
- * @return string containing data from the file (default coding is used)
- * @throws IOException
- * thrown when there are some problems with a file
- */
- protected String fileToString(final String fileName) throws IOException {
- BufferedReader reader = new BufferedReader(new FileReader(fileName));
- String line = null;
- StringBuilder stringBuilder = new StringBuilder();
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- reader.close();
-
- return stringBuilder.toString();
- }
-
- /**
- * Method that reads all data from inputstream and transform it into a string.
- * UTF-8 coding is used.
- *
- * @param inputStream
- * stream from which we read data
- * @return string representing all data from input stream
- * @throws IOException
- * thrown if there are some problems with input stream
- */
- protected String inputStreamToString(final InputStream inputStream) throws IOException {
- StringWriter writer = new StringWriter();
- IOUtils.copy(inputStream, writer, "UTF-8");
- String result = writer.toString();
- return result;
- }
-
- /**
- * Method that encode string into a string that can be used in xml file.
- *
- * @param string
- * string to be escaped
- * @return escaped string, ready to be used in xml
- */
- protected String escapeXml(final String string) {
- if (string == null) {
- return null;
- }
- // quite expensive
- return StringEscapeUtils.escapeXml(string).replaceAll("\n", " ").replace("\r", " ");
- }
-
-}
+package lcsb.mapviewer.common;
+
+import java.awt.Color;
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringEscapeUtils;
+import org.apache.log4j.Logger;
+import org.w3c.dom.Document;
+import org.w3c.dom.NamedNodeMap;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+
+/**
+ * Abstract class with methods which help in parsing xml using DOM.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class XmlParser {
+ /**
+ * Base of the hex representation.
+ */
+ private static final int HEX_BASE = 16;
+
+ /**
+ * {@link DocumentBuilderFactory} used to create {@link DocumentBuilder}
+ * objects that will manipulate xml nodes.
+ */
+ private static DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(XmlParser.class.getName());
+
+ /**
+ * DOM document builder used for xml transformations.
+ */
+ private DocumentBuilder db;
+
+ /**
+ * Default constructor that prevents from instatiation of the class and
+ * initializes fields.
+ */
+ protected XmlParser() {
+ try {
+ db = documentBuilderFactory.newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ throw new InvalidStateException("Problem with xml parser");
+ }
+
+ }
+
+ /**
+ * Method returns the node of xml nodelist 'nodes' with 'tagName' name. If
+ * node could not be found then null is returned.
+ *
+ * @param tagName
+ * name of node to look for
+ * @param nodes
+ * list of nodes
+ * @return node from nodes list with the tagName name, <b>null</b> if such
+ * node doesn't exist
+ */
+ protected Node getNode(final String tagName, final NodeList nodes) {
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase(tagName)) {
+ return node;
+ }
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Method returns the child node of xml 'parentNode' with 'tagName' name. If
+ * node could not be found then null is returned.
+ *
+ * @param tagName
+ * name of node to look for
+ * @param parentNode
+ * parent node
+ * @return node from nodes list with the tagName name, <b>null</b> if such
+ * node doesn't exist
+ */
+ protected Node getNode(final String tagName, final Node parentNode) {
+ return getNode(tagName, parentNode.getChildNodes());
+ }
+
+ /**
+ * Method returns list of nodes with 'tagName' name. If node could not be
+ * found then empty list is returned.
+ *
+ * @param tagName
+ * name of node to look for
+ * @param nodes
+ * list of input nodes
+ * @return list of nodes with 'tagName' name
+ */
+ protected List<Node> getNodes(final String tagName, final NodeList nodes) {
+ List<Node> result = new ArrayList<Node>();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeName().equalsIgnoreCase(tagName)) {
+ result.add(node);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Method returns the value of node attribute. If attribute could not be found
+ * then "" is returned.
+ *
+ * @param attrName
+ * name of the attribute to look for
+ * @param node
+ * a node
+ * @return the value of node attribute, empty string("") if attribute doesn't
+ * exist
+ */
+ protected String getNodeAttr(final String attrName, final Node node) {
+ NamedNodeMap attrs = node.getAttributes();
+ for (int y = 0; y < attrs.getLength(); y++) {
+ Node attr = attrs.item(y);
+ if (attr.getNodeName().equalsIgnoreCase(attrName)) {
+ return attr.getNodeValue();
+ }
+ }
+ return "";
+ }
+
+ /**
+ * Method returns the text value of node. If text could not be found then ""
+ * is returned.
+ *
+ * @param node
+ * a node
+ * @return the text value of node or empty string ("") if the text could be
+ * found.
+ */
+ protected String getNodeValue(final Node node) {
+ if (node == null) {
+ return "";
+ }
+ NodeList childNodes = node.getChildNodes();
+ for (int x = 0; x < childNodes.getLength(); x++) {
+ Node data = childNodes.item(x);
+ if (data.getNodeType() == Node.TEXT_NODE) {
+ return data.getNodeValue();
+ }
+ }
+ return "";
+ }
+
+ /**
+ * Method returns the xml Document from input source given as a parameter.
+ *
+ * @param stream
+ * input stream with xml document
+ * @return Document node for the input stream
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ protected Document getXmlDocumentFromInputSource(final InputSource stream) throws InvalidXmlSchemaException {
+ try {
+ return db.parse(stream);
+ } catch (SAXException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser", e);
+ } catch (IOException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser", e);
+ }
+ }
+
+ /**
+ * Method returns the xml Document from text given as a source.
+ *
+ * @param text
+ * string representing xml document
+ * @return Document for the xml document given in the input
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ protected Document getXmlDocumentFromString(final String text) throws InvalidXmlSchemaException {
+ InputSource is = new InputSource();
+ is.setCharacterStream(new StringReader(text));
+ return getXmlDocumentFromInputSource(is);
+ }
+
+ /**
+ * Transforms node into string xml format.
+ *
+ * @param node
+ * node that should be transformed into xml string
+ * @return string representation of the xml node
+ */
+ protected String nodeToString(final Node node) {
+ return nodeToString(node, false);
+ }
+
+ /**
+ * Transforms node into string xml format.
+ *
+ * @param node
+ * node that should be transformed into xml string
+ * @param includeHeadNode
+ * should the top level node exist in the output
+ * @return string representation of the xml node
+ */
+ protected String nodeToString(final Node node, final boolean includeHeadNode) {
+ if (node == null) {
+ return null;
+ }
+ StringWriter sw = new StringWriter();
+ try {
+ Transformer t = TransformerFactory.newInstance().newTransformer();
+ t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ t.setOutputProperty(OutputKeys.INDENT, "yes");
+ t.setOutputProperty(OutputKeys.METHOD, "xml");
+
+ NodeList list = node.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node element = list.item(i);
+ t.transform(new DOMSource(element), new StreamResult(sw));
+ }
+ } catch (TransformerException te) {
+ logger.debug("nodeToString Transformer Exception");
+ }
+ if (includeHeadNode) {
+ return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+ }
+ return sw.toString();
+ }
+
+ /**
+ * This method transform color encoded in string (CellDesigner format) into
+ * Color.
+ *
+ * @param color
+ * string representing color
+ * @return Color object for the fiven string
+ */
+ protected Color stringToColor(final String color) {
+ try {
+ String alpha = color.substring(0, 2);
+ Color tmp = new Color(hexToInteger(color.substring(2)));
+ return new Color(tmp.getRed(), tmp.getGreen(), tmp.getBlue(), hexToInteger(alpha));
+ } catch (Exception e) {
+ throw new InvalidArgumentException("Invalid color string: " + color);
+ }
+ }
+
+ /**
+ * Transforms hex string into Integer.
+ *
+ * @param hexString
+ * string representation in hex base
+ * @return Integer value of the hex string
+ */
+ private Integer hexToInteger(String hexString) {
+ return Integer.valueOf(hexString, HEX_BASE);
+ }
+
+ /**
+ * Transforms Color object into string representing this color in RGB.
+ *
+ * @param color
+ * color that should be converted into string
+ * @return hex string representation of the color
+ */
+ protected String colorToString(final Color color) {
+ return String.format("%08X", color.getRGB());
+ }
+
+ /**
+ * Method that reads file and transforms it into a string.
+ *
+ * @param fileName
+ * path to a file
+ * @return string containing data from the file (default coding is used)
+ * @throws IOException
+ * thrown when there are some problems with a file
+ */
+ protected String fileToString(final String fileName) throws IOException {
+ BufferedReader reader = new BufferedReader(new FileReader(fileName));
+ String line = null;
+ StringBuilder stringBuilder = new StringBuilder();
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ reader.close();
+
+ return stringBuilder.toString();
+ }
+
+ /**
+ * Method that reads all data from inputstream and transform it into a string.
+ * UTF-8 coding is used.
+ *
+ * @param inputStream
+ * stream from which we read data
+ * @return string representing all data from input stream
+ * @throws IOException
+ * thrown if there are some problems with input stream
+ */
+ protected String inputStreamToString(final InputStream inputStream) throws IOException {
+ StringWriter writer = new StringWriter();
+ IOUtils.copy(inputStream, writer, "UTF-8");
+ String result = writer.toString();
+ return result;
+ }
+
+ /**
+ * Method that encode string into a string that can be used in xml file.
+ *
+ * @param string
+ * string to be escaped
+ * @return escaped string, ready to be used in xml
+ */
+ protected String escapeXml(final String string) {
+ if (string == null) {
+ return null;
+ }
+ // quite expensive
+ return StringEscapeUtils.escapeXml(string).replaceAll("\n", " ").replace("\r", " ");
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java b/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
index 8c28d0023086b0d7bd1c5ddd7411f715ac573f4a..561bc13f4a6559a40c55e197cb7153dc7adfbcbe 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.common;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.common.comparator.AllComparatorTests;
-import lcsb.mapviewer.common.exception.AllExceptionTests;
-import lcsb.mapviewer.common.geometry.AllGeometryTests;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllComparatorTests.class, //
- AllExceptionTests.class, //
- AllGeometryTests.class, //
- ConfigurationTest.class, //
- EventStorageLoggerAppenderTest.class, //
- HttpConnectionMethodTypeTest.class, //
- MimeTypeTest.class, //
- ObjectUtilsTest.class, //
- PairTest.class, //
- SystemClipboardTest.class, //
- TextFileUtilsTest.class, //
- XmlParserTest.class, //
-})
-public class AllCommonTests {
-
-}
+package lcsb.mapviewer.common;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.common.comparator.AllComparatorTests;
+import lcsb.mapviewer.common.exception.AllExceptionTests;
+import lcsb.mapviewer.common.geometry.AllGeometryTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllComparatorTests.class, //
+ AllExceptionTests.class, //
+ AllGeometryTests.class, //
+ ConfigurationTest.class, //
+ EventStorageLoggerAppenderTest.class, //
+ HttpConnectionMethodTypeTest.class, //
+ MimeTypeTest.class, //
+ ObjectUtilsTest.class, //
+ PairTest.class, //
+ SystemClipboardTest.class, //
+ TextFileUtilsTest.class, //
+ XmlParserTest.class, //
+})
+public class AllCommonTests {
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/EventStorageLoggerAppenderTest.java b/commons/src/test/java/lcsb/mapviewer/common/EventStorageLoggerAppenderTest.java
index 94a339ade89d259461e6c5cdd0643f2797189746..9816f4b8aab08b9416ace661da88ea4b95fc72bb 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/EventStorageLoggerAppenderTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/EventStorageLoggerAppenderTest.java
@@ -1,58 +1,58 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class EventStorageLoggerAppenderTest {
- Logger logger = Logger.getLogger(EventStorageLoggerAppenderTest.class);
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testLogCatching() {
- try {
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- logger.addAppender(appender);
- logger.warn("test");
- logger.debug("1");
- logger.error("2");
- logger.info("3");
- logger.fatal("4");
- assertEquals(1, appender.getWarnings().size());
- logger.removeAppender(appender);
- logger.warn("test");
- assertEquals(1, appender.getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- appender.requiresLayout();
- appender.close();
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class EventStorageLoggerAppenderTest {
+ Logger logger = Logger.getLogger(EventStorageLoggerAppenderTest.class);
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testLogCatching() {
+ try {
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ logger.addAppender(appender);
+ logger.warn("test");
+ logger.debug("1");
+ logger.error("2");
+ logger.info("3");
+ logger.fatal("4");
+ assertEquals(1, appender.getWarnings().size());
+ logger.removeAppender(appender);
+ logger.warn("test");
+ assertEquals(1, appender.getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ appender.requiresLayout();
+ appender.close();
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/HttpConnectionMethodTypeTest.java b/commons/src/test/java/lcsb/mapviewer/common/HttpConnectionMethodTypeTest.java
index 2723073007567a139b4f430431eefbe5345d136d..9789b766e90765c181cda689521e5dcf13761b13 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/HttpConnectionMethodTypeTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/HttpConnectionMethodTypeTest.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class HttpConnectionMethodTypeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (HttpConnectionMethodType type : HttpConnectionMethodType.values()) {
- assertNotNull(type);
-
- // for coverage tests
- HttpConnectionMethodType.valueOf(type.toString());
- }
- }
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class HttpConnectionMethodTypeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (HttpConnectionMethodType type : HttpConnectionMethodType.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ HttpConnectionMethodType.valueOf(type.toString());
+ }
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java b/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java
index 50189c2ae3e701fdd09db1327aebb5531a13440c..9087471b074a6c1add706e3f1c7a3d6173f71334 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java
@@ -1,32 +1,32 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class MimeTypeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (MimeType type : MimeType.values()) {
- assertNotNull(type);
- assertNotNull(type.getTextRepresentation());
- assertFalse(type.getTextRepresentation().isEmpty());
-
- //for coverage tests
- MimeType.valueOf(type.toString());
- }
- }
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class MimeTypeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (MimeType type : MimeType.values()) {
+ assertNotNull(type);
+ assertNotNull(type.getTextRepresentation());
+ assertFalse(type.getTextRepresentation().isEmpty());
+
+ //for coverage tests
+ MimeType.valueOf(type.toString());
+ }
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/ObjectUtilsTest.java b/commons/src/test/java/lcsb/mapviewer/common/ObjectUtilsTest.java
index ff8b79effc9a6a3d43d3f3d886865f4664e8d23a..71ee157432a239e4e6027b9226274ca4f294abb2 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/ObjectUtilsTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/ObjectUtilsTest.java
@@ -1,58 +1,58 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.lang.reflect.Constructor;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-public class ObjectUtilsTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetIdOfObject() {
- Object obj = new Object() {
- @SuppressWarnings("unused")
- public int getId() {
- return 107;
- }
- };
- assertEquals((Integer) 107, ObjectUtils.getIdOfObject(obj));
- }
-
- @Test
- public void testGetIdOfObjectWithoutId() {
- Object obj = new Object();
- try {
- ObjectUtils.getIdOfObject(obj);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
- }
-
- @Test
- public void testPrivateConstructor() throws Exception {
- try {
- Constructor<?> constr = ObjectUtils.class.getDeclaredConstructor(new Class<?>[] {});
- constr.setAccessible(true);
- assertNotNull(constr.newInstance(new Object[] {}));
- } catch (Exception e) {
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.lang.reflect.Constructor;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+public class ObjectUtilsTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetIdOfObject() {
+ Object obj = new Object() {
+ @SuppressWarnings("unused")
+ public int getId() {
+ return 107;
+ }
+ };
+ assertEquals((Integer) 107, ObjectUtils.getIdOfObject(obj));
+ }
+
+ @Test
+ public void testGetIdOfObjectWithoutId() {
+ Object obj = new Object();
+ try {
+ ObjectUtils.getIdOfObject(obj);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+ }
+
+ @Test
+ public void testPrivateConstructor() throws Exception {
+ try {
+ Constructor<?> constr = ObjectUtils.class.getDeclaredConstructor(new Class<?>[] {});
+ constr.setAccessible(true);
+ assertNotNull(constr.newInstance(new Object[] {}));
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/PairTest.java b/commons/src/test/java/lcsb/mapviewer/common/PairTest.java
index 33178d5e6abde5b5bed736f29567bc26f3cfd10c..286787b3f276391b3d8c37a3432fa262827b8824 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/PairTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/PairTest.java
@@ -1,70 +1,70 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class PairTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() {
- Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
- assertEquals("test str", pair.getLeft());
- assertEquals((Integer) 12, pair.getRight());
- }
-
- @Test
- public void testEquals() {
- Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
- Pair<String, Integer> pair2 = new Pair<String, Integer>("test str", 12);
- Pair<String, String> pair3 = new Pair<String, String>("test str", "str");
- Pair<String, Integer> pair4 = new Pair<String, Integer>("test str", 124);
- Pair<String, Integer> pair5 = new Pair<String, Integer>("test str1", 12);
- assertTrue(pair.equals(pair2));
- assertFalse(pair.equals(pair3));
- assertFalse(pair.equals(pair4));
- assertFalse(pair.equals(pair5));
-
- assertTrue(pair2.equals(pair));
- assertFalse(pair3.equals(pair));
- assertFalse(pair4.equals(pair));
- assertFalse(pair5.equals(pair));
- assertFalse(pair4.equals(new Object()));
- }
-
- @Test
- public void testHashCode() {
- Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
- Pair<String, Integer> pair2 = new Pair<String, Integer>("test str", 12);
- Pair<String, Integer> pair3 = new Pair<String, Integer>("test str", 124);
- assertEquals(pair.hashCode(), pair2.hashCode());
- assertTrue(pair.hashCode() != pair3.hashCode());
- }
-
- @Test
- public void testNullEquals() {
- Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
- Pair<String, Integer> pair2 = null;
- assertFalse(pair.equals(pair2));
- }
-
- @Test
- public void testToString() {
- Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
- assertTrue(pair.toString().contains(pair.getLeft().toString()));
- assertTrue(pair.toString().contains(pair.getRight().toString()));
- }
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class PairTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() {
+ Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
+ assertEquals("test str", pair.getLeft());
+ assertEquals((Integer) 12, pair.getRight());
+ }
+
+ @Test
+ public void testEquals() {
+ Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
+ Pair<String, Integer> pair2 = new Pair<String, Integer>("test str", 12);
+ Pair<String, String> pair3 = new Pair<String, String>("test str", "str");
+ Pair<String, Integer> pair4 = new Pair<String, Integer>("test str", 124);
+ Pair<String, Integer> pair5 = new Pair<String, Integer>("test str1", 12);
+ assertTrue(pair.equals(pair2));
+ assertFalse(pair.equals(pair3));
+ assertFalse(pair.equals(pair4));
+ assertFalse(pair.equals(pair5));
+
+ assertTrue(pair2.equals(pair));
+ assertFalse(pair3.equals(pair));
+ assertFalse(pair4.equals(pair));
+ assertFalse(pair5.equals(pair));
+ assertFalse(pair4.equals(new Object()));
+ }
+
+ @Test
+ public void testHashCode() {
+ Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
+ Pair<String, Integer> pair2 = new Pair<String, Integer>("test str", 12);
+ Pair<String, Integer> pair3 = new Pair<String, Integer>("test str", 124);
+ assertEquals(pair.hashCode(), pair2.hashCode());
+ assertTrue(pair.hashCode() != pair3.hashCode());
+ }
+
+ @Test
+ public void testNullEquals() {
+ Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
+ Pair<String, Integer> pair2 = null;
+ assertFalse(pair.equals(pair2));
+ }
+
+ @Test
+ public void testToString() {
+ Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
+ assertTrue(pair.toString().contains(pair.getLeft().toString()));
+ assertTrue(pair.toString().contains(pair.getRight().toString()));
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java b/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java
index 88ba17059b9e2a6fd06cfd679dcf7e2e1f837aab..604262c4cfb9c4837aa6fe338a1d362d99c080dd 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java
@@ -1,98 +1,98 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.Transferable;
-import java.awt.datatransfer.UnsupportedFlavorException;
-import java.io.IOException;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SystemClipboardTest {
- Logger logger = Logger.getLogger(SystemClipboardTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testClipboard() throws Exception {
- try {
- SystemClipboard sc = new SystemClipboard();
- sc.setClipboardContents("TEST");
-
- SystemClipboard sc2 = new SystemClipboard();
- assertEquals("TEST",sc2.getClipboardContents());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidClipboard() throws Exception {
- try {
- SystemClipboard sc2 = new SystemClipboard();
-
- Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
- clipboard.setContents(new Transferable() {
-
- @Override
- public boolean isDataFlavorSupported(DataFlavor flavor) {
- return true;
- }
-
- @Override
- public DataFlavor[] getTransferDataFlavors() {
- return null;
- }
-
- @Override
- public Object getTransferData(DataFlavor flavor) throws UnsupportedFlavorException, IOException {
- throw new UnsupportedFlavorException(flavor);
- }
- }, sc2);
-
- assertEquals(null,sc2.getClipboardContents());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLostOwnership() throws Exception {
- try {
- SystemClipboard sc = new SystemClipboard();
- sc.lostOwnership(null, null);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEmpty() throws Exception {
- try {
- SystemClipboard sc2 = new SystemClipboard();
- sc2.setClipboardContents(null);
- assertNull(sc2.getClipboardContents());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.datatransfer.UnsupportedFlavorException;
+import java.io.IOException;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class SystemClipboardTest {
+ Logger logger = Logger.getLogger(SystemClipboardTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testClipboard() throws Exception {
+ try {
+ SystemClipboard sc = new SystemClipboard();
+ sc.setClipboardContents("TEST");
+
+ SystemClipboard sc2 = new SystemClipboard();
+ assertEquals("TEST",sc2.getClipboardContents());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidClipboard() throws Exception {
+ try {
+ SystemClipboard sc2 = new SystemClipboard();
+
+ Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+ clipboard.setContents(new Transferable() {
+
+ @Override
+ public boolean isDataFlavorSupported(DataFlavor flavor) {
+ return true;
+ }
+
+ @Override
+ public DataFlavor[] getTransferDataFlavors() {
+ return null;
+ }
+
+ @Override
+ public Object getTransferData(DataFlavor flavor) throws UnsupportedFlavorException, IOException {
+ throw new UnsupportedFlavorException(flavor);
+ }
+ }, sc2);
+
+ assertEquals(null,sc2.getClipboardContents());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLostOwnership() throws Exception {
+ try {
+ SystemClipboard sc = new SystemClipboard();
+ sc.lostOwnership(null, null);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEmpty() throws Exception {
+ try {
+ SystemClipboard sc2 = new SystemClipboard();
+ sc2.setClipboardContents(null);
+ assertNull(sc2.getClipboardContents());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java b/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java
index 6bc27c3ee4a6557d7a4f3d583b6b939775316e78..a0136bd8eb8fde74ad2bfc11111754be20cbefb7 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java
@@ -1,76 +1,76 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import java.io.ByteArrayInputStream;
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.lang.reflect.Constructor;
-import java.nio.charset.StandardCharsets;
-import java.util.Map;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class TextFileUtilsTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetHeaderParametersFromFile() throws Exception {
- try {
- String fileContent = "#header\n" + //
- "#param1=value1\n" + //
- "#\n" + //
- "no header\n" + //
- "#param2=value\n";
-
- Map<String, String> params = TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(fileContent.getBytes(StandardCharsets.UTF_8)));
- assertEquals(1, params.keySet().size());
- assertNull(params.get("param2"));
- assertEquals("value1", params.get("param1"));
- assertNull(params.get("header"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testParseHeader() throws Exception {
- try {
- InputStream is = new FileInputStream("testFiles/fileHeader.txt");
- Map<String, String> map = TextFileUtils.getHeaderParametersFromFile(is);
-
- assertEquals("1.0", map.get("VERSION"));
- assertEquals("example name", map.get("NAME"));
- assertEquals("layout description", map.get("DESCRIPTION"));
- assertEquals("", map.get("MISSING"));
- assertEquals("A=B", map.get("TRICKY"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPrivateConstructor() throws Exception {
- try {
- Constructor<?> constr = TextFileUtils.class.getDeclaredConstructor(new Class<?>[] {});
- constr.setAccessible(true);
- assertNotNull(constr.newInstance(new Object[] {}));
- } catch (Exception e) {
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import java.io.ByteArrayInputStream;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.lang.reflect.Constructor;
+import java.nio.charset.StandardCharsets;
+import java.util.Map;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class TextFileUtilsTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetHeaderParametersFromFile() throws Exception {
+ try {
+ String fileContent = "#header\n" + //
+ "#param1=value1\n" + //
+ "#\n" + //
+ "no header\n" + //
+ "#param2=value\n";
+
+ Map<String, String> params = TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(fileContent.getBytes(StandardCharsets.UTF_8)));
+ assertEquals(1, params.keySet().size());
+ assertNull(params.get("param2"));
+ assertEquals("value1", params.get("param1"));
+ assertNull(params.get("header"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testParseHeader() throws Exception {
+ try {
+ InputStream is = new FileInputStream("testFiles/fileHeader.txt");
+ Map<String, String> map = TextFileUtils.getHeaderParametersFromFile(is);
+
+ assertEquals("1.0", map.get("VERSION"));
+ assertEquals("example name", map.get("NAME"));
+ assertEquals("layout description", map.get("DESCRIPTION"));
+ assertEquals("", map.get("MISSING"));
+ assertEquals("A=B", map.get("TRICKY"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPrivateConstructor() throws Exception {
+ try {
+ Constructor<?> constr = TextFileUtils.class.getDeclaredConstructor(new Class<?>[] {});
+ constr.setAccessible(true);
+ assertNotNull(constr.newInstance(new Object[] {}));
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java b/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
index a2bd25fb3984cca2128a256b43a47a20f5dca638..5e2188cfd4ab7d7d36faeaf865a3a7376ac5bc3c 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
@@ -1,474 +1,474 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.Color;
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.lang.reflect.Field;
-import java.nio.charset.StandardCharsets;
-import java.util.List;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.apache.log4j.Logger;
-import org.apache.xerces.dom.DocumentImpl;
-import org.apache.xerces.dom.ElementImpl;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.w3c.dom.NamedNodeMap;
-import org.w3c.dom.Node;
-import org.xml.sax.InputSource;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-
-public class XmlParserTest {
- Logger logger = Logger.getLogger(XmlParserTest.class);
-
- XmlParser parser = new XmlParser();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testColorParsing() {
- try {
- String strColor = "ffcbcd09";
-
- Color c = parser.stringToColor(strColor);
- String resultString = parser.colorToString(c);
- assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
-
- Color c2 = parser.stringToColor(resultString);
-
- assertEquals(c.getRed(), c2.getRed());
- assertEquals(c.getGreen(), c2.getGreen());
- assertEquals(c.getBlue(), c2.getBlue());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidColorParsing() {
- try {
- String strColor = "hello world";
-
- parser.stringToColor(strColor);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColorParsingWithAlpha() {
- try {
- String strColor = "fecbcd09";
-
- Color c = parser.stringToColor(strColor);
- String resultString = parser.colorToString(c);
- assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
-
- Color c2 = parser.stringToColor(resultString);
-
- assertEquals(c.getRed(), c2.getRed());
- assertEquals(c.getGreen(), c2.getGreen());
- assertEquals(c.getBlue(), c2.getBlue());
- assertEquals(c.getAlpha(), c2.getAlpha());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetXmlDocumentFromString() throws Exception {
- try {
- Document validDoc = parser.getXmlDocumentFromString("<node>test</node>");
- assertNotNull(validDoc);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testNodeToString() throws Exception {
- try {
- String xml = "<test_node>test_x</test_node>";
- Document validDoc = parser.getXmlDocumentFromString(xml);
- String str = parser.nodeToString(validDoc);
- assertEquals(xml.trim(), str.trim());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEmptyNodeToString() throws Exception {
- try {
- String str = parser.nodeToString(null);
- assertNull(str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testNodeToStringWithHeader() throws Exception {
- try {
- String xml = "<test_node>test_x</test_node>";
- Document validDoc = parser.getXmlDocumentFromString(xml);
- String str = parser.nodeToString(validDoc, true);
- assertTrue(str.contains(xml));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidNodeToString() throws Exception {
- try {
- final DocumentImpl xmlDoc = new DocumentImpl();
-
- Element root = xmlDoc.createElement("booking");
-
- class Tmp extends ElementImpl {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public Tmp() {
- this.ownerDocument = xmlDoc;
- }
-
- @Override
- public NamedNodeMap getAttributes() {
- return null;
- }
-
- }
- ;
- Element el = new Tmp();
- root.appendChild(el);
- assertNotNull(parser.nodeToString(root, true));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetXmlDocumentFromInvalidString() throws Exception {
- try {
- parser.getXmlDocumentFromString("<node>test<node>");
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetXmlDocumentFromInvalidInputStream() throws Exception {
- try {
- parser.getXmlDocumentFromInputSource(new InputSource());
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEscapeXml() throws Exception {
- try {
- String str = parser.escapeXml("<xml>node</xml>");
- assertFalse(str.contains("<"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEscapeNullXml() throws Exception {
- try {
- String str = parser.escapeXml(null);
- assertNull(str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFileToString() throws Exception {
- try {
- String str = parser.fileToString("testFiles/test.txt");
- assertTrue(str.contains("test"));
- assertTrue(str.contains("file"));
- assertTrue(str.contains("with some content"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testInputStreamToString() throws Exception {
- try {
- InputStream stream = new ByteArrayInputStream("stream string".getBytes(StandardCharsets.UTF_8));
- String str = parser.inputStreamToString(stream);
- assertEquals("stream string", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodeValue() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node>content</node>");
- Node node = parser.getNode("node", document);
- String str = parser.getNodeValue(node);
- assertEquals("content", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodeValue2() throws Exception {
- try {
- String str = parser.getNodeValue(null);
- assertEquals("", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodeValue3() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node></node>");
- Node node = parser.getNode("node", document);
- String str = parser.getNodeValue(node);
- assertEquals("", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodeValue4() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node><subnode/></node>");
- Node node = parser.getNode("node", document);
- String str = parser.getNodeValue(node);
- assertEquals("", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testInputStreamToStringThrowsException() throws Exception {
- try {
- parser.inputStreamToString(new InputStream() {
- @Override
- public int read() throws IOException {
- throw new IOException();
- }
- });
- fail("Exception expected");
- } catch (IOException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFileToStringThrowsException() throws Exception {
- try {
- parser.fileToString("testFiles/unknown file.txt");
- fail("Exception expected");
- } catch (IOException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodeAttr() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node attr=\"val\">content</node>");
- Node node = parser.getNode("node", document);
- String str = parser.getNodeAttr("attr", node);
- assertEquals("val", str);
- str = parser.getNodeAttr("attr2", node);
- assertEquals("", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodes() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
- Node node = parser.getNode("node", document);
- List<Node> nodes = parser.getNodes("subnode", node.getChildNodes());
- assertEquals(2, nodes.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNode() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
- Node node = parser.getNode("node", document);
- Node child = parser.getNode("other", node.getChildNodes());
- assertNotNull(child);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNode2() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node attr=\"x\"><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
- Node node = parser.getNode("node", document);
- Node child = parser.getNode("other2", node.getChildNodes());
- assertNull(child);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNode3() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node attr=\"x\">xxx</node>");
- Node node = parser.getNode("node", document);
- Node child = parser.getNode("other2", node.getChildNodes());
- assertNull(child);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testExceptionInConstructor() throws Exception {
- DocumentBuilderFactory factory = null;
- Field privateStringField = XmlParser.class.getDeclaredField("documentBuilderFactory");
- try {
-
- privateStringField.setAccessible(true);
-
- factory = (DocumentBuilderFactory) privateStringField.get(parser);
- privateStringField.set(parser, new DocumentBuilderFactory() {
-
- @Override
- public void setFeature(String name, boolean value) throws ParserConfigurationException {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setAttribute(String name, Object value) throws IllegalArgumentException {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public DocumentBuilder newDocumentBuilder() throws ParserConfigurationException {
- throw new ParserConfigurationException();
- }
-
- @Override
- public boolean getFeature(String name) throws ParserConfigurationException {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public Object getAttribute(String name) throws IllegalArgumentException {
- // TODO Auto-generated method stub
- return null;
- }
- });
- new XmlParser();
- fail("Exception expected");
- } catch (InvalidStateException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- privateStringField.set(parser, factory);
- }
- }
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.lang.reflect.Field;
+import java.nio.charset.StandardCharsets;
+import java.util.List;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.apache.log4j.Logger;
+import org.apache.xerces.dom.DocumentImpl;
+import org.apache.xerces.dom.ElementImpl;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.NamedNodeMap;
+import org.w3c.dom.Node;
+import org.xml.sax.InputSource;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+
+public class XmlParserTest {
+ Logger logger = Logger.getLogger(XmlParserTest.class);
+
+ XmlParser parser = new XmlParser();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testColorParsing() {
+ try {
+ String strColor = "ffcbcd09";
+
+ Color c = parser.stringToColor(strColor);
+ String resultString = parser.colorToString(c);
+ assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
+
+ Color c2 = parser.stringToColor(resultString);
+
+ assertEquals(c.getRed(), c2.getRed());
+ assertEquals(c.getGreen(), c2.getGreen());
+ assertEquals(c.getBlue(), c2.getBlue());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidColorParsing() {
+ try {
+ String strColor = "hello world";
+
+ parser.stringToColor(strColor);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColorParsingWithAlpha() {
+ try {
+ String strColor = "fecbcd09";
+
+ Color c = parser.stringToColor(strColor);
+ String resultString = parser.colorToString(c);
+ assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
+
+ Color c2 = parser.stringToColor(resultString);
+
+ assertEquals(c.getRed(), c2.getRed());
+ assertEquals(c.getGreen(), c2.getGreen());
+ assertEquals(c.getBlue(), c2.getBlue());
+ assertEquals(c.getAlpha(), c2.getAlpha());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetXmlDocumentFromString() throws Exception {
+ try {
+ Document validDoc = parser.getXmlDocumentFromString("<node>test</node>");
+ assertNotNull(validDoc);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testNodeToString() throws Exception {
+ try {
+ String xml = "<test_node>test_x</test_node>";
+ Document validDoc = parser.getXmlDocumentFromString(xml);
+ String str = parser.nodeToString(validDoc);
+ assertEquals(xml.trim(), str.trim());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEmptyNodeToString() throws Exception {
+ try {
+ String str = parser.nodeToString(null);
+ assertNull(str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testNodeToStringWithHeader() throws Exception {
+ try {
+ String xml = "<test_node>test_x</test_node>";
+ Document validDoc = parser.getXmlDocumentFromString(xml);
+ String str = parser.nodeToString(validDoc, true);
+ assertTrue(str.contains(xml));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidNodeToString() throws Exception {
+ try {
+ final DocumentImpl xmlDoc = new DocumentImpl();
+
+ Element root = xmlDoc.createElement("booking");
+
+ class Tmp extends ElementImpl {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public Tmp() {
+ this.ownerDocument = xmlDoc;
+ }
+
+ @Override
+ public NamedNodeMap getAttributes() {
+ return null;
+ }
+
+ }
+ ;
+ Element el = new Tmp();
+ root.appendChild(el);
+ assertNotNull(parser.nodeToString(root, true));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetXmlDocumentFromInvalidString() throws Exception {
+ try {
+ parser.getXmlDocumentFromString("<node>test<node>");
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetXmlDocumentFromInvalidInputStream() throws Exception {
+ try {
+ parser.getXmlDocumentFromInputSource(new InputSource());
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEscapeXml() throws Exception {
+ try {
+ String str = parser.escapeXml("<xml>node</xml>");
+ assertFalse(str.contains("<"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEscapeNullXml() throws Exception {
+ try {
+ String str = parser.escapeXml(null);
+ assertNull(str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFileToString() throws Exception {
+ try {
+ String str = parser.fileToString("testFiles/test.txt");
+ assertTrue(str.contains("test"));
+ assertTrue(str.contains("file"));
+ assertTrue(str.contains("with some content"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testInputStreamToString() throws Exception {
+ try {
+ InputStream stream = new ByteArrayInputStream("stream string".getBytes(StandardCharsets.UTF_8));
+ String str = parser.inputStreamToString(stream);
+ assertEquals("stream string", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodeValue() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node>content</node>");
+ Node node = parser.getNode("node", document);
+ String str = parser.getNodeValue(node);
+ assertEquals("content", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodeValue2() throws Exception {
+ try {
+ String str = parser.getNodeValue(null);
+ assertEquals("", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodeValue3() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node></node>");
+ Node node = parser.getNode("node", document);
+ String str = parser.getNodeValue(node);
+ assertEquals("", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodeValue4() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node><subnode/></node>");
+ Node node = parser.getNode("node", document);
+ String str = parser.getNodeValue(node);
+ assertEquals("", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testInputStreamToStringThrowsException() throws Exception {
+ try {
+ parser.inputStreamToString(new InputStream() {
+ @Override
+ public int read() throws IOException {
+ throw new IOException();
+ }
+ });
+ fail("Exception expected");
+ } catch (IOException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFileToStringThrowsException() throws Exception {
+ try {
+ parser.fileToString("testFiles/unknown file.txt");
+ fail("Exception expected");
+ } catch (IOException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodeAttr() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node attr=\"val\">content</node>");
+ Node node = parser.getNode("node", document);
+ String str = parser.getNodeAttr("attr", node);
+ assertEquals("val", str);
+ str = parser.getNodeAttr("attr2", node);
+ assertEquals("", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodes() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
+ Node node = parser.getNode("node", document);
+ List<Node> nodes = parser.getNodes("subnode", node.getChildNodes());
+ assertEquals(2, nodes.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNode() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
+ Node node = parser.getNode("node", document);
+ Node child = parser.getNode("other", node.getChildNodes());
+ assertNotNull(child);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNode2() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node attr=\"x\"><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
+ Node node = parser.getNode("node", document);
+ Node child = parser.getNode("other2", node.getChildNodes());
+ assertNull(child);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNode3() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node attr=\"x\">xxx</node>");
+ Node node = parser.getNode("node", document);
+ Node child = parser.getNode("other2", node.getChildNodes());
+ assertNull(child);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testExceptionInConstructor() throws Exception {
+ DocumentBuilderFactory factory = null;
+ Field privateStringField = XmlParser.class.getDeclaredField("documentBuilderFactory");
+ try {
+
+ privateStringField.setAccessible(true);
+
+ factory = (DocumentBuilderFactory) privateStringField.get(parser);
+ privateStringField.set(parser, new DocumentBuilderFactory() {
+
+ @Override
+ public void setFeature(String name, boolean value) throws ParserConfigurationException {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setAttribute(String name, Object value) throws IllegalArgumentException {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public DocumentBuilder newDocumentBuilder() throws ParserConfigurationException {
+ throw new ParserConfigurationException();
+ }
+
+ @Override
+ public boolean getFeature(String name) throws ParserConfigurationException {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public Object getAttribute(String name) throws IllegalArgumentException {
+ // TODO Auto-generated method stub
+ return null;
+ }
+ });
+ new XmlParser();
+ fail("Exception expected");
+ } catch (InvalidStateException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ privateStringField.set(parser, factory);
+ }
+ }
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/BellExport.java b/console/src/main/java/lcsb/mapviewer/run/BellExport.java
index d22ed9fe9d2fad860c946711568b323bab20a41c..d280b3888757d33320307ae93abad8dc409a848e 100644
--- a/console/src/main/java/lcsb/mapviewer/run/BellExport.java
+++ b/console/src/main/java/lcsb/mapviewer/run/BellExport.java
@@ -1,140 +1,140 @@
-package lcsb.mapviewer.run;
-
-import lcsb.mapviewer.annotation.services.ModelAnnotator;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.ApplicationContextLoader;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.services.interfaces.IExporterService;
-import lcsb.mapviewer.services.interfaces.IExporterService.ExporterParameters;
-import lcsb.mapviewer.services.utils.data.ExportFileType;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * This class prepare data for Bell format (further transformation is done by
- * Marek).
- *
- * @author Piotr Gawron
- *
- */
-public class BellExport {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(BellExport.class.getName());
-
- /**
- * Object that performs different types of export transformation.
- */
- @Autowired
- private IExporterService exporter;
-
- /**
- * Object used to annotate the model.
- */
- @Autowired
- private ModelAnnotator modelAnnotator;
-
- /**
- * Object used to annotate the model.
- */
- @Autowired
- private DbUtils dbUtils;
-
- /**
- * Static main method used to run this stand alone code.
- *
- * @param args
- * command line arguments
- */
- public static void main(String[] args) {
- ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
- BellExport main = new BellExport();
- ApplicationContextLoader.injectDependencies(main);
- main.run();
- }
-
- /**
- * Default constructor.
- */
- public BellExport() {
-
- }
-
- /**
- * Method that export pd map into file that can be exported to bell (by
- * Marek).
- *
- */
- private void run() {
- CellDesignerXmlParser p = new CellDesignerXmlParser();
- try {
- String filename = PdMapAnnotations.getLastPdFilename();
- String version = PdMapAnnotations.getLastPdVersion();
-
- //filename = "testFiles/other_full/ASTHMAP18000X8000V1_38.xml";
- //version = "1.1.38";
- dbUtils.createSessionForCurrentThread();
- Model model = p.createModel(new ConverterParams().filename(filename));
-
- modelAnnotator.performAnnotations(model, new IProgressUpdater() {
-
- @Override
- public void setProgress(double progress) {
- // TODO Auto-generated method stub
-
- }
- });
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
- fileName("out/bell/" + version + "-reactions.txt").//
- fileType(ExportFileType.TAB_SEPARATED).//
- type(Species.class).//
- moleculeEdges(false);
-
- exporter.exportReactions(params);
-
- params = new IExporterService.ExporterParameters().model(model).//
- fileName("out/bell/" + version + "-species.txt").//
- fileType(ExportFileType.TAB_SEPARATED).//
- type(Species.class).//
-// column(ExportColumn.FULL).//
- moleculeEdges(false);
- exporter.exportSpecies(params);
-
- params = new IExporterService.ExporterParameters().model(model).//
- fileName("out/bell/" + version + "-compartments.txt").//
- fileType(ExportFileType.TAB_SEPARATED).//
- type(Object.class); //
-// column(ExportColumn.FULL);
- exporter.exportCompartments(params);
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- } finally {
- dbUtils.closeSessionForCurrentThread();
- }
- }
-
- /**
- * @return the modelAnnotator
- * @see #modelAnnotator
- */
- public ModelAnnotator getModelAnnotator() {
- return modelAnnotator;
- }
-
- /**
- * @param modelAnnotator
- * the modelAnnotator to set
- * @see #modelAnnotator
- */
- public void setModelAnnotator(ModelAnnotator modelAnnotator) {
- this.modelAnnotator = modelAnnotator;
- }
-}
+package lcsb.mapviewer.run;
+
+import lcsb.mapviewer.annotation.services.ModelAnnotator;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.persist.ApplicationContextLoader;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.services.interfaces.IExporterService;
+import lcsb.mapviewer.services.interfaces.IExporterService.ExporterParameters;
+import lcsb.mapviewer.services.utils.data.ExportFileType;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * This class prepare data for Bell format (further transformation is done by
+ * Marek).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class BellExport {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(BellExport.class.getName());
+
+ /**
+ * Object that performs different types of export transformation.
+ */
+ @Autowired
+ private IExporterService exporter;
+
+ /**
+ * Object used to annotate the model.
+ */
+ @Autowired
+ private ModelAnnotator modelAnnotator;
+
+ /**
+ * Object used to annotate the model.
+ */
+ @Autowired
+ private DbUtils dbUtils;
+
+ /**
+ * Static main method used to run this stand alone code.
+ *
+ * @param args
+ * command line arguments
+ */
+ public static void main(String[] args) {
+ ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+ BellExport main = new BellExport();
+ ApplicationContextLoader.injectDependencies(main);
+ main.run();
+ }
+
+ /**
+ * Default constructor.
+ */
+ public BellExport() {
+
+ }
+
+ /**
+ * Method that export pd map into file that can be exported to bell (by
+ * Marek).
+ *
+ */
+ private void run() {
+ CellDesignerXmlParser p = new CellDesignerXmlParser();
+ try {
+ String filename = PdMapAnnotations.getLastPdFilename();
+ String version = PdMapAnnotations.getLastPdVersion();
+
+ //filename = "testFiles/other_full/ASTHMAP18000X8000V1_38.xml";
+ //version = "1.1.38";
+ dbUtils.createSessionForCurrentThread();
+ Model model = p.createModel(new ConverterParams().filename(filename));
+
+ modelAnnotator.performAnnotations(model, new IProgressUpdater() {
+
+ @Override
+ public void setProgress(double progress) {
+ // TODO Auto-generated method stub
+
+ }
+ });
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
+ fileName("out/bell/" + version + "-reactions.txt").//
+ fileType(ExportFileType.TAB_SEPARATED).//
+ type(Species.class).//
+ moleculeEdges(false);
+
+ exporter.exportReactions(params);
+
+ params = new IExporterService.ExporterParameters().model(model).//
+ fileName("out/bell/" + version + "-species.txt").//
+ fileType(ExportFileType.TAB_SEPARATED).//
+ type(Species.class).//
+// column(ExportColumn.FULL).//
+ moleculeEdges(false);
+ exporter.exportSpecies(params);
+
+ params = new IExporterService.ExporterParameters().model(model).//
+ fileName("out/bell/" + version + "-compartments.txt").//
+ fileType(ExportFileType.TAB_SEPARATED).//
+ type(Object.class); //
+// column(ExportColumn.FULL);
+ exporter.exportCompartments(params);
+
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ } finally {
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
+
+ /**
+ * @return the modelAnnotator
+ * @see #modelAnnotator
+ */
+ public ModelAnnotator getModelAnnotator() {
+ return modelAnnotator;
+ }
+
+ /**
+ * @param modelAnnotator
+ * the modelAnnotator to set
+ * @see #modelAnnotator
+ */
+ public void setModelAnnotator(ModelAnnotator modelAnnotator) {
+ this.modelAnnotator = modelAnnotator;
+ }
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
index 09c6c27d63149aa7e9a22b20679690168d55f4ee..3f6ad5730de29c4a0911953101be19b19fb5044f 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
@@ -1,467 +1,467 @@
-package lcsb.mapviewer.run;
-
-import java.awt.geom.Point2D;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.io.UnsupportedEncodingException;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.annotation.services.MiriamConnector;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-
-/**
- * This class is entry point for console tool to convert data from tab separated
- * file a CellDesigner format.
- *
- * @author Piotr Gawron
- *
- */
-public class ConsoleConverter {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(ConsoleConverter.class);
-
- /**
- * Options from the input.
- */
- private RunOptions inputOptions;
-
- /**
- * Connector used for accessing data from miriam registry.
- */
- private MiriamConnector mc = new MiriamConnector();
-
- /**
- * Util class used to access some information about {@link Element}.
- */
- private ElementUtils elementUtils = new ElementUtils();
-
- /**
- * Default constructor.
- *
- * @param args
- * parameters with which the program was run
- */
- public ConsoleConverter(String[] args) {
- inputOptions = new RunOptions(args);
- }
-
- /**
- * Main entry point to the program.
- *
- * @param args
- * parameters with which the program was run
- */
- public static void main(String[] args) {
-// ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
- ConsoleConverter main = new ConsoleConverter(args);
-// ApplicationContextLoader.injectDependencies(main);
- try {
- main.run();
- } catch (InvalidInputDataExecption e) {
- main.logger.error(e, e);
- }
- }
-
- /**
- * This method transform {@link #inputOptions input data}.
- *
- * @throws InvalidInputDataExecption
- * thrown when the input data are invalid
- */
- private void run() throws InvalidInputDataExecption {
- if (inputOptions.isFormat()) {
- inputOptions.printFormat();
- } else if (!inputOptions.isValidInput() || inputOptions.isHelpOption()) {
- inputOptions.printHelp();
- } else {
- logger.debug("Running...");
-
- String nodesFilename = inputOptions.getNodesFilename();
-
- Model model = new ModelFullIndexed(null);
- model.setWidth(inputOptions.getModelSize());
- model.setHeight(inputOptions.getModelSize());
- model.addCompartment(new Compartment("default"));
-
- Set<Element> elements = null;
- try {
- elements = getNodes(nodesFilename);
- } catch (IOException e) {
- throw new InvalidInputDataExecption("Problem with input file: " + nodesFilename, e);
- }
-
- for (Element element : elements) {
- model.addElement(element);
- }
-
- double middleX = inputOptions.getModelSize() / 2;
- double middleY = inputOptions.getModelSize() / 2;
-
- double size = model.getSpecies().size();
- double x = 0;
-
- for (Species species : model.getSpecies()) {
- SpeciesAlias alias = new SpeciesAlias(species);
- alias.setAliasId("al" + species.getElementId());
- alias.setWidth(inputOptions.getAliasWidth());
- alias.setHeight(inputOptions.getAliasHeight());
- double angle = x / size * 2 * Math.PI;
- alias.setX(middleX + Math.sin(angle) * inputOptions.getRadius());
- alias.setY(middleY + Math.cos(angle) * inputOptions.getRadius());
- model.addAlias(alias);
- x++;
- }
-
- String reactionsFilename = inputOptions.getReactionsFilename();
-
- List<Reaction> reactions;
- try {
- reactions = getReactions(reactionsFilename, model);
- } catch (IOException e) {
- throw new InvalidInputDataExecption("Problem with input file: " + reactionsFilename, e);
- }
- model.addReactions(reactions);
- String outputFilename = inputOptions.getOutputFilename();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- PrintWriter writer = null;
- try {
- writer = new PrintWriter(outputFilename, "UTF-8");
- writer.println(parser.toXml(model));
- } catch (FileNotFoundException e) {
- throw new InvalidInputDataExecption("Problem with output file: " + outputFilename, e);
- } catch (UnsupportedEncodingException e) {
- logger.error(e, e);
- } catch (InconsistentModelException e) {
- throw new InvalidStateException(e);
- } finally {
- writer.close();
- }
-
- }
- }
-
- /**
- * Returns list of {@link Reaction reactions} obtained from input file.
- *
- * @param filename
- * file with information about reactions
- * @param model
- * {@link Model} where the data about nodes is stored
- * @return list of {@link Reaction reactions} obtained from input file
- * @throws InvalidInputDataExecption
- * thrown when the file is invalid
- * @throws IOException
- * thrown when there is a problem with acceesing input file
- */
- private List<Reaction> getReactions(String filename, Model model) throws InvalidInputDataExecption, IOException {
- List<Reaction> result = new ArrayList<Reaction>();
- Integer identifierColumn = null;
- Integer typeColumn = null;
- Integer reactantsColumn = null;
- Integer modifiersColumn = null;
- Integer productsColumn = null;
- Integer annotationsColumn = null;
- Set<Integer> ids = new HashSet<Integer>();
- BufferedReader br = new BufferedReader(new FileReader(new File(filename)));
- try {
- String line = br.readLine();
- String[] cols = line.split("\t", -1);
- int columns = cols.length;
- for (int i = 0; i < cols.length; i++) {
- if (cols[i].equalsIgnoreCase(RunOptions.IDENTIFIER_REACTIONS_HEADER)) {
- identifierColumn = i;
- } else if (cols[i].equalsIgnoreCase(RunOptions.TYPE_REACTIONS_HEADER)) {
- typeColumn = i;
- } else if (cols[i].equalsIgnoreCase(RunOptions.REACTANTS_REACTIONS_HEADER)) {
- reactantsColumn = i;
- } else if (cols[i].equalsIgnoreCase(RunOptions.MODIFIERS_REACTIONS_HEADER)) {
- modifiersColumn = i;
- } else if (cols[i].equalsIgnoreCase(RunOptions.PRODUCTS_REACTIONS_HEADER)) {
- productsColumn = i;
- } else if (cols[i].equalsIgnoreCase(RunOptions.ANNOTATIONS_REACTIONS_HEADER)) {
- annotationsColumn = i;
- } else {
- throw new InvalidInputDataExecption("Unknown column name " + cols[i], filename);
- }
- }
- if (identifierColumn == null) {
- throw new InvalidInputDataExecption("No \"" + RunOptions.IDENTIFIER_REACTIONS_HEADER + "\" defined.", filename);
- } else if (typeColumn == null) {
- throw new InvalidInputDataExecption("No \"" + RunOptions.TYPE_REACTIONS_HEADER + "\" defined.", filename);
- } else if (reactantsColumn == null) {
- throw new InvalidInputDataExecption("No \"" + RunOptions.REACTANTS_REACTIONS_HEADER + "\" defined.", filename);
- } else if (modifiersColumn == null) {
- throw new InvalidInputDataExecption("No \"" + RunOptions.MODIFIERS_REACTIONS_HEADER + "\" defined.", filename);
- } else if (productsColumn == null) {
- throw new InvalidInputDataExecption("No \"" + RunOptions.PRODUCTS_REACTIONS_HEADER + "\" defined.", filename);
- } else if (annotationsColumn == null) {
- throw new InvalidInputDataExecption("No \"" + RunOptions.ANNOTATIONS_REACTIONS_HEADER + "\" defined.", filename);
- }
- int row = 2;
- while ((line = br.readLine()) != null) {
- cols = line.split("\t", -1);
- if (cols.length != columns) {
- throw new InvalidInputDataExecption("Invalid number of columns in row " + row, filename);
- }
- String id = cols[identifierColumn];
- if (ids.contains(id)) {
- throw new InvalidInputDataExecption("Id \"" + id + "\" is not unique.", filename);
- }
-
- String className = cols[typeColumn];
- Class<? extends AnnotatedObject> clazz = elementUtils.getClassByName(className);
- if (clazz == null) {
- throw new InvalidInputDataExecption("Unknown element type: " + className, filename);
- }
- List<Product> products = new ArrayList<Product>();
- String productString = cols[productsColumn];
- for (String string : productString.split(",")) {
- if (!string.isEmpty()) {
- Element element = model.getSpeciesBySpeciesId(string.trim());
- SpeciesAlias alias = model.getAliasesBySpeciesId(string.trim()).get(0);
- Product product = new Product(alias, element);
- products.add(product);
- }
- }
- if (products.size() == 0) {
- throw new InvalidInputDataExecption("List of products cannot be empty (row: " + row + ")", filename);
- }
-
- List<Reactant> reactants = new ArrayList<Reactant>();
- String reactantString = cols[reactantsColumn];
- for (String string : reactantString.split(",")) {
- if (!string.isEmpty()) {
- Element element = model.getSpeciesBySpeciesId(string.trim());
- SpeciesAlias alias = model.getAliasesBySpeciesId(string.trim()).get(0);
- Reactant product = new Reactant(alias, element);
- reactants.add(product);
- }
- }
- if (reactants.size() == 0) {
- throw new InvalidInputDataExecption("List of reactants cannot be empty (row: " + row + ")", filename);
- }
-
- List<Modifier> modifiers = new ArrayList<Modifier>();
- String modifierString = cols[modifiersColumn];
- for (String string : modifierString.split(",")) {
- if (!string.isEmpty()) {
- Element element = model.getSpeciesBySpeciesId(string.trim());
- SpeciesAlias alias = model.getAliasesBySpeciesId(string.trim()).get(0);
- Modifier modifier = new Catalysis(alias, element);
- modifiers.add(modifier);
- }
- }
- Alias alias1 = products.get(0).getAlias();
- Alias alias2 = reactants.get(0).getAlias();
-
- Point2D middle = new Point2D.Double((alias1.getCenterX() + alias2.getCenterX()) / 2, (alias1.getCenterY() + alias2.getCenterY()) / 2);
-
- Set<MiriamData> annotations = new HashSet<MiriamData>();
- if (annotationsColumn != null) {
- String[] annotationString = cols[annotationsColumn].split(",");
- for (String string : annotationString) {
- if (!string.isEmpty()) {
- try {
- annotations.add(MiriamType.getMiriamByUri(string));
- } catch (InvalidArgumentException e) {
- throw new InvalidInputDataExecption("Invalid miriam urn: " + string, filename);
- }
- }
- }
- }
-
- try {
- if (!Reaction.class.isAssignableFrom(clazz)) {
- throw new InvalidInputDataExecption("Invalid reaction type type: " + className, filename);
- }
- Reaction reaction = (Reaction) clazz.newInstance();
- for (Product product : products) {
- product.setLine(new PolylineData(middle, product.getAlias().getCenter()));
- reaction.addProduct(product);
- }
- for (Reactant reactant : reactants) {
- reactant.setLine(new PolylineData(reactant.getAlias().getCenter(), middle));
- reaction.addReactant(reactant);
- }
- for (Modifier modifier : modifiers) {
- modifier.setLine(new PolylineData(middle, modifier.getAlias().getCenter()));
- reaction.addModifier(modifier);
- }
- reaction.addMiriamData(annotations);
- reaction.setElementId(id);
- result.add(reaction);
- } catch (InstantiationException e) {
- throw new InvalidStateException(e);
- } catch (IllegalAccessException e) {
- throw new InvalidStateException(e);
- }
- row++;
- }
- } finally {
- br.close();
- }
- return result;
- }
-
- /**
- * This method parses the data from input file into set of {@link Element
- * elements}.
- *
- * @param filename
- * nam of input file
- * @return set of {@link Element elements}
- * @throws InvalidInputDataExecption
- * thrown when the input data is invalid
- * @throws IOException
- * thrown when there is a problem with input file
- */
- private Set<Element> getNodes(String filename) throws InvalidInputDataExecption, IOException {
- ElementUtils elementUtils = new ElementUtils();
-
- Set<Element> result = new HashSet<Element>();
- Set<String> ids = new HashSet<String>();
-
- Integer identifierColumn = null;
- Integer typeColumn = null;
- Integer nameColumn = null;
- Integer annotationsColumn = null;
-
- BufferedReader br = new BufferedReader(new FileReader(new File(filename)));
- try {
- String line = br.readLine();
- String[] cols = line.split("\t", -1);
- int columns = cols.length;
- for (int i = 0; i < cols.length; i++) {
- if (cols[i].equalsIgnoreCase(RunOptions.IDENTIFIER_NODES_HEADER)) {
- identifierColumn = i;
- } else if (cols[i].equalsIgnoreCase(RunOptions.TYPE_NODES_HEADER)) {
- typeColumn = i;
- } else if (cols[i].equalsIgnoreCase(RunOptions.NAME_NODES_HEADER)) {
- nameColumn = i;
- } else if (cols[i].equalsIgnoreCase(RunOptions.ANNOTATIONS_NODES_HEADER)) {
- annotationsColumn = i;
- } else {
- throw new InvalidInputDataExecption("Unknown column name " + cols[i], filename);
- }
- }
- if (identifierColumn == null) {
- throw new InvalidInputDataExecption("No \"" + RunOptions.IDENTIFIER_NODES_HEADER + "\" defined.", filename);
- }
- if (typeColumn == null) {
- throw new InvalidInputDataExecption("No \"" + RunOptions.TYPE_NODES_HEADER + "\" defined.", filename);
- }
- if (nameColumn == null) {
- throw new InvalidInputDataExecption("No \"" + RunOptions.NAME_NODES_HEADER + "\" defined.", filename);
- }
- int row = 2;
- while ((line = br.readLine()) != null) {
- if (line.isEmpty()) {
- continue;
- }
- cols = line.split("\t", -1);
- if (cols.length != columns) {
- throw new InvalidInputDataExecption(
- "Invalid number of columns in row " + row + ". Expected " + columns + ", but " + cols.length + " found", filename);
- }
- String id = cols[identifierColumn];
- if (ids.contains(id)) {
- throw new InvalidInputDataExecption("Id \"" + id + "\" is not unique.", filename);
- }
-
- String className = cols[typeColumn];
- Class<? extends AnnotatedObject> clazz = elementUtils.getClassByName(className);
- if (clazz == null) {
- throw new InvalidInputDataExecption("Unknown element type: " + className, filename);
- }
- String name = cols[nameColumn];
- if (name.isEmpty()) {
- throw new InvalidInputDataExecption("Name cannot be empty (row " + row + ").", filename);
- }
- Set<MiriamData> annotations = new HashSet<MiriamData>();
- if (annotationsColumn != null) {
- String[] annotationString = cols[annotationsColumn].split(",");
- for (String string : annotationString) {
- if (!string.isEmpty()) {
- try {
- annotations.add(MiriamType.getMiriamByUri(string));
- } catch (InvalidArgumentException e) {
- throw new InvalidInputDataExecption("Invalid miriam urn: " + string, filename);
- }
- }
- }
- }
-
- try {
- if (!Element.class.isAssignableFrom(clazz)) {
- throw new InvalidInputDataExecption("Invliad element type: " + className, filename);
- }
- Element element = (Element) clazz.newInstance();
- element.setName(name);
- element.addMiriamData(annotations);
- element.setElementId(id);
- result.add(element);
- } catch (InstantiationException e) {
- throw new InvalidStateException(e);
- } catch (IllegalAccessException e) {
- throw new InvalidStateException(e);
- }
- row++;
- }
- } finally {
- br.close();
- }
-
- return result;
- }
-
- /**
- * @return the mc
- * @see #mc
- */
- public MiriamConnector getMc() {
- return mc;
- }
-
- /**
- * @param mc
- * the mc to set
- * @see #mc
- */
- public void setMc(MiriamConnector mc) {
- this.mc = mc;
- }
-}
+package lcsb.mapviewer.run;
+
+import java.awt.geom.Point2D;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.annotation.services.MiriamConnector;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+/**
+ * This class is entry point for console tool to convert data from tab separated
+ * file a CellDesigner format.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ConsoleConverter {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(ConsoleConverter.class);
+
+ /**
+ * Options from the input.
+ */
+ private RunOptions inputOptions;
+
+ /**
+ * Connector used for accessing data from miriam registry.
+ */
+ private MiriamConnector mc = new MiriamConnector();
+
+ /**
+ * Util class used to access some information about {@link Element}.
+ */
+ private ElementUtils elementUtils = new ElementUtils();
+
+ /**
+ * Default constructor.
+ *
+ * @param args
+ * parameters with which the program was run
+ */
+ public ConsoleConverter(String[] args) {
+ inputOptions = new RunOptions(args);
+ }
+
+ /**
+ * Main entry point to the program.
+ *
+ * @param args
+ * parameters with which the program was run
+ */
+ public static void main(String[] args) {
+// ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+ ConsoleConverter main = new ConsoleConverter(args);
+// ApplicationContextLoader.injectDependencies(main);
+ try {
+ main.run();
+ } catch (InvalidInputDataExecption e) {
+ main.logger.error(e, e);
+ }
+ }
+
+ /**
+ * This method transform {@link #inputOptions input data}.
+ *
+ * @throws InvalidInputDataExecption
+ * thrown when the input data are invalid
+ */
+ private void run() throws InvalidInputDataExecption {
+ if (inputOptions.isFormat()) {
+ inputOptions.printFormat();
+ } else if (!inputOptions.isValidInput() || inputOptions.isHelpOption()) {
+ inputOptions.printHelp();
+ } else {
+ logger.debug("Running...");
+
+ String nodesFilename = inputOptions.getNodesFilename();
+
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(inputOptions.getModelSize());
+ model.setHeight(inputOptions.getModelSize());
+ model.addCompartment(new Compartment("default"));
+
+ Set<Element> elements = null;
+ try {
+ elements = getNodes(nodesFilename);
+ } catch (IOException e) {
+ throw new InvalidInputDataExecption("Problem with input file: " + nodesFilename, e);
+ }
+
+ for (Element element : elements) {
+ model.addElement(element);
+ }
+
+ double middleX = inputOptions.getModelSize() / 2;
+ double middleY = inputOptions.getModelSize() / 2;
+
+ double size = model.getSpecies().size();
+ double x = 0;
+
+ for (Species species : model.getSpecies()) {
+ SpeciesAlias alias = new SpeciesAlias(species);
+ alias.setAliasId("al" + species.getElementId());
+ alias.setWidth(inputOptions.getAliasWidth());
+ alias.setHeight(inputOptions.getAliasHeight());
+ double angle = x / size * 2 * Math.PI;
+ alias.setX(middleX + Math.sin(angle) * inputOptions.getRadius());
+ alias.setY(middleY + Math.cos(angle) * inputOptions.getRadius());
+ model.addAlias(alias);
+ x++;
+ }
+
+ String reactionsFilename = inputOptions.getReactionsFilename();
+
+ List<Reaction> reactions;
+ try {
+ reactions = getReactions(reactionsFilename, model);
+ } catch (IOException e) {
+ throw new InvalidInputDataExecption("Problem with input file: " + reactionsFilename, e);
+ }
+ model.addReactions(reactions);
+ String outputFilename = inputOptions.getOutputFilename();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ PrintWriter writer = null;
+ try {
+ writer = new PrintWriter(outputFilename, "UTF-8");
+ writer.println(parser.toXml(model));
+ } catch (FileNotFoundException e) {
+ throw new InvalidInputDataExecption("Problem with output file: " + outputFilename, e);
+ } catch (UnsupportedEncodingException e) {
+ logger.error(e, e);
+ } catch (InconsistentModelException e) {
+ throw new InvalidStateException(e);
+ } finally {
+ writer.close();
+ }
+
+ }
+ }
+
+ /**
+ * Returns list of {@link Reaction reactions} obtained from input file.
+ *
+ * @param filename
+ * file with information about reactions
+ * @param model
+ * {@link Model} where the data about nodes is stored
+ * @return list of {@link Reaction reactions} obtained from input file
+ * @throws InvalidInputDataExecption
+ * thrown when the file is invalid
+ * @throws IOException
+ * thrown when there is a problem with acceesing input file
+ */
+ private List<Reaction> getReactions(String filename, Model model) throws InvalidInputDataExecption, IOException {
+ List<Reaction> result = new ArrayList<Reaction>();
+ Integer identifierColumn = null;
+ Integer typeColumn = null;
+ Integer reactantsColumn = null;
+ Integer modifiersColumn = null;
+ Integer productsColumn = null;
+ Integer annotationsColumn = null;
+ Set<Integer> ids = new HashSet<Integer>();
+ BufferedReader br = new BufferedReader(new FileReader(new File(filename)));
+ try {
+ String line = br.readLine();
+ String[] cols = line.split("\t", -1);
+ int columns = cols.length;
+ for (int i = 0; i < cols.length; i++) {
+ if (cols[i].equalsIgnoreCase(RunOptions.IDENTIFIER_REACTIONS_HEADER)) {
+ identifierColumn = i;
+ } else if (cols[i].equalsIgnoreCase(RunOptions.TYPE_REACTIONS_HEADER)) {
+ typeColumn = i;
+ } else if (cols[i].equalsIgnoreCase(RunOptions.REACTANTS_REACTIONS_HEADER)) {
+ reactantsColumn = i;
+ } else if (cols[i].equalsIgnoreCase(RunOptions.MODIFIERS_REACTIONS_HEADER)) {
+ modifiersColumn = i;
+ } else if (cols[i].equalsIgnoreCase(RunOptions.PRODUCTS_REACTIONS_HEADER)) {
+ productsColumn = i;
+ } else if (cols[i].equalsIgnoreCase(RunOptions.ANNOTATIONS_REACTIONS_HEADER)) {
+ annotationsColumn = i;
+ } else {
+ throw new InvalidInputDataExecption("Unknown column name " + cols[i], filename);
+ }
+ }
+ if (identifierColumn == null) {
+ throw new InvalidInputDataExecption("No \"" + RunOptions.IDENTIFIER_REACTIONS_HEADER + "\" defined.", filename);
+ } else if (typeColumn == null) {
+ throw new InvalidInputDataExecption("No \"" + RunOptions.TYPE_REACTIONS_HEADER + "\" defined.", filename);
+ } else if (reactantsColumn == null) {
+ throw new InvalidInputDataExecption("No \"" + RunOptions.REACTANTS_REACTIONS_HEADER + "\" defined.", filename);
+ } else if (modifiersColumn == null) {
+ throw new InvalidInputDataExecption("No \"" + RunOptions.MODIFIERS_REACTIONS_HEADER + "\" defined.", filename);
+ } else if (productsColumn == null) {
+ throw new InvalidInputDataExecption("No \"" + RunOptions.PRODUCTS_REACTIONS_HEADER + "\" defined.", filename);
+ } else if (annotationsColumn == null) {
+ throw new InvalidInputDataExecption("No \"" + RunOptions.ANNOTATIONS_REACTIONS_HEADER + "\" defined.", filename);
+ }
+ int row = 2;
+ while ((line = br.readLine()) != null) {
+ cols = line.split("\t", -1);
+ if (cols.length != columns) {
+ throw new InvalidInputDataExecption("Invalid number of columns in row " + row, filename);
+ }
+ String id = cols[identifierColumn];
+ if (ids.contains(id)) {
+ throw new InvalidInputDataExecption("Id \"" + id + "\" is not unique.", filename);
+ }
+
+ String className = cols[typeColumn];
+ Class<? extends AnnotatedObject> clazz = elementUtils.getClassByName(className);
+ if (clazz == null) {
+ throw new InvalidInputDataExecption("Unknown element type: " + className, filename);
+ }
+ List<Product> products = new ArrayList<Product>();
+ String productString = cols[productsColumn];
+ for (String string : productString.split(",")) {
+ if (!string.isEmpty()) {
+ Element element = model.getSpeciesBySpeciesId(string.trim());
+ SpeciesAlias alias = model.getAliasesBySpeciesId(string.trim()).get(0);
+ Product product = new Product(alias, element);
+ products.add(product);
+ }
+ }
+ if (products.size() == 0) {
+ throw new InvalidInputDataExecption("List of products cannot be empty (row: " + row + ")", filename);
+ }
+
+ List<Reactant> reactants = new ArrayList<Reactant>();
+ String reactantString = cols[reactantsColumn];
+ for (String string : reactantString.split(",")) {
+ if (!string.isEmpty()) {
+ Element element = model.getSpeciesBySpeciesId(string.trim());
+ SpeciesAlias alias = model.getAliasesBySpeciesId(string.trim()).get(0);
+ Reactant product = new Reactant(alias, element);
+ reactants.add(product);
+ }
+ }
+ if (reactants.size() == 0) {
+ throw new InvalidInputDataExecption("List of reactants cannot be empty (row: " + row + ")", filename);
+ }
+
+ List<Modifier> modifiers = new ArrayList<Modifier>();
+ String modifierString = cols[modifiersColumn];
+ for (String string : modifierString.split(",")) {
+ if (!string.isEmpty()) {
+ Element element = model.getSpeciesBySpeciesId(string.trim());
+ SpeciesAlias alias = model.getAliasesBySpeciesId(string.trim()).get(0);
+ Modifier modifier = new Catalysis(alias, element);
+ modifiers.add(modifier);
+ }
+ }
+ Alias alias1 = products.get(0).getAlias();
+ Alias alias2 = reactants.get(0).getAlias();
+
+ Point2D middle = new Point2D.Double((alias1.getCenterX() + alias2.getCenterX()) / 2, (alias1.getCenterY() + alias2.getCenterY()) / 2);
+
+ Set<MiriamData> annotations = new HashSet<MiriamData>();
+ if (annotationsColumn != null) {
+ String[] annotationString = cols[annotationsColumn].split(",");
+ for (String string : annotationString) {
+ if (!string.isEmpty()) {
+ try {
+ annotations.add(MiriamType.getMiriamByUri(string));
+ } catch (InvalidArgumentException e) {
+ throw new InvalidInputDataExecption("Invalid miriam urn: " + string, filename);
+ }
+ }
+ }
+ }
+
+ try {
+ if (!Reaction.class.isAssignableFrom(clazz)) {
+ throw new InvalidInputDataExecption("Invalid reaction type type: " + className, filename);
+ }
+ Reaction reaction = (Reaction) clazz.newInstance();
+ for (Product product : products) {
+ product.setLine(new PolylineData(middle, product.getAlias().getCenter()));
+ reaction.addProduct(product);
+ }
+ for (Reactant reactant : reactants) {
+ reactant.setLine(new PolylineData(reactant.getAlias().getCenter(), middle));
+ reaction.addReactant(reactant);
+ }
+ for (Modifier modifier : modifiers) {
+ modifier.setLine(new PolylineData(middle, modifier.getAlias().getCenter()));
+ reaction.addModifier(modifier);
+ }
+ reaction.addMiriamData(annotations);
+ reaction.setElementId(id);
+ result.add(reaction);
+ } catch (InstantiationException e) {
+ throw new InvalidStateException(e);
+ } catch (IllegalAccessException e) {
+ throw new InvalidStateException(e);
+ }
+ row++;
+ }
+ } finally {
+ br.close();
+ }
+ return result;
+ }
+
+ /**
+ * This method parses the data from input file into set of {@link Element
+ * elements}.
+ *
+ * @param filename
+ * nam of input file
+ * @return set of {@link Element elements}
+ * @throws InvalidInputDataExecption
+ * thrown when the input data is invalid
+ * @throws IOException
+ * thrown when there is a problem with input file
+ */
+ private Set<Element> getNodes(String filename) throws InvalidInputDataExecption, IOException {
+ ElementUtils elementUtils = new ElementUtils();
+
+ Set<Element> result = new HashSet<Element>();
+ Set<String> ids = new HashSet<String>();
+
+ Integer identifierColumn = null;
+ Integer typeColumn = null;
+ Integer nameColumn = null;
+ Integer annotationsColumn = null;
+
+ BufferedReader br = new BufferedReader(new FileReader(new File(filename)));
+ try {
+ String line = br.readLine();
+ String[] cols = line.split("\t", -1);
+ int columns = cols.length;
+ for (int i = 0; i < cols.length; i++) {
+ if (cols[i].equalsIgnoreCase(RunOptions.IDENTIFIER_NODES_HEADER)) {
+ identifierColumn = i;
+ } else if (cols[i].equalsIgnoreCase(RunOptions.TYPE_NODES_HEADER)) {
+ typeColumn = i;
+ } else if (cols[i].equalsIgnoreCase(RunOptions.NAME_NODES_HEADER)) {
+ nameColumn = i;
+ } else if (cols[i].equalsIgnoreCase(RunOptions.ANNOTATIONS_NODES_HEADER)) {
+ annotationsColumn = i;
+ } else {
+ throw new InvalidInputDataExecption("Unknown column name " + cols[i], filename);
+ }
+ }
+ if (identifierColumn == null) {
+ throw new InvalidInputDataExecption("No \"" + RunOptions.IDENTIFIER_NODES_HEADER + "\" defined.", filename);
+ }
+ if (typeColumn == null) {
+ throw new InvalidInputDataExecption("No \"" + RunOptions.TYPE_NODES_HEADER + "\" defined.", filename);
+ }
+ if (nameColumn == null) {
+ throw new InvalidInputDataExecption("No \"" + RunOptions.NAME_NODES_HEADER + "\" defined.", filename);
+ }
+ int row = 2;
+ while ((line = br.readLine()) != null) {
+ if (line.isEmpty()) {
+ continue;
+ }
+ cols = line.split("\t", -1);
+ if (cols.length != columns) {
+ throw new InvalidInputDataExecption(
+ "Invalid number of columns in row " + row + ". Expected " + columns + ", but " + cols.length + " found", filename);
+ }
+ String id = cols[identifierColumn];
+ if (ids.contains(id)) {
+ throw new InvalidInputDataExecption("Id \"" + id + "\" is not unique.", filename);
+ }
+
+ String className = cols[typeColumn];
+ Class<? extends AnnotatedObject> clazz = elementUtils.getClassByName(className);
+ if (clazz == null) {
+ throw new InvalidInputDataExecption("Unknown element type: " + className, filename);
+ }
+ String name = cols[nameColumn];
+ if (name.isEmpty()) {
+ throw new InvalidInputDataExecption("Name cannot be empty (row " + row + ").", filename);
+ }
+ Set<MiriamData> annotations = new HashSet<MiriamData>();
+ if (annotationsColumn != null) {
+ String[] annotationString = cols[annotationsColumn].split(",");
+ for (String string : annotationString) {
+ if (!string.isEmpty()) {
+ try {
+ annotations.add(MiriamType.getMiriamByUri(string));
+ } catch (InvalidArgumentException e) {
+ throw new InvalidInputDataExecption("Invalid miriam urn: " + string, filename);
+ }
+ }
+ }
+ }
+
+ try {
+ if (!Element.class.isAssignableFrom(clazz)) {
+ throw new InvalidInputDataExecption("Invliad element type: " + className, filename);
+ }
+ Element element = (Element) clazz.newInstance();
+ element.setName(name);
+ element.addMiriamData(annotations);
+ element.setElementId(id);
+ result.add(element);
+ } catch (InstantiationException e) {
+ throw new InvalidStateException(e);
+ } catch (IllegalAccessException e) {
+ throw new InvalidStateException(e);
+ }
+ row++;
+ }
+ } finally {
+ br.close();
+ }
+
+ return result;
+ }
+
+ /**
+ * @return the mc
+ * @see #mc
+ */
+ public MiriamConnector getMc() {
+ return mc;
+ }
+
+ /**
+ * @param mc
+ * the mc to set
+ * @see #mc
+ */
+ public void setMc(MiriamConnector mc) {
+ this.mc = mc;
+ }
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/PdMapAnnotations.java b/console/src/main/java/lcsb/mapviewer/run/PdMapAnnotations.java
index fdd4685430be8a8253a85e4d7e84b4f8d051dbf9..2ddc3a1ee4c4d397ffac106c40e9853ba427eadd 100644
--- a/console/src/main/java/lcsb/mapviewer/run/PdMapAnnotations.java
+++ b/console/src/main/java/lcsb/mapviewer/run/PdMapAnnotations.java
@@ -1,82 +1,82 @@
-package lcsb.mapviewer.run;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * Class with some PD map specific information.
- *
- * @author Piotr Gawron
- *
- */
-public final class PdMapAnnotations {
-
- /**
- * Default class constructor. Prevent initialization.
- */
- private PdMapAnnotations() {
-
- }
-
- /**
- * Returns url to pdmap with reaction selected on it.
- *
- * @param reaction
- * reaction to be selected
- * @return url to the reaction in pd map
- */
- public static String getLinkForReaction(Reaction reaction) {
- return Configuration.PUBLICALY_AVAILABLE_PD_MAP + "&search=reaction:" + reaction.getIdReaction();
- }
-
- /**
- * Returns filename of the last available version of pd project from testFiles
- * directory.
- *
- * @return filename of the last available version of pd project
- * @throws FileNotFoundException
- * thrown when file cannpt be found
- */
- public static String getLastPdFilename() throws FileNotFoundException {
- String result = null;
- File folder = new File("testFiles/PD_full/");
- File[] listOfFiles = folder.listFiles();
-
- for (int i = 0; i < listOfFiles.length; i++) {
-
- if (listOfFiles[i].isFile() && listOfFiles[i].getAbsolutePath().toLowerCase().endsWith("xml")) {
- if (result == null) {
- result = listOfFiles[i].getAbsolutePath();
- } else {
- if (result.compareTo(listOfFiles[i].getAbsolutePath()) < 0) {
- result = listOfFiles[i].getAbsolutePath();
- }
- }
- }
- }
- if (result == null) {
- throw new FileNotFoundException();
- } else {
- return result;
- }
- }
-
- /**
- * Returns version of the last pd file project.
- *
- * @return version of the last pd file project
- */
- public static String getLastPdVersion() {
- String result = null;
- try {
- String[] tokens = getLastPdFilename().split("[\\/\\\\]");
- result = tokens[tokens.length - 1].replace(".xml", "");
- } catch (FileNotFoundException e) {
- return null;
- }
- return result;
- }
-}
+package lcsb.mapviewer.run;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * Class with some PD map specific information.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class PdMapAnnotations {
+
+ /**
+ * Default class constructor. Prevent initialization.
+ */
+ private PdMapAnnotations() {
+
+ }
+
+ /**
+ * Returns url to pdmap with reaction selected on it.
+ *
+ * @param reaction
+ * reaction to be selected
+ * @return url to the reaction in pd map
+ */
+ public static String getLinkForReaction(Reaction reaction) {
+ return Configuration.PUBLICALY_AVAILABLE_PD_MAP + "&search=reaction:" + reaction.getIdReaction();
+ }
+
+ /**
+ * Returns filename of the last available version of pd project from testFiles
+ * directory.
+ *
+ * @return filename of the last available version of pd project
+ * @throws FileNotFoundException
+ * thrown when file cannpt be found
+ */
+ public static String getLastPdFilename() throws FileNotFoundException {
+ String result = null;
+ File folder = new File("testFiles/PD_full/");
+ File[] listOfFiles = folder.listFiles();
+
+ for (int i = 0; i < listOfFiles.length; i++) {
+
+ if (listOfFiles[i].isFile() && listOfFiles[i].getAbsolutePath().toLowerCase().endsWith("xml")) {
+ if (result == null) {
+ result = listOfFiles[i].getAbsolutePath();
+ } else {
+ if (result.compareTo(listOfFiles[i].getAbsolutePath()) < 0) {
+ result = listOfFiles[i].getAbsolutePath();
+ }
+ }
+ }
+ }
+ if (result == null) {
+ throw new FileNotFoundException();
+ } else {
+ return result;
+ }
+ }
+
+ /**
+ * Returns version of the last pd file project.
+ *
+ * @return version of the last pd file project
+ */
+ public static String getLastPdVersion() {
+ String result = null;
+ try {
+ String[] tokens = getLastPdFilename().split("[\\/\\\\]");
+ result = tokens[tokens.length - 1].replace(".xml", "");
+ } catch (FileNotFoundException e) {
+ return null;
+ }
+ return result;
+ }
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java b/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
index d155f5dcd01d738514ff858668c160e0b3a1c7f2..74ea907a171577ae1ca7cedcd3dcca5097a91194 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
@@ -1,405 +1,405 @@
-package lcsb.mapviewer.run;
-
-import static org.junit.Assert.fail;
-
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.io.UnsupportedEncodingException;
-import java.text.DecimalFormat;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.ApplicationContextLoader;
-import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
-import lcsb.mapviewer.reactome.model.ReactomeReactionlikeEvent;
-import lcsb.mapviewer.reactome.utils.ComparatorException;
-import lcsb.mapviewer.reactome.utils.DataFormatter;
-import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
-import lcsb.mapviewer.reactome.utils.ReactionComparator;
-import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
-import lcsb.mapviewer.reactome.utils.comparators.MatchResult;
-import lcsb.mapviewer.reactome.utils.comparators.MatchResult.MatchStatus;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.PropertyConfigurator;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * This class generates report of comparison between data on PD-map and
- * reactome.
- *
- * @author Piotr Gawron
- *
- */
-
-public class ReactomeComparison {
- /**
- * Number of nanoseconds in second :).
- */
- private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
-
- /**
- * Local model used for comparison.
- */
- private Model model;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ReactomeComparison.class);
-
-
- /**
- * Comparator of reactions between our model and reactome.
- */
- @Autowired
- private ReactionComparator reactionComparator;
-
- /**
- * Class used for accessing reactome data.
- */
- @Autowired
- private DataSourceUpdater rc;
-
- /**
- * Util class used for manipulating information in reactome objects.
- */
- @Autowired
- private ReactomeQueryUtil rcu;
-
- /**
- * Formatter used for reaction comparison.
- */
- @Autowired
- private DataFormatter dataFormatter;
-
- /**
- * Static main method used to run this stand alone code.
- *
- * @param args
- * command line arguments
- */
- public static void main(String[] args) {
- long startTime = System.nanoTime();
- PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
- ReactomeComparison main = new ReactomeComparison();
- ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
- ApplicationContextLoader.injectDependencies(main);
- main.run();
- long endTime = System.nanoTime();
-
- long duration = endTime - startTime;
- double sec = duration / NANOSECONDS_IN_SECOND;
- System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
- }
-
- /**
- * Executes comparison between model and reactome representation.
- */
- public void run() {
- try {
- model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
-
- Set<String> list = new HashSet<String>();
-
- for (Element element : model.getElements()) {
- if (element instanceof Species) {
- list.add(((Species) element).getName());
- }
- }
- logger.debug("Species: " + list.size());
-
- List<String> ids = new ArrayList<String>();
- for (Reaction reaction : model.getReactions()) {
- ids.add(reaction.getIdReaction());
- }
- Collections.sort(ids);
- List<MatchResult> results = new ArrayList<MatchResult>();
-
- printHeader();
- int i = 0;
- for (String string : ids) {
- Reaction reaction = model.getReactionByReactionId(string);
- logger.info("Reaction: " + string + "; " + (i++) + "/" + ids.size());
- if (rcu.getReactomeIdentifierForReaction(reaction) != null) {
- MatchResult result = checkReaction(string);
- if (result != null) {
- results.add(result);
- printResult(result);
- }
- } else {
- ReactomeReactionlikeEvent reactomReaction = rcu.getSimilarReaction(reaction);
- if (reactomReaction != null) {
- MatchResult matchResult = new MatchResult();
- matchResult.setStatus(MatchStatus.SIMILAR_REACTION_FOUND);
- matchResult.setLocalReaction(reaction);
- matchResult.setReactomeReaction(reactomReaction);
- results.add(matchResult);
- printResult(matchResult);
-
- }
- }
- }
- printFooter(results);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
-
- }
-
- /**
- * Prints report footer.
- *
- * @param results
- * results used in the report
- */
- private void printFooter(List<MatchResult> results) {
- writer.println("</table>");
-
- int ok = 0;
- int mismatch = 0;
- int severe = 0;
- int similar = 0;
- for (MatchResult matchResult : results) {
- if (matchResult.getStatus() == MatchStatus.OK) {
- ok++;
- } else if (matchResult.getStatus() == MatchStatus.MISMATCH) {
- mismatch++;
- } else if (matchResult.getStatus() == MatchStatus.SIMILAR_REACTION_FOUND) {
- similar++;
- } else {
- severe++;
- }
- }
- writer.println("<p>Reactions checked: " + (results.size()) + "</p>");
- writer.println("<p>OK: " + ok + "</p>");
- writer.println("<p>MISMATCH: " + mismatch + "</p>");
- writer.println("<p>SEVERE PROBLEMS: " + severe + "</p>");
- writer.println("<p>SIMILAR: " + similar + "</p>");
-
- writer.println("</body></html>");
- writer.close();
-
- }
-
- /**
- * Object to which the report is written.
- */
- private PrintWriter writer;
-
- /**
- * Creates report stream and prints header of the report.
- *
- * @throws FileNotFoundException
- * if there is a problem with creating report file
- * @throws UnsupportedEncodingException
- * thrown when there are problems with encoding
- */
- private void printHeader() throws FileNotFoundException, UnsupportedEncodingException {
- writer = new PrintWriter("out/report/report.html", "UTF-8");
- writer.println("<html><head></head><body>");
- writer.println("<table cellspacing=\"0\">");
-
- String resultString = "<tr>";
- resultString += "<td" + style + ">Reaction</td>";
- resultString += "<td" + style + ">REACTOME ID</td>";
- resultString += "<td" + style + ">Status</td>";
- resultString += "<td" + style + ">Similarity</td>";
- resultString += "<td" + style + ">Unknown reaction input</td>";
- resultString += "<td" + style + ">Unknown reaction modifier</td>";
- resultString += "<td" + style + ">Unknown reaction output</td>";
- resultString += "<td" + style + ">Unknown reactome input</td>";
- resultString += "<td" + style + ">Unknown reactome modifier</td>";
- resultString += "<td" + style + ">Unknown reactome output</td>";
- resultString += "</tr>";
- writer.println(resultString);
-
- }
-
- /**
- * Formatter of decimal numbers.
- */
- private DecimalFormat df = new DecimalFormat("#.##");
-
- /**
- * Style used by report cells.
- */
- private String style = " style=\"border-width:1;border-style:solid;border-color:#000000;\" ";
-
- /**
- * Prints result row.
- *
- * @param result
- * result to be printed
- * @throws IOException
- * @throws AnnotatorException
- */
- private void printResult(MatchResult result) throws IOException, AnnotatorException {
- String color = "#000000";
- String status = "";
- String error = "";
- switch (result.getStatus()) {
- case OK:
- color = "#52D017";
- status = "OK";
- error = "<td colspan=\"6\" " + style + "></td>";
- return;
- case SIMILAR_REACTION_FOUND:
- color = "#5757E0";
- status = "SIMILAR";
- error = "<td colspan=\"6\" " + style + "></td>";
- return;
- case MISMATCH:
- color = "#FFFF00";
- status = "MISMATCH";
- error += "<td" + style + ">" + dataFormatter.getInvalidLocalInputString(result) + " </td>";
- error += "<td" + style + ">" + dataFormatter.getInvalidLocalModifierString(result) + " </td>";
- error += "<td" + style + ">" + dataFormatter.getInvalidLocalOutputString(result) + " </td>";
- error += "<td" + style + ">" + dataFormatter.getInvalidReactomeInputString(result) + " </td>";
- error += "<td" + style + ">" + dataFormatter.getInvalidReactomeModifierString(result) + " </td>";
- error += "<td" + style + ">" + dataFormatter.getInvalidReactomeOutputString(result) + " </td>";
- break;
- case INVALID_REACTOME_ID:
- color = "#FF0000";
- status = "REACTOME id does not point to reaction";
- error = "<td colspan=\"6\" " + style + "></td>";
- return;
- case INVALID_REACTION_WITH_PHEONTYPE:
- color = "#FF0000";
- status = "Impossible to map reaction to reactome - reaction contains Phenotype";
- error = "<td colspan=\"6\" " + style + "></td>";
- return;
- default:
- return;
- }
- String resultString = "<tr bgcolor = \"" + color + "\">";
- String reactionId = result.getLocalReaction().getIdReaction();
- String reactomId = null;
- reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
-
- resultString += "<td" + style + "><a target=\"_blank\" href=\"" + PdMapAnnotations.getLinkForReaction(result.getLocalReaction()) + "\">" + reactionId
- + "</a> ";
- resultString += "<a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
-
- if (result.getReactomeReaction() != null) {
- reactomId = result.getReactomeReaction().getStableIdentifier().getIdentifier() + "."
- + result.getReactomeReaction().getStableIdentifier().getIdentifierVersion();
- } else {
- reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
- }
-
- resultString += "<td" + style + "><a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
- resultString += "<td" + style + ">" + status + "</td>";
- resultString += "<td" + style + ">" + df.format(result.getScore() * IProgressUpdater.MAX_PROGRESS) + "%</td>";
- resultString += error;
- resultString += "</tr>";
- writer.println(resultString);
- System.out.println(resultString);
- }
-
- /**
- * Compares our model reaction to reactome representation.
- *
- * @param id
- * identifier of our reaction
- * @return result of reaction comparison
- * @throws IOException
- * thrown whene there are problems accessing reactome reaction
- * @throws ComparatorException
- */
- private MatchResult checkReaction(String id) throws IOException, ComparatorException {
- return checkReaction(model.getReactionByReactionId(id));
- }
-
- /**
- * Compares our model reaction to reactome representation.
- *
- * @param reaction
- * our reaction
- * @return result of reaction comparison
- * @throws IOException
- * thrown whene there are problems accessing reactome reaction
- * @throws ComparatorException
- */
- private MatchResult checkReaction(Reaction reaction) throws IOException, ComparatorException {
- String stableIdentifier = rcu.getReactomeIdentifierForReaction(reaction);
- if (stableIdentifier != null) {
- String identifier = stableIdentifier.split("\\.")[0];
- String version = stableIdentifier.split("\\.")[1];
-
- ReactomeDatabaseObject object = rc.getFullObjectForStableIdentifier(identifier, version);
- if (object != null && object instanceof ReactomeReactionlikeEvent) {
- return reactionComparator.compareReactions(reaction, (ReactomeReactionlikeEvent) object);
-
- } else {
- MatchResult result = new MatchResult();
- result.setLocalReaction(reaction);
- result.setStatus(MatchStatus.INVALID_REACTOME_ID);
- return result;
- }
- }
- return null;
- }
-
- /**
- * @return the reactionComparator
- */
- public ReactionComparator getReactionComparator() {
- return reactionComparator;
- }
-
- /**
- * @param reactionComparator
- * the reactionComparator to set
- */
- public void setReactionComparator(ReactionComparator reactionComparator) {
- this.reactionComparator = reactionComparator;
- }
-
- /**
- * @return the dataFormatter
- */
- public DataFormatter getDataFormatter() {
- return dataFormatter;
- }
-
- /**
- * @param dataFormatter
- * the dataFormatter to set
- */
- public void setDataFormatter(DataFormatter dataFormatter) {
- this.dataFormatter = dataFormatter;
- }
-
- /**
- * @return the rc
- * @see #rc
- */
- public DataSourceUpdater getRc() {
- return rc;
- }
-
- /**
- * @param rc
- * the rc to set
- * @see #rc
- */
- public void setRc(DataSourceUpdater rc) {
- this.rc = rc;
- }
-
-}
+package lcsb.mapviewer.run;
+
+import static org.junit.Assert.fail;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.UnsupportedEncodingException;
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.persist.ApplicationContextLoader;
+import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
+import lcsb.mapviewer.reactome.model.ReactomeReactionlikeEvent;
+import lcsb.mapviewer.reactome.utils.ComparatorException;
+import lcsb.mapviewer.reactome.utils.DataFormatter;
+import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
+import lcsb.mapviewer.reactome.utils.ReactionComparator;
+import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
+import lcsb.mapviewer.reactome.utils.comparators.MatchResult;
+import lcsb.mapviewer.reactome.utils.comparators.MatchResult.MatchStatus;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.PropertyConfigurator;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * This class generates report of comparison between data on PD-map and
+ * reactome.
+ *
+ * @author Piotr Gawron
+ *
+ */
+
+public class ReactomeComparison {
+ /**
+ * Number of nanoseconds in second :).
+ */
+ private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
+
+ /**
+ * Local model used for comparison.
+ */
+ private Model model;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ReactomeComparison.class);
+
+
+ /**
+ * Comparator of reactions between our model and reactome.
+ */
+ @Autowired
+ private ReactionComparator reactionComparator;
+
+ /**
+ * Class used for accessing reactome data.
+ */
+ @Autowired
+ private DataSourceUpdater rc;
+
+ /**
+ * Util class used for manipulating information in reactome objects.
+ */
+ @Autowired
+ private ReactomeQueryUtil rcu;
+
+ /**
+ * Formatter used for reaction comparison.
+ */
+ @Autowired
+ private DataFormatter dataFormatter;
+
+ /**
+ * Static main method used to run this stand alone code.
+ *
+ * @param args
+ * command line arguments
+ */
+ public static void main(String[] args) {
+ long startTime = System.nanoTime();
+ PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
+ ReactomeComparison main = new ReactomeComparison();
+ ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+ ApplicationContextLoader.injectDependencies(main);
+ main.run();
+ long endTime = System.nanoTime();
+
+ long duration = endTime - startTime;
+ double sec = duration / NANOSECONDS_IN_SECOND;
+ System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
+ }
+
+ /**
+ * Executes comparison between model and reactome representation.
+ */
+ public void run() {
+ try {
+ model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
+
+ Set<String> list = new HashSet<String>();
+
+ for (Element element : model.getElements()) {
+ if (element instanceof Species) {
+ list.add(((Species) element).getName());
+ }
+ }
+ logger.debug("Species: " + list.size());
+
+ List<String> ids = new ArrayList<String>();
+ for (Reaction reaction : model.getReactions()) {
+ ids.add(reaction.getIdReaction());
+ }
+ Collections.sort(ids);
+ List<MatchResult> results = new ArrayList<MatchResult>();
+
+ printHeader();
+ int i = 0;
+ for (String string : ids) {
+ Reaction reaction = model.getReactionByReactionId(string);
+ logger.info("Reaction: " + string + "; " + (i++) + "/" + ids.size());
+ if (rcu.getReactomeIdentifierForReaction(reaction) != null) {
+ MatchResult result = checkReaction(string);
+ if (result != null) {
+ results.add(result);
+ printResult(result);
+ }
+ } else {
+ ReactomeReactionlikeEvent reactomReaction = rcu.getSimilarReaction(reaction);
+ if (reactomReaction != null) {
+ MatchResult matchResult = new MatchResult();
+ matchResult.setStatus(MatchStatus.SIMILAR_REACTION_FOUND);
+ matchResult.setLocalReaction(reaction);
+ matchResult.setReactomeReaction(reactomReaction);
+ results.add(matchResult);
+ printResult(matchResult);
+
+ }
+ }
+ }
+ printFooter(results);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+
+ }
+
+ /**
+ * Prints report footer.
+ *
+ * @param results
+ * results used in the report
+ */
+ private void printFooter(List<MatchResult> results) {
+ writer.println("</table>");
+
+ int ok = 0;
+ int mismatch = 0;
+ int severe = 0;
+ int similar = 0;
+ for (MatchResult matchResult : results) {
+ if (matchResult.getStatus() == MatchStatus.OK) {
+ ok++;
+ } else if (matchResult.getStatus() == MatchStatus.MISMATCH) {
+ mismatch++;
+ } else if (matchResult.getStatus() == MatchStatus.SIMILAR_REACTION_FOUND) {
+ similar++;
+ } else {
+ severe++;
+ }
+ }
+ writer.println("<p>Reactions checked: " + (results.size()) + "</p>");
+ writer.println("<p>OK: " + ok + "</p>");
+ writer.println("<p>MISMATCH: " + mismatch + "</p>");
+ writer.println("<p>SEVERE PROBLEMS: " + severe + "</p>");
+ writer.println("<p>SIMILAR: " + similar + "</p>");
+
+ writer.println("</body></html>");
+ writer.close();
+
+ }
+
+ /**
+ * Object to which the report is written.
+ */
+ private PrintWriter writer;
+
+ /**
+ * Creates report stream and prints header of the report.
+ *
+ * @throws FileNotFoundException
+ * if there is a problem with creating report file
+ * @throws UnsupportedEncodingException
+ * thrown when there are problems with encoding
+ */
+ private void printHeader() throws FileNotFoundException, UnsupportedEncodingException {
+ writer = new PrintWriter("out/report/report.html", "UTF-8");
+ writer.println("<html><head></head><body>");
+ writer.println("<table cellspacing=\"0\">");
+
+ String resultString = "<tr>";
+ resultString += "<td" + style + ">Reaction</td>";
+ resultString += "<td" + style + ">REACTOME ID</td>";
+ resultString += "<td" + style + ">Status</td>";
+ resultString += "<td" + style + ">Similarity</td>";
+ resultString += "<td" + style + ">Unknown reaction input</td>";
+ resultString += "<td" + style + ">Unknown reaction modifier</td>";
+ resultString += "<td" + style + ">Unknown reaction output</td>";
+ resultString += "<td" + style + ">Unknown reactome input</td>";
+ resultString += "<td" + style + ">Unknown reactome modifier</td>";
+ resultString += "<td" + style + ">Unknown reactome output</td>";
+ resultString += "</tr>";
+ writer.println(resultString);
+
+ }
+
+ /**
+ * Formatter of decimal numbers.
+ */
+ private DecimalFormat df = new DecimalFormat("#.##");
+
+ /**
+ * Style used by report cells.
+ */
+ private String style = " style=\"border-width:1;border-style:solid;border-color:#000000;\" ";
+
+ /**
+ * Prints result row.
+ *
+ * @param result
+ * result to be printed
+ * @throws IOException
+ * @throws AnnotatorException
+ */
+ private void printResult(MatchResult result) throws IOException, AnnotatorException {
+ String color = "#000000";
+ String status = "";
+ String error = "";
+ switch (result.getStatus()) {
+ case OK:
+ color = "#52D017";
+ status = "OK";
+ error = "<td colspan=\"6\" " + style + "></td>";
+ return;
+ case SIMILAR_REACTION_FOUND:
+ color = "#5757E0";
+ status = "SIMILAR";
+ error = "<td colspan=\"6\" " + style + "></td>";
+ return;
+ case MISMATCH:
+ color = "#FFFF00";
+ status = "MISMATCH";
+ error += "<td" + style + ">" + dataFormatter.getInvalidLocalInputString(result) + " </td>";
+ error += "<td" + style + ">" + dataFormatter.getInvalidLocalModifierString(result) + " </td>";
+ error += "<td" + style + ">" + dataFormatter.getInvalidLocalOutputString(result) + " </td>";
+ error += "<td" + style + ">" + dataFormatter.getInvalidReactomeInputString(result) + " </td>";
+ error += "<td" + style + ">" + dataFormatter.getInvalidReactomeModifierString(result) + " </td>";
+ error += "<td" + style + ">" + dataFormatter.getInvalidReactomeOutputString(result) + " </td>";
+ break;
+ case INVALID_REACTOME_ID:
+ color = "#FF0000";
+ status = "REACTOME id does not point to reaction";
+ error = "<td colspan=\"6\" " + style + "></td>";
+ return;
+ case INVALID_REACTION_WITH_PHEONTYPE:
+ color = "#FF0000";
+ status = "Impossible to map reaction to reactome - reaction contains Phenotype";
+ error = "<td colspan=\"6\" " + style + "></td>";
+ return;
+ default:
+ return;
+ }
+ String resultString = "<tr bgcolor = \"" + color + "\">";
+ String reactionId = result.getLocalReaction().getIdReaction();
+ String reactomId = null;
+ reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
+
+ resultString += "<td" + style + "><a target=\"_blank\" href=\"" + PdMapAnnotations.getLinkForReaction(result.getLocalReaction()) + "\">" + reactionId
+ + "</a> ";
+ resultString += "<a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
+
+ if (result.getReactomeReaction() != null) {
+ reactomId = result.getReactomeReaction().getStableIdentifier().getIdentifier() + "."
+ + result.getReactomeReaction().getStableIdentifier().getIdentifierVersion();
+ } else {
+ reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
+ }
+
+ resultString += "<td" + style + "><a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
+ resultString += "<td" + style + ">" + status + "</td>";
+ resultString += "<td" + style + ">" + df.format(result.getScore() * IProgressUpdater.MAX_PROGRESS) + "%</td>";
+ resultString += error;
+ resultString += "</tr>";
+ writer.println(resultString);
+ System.out.println(resultString);
+ }
+
+ /**
+ * Compares our model reaction to reactome representation.
+ *
+ * @param id
+ * identifier of our reaction
+ * @return result of reaction comparison
+ * @throws IOException
+ * thrown whene there are problems accessing reactome reaction
+ * @throws ComparatorException
+ */
+ private MatchResult checkReaction(String id) throws IOException, ComparatorException {
+ return checkReaction(model.getReactionByReactionId(id));
+ }
+
+ /**
+ * Compares our model reaction to reactome representation.
+ *
+ * @param reaction
+ * our reaction
+ * @return result of reaction comparison
+ * @throws IOException
+ * thrown whene there are problems accessing reactome reaction
+ * @throws ComparatorException
+ */
+ private MatchResult checkReaction(Reaction reaction) throws IOException, ComparatorException {
+ String stableIdentifier = rcu.getReactomeIdentifierForReaction(reaction);
+ if (stableIdentifier != null) {
+ String identifier = stableIdentifier.split("\\.")[0];
+ String version = stableIdentifier.split("\\.")[1];
+
+ ReactomeDatabaseObject object = rc.getFullObjectForStableIdentifier(identifier, version);
+ if (object != null && object instanceof ReactomeReactionlikeEvent) {
+ return reactionComparator.compareReactions(reaction, (ReactomeReactionlikeEvent) object);
+
+ } else {
+ MatchResult result = new MatchResult();
+ result.setLocalReaction(reaction);
+ result.setStatus(MatchStatus.INVALID_REACTOME_ID);
+ return result;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * @return the reactionComparator
+ */
+ public ReactionComparator getReactionComparator() {
+ return reactionComparator;
+ }
+
+ /**
+ * @param reactionComparator
+ * the reactionComparator to set
+ */
+ public void setReactionComparator(ReactionComparator reactionComparator) {
+ this.reactionComparator = reactionComparator;
+ }
+
+ /**
+ * @return the dataFormatter
+ */
+ public DataFormatter getDataFormatter() {
+ return dataFormatter;
+ }
+
+ /**
+ * @param dataFormatter
+ * the dataFormatter to set
+ */
+ public void setDataFormatter(DataFormatter dataFormatter) {
+ this.dataFormatter = dataFormatter;
+ }
+
+ /**
+ * @return the rc
+ * @see #rc
+ */
+ public DataSourceUpdater getRc() {
+ return rc;
+ }
+
+ /**
+ * @param rc
+ * the rc to set
+ * @see #rc
+ */
+ public void setRc(DataSourceUpdater rc) {
+ this.rc = rc;
+ }
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java b/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
index 40882f8f5de10bea924cf71b6390f23c524cee7d..556976542d2f47a551e080ef9f2594a0c8c2b971 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
@@ -1,616 +1,616 @@
-package lcsb.mapviewer.run;
-
-import java.awt.Rectangle;
-import java.awt.geom.Point2D;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.ApplicationContextLoader;
-import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
-import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
-import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.PropertyConfigurator;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * This class create a data that could be used by visualized in reactome
- * visualization framework. It was developed only for test purpose and has no
- * real value.
- */
-public class ReactomeExport {
- /**
- * Size of the map to vizualize.
- */
- private static final int DEFAULT_SIZE = 30000;
- /**
- * Bounds of the map to vizualize.
- */
- private static Rectangle bound = new Rectangle(0, 0, DEFAULT_SIZE, DEFAULT_SIZE);
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ReactomeExport.class.getName());
-
- /**
- * Class used for accessing reactome data.
- */
- @Autowired
- private DataSourceUpdater rc;
-
- /**
- * Util class used for manipulating information in reactome objects.
- */
- @Autowired
- private ReactomeQueryUtil rcu;
-
- /**
- * Static main method used to run this stand alone code.
- *
- * @param args
- * command line arguments
- */
- public static void main(String[] args) {
- PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
- ReactomeExport main = new ReactomeExport();
- ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
- ApplicationContextLoader.injectDependencies(main);
- main.run();
-
- }
-
- /**
- * String containing the result of export.
- */
- private String result = "";
-
- /**
- * Adds text to the output.
- *
- * @param str
- * text to add
- */
- private void print(String str) {
- result += str;
- }
-
- /**
- * Identifier counter used for generating identifiers in the reactome
- * visualization model.
- */
- private int id = 0;
-
- /**
- * Map between aliases in our model and identifiers that will be used in the
- * reactome vizualization model.
- */
- private Map<Alias, Integer> tempIds = new HashMap<Alias, Integer>();
-
- /**
- * Creates reactome identifier for alias.
- *
- * @param alias
- * object for which identifier is created
- * @return identifier of the alias
- */
- public int addElement(Alias alias) {
- int result = -1;
- if (tempIds.containsKey(alias)) {
- result = tempIds.get(alias);
- } else {
- tempIds.put(alias, ++id);
- result = id;
-
- if (alias instanceof ComplexAlias) {
- for (Alias a : ((ComplexAlias) alias).getAliases()) {
- addElement(a);
- }
- } else if (alias instanceof CompartmentAlias) {
- for (Alias a : ((CompartmentAlias) alias).getAliases()) {
- addElement(a);
- }
- }
- }
-
- return result;
- }
-
- /**
- * Creates file with reactome vizualization.
- */
- private void run() {
- CellDesignerXmlParser p = new CellDesignerXmlParser();
- try {
- Model model = p.createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
- print("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
- print("<Process reactomeId=\"0\">\n");
- print("<Properties>\n");
- print("<displayName>PD map</displayName>\n");
- print("</Properties>\n");
- printAliases(model);
- printReactions(model);
- print("</Process>\n");
-
- PrintWriter writer = new PrintWriter("out/report/reactome-viewer.xml", "UTF-8");
- writer.print(result);
- writer.close();
-
- } catch (Exception e) {
- logger.error(e.getMessage());
- e.printStackTrace();
- }
-
- }
-
- /**
- * Creates representation of the aliases in the reactome visualization model.
- *
- * @param model
- * our model to be visualized
- * @throws IOException
- * thrown when there are problems accessing reactome database
- */
- private void printAliases(Model model) throws IOException {
- print("<Nodes>\n");
- List<Alias> aliases = new ArrayList<Alias>();
- aliases.addAll(model.getAliases());
- Collections.sort(aliases, Alias.SIZE_COMPARATOR);
- for (Alias alias : aliases) {
- if (!aliasFeasible(alias)) {
- continue;
- }
- int currId = addElement(alias);
- Element element = null;
- Map<String, String> parameters = new HashMap<String, String>();
- Map<String, String> attributes = new HashMap<String, String>();
-
- attributes.put("id", currId + "");
- attributes.put("position", (int) alias.getCenterX() + " " + (int) alias.getCenterY());
- attributes.put("bounds", alias.getX().intValue() + " " + alias.getY().intValue() + " " + alias.getWidth().intValue() + " "
- + alias.getHeight().intValue());
- attributes.put("textPosition", (int) alias.getCenterX() + " " + (int) alias.getCenterY());
- attributes.put("reactomeId", "0");
-
- Set<Integer> components = new HashSet<Integer>();
- String type = "";
- if (alias instanceof SpeciesAlias) {
- element = ((SpeciesAlias) alias).getSpecies();
- String stableIdentifier = rcu.getReactomeIdentifierForSpecies(((SpeciesAlias) alias).getSpecies());
- if (stableIdentifier != null) {
- ReactomeDatabaseObject obj = rc.getFullObjectForStableIdentifier(stableIdentifier);
- if (obj != null && obj.getDbId() != null) {
- attributes.put("reactomeId", obj.getDbId() + "");
- }
- }
- parameters.put("displayName", ((Species) element).getName());
- if (alias instanceof ComplexAlias) {
- for (Alias a : ((ComplexAlias) alias).getAliases()) {
- components.add(addElement(a));
- }
- }
- }
- if (alias instanceof CompartmentAlias) {
- element = ((CompartmentAlias) alias).getCompartment();
- parameters.put("displayName", ((Compartment) element).getName());
- for (Alias a : ((CompartmentAlias) alias).getAliases()) {
- components.add(addElement(a));
- }
- }
-
- if (element instanceof ComplexSpecies) {
- type = "org.gk.render.RenderableComplex";
- attributes.put("hideComponents", "true");
- attributes.put("textPosition", (int) alias.getCenterX() + " " + (int) (alias.getY() + alias.getHeight()));
- } else if (element instanceof SimpleMolecule) {
- type = "org.gk.render.RenderableChemical";
- } else if (element instanceof Ion) {
- type = "org.gk.render.RenderableChemical";
- } else if (element instanceof Protein) {
- type = "org.gk.render.RenderableProtein";
- } else if (element instanceof Species) {
- type = "org.gk.render.RenderableEntity";
- } else if (element instanceof Compartment) {
- type = "org.gk.render.RenderableCompartment";
- } else {
- logger.debug("Ignoring: " + parameters.get("displayName") + "(" + element.getClass() + ")");
- continue;
- }
- print("<" + type);
- for (String string : attributes.keySet()) {
- print(" " + string + "=\"" + attributes.get(string) + "\"");
- }
- print(">");
- for (String key : parameters.keySet()) {
- print("<" + key + ">" + parameters.get(key) + "</" + key + ">");
- }
-
- if (components.size() != 0) {
- print("\n <Components>\n");
- for (Integer i : components) {
- print(" <Component id=\"" + i + "\"/>\n");
- }
- print(" </Components>\n");
- }
- print("</" + type + ">\n");
-
- }
- print("</Nodes>\n");
- }
-
- /**
- * Creates reactions in reactome visuazliation model from our model.
- *
- * @param model
- * model to be visualized
- * @throws IOException
- * thrown when there are problems with accessing reactome database
- */
- private void printReactions(Model model) throws IOException {
- print("<Edges>\n");
- for (Reaction reaction : model.getReactions()) {
- if (!isReactionFeasible(reaction)) {
- continue;
- }
- int currId = ++id;
- Map<String, String> parameters = new HashMap<String, String>();
- Map<Integer, String> inputs = new HashMap<Integer, String>();
- Map<Integer, String> outputs = new HashMap<Integer, String>();
- Map<Integer, String> catalysts = new HashMap<Integer, String>();
-
- Map<String, String> attributes = new HashMap<String, String>();
-
- attributes.put("id", currId + "");
- attributes.put("position", (int) reaction.getCenterPoint().getX() + " " + (int) reaction.getCenterPoint().getY());
- attributes.put("points", getReactionMiddlePoints(reaction));
- attributes.put("lineWidth", "1.0");
- attributes.put("reactomeId", "0");
-
- parameters.put("displayName", reaction.getIdReaction());
-
- String stableIdentifier = rcu.getReactomeIdentifierForReaction(reaction);
- if (stableIdentifier != null) {
- ReactomeDatabaseObject obj = rc.getFullObjectForStableIdentifier(stableIdentifier);
- if (obj != null && obj.getDbId() != null) {
- attributes.put("reactomeId", obj.getDbId() + "");
- }
- }
-
- for (ReactionNode node : reaction.getReactionNodes()) {
- Integer id = tempIds.get(node.getAlias());
- if (node instanceof Reactant) {
- inputs.put(id, getInputString((Reactant) node));
- } else if (node instanceof Product) {
- outputs.put(id, getOutputString((Product) node));
- } else if (node instanceof Modifier) {
- catalysts.put(id, getModifierString((Modifier) node));
- }
- }
-
- String type = "org.gk.render.RenderableReaction";
-
- print("<" + type);
- for (String string : attributes.keySet()) {
- print(" " + string + "=\"" + attributes.get(string) + "\"");
- }
- print(">\n");
- print(" <Properties>\n");
- for (String key : parameters.keySet()) {
- print(" <" + key + ">" + parameters.get(key) + "</" + key + ">\n");
- }
- print(" </Properties>\n");
-
- if (inputs.size() != 0) {
- print(" <Inputs>\n");
- for (Integer i : inputs.keySet()) {
- print(" <Input id=\"" + i + "\" points=\"" + inputs.get(i) + "\"/>\n");
- }
- print(" </Inputs>\n");
- }
- if (outputs.size() != 0) {
- print(" <Outputs>\n");
- for (Integer i : outputs.keySet()) {
- print(" <Output id=\"" + i + "\" points=\"" + outputs.get(i) + "\"/>\n");
- }
- print(" </Outputs>\n");
- }
- if (catalysts.size() != 0) {
- print(" <Catalysts>\n");
- for (Integer i : catalysts.keySet()) {
- print(" <Catalyst id=\"" + i + "\" points=\"" + catalysts.get(i) + "\"/>\n");
- }
- print(" </Catalysts>\n");
- }
- print("</" + type + ">\n");
-
- }
-
- print("</Edges>\n");
- }
-
- /**
- * Returns string representing modifier.
- *
- * @param node
- * modifier in our model
- * @return string representing modifier that can be used in reactome
- * visualization
- */
- private String getModifierString(ReactionNode node) {
- String result = null;
- List<Point2D> points = node.getLine().getPoints();
- for (int i = 0; i < points.size() - 1; i++) {
- if (result == null) {
- result = "";
- } else {
- result += ", ";
- }
- Point2D point = points.get(i);
- result += (int) point.getX() + " " + (int) point.getY();
- }
- return result;
- }
-
- /**
- * Returns string representing product.
- *
- * @param node
- * product in our model
- * @return string representing product that can be used in reactome
- * visualization
- */
- private String getOutputString(ReactionNode node) {
- for (NodeOperator tmpNode : node.getReaction().getOperators()) {
- if (tmpNode.isProductOperator()) {
- String result = null;
- List<Point2D> points = node.getLine().getPoints();
- for (int i = points.size() - 1; i >= 0; i--) {
- if (result == null) {
- result = "";
- } else {
- result += ", ";
- }
- Point2D point = points.get(i);
- result += (int) point.getX() + " " + (int) point.getY();
- }
- return result;
- }
- }
- Point2D point = node.getLine().getEndPoint();
- String result = (int) point.getX() + " " + (int) point.getY();
- return result;
- }
-
- /**
- * Returns string representing reactant.
- *
- * @param node
- * reactant in our model
- * @return string representing reactant that can be used in reactome
- * visualization
- */
- private String getInputString(ReactionNode node) {
- for (NodeOperator tmpNode : node.getReaction().getOperators()) {
- if (tmpNode.isReactantOperator()) {
- String result = null;
- List<Point2D> points = node.getLine().getPoints();
- for (int i = 0; i < points.size(); i++) {
- if (result == null) {
- result = "";
- } else {
- result += ", ";
- }
- Point2D point = points.get(i);
- result += (int) point.getX() + " " + (int) point.getY();
- }
- return result;
- }
- }
- Point2D point = node.getLine().getPoints().get(0);
- String result = (int) point.getX() + " " + (int) point.getY();
- return result;
- }
-
- /**
- * Check if reaction can be easily transformed into reactome vizualization
- * tool.
- *
- * @param reaction
- * reaction to be checked
- * @return <code>true</code> if reaction can be easily transformed,
- * <code>false</code> otherwise
- */
- private boolean isReactionFeasible(Reaction reaction) {
- for (ReactionNode node : reaction.getReactionNodes()) {
- if (!aliasFeasible(node.getAlias())) {
- return false;
- }
- }
- int counter = 0;
- for (NodeOperator node : reaction.getOperators()) {
- if (node.isProductOperator()) {
- counter++;
- }
- if (counter > 1) {
- logger.debug("To many operators in the input: " + reaction.getIdReaction());
- return false;
- }
- }
- counter = 0;
- for (NodeOperator node : reaction.getOperators()) {
- if (node.isReactantOperator()) {
- counter++;
- }
- if (counter > 1) {
- logger.debug("To many operators in the output: " + reaction.getIdReaction());
- return false;
- }
- }
- counter = 0;
- for (NodeOperator node : reaction.getOperators()) {
- if (node.isModifierOperator()) {
- logger.debug("To complicated catalyst: " + reaction.getIdReaction());
- return false;
- }
- }
- return true;
- }
-
- /**
- * Returns string representing reaction line.
- *
- * @param reaction
- * reaction to be transformed
- * @return string representing reaction line
- */
- private String getReactionMiddlePoints(Reaction reaction) {
- String result = null;
- NodeOperator node = null;
- for (NodeOperator n : reaction.getOperators()) {
- if (n.isReactantOperator()) {
- node = n;
- }
- }
- if (node != null) {
- for (Point2D point : node.getLine().getPoints()) {
- if (result == null) {
- result = (int) point.getX() + " " + (int) point.getY();
- } else {
- result += ", " + (int) point.getX() + " " + (int) point.getY();
- }
- }
- } else {
- AbstractNode tmp = null;
- for (AbstractNode reactionNode : reaction.getNodes()) {
- if (reactionNode instanceof Reactant) {
- tmp = reactionNode;
- }
- }
- List<Point2D> points = tmp.getLine().getPoints();
- for (int i = 0; i < points.size(); i++) {
- Point2D point = points.get(i);
- if (result == null) {
- result = (int) point.getX() + " " + (int) point.getY();
- } else {
- result += ", " + (int) point.getX() + " " + (int) point.getY();
- }
- }
- }
-
- node = null;
- for (NodeOperator n : reaction.getOperators()) {
- if (n.isProductOperator()) {
- node = n;
- }
- }
- if (node != null) {
- List<Point2D> points = node.getLine().getPoints();
- for (int i = points.size() - 1; i >= 0; i--) {
- Point2D point = points.get(i);
- if (result == null) {
- result = (int) point.getX() + " " + (int) point.getY();
- } else {
- result += ", " + (int) point.getX() + " " + (int) point.getY();
- }
- }
- } else {
- AbstractNode tmp = null;
- for (AbstractNode reactionNode : reaction.getNodes()) {
- if (reactionNode instanceof Product) {
- tmp = reactionNode;
- }
- }
- List<Point2D> points = tmp.getLine().getPoints();
- for (int i = 0; i < points.size(); i++) {
- Point2D point = points.get(i);
- if (result == null) {
- result = (int) point.getX() + " " + (int) point.getY();
- } else {
- result += ", " + (int) point.getX() + " " + (int) point.getY();
- }
- }
- }
-
- return result;
- }
-
- /**
- * Checks if alias can be put into reactome vizualization.
- *
- * @param alias
- * alias to check
- * @return <code>true</code> if alias can be put into reactome vizualization,
- * <code>false</code> otherwise
- */
- public boolean aliasFeasible(Alias alias) {
- Point2D point = new Point2D.Double(alias.getX(), alias.getY());
- Point2D point2 = new Point2D.Double(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
- if (bound.contains(point) && bound.contains(point2)) {
- return true;
- }
- return false;
- }
-
- /**
- * @return the rc
- * @see #rc
- */
- public DataSourceUpdater getRc() {
- return rc;
- }
-
- /**
- * @param rc
- * the rc to set
- * @see #rc
- */
- public void setRc(DataSourceUpdater rc) {
- this.rc = rc;
- }
-
- /**
- * @return the rcu
- * @see #rcu
- */
- public ReactomeQueryUtil getRcu() {
- return rcu;
- }
-
- /**
- * @param rcu
- * the rcu to set
- * @see #rcu
- */
- public void setRcu(ReactomeQueryUtil rcu) {
- this.rcu = rcu;
- }
-
-}
+package lcsb.mapviewer.run;
+
+import java.awt.Rectangle;
+import java.awt.geom.Point2D;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.ComplexSpecies;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.persist.ApplicationContextLoader;
+import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
+import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
+import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.PropertyConfigurator;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * This class create a data that could be used by visualized in reactome
+ * visualization framework. It was developed only for test purpose and has no
+ * real value.
+ */
+public class ReactomeExport {
+ /**
+ * Size of the map to vizualize.
+ */
+ private static final int DEFAULT_SIZE = 30000;
+ /**
+ * Bounds of the map to vizualize.
+ */
+ private static Rectangle bound = new Rectangle(0, 0, DEFAULT_SIZE, DEFAULT_SIZE);
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ReactomeExport.class.getName());
+
+ /**
+ * Class used for accessing reactome data.
+ */
+ @Autowired
+ private DataSourceUpdater rc;
+
+ /**
+ * Util class used for manipulating information in reactome objects.
+ */
+ @Autowired
+ private ReactomeQueryUtil rcu;
+
+ /**
+ * Static main method used to run this stand alone code.
+ *
+ * @param args
+ * command line arguments
+ */
+ public static void main(String[] args) {
+ PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
+ ReactomeExport main = new ReactomeExport();
+ ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+ ApplicationContextLoader.injectDependencies(main);
+ main.run();
+
+ }
+
+ /**
+ * String containing the result of export.
+ */
+ private String result = "";
+
+ /**
+ * Adds text to the output.
+ *
+ * @param str
+ * text to add
+ */
+ private void print(String str) {
+ result += str;
+ }
+
+ /**
+ * Identifier counter used for generating identifiers in the reactome
+ * visualization model.
+ */
+ private int id = 0;
+
+ /**
+ * Map between aliases in our model and identifiers that will be used in the
+ * reactome vizualization model.
+ */
+ private Map<Alias, Integer> tempIds = new HashMap<Alias, Integer>();
+
+ /**
+ * Creates reactome identifier for alias.
+ *
+ * @param alias
+ * object for which identifier is created
+ * @return identifier of the alias
+ */
+ public int addElement(Alias alias) {
+ int result = -1;
+ if (tempIds.containsKey(alias)) {
+ result = tempIds.get(alias);
+ } else {
+ tempIds.put(alias, ++id);
+ result = id;
+
+ if (alias instanceof ComplexAlias) {
+ for (Alias a : ((ComplexAlias) alias).getAliases()) {
+ addElement(a);
+ }
+ } else if (alias instanceof CompartmentAlias) {
+ for (Alias a : ((CompartmentAlias) alias).getAliases()) {
+ addElement(a);
+ }
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * Creates file with reactome vizualization.
+ */
+ private void run() {
+ CellDesignerXmlParser p = new CellDesignerXmlParser();
+ try {
+ Model model = p.createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
+ print("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
+ print("<Process reactomeId=\"0\">\n");
+ print("<Properties>\n");
+ print("<displayName>PD map</displayName>\n");
+ print("</Properties>\n");
+ printAliases(model);
+ printReactions(model);
+ print("</Process>\n");
+
+ PrintWriter writer = new PrintWriter("out/report/reactome-viewer.xml", "UTF-8");
+ writer.print(result);
+ writer.close();
+
+ } catch (Exception e) {
+ logger.error(e.getMessage());
+ e.printStackTrace();
+ }
+
+ }
+
+ /**
+ * Creates representation of the aliases in the reactome visualization model.
+ *
+ * @param model
+ * our model to be visualized
+ * @throws IOException
+ * thrown when there are problems accessing reactome database
+ */
+ private void printAliases(Model model) throws IOException {
+ print("<Nodes>\n");
+ List<Alias> aliases = new ArrayList<Alias>();
+ aliases.addAll(model.getAliases());
+ Collections.sort(aliases, Alias.SIZE_COMPARATOR);
+ for (Alias alias : aliases) {
+ if (!aliasFeasible(alias)) {
+ continue;
+ }
+ int currId = addElement(alias);
+ Element element = null;
+ Map<String, String> parameters = new HashMap<String, String>();
+ Map<String, String> attributes = new HashMap<String, String>();
+
+ attributes.put("id", currId + "");
+ attributes.put("position", (int) alias.getCenterX() + " " + (int) alias.getCenterY());
+ attributes.put("bounds", alias.getX().intValue() + " " + alias.getY().intValue() + " " + alias.getWidth().intValue() + " "
+ + alias.getHeight().intValue());
+ attributes.put("textPosition", (int) alias.getCenterX() + " " + (int) alias.getCenterY());
+ attributes.put("reactomeId", "0");
+
+ Set<Integer> components = new HashSet<Integer>();
+ String type = "";
+ if (alias instanceof SpeciesAlias) {
+ element = ((SpeciesAlias) alias).getSpecies();
+ String stableIdentifier = rcu.getReactomeIdentifierForSpecies(((SpeciesAlias) alias).getSpecies());
+ if (stableIdentifier != null) {
+ ReactomeDatabaseObject obj = rc.getFullObjectForStableIdentifier(stableIdentifier);
+ if (obj != null && obj.getDbId() != null) {
+ attributes.put("reactomeId", obj.getDbId() + "");
+ }
+ }
+ parameters.put("displayName", ((Species) element).getName());
+ if (alias instanceof ComplexAlias) {
+ for (Alias a : ((ComplexAlias) alias).getAliases()) {
+ components.add(addElement(a));
+ }
+ }
+ }
+ if (alias instanceof CompartmentAlias) {
+ element = ((CompartmentAlias) alias).getCompartment();
+ parameters.put("displayName", ((Compartment) element).getName());
+ for (Alias a : ((CompartmentAlias) alias).getAliases()) {
+ components.add(addElement(a));
+ }
+ }
+
+ if (element instanceof ComplexSpecies) {
+ type = "org.gk.render.RenderableComplex";
+ attributes.put("hideComponents", "true");
+ attributes.put("textPosition", (int) alias.getCenterX() + " " + (int) (alias.getY() + alias.getHeight()));
+ } else if (element instanceof SimpleMolecule) {
+ type = "org.gk.render.RenderableChemical";
+ } else if (element instanceof Ion) {
+ type = "org.gk.render.RenderableChemical";
+ } else if (element instanceof Protein) {
+ type = "org.gk.render.RenderableProtein";
+ } else if (element instanceof Species) {
+ type = "org.gk.render.RenderableEntity";
+ } else if (element instanceof Compartment) {
+ type = "org.gk.render.RenderableCompartment";
+ } else {
+ logger.debug("Ignoring: " + parameters.get("displayName") + "(" + element.getClass() + ")");
+ continue;
+ }
+ print("<" + type);
+ for (String string : attributes.keySet()) {
+ print(" " + string + "=\"" + attributes.get(string) + "\"");
+ }
+ print(">");
+ for (String key : parameters.keySet()) {
+ print("<" + key + ">" + parameters.get(key) + "</" + key + ">");
+ }
+
+ if (components.size() != 0) {
+ print("\n <Components>\n");
+ for (Integer i : components) {
+ print(" <Component id=\"" + i + "\"/>\n");
+ }
+ print(" </Components>\n");
+ }
+ print("</" + type + ">\n");
+
+ }
+ print("</Nodes>\n");
+ }
+
+ /**
+ * Creates reactions in reactome visuazliation model from our model.
+ *
+ * @param model
+ * model to be visualized
+ * @throws IOException
+ * thrown when there are problems with accessing reactome database
+ */
+ private void printReactions(Model model) throws IOException {
+ print("<Edges>\n");
+ for (Reaction reaction : model.getReactions()) {
+ if (!isReactionFeasible(reaction)) {
+ continue;
+ }
+ int currId = ++id;
+ Map<String, String> parameters = new HashMap<String, String>();
+ Map<Integer, String> inputs = new HashMap<Integer, String>();
+ Map<Integer, String> outputs = new HashMap<Integer, String>();
+ Map<Integer, String> catalysts = new HashMap<Integer, String>();
+
+ Map<String, String> attributes = new HashMap<String, String>();
+
+ attributes.put("id", currId + "");
+ attributes.put("position", (int) reaction.getCenterPoint().getX() + " " + (int) reaction.getCenterPoint().getY());
+ attributes.put("points", getReactionMiddlePoints(reaction));
+ attributes.put("lineWidth", "1.0");
+ attributes.put("reactomeId", "0");
+
+ parameters.put("displayName", reaction.getIdReaction());
+
+ String stableIdentifier = rcu.getReactomeIdentifierForReaction(reaction);
+ if (stableIdentifier != null) {
+ ReactomeDatabaseObject obj = rc.getFullObjectForStableIdentifier(stableIdentifier);
+ if (obj != null && obj.getDbId() != null) {
+ attributes.put("reactomeId", obj.getDbId() + "");
+ }
+ }
+
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ Integer id = tempIds.get(node.getAlias());
+ if (node instanceof Reactant) {
+ inputs.put(id, getInputString((Reactant) node));
+ } else if (node instanceof Product) {
+ outputs.put(id, getOutputString((Product) node));
+ } else if (node instanceof Modifier) {
+ catalysts.put(id, getModifierString((Modifier) node));
+ }
+ }
+
+ String type = "org.gk.render.RenderableReaction";
+
+ print("<" + type);
+ for (String string : attributes.keySet()) {
+ print(" " + string + "=\"" + attributes.get(string) + "\"");
+ }
+ print(">\n");
+ print(" <Properties>\n");
+ for (String key : parameters.keySet()) {
+ print(" <" + key + ">" + parameters.get(key) + "</" + key + ">\n");
+ }
+ print(" </Properties>\n");
+
+ if (inputs.size() != 0) {
+ print(" <Inputs>\n");
+ for (Integer i : inputs.keySet()) {
+ print(" <Input id=\"" + i + "\" points=\"" + inputs.get(i) + "\"/>\n");
+ }
+ print(" </Inputs>\n");
+ }
+ if (outputs.size() != 0) {
+ print(" <Outputs>\n");
+ for (Integer i : outputs.keySet()) {
+ print(" <Output id=\"" + i + "\" points=\"" + outputs.get(i) + "\"/>\n");
+ }
+ print(" </Outputs>\n");
+ }
+ if (catalysts.size() != 0) {
+ print(" <Catalysts>\n");
+ for (Integer i : catalysts.keySet()) {
+ print(" <Catalyst id=\"" + i + "\" points=\"" + catalysts.get(i) + "\"/>\n");
+ }
+ print(" </Catalysts>\n");
+ }
+ print("</" + type + ">\n");
+
+ }
+
+ print("</Edges>\n");
+ }
+
+ /**
+ * Returns string representing modifier.
+ *
+ * @param node
+ * modifier in our model
+ * @return string representing modifier that can be used in reactome
+ * visualization
+ */
+ private String getModifierString(ReactionNode node) {
+ String result = null;
+ List<Point2D> points = node.getLine().getPoints();
+ for (int i = 0; i < points.size() - 1; i++) {
+ if (result == null) {
+ result = "";
+ } else {
+ result += ", ";
+ }
+ Point2D point = points.get(i);
+ result += (int) point.getX() + " " + (int) point.getY();
+ }
+ return result;
+ }
+
+ /**
+ * Returns string representing product.
+ *
+ * @param node
+ * product in our model
+ * @return string representing product that can be used in reactome
+ * visualization
+ */
+ private String getOutputString(ReactionNode node) {
+ for (NodeOperator tmpNode : node.getReaction().getOperators()) {
+ if (tmpNode.isProductOperator()) {
+ String result = null;
+ List<Point2D> points = node.getLine().getPoints();
+ for (int i = points.size() - 1; i >= 0; i--) {
+ if (result == null) {
+ result = "";
+ } else {
+ result += ", ";
+ }
+ Point2D point = points.get(i);
+ result += (int) point.getX() + " " + (int) point.getY();
+ }
+ return result;
+ }
+ }
+ Point2D point = node.getLine().getEndPoint();
+ String result = (int) point.getX() + " " + (int) point.getY();
+ return result;
+ }
+
+ /**
+ * Returns string representing reactant.
+ *
+ * @param node
+ * reactant in our model
+ * @return string representing reactant that can be used in reactome
+ * visualization
+ */
+ private String getInputString(ReactionNode node) {
+ for (NodeOperator tmpNode : node.getReaction().getOperators()) {
+ if (tmpNode.isReactantOperator()) {
+ String result = null;
+ List<Point2D> points = node.getLine().getPoints();
+ for (int i = 0; i < points.size(); i++) {
+ if (result == null) {
+ result = "";
+ } else {
+ result += ", ";
+ }
+ Point2D point = points.get(i);
+ result += (int) point.getX() + " " + (int) point.getY();
+ }
+ return result;
+ }
+ }
+ Point2D point = node.getLine().getPoints().get(0);
+ String result = (int) point.getX() + " " + (int) point.getY();
+ return result;
+ }
+
+ /**
+ * Check if reaction can be easily transformed into reactome vizualization
+ * tool.
+ *
+ * @param reaction
+ * reaction to be checked
+ * @return <code>true</code> if reaction can be easily transformed,
+ * <code>false</code> otherwise
+ */
+ private boolean isReactionFeasible(Reaction reaction) {
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ if (!aliasFeasible(node.getAlias())) {
+ return false;
+ }
+ }
+ int counter = 0;
+ for (NodeOperator node : reaction.getOperators()) {
+ if (node.isProductOperator()) {
+ counter++;
+ }
+ if (counter > 1) {
+ logger.debug("To many operators in the input: " + reaction.getIdReaction());
+ return false;
+ }
+ }
+ counter = 0;
+ for (NodeOperator node : reaction.getOperators()) {
+ if (node.isReactantOperator()) {
+ counter++;
+ }
+ if (counter > 1) {
+ logger.debug("To many operators in the output: " + reaction.getIdReaction());
+ return false;
+ }
+ }
+ counter = 0;
+ for (NodeOperator node : reaction.getOperators()) {
+ if (node.isModifierOperator()) {
+ logger.debug("To complicated catalyst: " + reaction.getIdReaction());
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Returns string representing reaction line.
+ *
+ * @param reaction
+ * reaction to be transformed
+ * @return string representing reaction line
+ */
+ private String getReactionMiddlePoints(Reaction reaction) {
+ String result = null;
+ NodeOperator node = null;
+ for (NodeOperator n : reaction.getOperators()) {
+ if (n.isReactantOperator()) {
+ node = n;
+ }
+ }
+ if (node != null) {
+ for (Point2D point : node.getLine().getPoints()) {
+ if (result == null) {
+ result = (int) point.getX() + " " + (int) point.getY();
+ } else {
+ result += ", " + (int) point.getX() + " " + (int) point.getY();
+ }
+ }
+ } else {
+ AbstractNode tmp = null;
+ for (AbstractNode reactionNode : reaction.getNodes()) {
+ if (reactionNode instanceof Reactant) {
+ tmp = reactionNode;
+ }
+ }
+ List<Point2D> points = tmp.getLine().getPoints();
+ for (int i = 0; i < points.size(); i++) {
+ Point2D point = points.get(i);
+ if (result == null) {
+ result = (int) point.getX() + " " + (int) point.getY();
+ } else {
+ result += ", " + (int) point.getX() + " " + (int) point.getY();
+ }
+ }
+ }
+
+ node = null;
+ for (NodeOperator n : reaction.getOperators()) {
+ if (n.isProductOperator()) {
+ node = n;
+ }
+ }
+ if (node != null) {
+ List<Point2D> points = node.getLine().getPoints();
+ for (int i = points.size() - 1; i >= 0; i--) {
+ Point2D point = points.get(i);
+ if (result == null) {
+ result = (int) point.getX() + " " + (int) point.getY();
+ } else {
+ result += ", " + (int) point.getX() + " " + (int) point.getY();
+ }
+ }
+ } else {
+ AbstractNode tmp = null;
+ for (AbstractNode reactionNode : reaction.getNodes()) {
+ if (reactionNode instanceof Product) {
+ tmp = reactionNode;
+ }
+ }
+ List<Point2D> points = tmp.getLine().getPoints();
+ for (int i = 0; i < points.size(); i++) {
+ Point2D point = points.get(i);
+ if (result == null) {
+ result = (int) point.getX() + " " + (int) point.getY();
+ } else {
+ result += ", " + (int) point.getX() + " " + (int) point.getY();
+ }
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * Checks if alias can be put into reactome vizualization.
+ *
+ * @param alias
+ * alias to check
+ * @return <code>true</code> if alias can be put into reactome vizualization,
+ * <code>false</code> otherwise
+ */
+ public boolean aliasFeasible(Alias alias) {
+ Point2D point = new Point2D.Double(alias.getX(), alias.getY());
+ Point2D point2 = new Point2D.Double(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
+ if (bound.contains(point) && bound.contains(point2)) {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * @return the rc
+ * @see #rc
+ */
+ public DataSourceUpdater getRc() {
+ return rc;
+ }
+
+ /**
+ * @param rc
+ * the rc to set
+ * @see #rc
+ */
+ public void setRc(DataSourceUpdater rc) {
+ this.rc = rc;
+ }
+
+ /**
+ * @return the rcu
+ * @see #rcu
+ */
+ public ReactomeQueryUtil getRcu() {
+ return rcu;
+ }
+
+ /**
+ * @param rcu
+ * the rcu to set
+ * @see #rcu
+ */
+ public void setRcu(ReactomeQueryUtil rcu) {
+ this.rcu = rcu;
+ }
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java b/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
index 63122b2de227619902b2ede55095d1836c425479..32f4a07f0f161fd877a11d9262cfcfb16199b9b1 100644
--- a/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
+++ b/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
@@ -1,116 +1,116 @@
-package lcsb.mapviewer.run;
-
-import java.io.FileNotFoundException;
-import java.text.DecimalFormat;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-
-/**
- * This class is a snippet for Vibine collaboration project. It shows how to
- * access our internal data structures and source files.
- *
- * @author Piotr Gawron
- *
- */
-public class VibineSnippet {
-
- /**
- * Number of nanoseconds in second.
- */
- private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
-
- /**
- * CellDesigner file on with some data that is used in this snippet (it's PD
- * map from June 2015).
- */
- private static final String INPUT_FILE = "testFiles/pd_full/PD_150625_3.xml";
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(VibineSnippet.class);
-
- /**
- * Main entry point to the program.
- *
- * @param args
- * parameters with which the program was run
- */
- public static void main(String[] args) {
- VibineSnippet main = new VibineSnippet();
- long startTime = System.nanoTime();
-
- try {
- main.run();
- } catch (Exception e) {
- main.logger.error(e, e);
- } finally {
- long endTime = System.nanoTime();
- long duration = endTime - startTime;
- double sec = duration / NANOSECONDS_IN_SECOND;
- System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
- }
- }
-
- /**
- * This method transform {@link #inputOptions input data}.
- *
- * @throws FileNotFoundException
- *
- * @throws Exception
- * thrown when the there is a problem...
- */
- private void run() throws Exception {
- logger.debug("Opening file: " + INPUT_FILE);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- Model model = parser.createModel(new ConverterParams().filename(INPUT_FILE));
-
- logger.debug("File processed.");
-
- logger.debug("-------------------------------");
- logger.debug("Number of elements: " + model.getElements().size());
- logger.debug("Number of aliases for these elements: " + model.getAliases().size());
-
- logger.debug("Number of reactions: " + model.getReactions().size());
-
- logger.debug("-------------------------------");
- String speciesId = "s4351";
- String reactionId = "re332";
- Element element = model.getElementByElementId(speciesId);
-
- List<SpeciesAlias> aliases = model.getAliasesBySpeciesId(speciesId);
-
- logger.debug("Element with id: " + speciesId);
- logger.debug("Element type: " + element.getClass());
- logger.debug("Element name: " + element.getName());
- logger.debug("Element is located in " + aliases.size() + " places on the map.");
- logger.debug("Here are coordinates: ");
- for (SpeciesAlias speciesAlias : aliases) {
- logger.debug(
- speciesAlias.getAliasId() + " - " + speciesAlias.getX() + "," + speciesAlias.getY() + "," + speciesAlias.getWidth() + ","
- + speciesAlias.getHeight());
- }
-
- logger.debug("-------------------------------");
- Reaction reaction = model.getReactionByReactionId(reactionId);
-
- logger.debug("Reaction with id: " + reactionId);
- logger.debug("Reaction has " + reaction.getReactionNodes().size() + " members.");
- for (ReactionNode node : reaction.getReactionNodes()) {
- logger.debug(
- node.getClass().getSimpleName() + "; points to " + node.getElement().getClass().getSimpleName() + "[" + node.getElement().getElementId() + "]");
- }
- logger.debug("-------------------------------");
- }
-
-}
+package lcsb.mapviewer.run;
+
+import java.io.FileNotFoundException;
+import java.text.DecimalFormat;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+
+/**
+ * This class is a snippet for Vibine collaboration project. It shows how to
+ * access our internal data structures and source files.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class VibineSnippet {
+
+ /**
+ * Number of nanoseconds in second.
+ */
+ private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
+
+ /**
+ * CellDesigner file on with some data that is used in this snippet (it's PD
+ * map from June 2015).
+ */
+ private static final String INPUT_FILE = "testFiles/pd_full/PD_150625_3.xml";
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(VibineSnippet.class);
+
+ /**
+ * Main entry point to the program.
+ *
+ * @param args
+ * parameters with which the program was run
+ */
+ public static void main(String[] args) {
+ VibineSnippet main = new VibineSnippet();
+ long startTime = System.nanoTime();
+
+ try {
+ main.run();
+ } catch (Exception e) {
+ main.logger.error(e, e);
+ } finally {
+ long endTime = System.nanoTime();
+ long duration = endTime - startTime;
+ double sec = duration / NANOSECONDS_IN_SECOND;
+ System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
+ }
+ }
+
+ /**
+ * This method transform {@link #inputOptions input data}.
+ *
+ * @throws FileNotFoundException
+ *
+ * @throws Exception
+ * thrown when the there is a problem...
+ */
+ private void run() throws Exception {
+ logger.debug("Opening file: " + INPUT_FILE);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = parser.createModel(new ConverterParams().filename(INPUT_FILE));
+
+ logger.debug("File processed.");
+
+ logger.debug("-------------------------------");
+ logger.debug("Number of elements: " + model.getElements().size());
+ logger.debug("Number of aliases for these elements: " + model.getAliases().size());
+
+ logger.debug("Number of reactions: " + model.getReactions().size());
+
+ logger.debug("-------------------------------");
+ String speciesId = "s4351";
+ String reactionId = "re332";
+ Element element = model.getElementByElementId(speciesId);
+
+ List<SpeciesAlias> aliases = model.getAliasesBySpeciesId(speciesId);
+
+ logger.debug("Element with id: " + speciesId);
+ logger.debug("Element type: " + element.getClass());
+ logger.debug("Element name: " + element.getName());
+ logger.debug("Element is located in " + aliases.size() + " places on the map.");
+ logger.debug("Here are coordinates: ");
+ for (SpeciesAlias speciesAlias : aliases) {
+ logger.debug(
+ speciesAlias.getAliasId() + " - " + speciesAlias.getX() + "," + speciesAlias.getY() + "," + speciesAlias.getWidth() + ","
+ + speciesAlias.getHeight());
+ }
+
+ logger.debug("-------------------------------");
+ Reaction reaction = model.getReactionByReactionId(reactionId);
+
+ logger.debug("Reaction with id: " + reactionId);
+ logger.debug("Reaction has " + reaction.getReactionNodes().size() + " members.");
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ logger.debug(
+ node.getClass().getSimpleName() + "; points to " + node.getElement().getClass().getSimpleName() + "[" + node.getElement().getElementId() + "]");
+ }
+ logger.debug("-------------------------------");
+ }
+
+}
diff --git a/console/src/test/java/lcsb/mapviewer/run/PdMapAnnotationsTest.java b/console/src/test/java/lcsb/mapviewer/run/PdMapAnnotationsTest.java
index 587c9303334d670260742eb058dc8ca7628335ac..3c0f4bfef1b829047e4f6f66437ec988815b9628 100644
--- a/console/src/test/java/lcsb/mapviewer/run/PdMapAnnotationsTest.java
+++ b/console/src/test/java/lcsb/mapviewer/run/PdMapAnnotationsTest.java
@@ -1,40 +1,40 @@
-package lcsb.mapviewer.run;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.File;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.run.PdMapAnnotations;
-
-public class PdMapAnnotationsTest {
- Logger logger = Logger.getLogger(PdMapAnnotationsTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() {
- try {
- String fileName = PdMapAnnotations.getLastPdFilename();
- assertNotNull(fileName);
- File file = new File(fileName);
- assertTrue(file.exists());
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception occurred");
- }
- }
-
-}
+package lcsb.mapviewer.run;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.File;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.run.PdMapAnnotations;
+
+public class PdMapAnnotationsTest {
+ Logger logger = Logger.getLogger(PdMapAnnotationsTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() {
+ try {
+ String fileName = PdMapAnnotations.getLastPdFilename();
+ assertNotNull(fileName);
+ File file = new File(fileName);
+ assertTrue(file.exists());
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception occurred");
+ }
+ }
+
+}
diff --git a/console/testFiles/pd_full/PD_151217_2/layouts/PD substantia nigra.txt b/console/testFiles/pd_full/PD_151217_2/layouts/PD substantia nigra.txt
index 8f57d5c9d21132e0b5eebbd5c953a7922f207282..5ed3ee874243594bd2a73e646c0d5cf2d9cc11d2 100644
--- a/console/testFiles/pd_full/PD_151217_2/layouts/PD substantia nigra.txt
+++ b/console/testFiles/pd_full/PD_151217_2/layouts/PD substantia nigra.txt
@@ -1,4342 +1,4342 @@
-# VERSION=1.0
-# NAME=PD substantia nigra
+# VERSION=1.0
+# NAME=PD substantia nigra
# DESCRIPTION=Differential transcriptome expression from post mortem tissue. Meta-analysis from 8 published datasets, FDR = 0.05, see PMIDs 23832570 and 25447234.
-name value
-GBE1 -0,943978048
-SLC18A2 -0,941309505
-KCNJ6 -0,894120983
-DLK1 -0,887122171
-PTDSS1 -0,851959645
-FGF13 -0,842876271
-PCDH8 -0,83524894
-ZNF226 -0,82900335
-SLC6A3 -0,824713365
-PIP5K1B -0,812285785
-DENR -0,81101551
-TPBG -0,806963209
-PRKAR2B -0,805288865
-OSBPL10 -0,80406299
-ALDH1A1 -0,795042129
-GGCX -0,795035797
-ACP2 -0,794853979
-SLITRK5 -0,793842132
-FAM70A -0,793715412
-HPRT1 -0,792370336
-CCNH -0,790971864
-MYRIP -0,78490295
-TUBB2A -0,783142444
-ACTR10 -0,782043082
-BASP1 -0,778702387
-CADPS2 -0,777552826
-PID1 -0,775106213
-SV2C -0,774895093
-RBM3 -0,77091551
-REEP1 -0,770000111
-RIMBP2 -0,766421185
-CNIH3 -0,765790316
-DMXL2 -0,765309344
-LOC10431 -0,762992699
-SV2B -0,759985564
-AGK -0,756506198
-RCAN2 -0,753762002
-LPPR4 -0,753018962
-RALYL -0,75270126
-L1CAM -0,751978689
-BCAS2 -0,751241508
-LOC100131795 -0,750350108
-TH -0,748260596
-AV756161 -0,747351587
-TRIM36 -0,746057792
-MPPED2 -0,743864716
-NELL2 -0,742513977
-MAGED1 -0,739190733
-LRRC49 -0,738776851
-SYNGR3 -0,734846774
-ERC2 -0,734619705
-VBP1 -0,73223558
-UQCC -0,729749962
-DCLK1 -0,725139215
-GSS -0,724321987
-OPA1 -0,723790592
-PPP2R2B -0,720892147
-COPS4 -0,720599852
-NSF -0,720580224
-DLD -0,72035948
-DYNC1I1 -0,719837984
-GABARAPL3 -0,717235008
-GPRASP1 -0,71302626
-NAP1L2 -0,712876929
-AMPH -0,711957162
-PNMAL1 -0,70952389
-RGS6 -0,706463
-LDB2 -0,704777497
-TTC19 -0,704232585
-SCN3B -0,703738866
-ATPIF1 -0,702603531
-BEX1 -0,700382911
-LMO3 -0,699029823
-TBC1D9 -0,698189481
-NDUFS1 -0,697230219
-INSM1 -0,696524737
-PARL -0,696362568
-MRPL15 -0,688780959
-C3orf14 -0,687875821
-C19orf62 -0,687403479
-PCYOX1L -0,686812669
-VRK1 -0,685016241
-MDH2 -0,684889561
-SMYD3 -0,684642724
-ASAH1 -0,68459801
-GSTA4 -0,684021936
-NDUFA9 -0,683116722
-ATP5C1 -0,682289667
-DDX25 -0,681511867
-GNG3 -0,681122999
-MUDENG -0,67996077
-SCG2 -0,679728044
-MOAP1 -0,679575281
-SYT1 -0,678979261
-ATP6V1H -0,6786546
-SHOC2 -0,677754756
-PCSK1 -0,677441918
-LBH -0,67710638
-HK1 -0,676818391
-KIAA0319 -0,676346138
-SMAP1 -0,67618103
-EHBP1 -0,675429621
-RAP1GAP2 -0,673705297
-FABP7 -0,673485271
-LRRN3 -0,6731503
-AHNAK2 -0,672875949
-DHDDS -0,671959403
-SNAPC5 -0,670824633
-C17orf108 -0,670563093
-AL390170 -0,67026906
-PTS -0,669577055
-NUDT11 -0,668061506
-HMP19 -0,66794356
-IMMT -0,667541939
-RGS4 -0,667109174
-RET -0,667088994
-PBLD -0,666164981
-AP3M2 -0,666056972
-WDR7 -0,665751643
-ATP6V0D1 -0,665487037
-RTF1 -0,664652469
-TUBB3 -0,664644351
-CHCHD2 -0,664529051
-DYNLT3 -0,663584428
-RAB6B -0,662755469
-CHGB -0,661865706
-NGFRAP1 -0,659441958
-AZIN1 -0,659394366
-EN1 -0,659313013
-SNX10 -0,659251628
-MIA3 -0,65882244
-ANK1 -0,657621479
-NR4A2 -0,65598531
-ANAPC13 -0,655864214
-RGS7 -0,654445938
-NME5 -0,652754395
-TXNDC9 -0,652019899
-PPIP5K2 -0,651763237
-RFK -0,651442652
-BE674466 -0,651048329
-PEG10 -0,650932122
-PIAS2 -0,650823358
-CUX2 -0,649970555
-SEPT6 -0,649422911
-FKBP1B -0,649416387
-C12orf10 -0,648407487
-HMGCS1 -0,648164918
-WDR61 -0,648133373
-GFPT1 -0,647751981
-MLLT11 -0,647471245
-AGTR1 -0,645674318
-CSNK1D -0,645408463
-WDR47 -0,64495088
-PSMD14 -0,644669314
-CISD1 -0,643780748
-PSMD11 -0,642982055
-KCNS3 -0,642919136
-TIMM8B -0,642730563
-RUNDC3B -0,641744336
-ANKRD6 -0,640032629
-MDH1 -0,639623665
-STMN2 -0,639070421
-BAI3 -0,638894116
-STX12 -0,638382169
-NECAP1 -0,638376593
-NIT2 -0,638223243
-CIRBP -0,637859912
-XK -0,636787355
-KIAA1797 -0,636384728
-ICMT -0,636379567
-GALT -0,636138691
-SPINT2 -0,635454321
-PAIP1 -0,634724103
-TAGLN3 -0,63459569
-CADPS -0,634245008
-GALNT11 -0,634168707
-SLC9A6 -0,632805526
-ANKRD34C -0,63217094
-COPG2IT1 -0,63213856
-VPS4B -0,63135628
-ATP6V0E2 -0,631164455
-SC5DL -0,631137699
-CNPY2 -0,630875303
-GCC2 -0,630691438
-CRYZL1 -0,63015348
-MOBKL3 -0,630076244
-SNCA -0,629316875
-STAM -0,628134338
-TUBA4A -0,627764216
-MAK16 -0,627148096
-FRY -0,626684765
-UBE2V2 -0,626378865
-RWDD2B -0,626170788
-FBXO9 -0,62572532
-FLJ41278 -0,6251633
-SLC30A9 -0,624759053
-LOC100132015 -0,623179237
-EXOG -0,622056922
-RAP1GAP -0,618803848
-DYNC1LI1 -0,618641756
-HARS -0,618639749
-NDUFA5 -0,618245275
-SPCS1 -0,618130333
-PSMB7 -0,618122572
-NETO2 -0,618103081
-ATP5G3 -0,617855025
-UCHL1 -0,617452524
-FAM127A -0,616124191
-TSSC1 -0,615619431
-CBLN1 -0,615519237
-CYB5R1 -0,615294192
-PSMG1 -0,61487171
-AKAP12 -0,614821543
-CYB561 -0,614281499
-KCND3 -0,613554227
-GABRB1 -0,613364723
-SLIT1 -0,613251897
-HN1 -0,612796898
-F8 -0,612749576
-VSNL1 -0,611517123
-ATP5A1 -0,611141848
-ARMCX5 -0,610703909
-AI097640 -0,610659067
-CERK -0,610508368
-TMX4 -0,610174408
-TSPAN13 -0,609932725
-CAMLG -0,609409157
-NDUFA7 -0,609351405
-STRAP -0,609237631
-RTCD1 -0,607502869
-ORC5L -0,606910471
-SCG5 -0,606870723
-HSPA12A -0,606863939
-VAV3 -0,606070683
-TUBB2C -0,60582666
-DCTN2 -0,605238426
-OCRL -0,604661192
-HPCAL4 -0,604023171
-ARL1 -0,604008234
-CDK14 -0,603712397
-TLK1 -0,603591955
-BLVRA -0,603201697
-NEFL -0,602887281
-SLC25A32 -0,602708801
-ATXN10 -0,602624835
-UQCRC2 -0,601726567
-SLC25A3 -0,601470752
-MYL12B -0,601373186
-CDS2 -0,601292766
-DDC -0,601079077
-BSCL2 -0,6009448
-CACNB3 -0,598982611
-RIMS3 -0,598771066
-LASS6 -0,598387226
-FIBP -0,598382328
-LRPPRC -0,598144321
-PYROXD1 -0,598012671
-MAP3K9 -0,597438703
-CHL1 -0,5969101
-FJX1 -0,596748319
-PFN2 -0,596551333
-ATMIN -0,59649395
-LIN7B -0,596058244
-AV704232 -0,595274626
-PPP2R5C -0,594797769
-SNAP91 -0,59414072
-AKT3 -0,593859242
-NDUFAB1 -0,593111219
-CCDC28A -0,59307395
-GLOD4 -0,592429097
-STXBP1 -0,591440124
-HLTF -0,591296161
-CRMP1 -0,590916915
-KIAA0513 -0,590696005
-GHITM -0,590624599
-ATP6V1B2 -0,590367192
-USP14 -0,589739205
-RNFT2 -0,589705749
-SCG3 -0,589375952
-ATP5B -0,588999541
-FAM136A -0,588982627
-UBE2N -0,588308222
-ANXA6 -0,588071667
-MRTO4 -0,58799806
-SNRK -0,587183425
-CACNA2D2 -0,587134808
-IFT57 -0,586933566
-PPP3CB -0,586906049
-RICH2 -0,586554767
-ME3 -0,586514247
-THOC7 -0,585617181
-FAM188A -0,584083221
-EIF2B3 -0,582997986
-CNTNAP1 -0,582856877
-SCRN1 -0,582791752
-ACAT1 -0,582760841
-IDI1 -0,582694626
-PBX1 -0,582658829
-CDC42 -0,582658446
-NBEA -0,582614884
-PPP1R2 -0,581839918
-ACTR6 -0,581817384
-TAF9 -0,581794162
-NIPSNAP1 -0,581711722
-SEC61A2 -0,58139821
-WDR37 -0,581272248
-VWA5A -0,581248993
-CDC27 -0,580500838
-MYT1L -0,580491453
-PSMC1 -0,580473356
-KATNB1 -0,578133005
-ZWINT -0,577661475
-C12orf24 -0,577181135
-SLC25A46 -0,577144749
-DOLK -0,576794187
-APOO -0,576716633
-GCH1 -0,576494714
-TBC1D30 -0,575582077
-DCTN3 -0,575526778
-FBXL2 -0,575141782
-KIFAP3 -0,574923419
-CMAS -0,574834972
-C18orf10 -0,574780811
-PNMA2 -0,574504978
-PDHX -0,574434123
-SAMM50 -0,574204311
-NDUFA2 -0,574087728
-NPTN -0,573534504
-HIGD1A -0,573110642
-CYC1 -0,573010558
-HMGCR -0,572959475
-TRAPPC2L -0,572517332
-IMPA1 -0,572397104
-IMPACT -0,572070372
-KIAA0802 -0,572067617
-DSTN -0,571964512
-C5orf44 -0,571958339
-CCK -0,571148184
-OGDHL -0,571078621
-TCP11L1 -0,570951095
-RNF14 -0,569913578
-IARS -0,569079443
-CDH8 -0,569072707
-RNF41 -0,568830451
-SCN3A -0,568276898
-PSMD12 -0,567936617
-TNFRSF21 -0,567631199
-FIG4 -0,566751868
-DDX24 -0,566446037
-MARK1 -0,566206858
-ATP8A2 -0,565754513
-ACLY -0,565055263
-DDX42 -0,564984354
-KIF3C -0,564949485
-PIN1 -0,564290859
-PSEN2 -0,564206755
-TERF2IP -0,564084181
-VDAC3 -0,563895581
-B3GNT1 -0,563686309
-CHN1 -0,563660153
-GLO1 -0,561564055
-RAB11A -0,561549092
-PRPS1 -0,561391557
-MAP2 -0,561080301
-NHP2 -0,56096586
-DNAJA2 -0,560780556
-NDRG4 -0,560771764
-HNRNPA0 -0,560406816
-NDUFV2 -0,559975953
-ADH5 -0,559909821
-FAM3C -0,559672666
-COPS7A -0,559265307
-SULT4A1 -0,558733244
-MATN3 -0,558346148
-TMEM14A -0,557817575
-HRASLS -0,557799459
-TMEM14B -0,557593404
-TTC1 -0,557573183
-R3HDM1 -0,557428266
-AUH -0,55725646
-C5orf22 -0,55714645
-TUBB -0,557095971
-C5orf13 -0,55663948
-COX7A2L -0,556219721
-POMP -0,556110434
-ATP5J2 -0,555267292
-ZNF204P -0,555121445
-INA -0,554984251
-NUP93 -0,55488654
-STAU2 -0,55454534
-VAT1 -0,554180752
-DDB1 -0,554146967
-THY1 -0,554057809
-SRPRB -0,553818923
-IMP4 -0,553554219
-SRP19 -0,552319097
-FUCA1 -0,551919323
-PRKCZ -0,551777138
-CD2BP2 -0,55167071
-C12orf43 -0,551436389
-SUSD4 -0,55137396
-W88821 -0,551080268
-LSM4 -0,550328209
-SNAP25 -0,550276399
-ACSL6 -0,549806401
-MYH10 -0,549550685
-DDHD2 -0,548942799
-PRKACA -0,548422775
-CHRNB3 -0,547701041
-NEFM -0,547618123
-PLD3 -0,547495065
-GSPT2 -0,547329995
-ATP6V1E1 -0,546911033
-GABBR2 -0,546899558
-IPW -0,546596796
-SCAMP5 -0,546380917
-RFPL1S -0,545994554
-BSN -0,545979557
-MAGI1 -0,54490486
-DRG1 -0,544733954
-PITPNB -0,544704547
-LETMD1 -0,544636809
-AI263044 -0,544470885
-STOML1 -0,544383238
-GBAS -0,544103215
-RAB3GAP1 -0,543092086
-ACTG1 -0,54300405
-PPME1 -0,542943175
-AFG3L2 -0,542490245
-DNAJC6 -0,541912283
-TUBA1B -0,541625287
-ABCE1 -0,541581351
-ARF3 -0,541401116
-SRSF3 -0,54134715
-NEFH -0,540578844
-ADK -0,540377244
-TIMM17A -0,540158649
-ELOVL6 -0,540054201
-FAM189A1 -0,539987546
-ATP6V1A -0,539816156
-OAT -0,53960074
-KIAA0284 -0,539436564
-SLC25A12 -0,538986194
-AP3D1 -0,538816413
-ISCU -0,53848727
-CDH10 -0,538458105
-APEH -0,538385859
-TMEM35 -0,537944022
-NDFIP1 -0,537769873
-U79277 -0,537586945
-SYNGR1 -0,53757151
-MEAF6 -0,537175986
-DNM1 -0,536361784
-DEF8 -0,536162488
-PDXK -0,536128962
-RIT2 -0,536060129
-AACS -0,535868362
-RAB3A -0,535840143
-LXN -0,535676847
-CCBL2 -0,53559953
-ATXN7L3B -0,535570224
-RCN2 -0,535264733
-SDC2 -0,535187449
-NRXN3 -0,534911729
-SDC1 -0,534748047
-PSMD1 -0,534162775
-UBA5 -0,534098166
-PEX11B -0,533915774
-RAP1GDS1 -0,533764019
-NUPL1 -0,533680375
-ARMCX1 -0,533607326
-SDHAP1 -0,533209621
-PJA2 -0,532853246
-ACOT7 -0,532662038
-SEZ6L -0,532618647
-CELF2 -0,532603645
-CXorf40A -0,532513065
-NDUFB5 -0,532279155
-GARS -0,532224902
-NRG1 -0,532009485
-SEC31B -0,53180843
-ME1 -0,531466374
-PSMD8 -0,531445018
-MSL1 -0,531268404
-PCLO -0,531166247
-RAB14 -0,531006634
-MAGED2 -0,530858407
-EIF3K -0,530846086
-MMD -0,530845303
-MYO5A -0,530805656
-NCRNA00094 -0,530597959
-KIAA1107 -0,53057188
-KIAA0564 -0,530294183
-PSMB2 -0,530140819
-C1orf114 -0,530111522
-GCLM -0,529867963
-NDN -0,529086871
-SRD5A1 -0,528786683
-DNAJB9 -0,528374918
-SLC7A8 -0,528181836
-CLIP3 -0,527794519
-NDUFB1 -0,527724864
-CLSTN2 -0,52726691
-C14orf156 -0,527148764
-CIAPIN1 -0,527136633
-ATP5F1 -0,527047789
-PSMB5 -0,526841307
-FAM32A -0,526499611
-KIAA1644 -0,526147045
-RTN1 -0,526062751
-EXOSC9 -0,525622526
-PFKM -0,525053758
-TCF25 -0,524910517
-ATP5O -0,524889972
-PTPRN2 -0,524794642
-SNX4 -0,524373257
-ATP6V1G2 -0,524016622
-SLC35E3 -0,523930118
-SLC2A6 -0,52364368
-SUCLA2 -0,523588063
-PLCB1 -0,523263994
-TMEM30A -0,521872901
-PDE4D -0,521870014
-RAB5A -0,521632556
-MAPK9 -0,521572661
-CAP2 -0,521120749
-RPS6KA3 -0,520660932
-GNAO1 -0,520506337
-PSMD6 -0,520132666
-TBCE -0,519679173
-C9orf125 -0,519623009
-MN1 -0,51937171
-MFSD1 -0,51842841
-KIF3A -0,518357676
-SHFM1 -0,517546292
-NRIP3 -0,516545986
-ANKMY2 -0,516365077
-CDK5 -0,516196782
-REEP5 -0,516165841
-SLC1A1 -0,516141732
-UBE2K -0,516036367
-SMEK2 -0,515537555
-PI4K2A -0,515462049
-TTC39A -0,514924765
-GUCY1B3 -0,514788287
-QPCT -0,514170797
-ST6GALNAC5 -0,514077764
-ATP6V1F -0,513941613
-HSD17B12 -0,513489073
-PPFIA2 -0,51321383
-PLCH1 -0,512855521
-CNTN6 -0,512564243
-ENTPD6 -0,512350634
-ALAS1 -0,512141897
-RUNDC3A -0,511994377
-PCMT1 -0,511547085
-IDS -0,511290223
-PLEKHB2 -0,510964275
-CDO1 -0,510668427
-NDUFB6 -0,510219117
-COX6C -0,509869079
-OPTN -0,509603205
-PSMA1 -0,509510596
-STS -0,509361214
-TIMM10 -0,509318807
-C1D -0,509252454
-GAP43 -0,509215292
-CCDC6 -0,509150548
-TRIM37 -0,509012308
-ATP2B2 -0,508803511
-PGAM1 -0,50863259
-GGNBP2 -0,508616013
-SRP72 -0,508482078
-TCEAL2 -0,508464868
-SV2A -0,508330914
-CDK5R2 -0,508227652
-FHOD3 -0,508155146
-FECH -0,508046235
-ATP2A3 -0,507932978
-SUB1 -0,507787459
-ACO2 -0,507726776
-C20orf3 -0,507526055
-SEC22B -0,507453281
-VPS35 -0,507278509
-MRPS33 -0,507141908
-TXNL4A -0,50704416
-ARHGEF9 -0,506224253
-RBM9 -0,506096633
-TMEM135 -0,506088817
-UHRF1BP1L -0,505757524
-ME2 -0,505446593
-BZRAP1 -0,505378895
-MCAT -0,50534007
-AKAP6 -0,505213579
-COPS3 -0,505110121
-MRPS35 -0,505107922
-YWHAB -0,505015581
-PEX7 -0,504955276
-COPS8 -0,504746043
-OXCT1 -0,504643125
-MAD2L1 -0,504589351
-MCTS1 -0,504510155
-LGALS8 -0,50448664
-ACP1 -0,504339709
-MX1 -0,50393674
-NCALD -0,50389725
-TASP1 -0,503797818
-AGTPBP1 -0,503605082
-RNF128 -0,503554068
-PSMD13 -0,503503704
-TXN -0,50336484
-NHLH2 -0,50325399
-USP12 -0,503149229
-PFDN4 -0,502988386
-NAP1L3 -0,502893901
-MRPL20 -0,502624211
-ACSL3 -0,502355771
-MTPAP -0,502307088
-PMPCB -0,502239978
-SH3GL3 -0,502227406
-API5 -0,502196949
-CAPNS1 -0,5020898
-YWHAZ -0,501747483
-TOMM70A -0,501591565
-STX18 -0,501503813
-HNRNPK -0,501464694
-LRP1B -0,501433491
-CDC123 -0,500993468
-DCTN6 -0,500740808
-VAPB -0,500599356
-CCDC56 -0,499906136
-GOT2 -0,499477446
-RHEB -0,499343134
-PSMD2 -0,499333749
-YPEL5 -0,49910251
-ATP5G1 -0,499077107
-TUBA1A -0,498949544
-GSTM3 -0,498766376
-EPB41L1 -0,498605796
-EPS15 -0,498447403
-ENO2 -0,498261848
-ASMTL -0,498100631
-FH -0,498098378
-CLTC -0,497596743
-PSMA3 -0,497405846
-UROS -0,497291028
-OLFM1 -0,496832922
-ATP6V1G1 -0,496818916
-B3GALNT1 -0,496135395
-PHLPP2 -0,496077027
-TSPYL1 -0,495383913
-SERINC1 -0,49538338
-RPL15 -0,495355843
-ITFG1 -0,495195881
-PDHB -0,494999933
-RABL3 -0,494855325
-TMEM22 -0,49462563
-MCFD2 -0,494506103
-GABARAPL1 -0,494373853
-MAGEL2 -0,493987847
-VPS33B -0,493750355
-CDIPT -0,493440531
-ATP6V0B -0,493438352
-CLGN -0,493358721
-SEC23A -0,493255831
-C7orf43 -0,49286586
-ARL3 -0,492481932
-SLC12A5 -0,492392187
-LAPTM4B -0,492348426
-LOC285359 -0,492290998
-LARP1 -0,49192011
-YME1L1 -0,491725992
-RAB2A -0,491586306
-SPATA20 -0,490991626
-ASH2L -0,490785052
-PTBP2 -0,490747846
-WTAP -0,490599757
-NANS -0,490410248
-SCFD1 -0,490269997
-EPB49 -0,489916122
-TUFT1 -0,489843226
-POP4 -0,489594415
-CACNA1G -0,489236615
-PRPF19 -0,48917604
-NCOA4 -0,488872014
-C1orf216 -0,488856307
-TXNL1 -0,488777426
-AMPD2 -0,48875487
-ASL -0,488300478
-PFDN1 -0,48807629
-EXTL2 -0,488020888
-RPA3 -0,48773487
-ACVR1B -0,487609726
-ANKRD46 -0,487476076
-GRIA1 -0,48726366
-PSMB6 -0,487099126
-CAPRIN2 -0,486969775
-SRGAP3 -0,48684289
-ARPC5L -0,486786621
-PSME3 -0,486309204
-NME2 -0,486066455
-ISCA1 -0,485683262
-ZNF365 -0,485504618
-PINK1 -0,485341061
-RWDD2A -0,48504437
-EXOC1 -0,484927354
-ECE2 -0,484617735
-WDR77 -0,484600271
-AI890972 -0,484490353
-ERBB4 -0,484253264
-PSMD4 -0,483962197
-RAB6C -0,483864006
-CSTF3 -0,483798153
-NIPA2 -0,483638091
-AK5 -0,483482302
-C17orf91 -0,483141592
-INPP4B -0,482534933
-PJA1 -0,482372063
-BE551361 -0,482367089
-B4GALT5 -0,48224903
-MTX2 -0,481915827
-MGST3 -0,481667788
-TRMT11 -0,481613419
-PTPRN -0,481522612
-DNAJC12 -0,48150495
-FTSJ2 -0,481162212
-CCT8 -0,48112028
-PGAP1 -0,481030935
-SLC25A44 -0,480898127
-AMIGO2 -0,480319409
-SCAMP1 -0,480275681
-RBKS -0,480222
-SYN1 -0,48014199
-APEX1 -0,479680328
-AL157484 -0,4790893
-PAK3 -0,479026618
-SLC25A13 -0,478484409
-EIF1B -0,478403329
-DLAT -0,478235597
-AI375694 -0,47804406
-PMS2L1 -0,477748782
-DYNC2LI1 -0,477528415
-RANBP9 -0,477445784
-PTPN20A -0,476653786
-ZMYM4 -0,476508652
-UQCRQ -0,476353248
-EXOSC7 -0,476299374
-NDUFB3 -0,476207507
-LCMT1 -0,476121484
-ZNF547 -0,47597802
-TBCA -0,475802982
-MAPK8IP3 -0,475554385
-N80935 -0,475378775
-SLC4A3 -0,475327531
-AASDHPPT -0,475086681
-CAND2 -0,475049952
-CXorf40B -0,474988185
-FXYD6 -0,47456179
-RNF10 -0,474499733
-ELOVL4 -0,474412575
-AAK1 -0,474378982
-SEH1L -0,474159291
-PTPRU -0,473978747
-LPGAT1 -0,473432618
-VPS24 -0,473360696
-MCF2 -0,473341916
-FAR2 -0,473007144
-CKMT1A -0,472884518
-TMED3 -0,472883274
-RNASEH1 -0,47283341
-NDUFA3 -0,472657747
-GLS -0,472644869
-FAM168A -0,472617309
-KLHDC10 -0,472577269
-GLRX5 -0,472478522
-SYT17 -0,472292582
-PAM -0,472018566
-CLTB -0,471770785
-COPS2 -0,470912718
-DDA1 -0,470419616
-PCSK2 -0,470372976
-SLC25A6 -0,470332168
-TPI1 -0,470300584
-MECR -0,47026417
-ORC4L -0,47025895
-ITPR1 -0,470228063
-HMG20A -0,470060529
-GNB5 -0,470039178
-TMEM208 -0,469963608
-NCAPG -0,469752447
-GLRB -0,469638821
-ATP6V1D -0,469577982
-AKAP11 -0,469501191
-SH3GL2 -0,46948768
-NISCH -0,469445416
-SIPA1L1 -0,469275377
-PFKP -0,469125064
-LYRM4 -0,469088537
-SLC4A1AP -0,46898494
-AP2A2 -0,468669242
-CX3CL1 -0,46850557
-WBP11 -0,468444743
-LASP1 -0,468444317
-GOT1 -0,468375399
-C6orf120 -0,468133996
-SPAG7 -0,468070563
-SERGEF -0,467688975
-TFB2M -0,4675501
-AP3B2 -0,467537408
-PAFAH1B1 -0,467362101
-BPGM -0,467130793
-CRAT -0,466839519
-DDX1 -0,466770911
-ADAM23 -0,46652833
-ASB6 -0,466473575
-PCDHA1 -0,466456945
-TUSC3 -0,465574044
-TCEA2 -0,465512943
-SMARCA4 -0,4653413
-DAPK1 -0,465142929
-DBNDD1 -0,464965333
-NDUFC2 -0,464959656
-IDH3B -0,464778307
-CDC37L1 -0,464692992
-WDR11 -0,464429092
-CD200 -0,464378251
-TUSC2 -0,464289641
-IRGQ -0,464009317
-CALY -0,463919598
-NNT -0,463872117
-MSH2 -0,463745236
-GYG1 -0,463657489
-FAM134C -0,463380379
-RTN2 -0,463379977
-RBM12 -0,463289569
-SYNJ1 -0,463207762
-ABCA5 -0,462881594
-ENTPD4 -0,462777994
-MAP2K4 -0,462732144
-AIMP2 -0,46256199
-PITPNA -0,462484131
-BNIP3 -0,461982272
-COPS5 -0,461956463
-BRE -0,461910476
-MIR21 -0,461667267
-ATP5S -0,46152488
-SIN3B -0,461515059
-NAT10 -0,461457105
-MTCH2 -0,461117099
-ACHE -0,461032229
-PSD3 -0,46079613
-UCHL3 -0,460466303
-SMPX -0,459975528
-USP11 -0,459753441
-RNF187 -0,459566796
-AAGAB -0,458932639
-ENY2 -0,458770966
-NDEL1 -0,458614173
-FAM184A -0,458384449
-TOX4 -0,458204483
-SLC25A15 -0,458110832
-SACM1L -0,458050139
-ADARB1 -0,458034616
-SPHK2 -0,457781426
-CES2 -0,457687554
-CYFIP2 -0,457201169
-KPNA2 -0,457034156
-ACTR1A -0,456856222
-SLC25A22 -0,456321526
-DPYSL3 -0,456025294
-PRKAR1A -0,455984698
-SIDT1 -0,455560984
-TIPRL -0,455474112
-EIF5 -0,455347544
-C16orf58 -0,455176502
-RAB7A -0,454946879
-MFSD6 -0,454914435
-NDUFS2 -0,454605666
-APOOL -0,454580027
-GNB1 -0,454284789
-SARS -0,454282127
-PIK3R3 -0,454240907
-SERINC3 -0,454097365
-ST3GAL5 -0,45407104
-DHRS11 -0,453695947
-NEDD8 -0,45367218
-RAB15 -0,453664346
-HSPA13 -0,453577406
-OLA1 -0,453153228
-C3orf18 -0,45312023
-AF131844 -0,453027105
-C12orf52 -0,452914604
-ACBD3 -0,452894377
-PCIF1 -0,452240197
-BMP2K -0,451224584
-TSPYL5 -0,450674174
-SEC63 -0,450642641
-C7orf44 -0,450408444
-PWP1 -0,450360796
-SLC25A14 -0,45012674
-SYP -0,449768016
-PRKCB -0,449564151
-KIF2A -0,449276369
-PEX26 -0,449100108
-SDHA -0,448617251
-PITRM1 -0,448602767
-PPA2 -0,448269554
-MAN2A2 -0,448177121
-FAM49A -0,448170721
-KCTD9 -0,448062861
-REEP2 -0,44801948
-NDUFS3 -0,447803075
-CHGA -0,447356315
-UBE2E3 -0,447311178
-LOC595101 -0,447006376
-RNF170 -0,446698112
-TMCO1 -0,446651514
-PCCB -0,446640741
-RAB1A -0,44645249
-ATP1A1 -0,446309137
-KIAA1045 -0,446174802
-CASD1 -0,445992918
-C3orf37 -0,445975885
-RAD17 -0,445659766
-BBS4 -0,445631347
-TBC1D19 -0,445509157
-TSG101 -0,445289202
-DKK3 -0,445181251
-KCNQ2 -0,444911548
-EIF4E -0,44477948
-LOC100134209 -0,444742688
-OSTF1 -0,444651424
-PPCS -0,444330494
-ATP13A2 -0,443924538
-DHRS7B -0,443866868
-TSN -0,443785273
-AI201594 -0,443780197
-UBE2J1 -0,443536878
-C12orf51 -0,443320039
-INPP5F -0,44324612
-KIAA0391 -0,443138749
-NDUFB8 -0,442168118
-COX8A -0,442151263
-PLCB4 -0,442128902
-UQCRC1 -0,442055114
-RNMT -0,442010619
-PSMB4 -0,441631296
-ATP9A -0,441570839
-COMMD8 -0,441419712
-STX7 -0,441415012
-UQCRFS1 -0,441387219
-ARMC8 -0,441335025
-USP33 -0,441131902
-SC4MOL -0,441051846
-AVL9 -0,440604375
-CORO1C -0,440555184
-ATP6V0A1 -0,440500219
-AKTIP -0,440321706
-C11orf49 -0,440065839
-ACCN1 -0,439959618
-DYNC1H1 -0,439954428
-RTN4 -0,439926435
-IFT52 -0,439664934
-ARIH1 -0,439616652
-SLC23A2 -0,439279622
-FDPS -0,439263979
-ZW10 -0,439088192
-C6orf211 -0,438493952
-CAPZA2 -0,438442617
-TRIM9 -0,43841496
-PANK2 -0,438226487
-SLC25A36 -0,437878589
-TM7SF2 -0,437751686
-GPD1L -0,437274057
-TM2D3 -0,437156245
-TBC1D22A -0,436837159
-AFF2 -0,436678505
-PSMA4 -0,43652406
-SCAPER -0,436328183
-KPNB1 -0,43624217
-C8orf33 -0,436164892
-RRAS2 -0,435924543
-PNMA1 -0,435862986
-DRD2 -0,435854058
-CCDC92 -0,435740221
-CYB5B -0,435703661
-DNM1L -0,435497666
-FAM98A -0,435109538
-CYCS -0,43500707
-UBE2B -0,434857087
-DCTPP1 -0,434751269
-ENC1 -0,434576571
-SAP18 -0,434463135
-MED7 -0,43446171
-UBXN6 -0,433506891
-MAEA -0,433493136
-C20orf27 -0,433220759
-ARFGEF2 -0,4331108
-FKBP9 -0,433030189
-COQ10B -0,432955202
-SNRNP25 -0,432902395
-PHKB -0,432809153
-CETN2 -0,432732838
-PIK3R4 -0,432641256
-EFR3A -0,432263211
-FAM162A -0,432255742
-LOC732160 -0,432226821
-SRPK2 -0,432044566
-USP9X -0,431489845
-DENND2A -0,431031563
-PPP2CA -0,430950806
-CHST1 -0,430892555
-OSBPL9 -0,430720865
-TPM3 -0,430527364
-UGP2 -0,430314768
-AL049387 -0,430134526
-ARHGDIG -0,429952838
-GPR161 -0,429932801
-HGSNAT -0,429440496
-TCEAL4 -0,429402449
-KHDC1 -0,429285977
-SPATA7 -0,428924113
-NIPSNAP3B -0,428922472
-NHP2L1 -0,42870798
-BZW2 -0,428685674
-BZW1 -0,428658261
-ABCF3 -0,428526247
-PEX19 -0,428349422
-POLR2K -0,42820853
-FAM134B -0,428156057
-TUBGCP4 -0,428150919
-CSNK2A1 -0,427824997
-PPP2R5D -0,427719013
-CEND1 -0,427667723
-RNF11 -0,427514623
-EBNA1BP2 -0,427275229
-SDHC -0,42690156
-ATP6AP2 -0,426823582
-MAPK1 -0,426681157
-YTHDC2 -0,425950246
-ACTR3B -0,425721173
-LRRC47 -0,424928312
-ANO10 -0,424906321
-MORF4L2 -0,424702281
-NAE1 -0,424669605
-GRSF1 -0,424576498
-UBE3C -0,42455123
-RRM1 -0,424268285
-IARS2 -0,424201991
-HINT1 -0,423973896
-B4GALT7 -0,423964657
-OBSL1 -0,423852756
-RPH3A -0,423713255
-PTPRM -0,423526608
-TRAP1 -0,423405292
-GSTO1 -0,423136683
-PGK1 -0,423107749
-KCTD2 -0,423033005
-AKAP9 -0,423014145
-KIAA0090 -0,422971022
-NIF3L1 -0,422805913
-SAE1 -0,422487927
-TRAPPC4 -0,422454822
-UBE3B -0,422322842
-MRPL13 -0,422291395
-ARF1 -0,422218883
-NCKAP1 -0,421739152
-COX11 -0,421717769
-XPA -0,421552598
-FKBP11 -0,421544606
-ZFAND1 -0,42136139
-RUSC1 -0,421250909
-PSMC2 -0,42099626
-MCM4 -0,420976269
-HEXA -0,420954607
-PDE4A -0,420795908
-VPS45 -0,420785909
-OGFOD1 -0,420640442
-ADPGK -0,420505817
-AP2M1 -0,420467875
-PSMD5 -0,420139323
-PGRMC1 -0,420109613
-CLASP2 -0,419942702
-CAMTA1 -0,419843296
-COX5A -0,419753275
-BCAP29 -0,419678508
-C21orf59 -0,419586484
-INSIG1 -0,419347593
-NDUFAF1 -0,419256514
-SNCG -0,419205938
-NCAN -0,418993508
-SLC24A3 -0,418714364
-MAP2K1 -0,418679322
-BRCC3 -0,418660516
-MYCBP2 -0,418420128
-PREPL -0,41818051
-TUFM -0,418149804
-LYRM2 -0,41810337
-ORC3L -0,417994092
-TSR2 -0,417894679
-SLC41A3 -0,41774061
-DZIP3 -0,417712026
-MRPS11 -0,417644175
-B4GALT6 -0,41761846
-CHD5 -0,417472
-TUBA1C -0,417351982
-OTUB1 -0,41729395
-DCAF6 -0,417154254
-UQCR10 -0,417021115
-BEX4 -0,416948363
-RTN3 -0,416868526
-GOLT1B -0,416408995
-MRPL3 -0,416396676
-DDX19A -0,416375948
-C4orf41 -0,416356919
-SEMA3G -0,416349944
-TUBA3D -0,416216957
-B4GALNT1 -0,415958605
-TOR1A -0,415819164
-SUPT16H -0,415597727
-ACTR3 -0,415469056
-ABCB9 -0,415410201
-SERF1B -0,415262572
-PSMC6 -0,415072747
-GALNT2 -0,414525722
-ARF5 -0,414370994
-TCEB1 -0,414262524
-FEN1 -0,414164817
-HS2ST1 -0,413801139
-FBXL15 -0,413238338
-ANAPC10 -0,413161353
-MAPK10 -0,413048251
-FGF12 -0,412576909
-GTF2B -0,412561968
-CALM3 -0,412474461
-C12orf5 -0,412385409
-BTRC -0,412323302
-UBXN8 -0,411884422
-G6PC3 -0,411853401
-MARK4 -0,411850043
-SDHB -0,411814414
-FXC1 -0,411804756
-KIAA1467 -0,411406746
-COL4A3BP -0,411372338
-MADD -0,411317373
-SLC25A11 -0,411257994
-APBB3 -0,411242683
-LDHB -0,411172229
-ENTPD3 -0,410988615
-CAMK2B -0,410817586
-C15orf24 -0,410807275
-RAB11FIP5 -0,410722406
-C18orf1 -0,410410534
-IL13RA2 -0,410393436
-TMEFF1 -0,40994415
-TAX1BP1 -0,409905258
-ABHD11 -0,409662969
-SETD4 -0,409479623
-NARS -0,409352949
-LOC441259 -0,409193342
-SMAD2 -0,408937637
-MAGEH1 -0,408820062
-LPIN2 -0,408744346
-WRB -0,408371938
-HSPB11 -0,408269901
-COMMD9 -0,407620354
-RMND1 -0,407542555
-RBP1 -0,407484296
-TSPAN7 -0,407465467
-YKT6 -0,407243851
-ATP5L -0,407238078
-STAT1 -0,407123963
-SPTAN1 -0,407085674
-SLBP -0,407034029
-FAM115A -0,407018502
-ATP1B1 -0,407007242
-GIN1 -0,406994648
-SLC25A4 -0,406703055
-RPAP3 -0,40653888
-ELAVL4 -0,406510215
-LDHA -0,406394191
-GABRG2 -0,406143723
-ACOT1 -0,406088493
-LZTFL1 -0,406077259
-LARP4 -0,406073312
-PTPRG -0,405852123
-DIRAS2 -0,405793372
-SNCB -0,405789504
-CDS1 -0,405765281
-ARL2BP -0,405758176
-BCL2L13 -0,405729545
-STAT4 -0,405634359
-C17orf75 -0,405632179
-ELAVL2 -0,405590653
-DNM3 -0,405342092
-SNX16 -0,404866663
-TACO1 -0,40485549
-HPGD -0,404805074
-CHMP2B -0,404775945
-DPP8 -0,404495701
-SYBU -0,403649563
-CHP -0,403478973
-GTF2H5 -0,403475179
-PPP2R5B -0,403191055
-TRAK1 -0,402996995
-ACSL4 -0,402921692
-RABGAP1L -0,402883713
-PSMB3 -0,402864552
-ASTN1 -0,402784524
-TIMM23B -0,402679864
-NDUFC1 -0,402669713
-GPM6A -0,402645229
-NCDN -0,402391637
-TMEM183A -0,402206694
-LACTB2 -0,402125728
-SFPQ -0,401934429
-SLC1A4 -0,401903736
-LOC731884 -0,401617561
-TTC3 -0,401599425
-APBA1 -0,401587582
-FAM20B -0,401527926
-ISOC1 -0,401479145
-TMEM70 -0,401425176
-GLUD1 -0,401204073
-NDUFA4 -0,401152135
-SHANK2 -0,401076931
-NDUFA6 -0,400922451
-FAM128A -0,400907344
-TSNAX -0,400758374
-BLCAP -0,400561763
-WASF3 -0,400514139
-MTMR6 -0,400412018
-CBARA1 -0,399961135
-SMCR7L -0,399645568
-REXO2 -0,399637796
-ASTN2 -0,399013865
-FBXO31 -0,398919379
-MRPS10 -0,398754479
-GNAL -0,398117434
-RDH11 -0,398104472
-ANKH -0,398086916
-EPHA5 -0,397910595
-DPY19L2P2 -0,397861593
-NRXN1 -0,39777997
-FOXA1 -0,397622781
-AGGF1 -0,397583973
-CLCN6 -0,397581706
-PRKAG1 -0,397496639
-GRM5 -0,397456403
-BCAT1 -0,397331444
-MAP1LC3B -0,397317027
-HMGCL -0,397130437
-IFIT5 -0,397045055
-FAM82B -0,397007464
-TMEM189-UBE2V1 -0,39671729
-TMEM160 -0,396535704
-PIGZ -0,396390486
-VDAC2 -0,3962914
-BCAP31 -0,396227306
-CUL2 -0,395939867
-C5orf30 -0,395902062
-VAMP4 -0,395520757
-CLTA -0,395495699
-NOS1AP -0,395452681
-YWHAH -0,395414553
-AGL -0,39537715
-PPIA -0,395286888
-POLR2E -0,395239973
-FAM190B -0,395231307
-CAND1 -0,395218949
-DIABLO -0,395167608
-FAM155A -0,395099838
-FAM174B -0,394929763
-ABCA11P -0,394841999
-LMF1 -0,394801997
-EIF3I -0,394774336
-RRAGA -0,39363313
-SLC25A5 -0,39336993
-BTBD3 -0,393323586
-SLC38A6 -0,393193457
-TSPYL4 -0,39289974
-NDUFA8 -0,392898828
-ERI3 -0,392853573
-CDH11 -0,392815946
-VPS11 -0,392712183
-RPP40 -0,39270293
-SMS -0,392616216
-USP4 -0,39251437
-RAN -0,392486577
-SYT11 -0,392234251
-SEC23IP -0,392233152
-SUPV3L1 -0,392124663
-TOX3 -0,392048323
-OSBPL3 -0,391742979
-ATP5J -0,391738382
-APC -0,391687772
-EIF2AK2 -0,391678642
-MPPE1 -0,391534871
-CHD3 -0,391021702
-BE858194 -0,390954653
-GPN2 -0,390821549
-TMEM97 -0,39059622
-BRF2 -0,390477924
-NSDHL -0,390017568
-LOC654342 -0,389476483
-SATB1 -0,389035394
-RPP14 -0,388984247
-C16orf68 -0,388858051
-PHF14 -0,388842446
-CKAP5 -0,388699527
-MMADHC -0,388406258
-MEST -0,388313548
-UQCRH -0,387974488
-GBAP1 -0,387823169
-PMPCA -0,387778282
-TMEM41B -0,387668262
-SCLY -0,387620138
-OXA1L -0,387520115
-CLPX -0,387517816
-EML1 -0,387443167
-DPP6 -0,387318033
-FBXO3 -0,387294212
-GAPDH -0,386769027
-ATP6V1C1 -0,386766958
-PRAF2 -0,386484628
-NAA35 -0,386425969
-EIF4H -0,386302469
-SGSH -0,386196526
-CLCN3 -0,386084887
-SMARCA1 -0,385880429
-FAM158A -0,385760557
-AP3S2 -0,385712457
-EIF1AX -0,385367803
-RNF115 -0,385287305
-GPI -0,385266179
-SEC62 -0,385020013
-G3BP2 -0,384968143
-NDUFV1 -0,38487232
-C19orf42 -0,384758261
-BEND5 -0,384699839
-KCNAB2 -0,384620267
-EVL -0,384619104
-MTMR9 -0,384460721
-SIRT3 -0,384239932
-CNIH -0,383916854
-TOLLIP -0,383913386
-C11orf2 -0,383735535
-NUDCD3 -0,383703548
-MED4 -0,383545823
-RABGEF1 -0,38353381
-PTN -0,383407974
-GBF1 -0,383365739
-C1orf163 -0,383317238
-LOC100129361 -0,383315417
-CUL4B -0,383032231
-OXR1 -0,382758654
-TRIM33 -0,382726006
-GPC5 -0,382713696
-C11orf51 -0,382673891
-MAN1C1 -0,382595078
-FGF9 -0,382294616
-SPOCK2 -0,382267861
-GLMN -0,382038722
-MPP1 -0,381567886
-KIF21B -0,381555674
-RND1 -0,381481938
-PEX1 -0,381462705
-C2orf34 -0,381417191
-OTUD3 -0,381344145
-MSRB2 -0,381206334
-CCDC85B -0,38118283
-RGS3 -0,380621769
-SERPINI1 -0,380596066
-C14orf2 -0,380470075
-IDH3G -0,380458518
-POLR2C -0,380378788
-CTNNA2 -0,380377628
-XRCC6 -0,380295972
-EIF3A -0,380281294
-CRBN -0,380214781
-RPS6KC1 -0,3801397
-NUDT2 -0,380057201
-GOLPH3L -0,379823471
-CSNK1A1 -0,379812095
-NDUFB2 -0,379757693
-FTO -0,37940886
-SLC6A15 -0,379271656
-PCP4 -0,379256762
-NIT1 -0,37912136
-CCNC -0,378699092
-DGKB -0,378485235
-RANBP6 -0,377965444
-DNAJC8 -0,377764456
-MAPRE2 -0,377675379
-ARFGAP2 -0,377574006
-BDNF -0,377511436
-HSD17B10 -0,376728332
-AKAP7 -0,376531212
-EHD1 -0,376479944
-PSMD10 -0,376243528
-FABP5L2 -0,376090187
-VAMP7 -0,376017526
-WBP4 -0,375749974
-MAP1B -0,375485017
-SMPDL3A -0,375390185
-GPR89C -0,375362209
-SEPT2 -0,37512019
-GPX3 -0,374915078
-AARSD1 -0,374664572
-HSPA9 -0,37466397
-MAP1A -0,374598439
-C16orf62 -0,374459363
-CARKD -0,374388504
-ASS1 -0,374197776
-WDR12 -0,374046313
-ABHD14A -0,37397421
-SPIN2B -0,373568971
-RAB6A -0,373528481
-PTPRF -0,373483075
-RRAGB -0,373427062
-STK39 -0,373365187
-COX7B -0,373307822
-PDCL -0,373110957
-ATP2A2 -0,373066228
-PPM1E -0,37285382
-TRMT61B -0,372798595
-C21orf33 -0,372766056
-MGMT -0,372730061
-LPHN3 -0,372647138
-WBP2 -0,372385809
-ACSBG1 -0,372296169
-PGRMC2 -0,372287654
-LRRC20 -0,372239514
-AGA -0,372171162
-NRCAM -0,372117405
-FUT9 -0,372053568
-C22orf28 -0,371916518
-MRPS15 -0,371914782
-UFM1 -0,371876489
-CAMK2G -0,371790847
-AVPI1 -0,371692415
-MAST2 -0,371637676
-PPP1R7 -0,371553142
-EEF1A2 -0,371514176
-ATP5D -0,371416456
-EEF1E1 -0,37139203
-NLRP1 -0,371368381
-PMS2CL -0,371209965
-CDK5R1 -0,371120209
-C2orf72 -0,371108998
-OAZ2 -0,3710748
-AL109698 -0,37073584
-INPP4A -0,370700597
-ERH -0,370513944
-CAMK1G -0,370474818
-MED24 -0,370430566
-DMXL1 -0,370287216
-COMMD4 -0,370258812
-NOMO3 -0,370043447
-MORF4 -0,369691968
-ZNHIT3 -0,369651044
-GDPD5 -0,369635923
-CUL5 -0,369519961
-AP1B1 -0,369511443
-YARS -0,369387873
-ABHD10 -0,36913324
-KCNB1 -0,369083149
-SKP1 -0,369015624
-FBXO28 -0,368924883
-ATR -0,368436696
-TMED2 -0,368132686
-ARPC1A -0,367983188
-PHYH -0,367958422
-MRPL22 -0,367879083
-SRRD -0,367868238
-WDYHV1 -0,367821841
-EIF3CL -0,367732775
-HMGB3 -0,367450086
-DENND1B -0,36732795
-ALDH5A1 -0,367318431
-CCNA1 -0,367103911
-FAM134A -0,367014983
-DZIP1 -0,366778091
-WASF1 -0,366602553
-ATXN3 -0,366426778
-CCDC25 -0,3658102
-ERP29 -0,365799413
-IVD -0,365499555
-SNX24 -0,365222253
-CDK20 -0,365176415
-TTC9 -0,365148586
-RBM8A -0,36488846
-AMACR -0,364562114
-TBPL1 -0,364450426
-PTPMT1 -0,364434415
-CANX -0,364232908
-ELAC2 -0,364131757
-EIF2S1 -0,364109368
-AKR1B1 -0,363915593
-ACADM -0,363858719
-RGS16 -0,363795844
-SLC20A1 -0,363602798
-MTUS2 -0,363384151
-ZMIZ2 -0,363364816
-NDUFS4 -0,363146027
-AW242701 -0,363104323
-SNAPC3 -0,363053639
-ENOPH1 -0,362868334
-LYRM1 -0,362706602
-TRMT12 -0,362561085
-BAALC -0,362539013
-CHMP1B -0,362404908
-ATP1A3 -0,362300724
-TOMM20 -0,362192747
-PEX14 -0,362047536
-EIF2AK1 -0,361934247
-CNNM2 -0,361790716
-PPOX -0,361753445
-TAC1 -0,361655557
-GLRX3 -0,361266708
-OBFC1 -0,360197329
-MFN2 -0,360036589
-DGCR14 -0,359808857
-FAM175B -0,359691136
-PARP2 -0,359639462
-GPR107 -0,359495249
-TUBGCP5 -0,35920098
-ENSA -0,359186957
-UMPS -0,358973056
-SSBP1 -0,358916914
-PFDN2 -0,358707301
-IFFO1 -0,35859667
-CCT2 -0,358497035
-PSMA5 -0,358414139
-ZC3H15 -0,358397302
-EPHX2 -0,358269729
-CALB1 -0,358259257
-POP7 -0,358253841
-MRPL12 -0,357874032
-DFNA5 -0,357815106
-PIAS1 -0,357740062
-ARL4C -0,35770713
-HRAS -0,357592893
-CEP68 -0,35754909
-SNRPA1 -0,357535253
-SCP2 -0,357518758
-C4orf27 -0,356816465
-TMEM185B -0,35662055
-SPAG16 -0,356585241
-ESYT1 -0,356493695
-PTP4A1 -0,356347412
-PDLIM2 -0,356333479
-MSRA -0,355999453
-UAP1 -0,355870622
-CDK16 -0,355785531
-MBOAT7 -0,355761708
-FARSA -0,355610517
-MRPS7 -0,355424517
-EPHB2 -0,355389176
-LOC729991-MEF2B -0,355378273
-PDHA1 -0,355252318
-ACTL6B -0,355166654
-SAR1A -0,355144478
-KDM1A -0,355067715
-PRDX3 -0,354963773
-ETF1 -0,354759299
-ARMCX2 -0,354758912
-IQSEC1 -0,35395949
-TIMM13 -0,353925241
-AP2B1 -0,353904118
-STYK1 -0,353863363
-CDK7 -0,353806664
-DLG3 -0,353783905
-SEPHS2 -0,353722454
-MTOR -0,353463273
-PPIH -0,353351383
-GRPEL1 -0,353254529
-C9orf91 -0,353075824
-RGS17 -0,353023569
-NTSR1 -0,352789658
-HNRNPH2 -0,352751195
-HCCS -0,3526918
-C2orf3 -0,352661516
-TFDP2 -0,352647453
-GOSR2 -0,352396188
-PSMB1 -0,352279045
-MPI -0,35224609
-DUSP26 -0,351953212
-HERC1 -0,351631367
-SORD -0,351295095
-TUBB2B -0,351140866
-LPCAT4 -0,351128323
-CFL1 -0,351124653
-ARPP19 -0,350935095
-MTMR4 -0,350923479
-COX7A2 -0,350878835
-PGM1 -0,350865278
-RHOQ -0,350802567
-CCDC53 -0,350756677
-UQCRB -0,350742301
-NAPA -0,350657124
-CSDC2 -0,35061274
-BECN1 -0,350596093
-GYG2 -0,350535323
-GPKOW -0,35045328
-FXYD7 -0,350387292
-CYLD -0,349973469
-CSPG5 -0,349825086
-TTC15 -0,349816074
-ILF2 -0,349761198
-STOML2 -0,349586681
-CACNB2 -0,349516102
-VARS -0,349372141
-ZSCAN18 -0,349241937
-PTRH2 -0,349224021
-P2RX5 -0,349175679
-RALB -0,349042784
-NUBPL -0,348899542
-NCBP2 -0,348786336
-DKFZp434H1419 -0,348772873
-UFSP2 -0,348370783
-ARHGEF17 -0,348050229
-FXR2 -0,34801331
-INSIG2 -0,347755165
-XRCC5 -0,347746659
-CLTCL1 -0,34759935
-TMEM177 -0,347585446
-VAMP2 -0,347189398
-EML2 -0,347084746
-SNUPN -0,346850632
-GPX4 -0,346688538
-RASA1 -0,346685342
-USP46 -0,346590476
-LSM5 -0,346546029
-SEC31A -0,34652486
-PALM2-AKAP2 -0,346447335
-CKAP2 -0,346385113
-ELOVL5 -0,346375127
-PMS2L3 -0,346133275
-PAQR3 -0,346117871
-ST8SIA3 -0,34604187
-FDX1 -0,34603415
-C12orf4 -0,345989709
-COQ7 -0,345988262
-UROD -0,345987158
-RPE65 -0,345902642
-DCK -0,345889475
-RARS -0,345819092
-CAPZA1 -0,345775372
-NRN1 -0,345693574
-RNF7 -0,345545425
-ABAT -0,345474072
-CRY2 -0,345467057
-HR -0,345290796
-CACNA2D3 -0,345213407
-TWIST1 -0,345148814
-P4HTM -0,345112277
-GDI1 -0,344731063
-GRIA3 -0,344721718
-D4S234E -0,344715573
-TMEM151B -0,344385728
-MPHOSPH6 -0,344298044
-PYGB -0,344201683
-MARCH6 -0,344086188
-AL050136 -0,343680587
-NDUFS6 -0,343667551
-TRAPPC9 -0,343555476
-PYGL -0,343533875
-EFNB3 -0,343417492
-SCD -0,343398039
-TFG -0,342863204
-PPFIA3 -0,342761025
-SENP6 -0,342750174
-KCMF1 -0,342689973
-GNAS -0,342684217
-MAPK6 -0,342588157
-PRMT5 -0,34246621
-SEPT11 -0,342460355
-MEIS3P1 -0,342265108
-FABP3 -0,3421554
-YIPF6 -0,3420929
-FABP6 -0,342074193
-SRSF9 -0,341825092
-AP1AR -0,341737984
-PKNOX2 -0,341609179
-PAK6 -0,341535575
-PRKAA1 -0,341378959
-UBA3 -0,34130955
-OAZ1 -0,341251276
-EID1 -0,340941987
-MRPS28 -0,340842312
-AA890010 -0,340724739
-OSBP -0,340497775
-ATP6V0C -0,34047911
-ARHGAP24 -0,340414643
-PNKP -0,340118439
-PSMD7 -0,340085658
-IPO9 -0,340071575
-ARF4 -0,339993296
-TERF2 -0,339818219
-SRSF2 -0,339525933
-PSMC5 -0,33950993
-TM9SF1 -0,339389717
-ACAT2 -0,339093022
-CDK8 -0,33909169
-KIAA0196 -0,338987444
-TFPT -0,338941882
-TRPC4AP -0,338718194
-TUBG1 -0,338211067
-SCN2B -0,338080627
-MTHFD1 -0,338071854
-ATPAF2 -0,338050158
-IGSF1 -0,337997383
-RGPD6 -0,337877048
-C16orf45 -0,33773508
-C10orf76 -0,337659307
-UBE2A -0,33762595
-PQLC1 -0,337612976
-SOD1 -0,337454918
-ARPC2 -0,337418781
-MEMO1 -0,33728488
-CSDE1 -0,337036578
-PHYHIP -0,336992273
-LYPLA1 -0,33698776
-NDUFA1 -0,336883322
-MARCKSL1 -0,336747008
-DCTN1 -0,336745427
-COX6A1 -0,336728807
-DPM1 -0,336614034
-ELP3 -0,336602956
-LOC653566 -0,336555692
-COX7BP1 -0,336528019
-CAPZB -0,336348777
-DCUN1D4 -0,335942405
-UCHL5 -0,335933871
-PSIP1 -0,335684272
-MRS2 -0,335589123
-RABGAP1 -0,335570544
-KCNA6 -0,335454989
-RAC1 -0,335429141
-ZMYM2 -0,33542626
-MRPL17 -0,335371398
-MLF1 -0,335274724
-RFC3 -0,33507418
-ARMCX3 -0,335005795
-GMDS -0,334931775
-KIAA0317 -0,334922749
-CAMSAP1 -0,334678333
-LSG1 -0,334628714
-PNPO -0,334625052
-THOC5 -0,334532053
-C11orf58 -0,334154436
-MTCH1 -0,334038037
-KAL1 -0,333848755
-OMG -0,333590731
-KLHL7 -0,333537148
-TTPAL -0,333489991
-GLA -0,333336937
-SEZ6L2 -0,333262252
-SNURF -0,333035272
-ARL6IP1 -0,332988884
-BFSP1 -0,332976059
-MAPKSP1 -0,332894473
-HABP4 -0,332672498
-SLC8A2 -0,332645114
-CKAP4 -0,332543738
-NPM1 -0,332250102
-CLSTN3 -0,332157745
-RUSC2 -0,33210981
-RCHY1 -0,331805148
-CACNA1D -0,331681156
-ZFAND5 -0,331302172
-TACC2 -0,331046487
-CHCHD3 -0,331008486
-RGS2 -0,330792786
-LDOC1 -0,330775706
-BTN2A1 -0,33075204
-WDR45 -0,330593865
-W87688 -0,330499179
-YWHAQ -0,330473094
-RAB3GAP2 -0,33029144
-HTRA2 -0,330240669
-SNRPD1 -0,330240562
-ANXA7 -0,330030639
-KIAA1024 -0,329770804
-RAD51C -0,329735785
-PRPF18 -0,329474331
-CCT6B -0,329361737
-ABCD3 -0,329205796
-PARN -0,329139621
-APOL2 -0,328983174
-MRPS18A -0,32863432
-RASL10A -0,328581006
-COG8 -0,328398026
-ZNF512B -0,327877848
-ATP5H -0,327758416
-PRDM4 -0,327710757
-TSPAN3 -0,327644045
-EPB41L3 -0,327416874
-APLNR -0,327394979
-TFR2 -0,327337619
-GADD45A -0,327012981
-POLR3F -0,326871651
-FASTKD3 -0,326789822
-TCERG1 -0,326746174
-VPS41 -0,326459968
-C17orf101 -0,325979143
-EXOC3 -0,325763291
-SLC25A17 -0,325666279
-GDAP1L1 -0,325526797
-HCFC1R1 -0,325022815
-SF3B5 -0,324878766
-TEX10 -0,324812522
-PSMA7 -0,324673715
-TCTN3 -0,324389244
-NOVA1 -0,32437578
-RABEPK -0,324366299
-ALG5 -0,324335095
-ENOSF1 -0,32427768
-SH3BGRL3 -0,32409913
-CTNND2 -0,324002004
-NKRF -0,323983769
-SLC6A1 -0,323833407
-MAPK1IP1L -0,323722226
-RAB22A -0,323713658
-GRP -0,323354345
-SDS -0,323335387
-IBTK -0,323304602
-CARS -0,322679359
-WWP1 -0,322463311
-ARL8B -0,322442301
-SLC19A2 -0,322361872
-F8A3 -0,322202521
-LPHN1 -0,322183082
-SMARCD3 -0,322148361
-GPN1 -0,322024809
-FAF2 -0,322014431
-SLC35B1 -0,321878066
-MPV17 -0,321698226
-TOM1 -0,321634922
-NEDD4L -0,321518057
-MRFAP1L1 -0,321393672
-C6orf62 -0,321303598
-POLR3B -0,321247444
-HTR2A -0,321189596
-CUL3 -0,321141566
-PSMD9 -0,321108014
-LRP3 -0,32099653
-TMEM62 -0,320873847
-PLS3 -0,320803014
-SUMO1 -0,32076762
-DLG4 -0,320617015
-ANKRD17 -0,320557554
-ARFIP2 -0,320500236
-HMGN4 -0,320196335
-PRKAG2 -0,319945607
-STAR -0,319749743
-NF1 -0,319726773
-ATOX1 -0,31967306
-UBE2M -0,319629201
-NDRG3 -0,319446308
-SNPH -0,319396594
-TPD52 -0,319178712
-PLK2 -0,319120325
-C1QBP -0,318975829
-SRSF8 -0,318843616
-USP22 -0,318806098
-GPD1 -0,318728943
-MAPK8IP2 -0,318691894
-USP20 -0,318610382
-RPA2 -0,31845096
-CCPG1 -0,318358561
-NQO2 -0,318256129
-POLR3C -0,318231923
-HBXIP -0,318079181
-MRPS31 -0,318018334
-SNRPB2 -0,31801084
-CACNG3 -0,317104885
-CCNE1 -0,316783937
-NDUFAF4 -0,316755785
-GRK6 -0,316405946
-ZER1 -0,316363024
-CHCHD7 -0,316179658
-C20orf29 -0,315860291
-AI693193 -0,315746456
-TPMT -0,315745725
-TPPP3 -0,315557058
-CTH -0,315210231
-HSDL2 -0,31516145
-MAPRE3 -0,314964867
-NLE1 -0,314918022
-ARHGEF4 -0,314777145
-STK19 -0,314737564
-AW503390 -0,314280211
-KIAA1279 -0,314104435
-CA14 -0,313849822
-CYP2E1 -0,313441486
-FHL1 -0,313417456
-MYL6B -0,313075964
-PACRG -0,3129322
-SCN2A -0,312912414
-POLR3G -0,312898745
-MED6 -0,312862133
-PCSK1N -0,312861133
-FLJ10038 -0,312756044
-PHTF1 -0,312716368
-PRPF4 -0,312654478
-RPRD1A -0,312642779
-HLF -0,312545473
-MTMR1 -0,312535102
-MFN1 -0,312461722
-C1orf50 -0,312398425
-QPRT -0,312349796
-ZDHHC6 -0,31229266
-ITGAE -0,311863717
-SLC18A1 -0,311739998
-CD83 -0,311711539
-GGCT -0,311631664
-KIAA0100 -0,311503156
-OPN3 -0,311374884
-SSX2IP -0,311111099
-NUCB2 -0,31105706
-UTP11L -0,311015852
-GOLGA8B -0,310924837
-UST -0,310734373
-PRKCI -0,310493775
-AP2S1 -0,310480065
-WBSCR22 -0,310476192
-PPP3CA -0,310434457
-PDSS2 -0,310396648
-PEG3 -0,310335546
-ATP5E -0,310319916
-GABRA5 -0,310200087
-AGPAT4 -0,310173061
-PDCD10 -0,310157516
-DDOST -0,310094837
-RPL23 -0,309992315
-HOMER1 -0,309485866
-C1orf123 -0,309187816
-POLE3 -0,309012195
-DDX41 -0,308923345
-HSD17B8 -0,308824584
-GMPR2 -0,308792858
-SCARB2 -0,308695909
-DGUOK -0,308606021
-MAGEF1 -0,308535371
-FOXA2 -0,308348483
-GLS2 -0,308287643
-TBCC -0,308286536
-FBXO41 -0,308255485
-SLC12A1 -0,308214984
-PELO -0,308137793
-KCNE1L -0,30811412
-RBBP4 -0,308007454
-UBL5 -0,307720013
-KLHL12 -0,307571676
-FTSJ1 -0,307464516
-ZFYVE16 -0,307366442
-PPT1 -0,3073579
-ZC3H13 -0,307293327
-DYRK1A -0,307183877
-PHACTR2 -0,306935621
-SLITRK3 -0,306872073
-PI4KA -0,306770561
-RNPS1 -0,306364972
-RALGAPB -0,306086767
-BRP44 -0,305953308
-BNIP1 -0,305883874
-SUPT4H1 -0,305675152
-BCKDK -0,30566687
-PLAA -0,305619464
-ACTR2 -0,305363631
-PION -0,305054773
-NFU1 -0,305010295
-CCT6A -0,304801168
-KIAA0427 -0,304585348
-EHD3 -0,304533089
-FAM63B -0,304437794
-STK25 -0,304425083
-POLB -0,304419007
-MRPL35 -0,304416576
-UBE2Z -0,3043165
-GSTZ1 -0,304133065
-AP3S1 -0,30395899
-SPATS2L -0,303776395
-LOC729580 -0,303766036
-RALGAPA1 -0,303697943
-PUF60 -0,303647762
-DAP3 -0,303640732
-AHI1 -0,303570806
-UBE2NL -0,303361552
-TMEM164 -0,303165514
-DOCK3 -0,303099341
-CADM3 -0,303050893
-ZNF219 -0,302968533
-PRKAR1B -0,302898104
-DOK5 -0,302798088
-ORMDL2 -0,302372011
-ACVR2A -0,302331205
-ALDOA -0,30171568
-ATRN -0,301666345
-COX7C -0,301597748
-PRKDC -0,301229867
-GNG10 -0,300757182
-SNX17 -0,300752701
-RBMS1 -0,300466996
-AJAP1 -0,300458474
-PREP -0,300414848
-ALDOC -0,300361514
-LAMA4 -0,300246196
-PI4KAP1 -0,300223018
-TMEM222 -0,30010369
-PIGB -0,299980372
-SSSCA1 -0,29997354
-DCUN1D1 -0,299517655
-DLSTP1 -0,299414392
-ITM2B -0,299325985
-AK025651 -0,299260618
-ACOT13 -0,299073057
-ZNF593 -0,298588283
-LOC100129250 -0,298385026
-H2AFY -0,298292243
-IGF1 -0,298232454
-KIAA0368 -0,29819687
-FKBP3 -0,298122528
-C12orf49 -0,297820161
-PRKRIR -0,297808472
-GLUD2 -0,297805688
-NBL1 -0,297799978
-PTPN4 -0,297657679
-LOC644617 -0,297586698
-IL33 -0,297538719
-CUL4A -0,29730361
-SIP1 -0,297199387
-POLDIP2 -0,297140479
-EBP -0,297109427
-FASTKD2 -0,296665172
-SMPD1 -0,296658212
-FAM55C -0,296650198
-TRPV2 -0,296465177
-DOPEY1 -0,29633822
-SCYL3 -0,296201386
-UBL3 -0,296188632
-STK38L -0,296164266
-APITD1 -0,296017845
-SFXN1 -0,295918484
-CPT1A -0,295754312
-USP8 -0,29570338
-MRPS30 -0,295702739
-ATG7 -0,295335659
-C10orf88 -0,29514056
-PIPOX -0,295018193
-RAC3 -0,294600261
-CIAO1 -0,294564961
-KLC2 -0,294523931
-LEPROTL1 -0,29448316
-ENDOD1 -0,294147277
-FEM1B -0,294007766
-IRS1 -0,293342341
-CYP51A1 -0,293155923
-DYNLRB1 -0,292974645
-TOM1L2 -0,292906836
-TDP2 -0,292808809
-MRPL49 -0,292778686
-LRP8 -0,292767989
-MOSPD1 -0,292730297
-C6orf134 -0,29255632
-TRPC1 -0,29249815
-RASL11B -0,292459191
-AL109671 -0,292334441
-TTC37 -0,292136499
-ODZ4 -0,292070818
-KIN -0,291741417
-KPNA1 -0,291721639
-CAST -0,291558763
-NDUFA13 -0,291524477
-AKR1A1 -0,29149158
-QARS -0,29146477
-MRPS22 -0,29145846
-MMACHC -0,291414294
-UBQLN2 -0,291358191
-PIK3CB -0,291242041
-COX6B1 -0,291081182
-PDK2 -0,290962723
-RABGGTB -0,290962562
-SR140 -0,290943983
-ATF2 -0,290881352
-FADS1 -0,290820194
-SRP14 -0,290691218
-RAD23B -0,290632171
-AHCY -0,290521401
-RINT1 -0,290502144
-SRP54 -0,290224786
-COX5B -0,289972152
-NBN -0,289962803
-DDX50 -0,289845246
-NUFIP1 -0,289611609
-HDGFRP3 -0,289540354
-HBA2 -0,289412602
-SRP9L1 -0,289377441
-ARFGEF1 -0,289327503
-FAM13B -0,289118442
-DIMT1L -0,288943725
-LPO -0,28888192
-VPS28 -0,288730564
-SSR3 -0,28867602
-SEPT7 -0,288663677
-NARS2 -0,288651232
-EMG1 -0,288493971
-HSPA8 -0,288488899
-TBC1D13 -0,288209587
-TTC35 -0,288076299
-GTPBP4 -0,287916733
-SPG7 -0,287774853
-PAFAH1B3 -0,28772138
-MAPT -0,28765216
-RERGL -0,287509361
-HNRNPD -0,287438947
-PLCL2 -0,287391702
-HLA-DPA1 -0,287200849
-CD55 -0,286966384
-IDH3A -0,286870398
-STXBP5L -0,286801199
-MAP3K12 -0,286334641
-PPP2R1A -0,286259611
-TMEM126B -0,286136364
-CDKN3 -0,286064506
-ABCC5 -0,286013319
-TMEM127 -0,285913561
-DNAJC2 -0,285585137
-SEC61G -0,285583827
-SSR1 -0,285489405
-AIMP1 -0,285281231
-YTHDF2 -0,285194578
-FAM86B1 -0,285046154
-CTBP1 -0,285027477
-CHRFAM7A -0,285001423
-SSBP3 -0,284934817
-MRPL46 -0,284930449
-TSPAN6 -0,284861931
-MYST2 -0,284824247
-GGH -0,284817124
-PRKACB -0,2847024
-C2orf47 -0,284692381
-NLK -0,284579832
-ASNS -0,28445955
-EXOC5 -0,28439526
-OAZ3 -0,284379411
-CTNNBIP1 -0,284364924
-PVR -0,284070802
-C16orf80 -0,284019987
-UBE3A -0,283816198
-EAPP -0,28376748
-IGSF3 -0,283764031
-KCND2 -0,283569047
-FOXK2 -0,283286684
-SLC35A2 -0,283204451
-TBCB -0,283168385
-SLC38A1 -0,283158141
-ACCN2 -0,283147998
-FAM149A -0,283126904
-TIMM22 -0,283102824
-EIF4ENIF1 -0,28310048
-THSD1P1 -0,282819454
-MAGED4 -0,282562753
-CLASP1 -0,282510547
-C1orf61 -0,282424601
-C6orf106 -0,282397365
-WDR44 -0,282155933
-GNL3 -0,282115302
-RCBTB1 -0,28192202
-OSTM1 -0,281535242
-AGPAT5 -0,281510168
-PRNP -0,281405094
-APPBP2 -0,281330465
-GAD1 -0,281295305
-NECAB3 -0,281056363
-ABCF1 -0,280961256
-DNAJC7 -0,280750506
-EPHB1 -0,280596899
-GPRC5A -0,280368026
-HSPA14 -0,280049432
-CLPTM1 -0,280042656
-SGPP1 -0,27999737
-ABCG4 -0,279891909
-GFRA1 -0,279146972
-ATP5SL -0,278849245
-CTSO -0,278677227
-DCTN4 -0,278556645
-MAP2K2 -0,278535478
-ZNF423 -0,278503712
-FUS -0,278285124
-ACTR8 -0,278282163
-PRR13 -0,278189761
-ZNF329 -0,278179162
-RNASEH2B -0,278151755
-LOC284244 -0,278099761
-FAM117A -0,277715513
-MREG -0,277651168
-C2orf18 -0,277609469
-AW612311 -0,277599115
-SYNRG -0,277434047
-SMARCE1 -0,277346186
-DNAJA3 -0,277188103
-PPP2R5E -0,2770317
-TMCO6 -0,276951805
-C6orf35 -0,276886272
-DDX18 -0,276619655
-TTLL1 -0,276373935
-LANCL1 -0,276361838
-SNRPE -0,276287655
-DTX4 -0,276233703
-IDH2 -0,276017451
-SACS -0,275814599
-ABHD2 -0,275491786
-VAMP1 -0,275092752
-AGPAT1 -0,27504004
-TYMS -0,274913065
-ZDHHC3 -0,27479568
-LMO1 -0,274566957
-UVRAG -0,274559415
-HBB -0,274385467
-PSMA2 -0,274273938
-CD24 -0,27422103
-GRAMD1B -0,27394685
-PRC1 -0,27393137
-YARS2 -0,27376193
-SIGMAR1 -0,273597834
-CPEB3 -0,273534888
-ARMC9 -0,273442678
-DNAJC10 -0,273369377
-TM9SF4 -0,27326642
-RBX1 -0,273166064
-C13orf1 -0,273151402
-PDCD4 -0,273130523
-LUZP2 -0,272843047
-APLP2 -0,272609838
-USO1 -0,272598741
-SH3BP5 -0,272512602
-PPP1R11 -0,272494252
-PEMT -0,272485616
-CDC16 -0,272287144
-LCMT2 -0,272235596
-DCX -0,271983078
-DDAH1 -0,271924121
-UBE2D2 -0,271815552
-TANK -0,271664689
-AW974666 -0,271662837
-USH1C -0,271630244
-BDH1 -0,271624449
-B9D1 -0,271589518
-BRD9 -0,271105209
-USP7 -0,271052865
-TRIM2 -0,270764995
-PARK7 -0,270634786
-NSFL1C -0,270597248
-COQ2 -0,269953826
-HNRPDL -0,269787459
-NOV -0,269731303
-SLC25A28 -0,269706278
-EXT2 -0,26958066
-VLDLR -0,269148459
-SLC4A4 -0,268895862
-SMURF1 -0,268798637
-ORC2L -0,268275919
-ZC4H2 -0,268056536
-SDHAF1 -0,267985583
-VDAC1 -0,267895013
-ALDH1A3 -0,267738476
-PNPLA4 -0,267586498
-HAGH -0,267406111
-CNTNAP2 -0,267355858
-KPNA3 -0,267278305
-LRBA -0,267216793
-DPYSL4 -0,267150239
-MCCC2 -0,26714725
-KBTBD4 -0,267031071
-DCTD -0,267005887
-C1orf21 -0,266982234
-C2orf43 -0,26679916
-SF3A3 -0,266732334
-PTPN3 -0,266674559
-FBXO21 -0,26664933
-CCT7 -0,266615147
-CLNS1A -0,266539743
-HAPLN1 -0,266160364
-SYT13 -0,26591944
-SENP5 -0,265695364
-HMGB2 -0,265556554
-CANT1 -0,265168032
-CGREF1 -0,265157579
-GRM1 -0,26510368
-ZFHX4 -0,265049797
-PVRL3 -0,264999073
-ADAR -0,264636454
-TRIM3 -0,264561355
-ANP32E -0,264413865
-PDLIM7 -0,264406742
-MLH1 -0,264377914
-PRKCA -0,264376056
-CYB5R3 -0,264120933
-PDE1A -0,263919942
-LOC100127998 -0,263915362
-WSB2 -0,263691169
-RPF1 -0,263404659
-CXCL12 -0,26333499
-TMEM66 -0,263285506
-EIF6 -0,263232223
-NFE2L1 -0,262789646
-KLHL20 -0,262772392
-PPM1H -0,262689193
-PIN4 -0,262483899
-TUBA4B -0,26241982
-ECT2 -0,262276809
-MGC5566 -0,261888759
-C9orf116 -0,261830489
-ASB1 -0,261751394
-ABCC8 -0,261735107
-ELOVL2 -0,261638578
-PHB2 -0,261466477
-ZNF580 -0,261379751
-DNAJC24 -0,261364702
-PSMB10 -0,261344946
-CSE1L -0,261292597
-ANKRD27 -0,261154598
-TUBG2 -0,261047779
-C6orf162 -0,261001828
-AL034399 -0,260886813
-GLT8D1 -0,26052144
-SRR -0,260520305
-MCC -0,260395686
-COX4I1 -0,260324715
-SEP15 -0,260222524
-RNF103 -0,260210477
-ZNF576 -0,260159221
-MGEA5 -0,260092677
-RSL24D1 -0,259958151
-USP13 -0,25969613
-MLLT3 -0,259631882
-SRI -0,259268888
-NCS1 -0,259133737
-MAPKAPK5 -0,259103348
-IQCG -0,25908825
-FN3KRP -0,258914892
-BCKDHB -0,258870249
-GOLGA5 -0,258736414
-RDBP -0,258483881
-SUPT7L -0,258355414
-METTL1 -0,258206012
-CREB3 -0,258159408
-TMEM111 -0,258136123
-NRSN2 -0,257397396
-CNTN1 -0,257314074
-COX10 -0,257277055
-SERPINB9 -0,257269621
-MTF2 -0,256976969
-EDNRB -0,25676028
-HSF2 -0,25652969
-POLR2L -0,256424652
-TRIM58 -0,256294322
-DACH1 -0,256241463
-UEVLD -0,256239024
-ATP1B3 -0,256215499
-SAP130 -0,256053262
-TRPC6 -0,255890704
-HERC6 -0,255794959
-NAV3 -0,255707496
-GOSR1 -0,25567987
-CNR1 -0,255506006
-PSME4 -0,25522233
-CAMKV -0,254605479
-ADSL -0,254512794
-BCS1L -0,254298738
-CCNB1 -0,253924801
-SNX2 -0,253887319
-ASAP2 -0,25387509
-WDR70 -0,253565737
-PTPRE -0,253309549
-SEPT5 -0,253058348
-SCML1 -0,253051964
-BCR -0,252946659
-MAGOH -0,252829021
-SEMA4F -0,25277628
-CLIP1 -0,252764211
-JMJD4 -0,252747043
-ZMYND11 -0,25273006
-CPSF6 -0,252574141
-PTPRA -0,252430519
-PLA2G12A -0,252393049
-MXRA5 -0,252290125
-RFX5 -0,252264534
-WARS -0,252174212
-HUS1 -0,252166663
-VCAM1 -0,251733145
-CEACAM21 -0,25171453
-RHOT1 -0,251514974
-EMD -0,251327933
-TSPYL2 -0,251307071
-THNSL1 -0,25130438
-NDUFB4 -0,251250318
-CHMP5 -0,251232028
-SKAP2 -0,251185084
-LRPAP1 -0,251070101
-COMMD3 -0,251069448
-ROGDI -0,250917557
-PPAP2B -0,25089017
-ADSS -0,250852878
-LGI2 -0,250809779
-CBX6 -0,250671998
-NELF -0,250584567
-DENND5B -0,250357567
-ATP2C1 -0,239139672
-SUMO2 -0,233193565
-KRAS -0,208565613
-PEX3 -0,200767265
-PRDX2 -0,195371323
-PDCD2 -0,194653063
-TM2D1 -0,189207426
-KHDRBS1 -0,16653347
-KLC1 -0,156510024
-ANK2 -0,155852142
-HBS1L -0,155006259
-NTRK3 -0,121314135
-PTPRO -0,110200451
-PLEKHA5 -0,10184855
-GCOM1 -0,091608137
-TIMM8A -0,084179504
-MKRN1 -0,074942655
-PLA2G4B -0,068760926
-RUFY3 -0,059042335
-RIMS2 -0,057507607
-C21orf2 -0,054091983
-METAP2 -0,053236401
-LRRC40 -0,040678287
-RPL10 -0,034862755
-RIOK3 -0,033313025
-SYNCRIP -0,027340658
-UNC45A -0,021866459
-MPZL1 -0,020796077
-RANBP1 -0,01610173
-ITGB1BP1 -0,011025016
-UBC -0,009666523
-RER1 -0,007044099
-PDS5B -0,005231512
-NCAM1 -0,004638056
-LIMCH1 0,003894784
-VPS13D 0,014841215
-WDFY3 0,017457694
-MRP63 0,023151675
-TSR1 0,064261585
-GRB10 0,066410415
-FAM128B 0,074972161
-PAK2 0,079518764
-PKP4 0,080237181
-TMEM144 0,083124821
-C3orf63 0,086752023
-DDAH2 0,250378216
-AF238870 0,250544885
-PTMS 0,250667518
-JAG1 0,250675664
-RPL32 0,25075902
-UXT 0,250812127
-HSP90B1 0,250888984
-SS18 0,250904748
-RND2 0,250918958
-CLEC4M 0,250931594
-AU147194 0,251115897
-IL1RAPL1 0,251119435
-EPB41L2 0,251131328
-TFDP3 0,251241244
-GAL3ST4 0,251281983
-EDN2 0,251371356
-SFTPC 0,251372616
-TRMT61A 0,251534845
-GPR4 0,251535902
-KEAP1 0,251692277
-RNF122 0,251718243
-NOTCH2 0,251745042
-WDR1 0,251871256
-NFX1 0,252023298
-DOHH 0,252100123
-NES 0,252167647
-SRSF10 0,252172984
-AQP3 0,252182392
-LOC728412 0,252404082
-RCN3 0,252455902
-CSNK1G1 0,252462493
-KCNS1 0,252601737
-CCDC71 0,252614101
-JUND 0,252645305
-LYST 0,252718314
-TPCN1 0,252770336
-MTA1 0,252823052
-RIN1 0,252841454
-ATHL1 0,252944239
-FTSJ3 0,253136044
-SERPINA1 0,253202139
-STARD7 0,2533744
-MRPL34 0,253425868
-PPID 0,25344089
-SH3PXD2A 0,253534644
-UBA7 0,253547625
-RUNX1 0,253686159
-ARNTL 0,253823553
-STAT6 0,253840779
-CASKIN2 0,25393147
-NFATC4 0,253965486
-LILRB2 0,254041373
-PPP1R13L 0,254173566
-RAP1A 0,254249533
-OTUD4 0,254380531
-ZNF516 0,254390037
-ZC3H14 0,254430628
-BTD 0,254441889
-ABHD4 0,254494909
-MT3 0,254554667
-PTCH1 0,254572046
-CDC42EP3 0,254591236
-LOC150776 0,254715807
-PTGES 0,254816225
-TPM2 0,254867646
-TAGLN 0,254960085
-AL050032 0,254984309
-HPN 0,25500915
-FLNC 0,255046574
-GJB3 0,255060346
-RAB40B 0,255071999
-CST1 0,255226531
-FGF21 0,255229382
-AW574933 0,255334628
-FGF5 0,255461872
-CLCN7 0,2555275
-BAHCC1 0,255618646
-FANCA 0,255627746
-CYBA 0,255682121
-TIE1 0,255683605
-ANKHD1-EIF4EBP3 0,255707685
-CDV3 0,255740411
-COL9A1 0,255878907
-TTC31 0,256049153
-ZIC1 0,256075896
-CCDC121 0,256090992
-FUT4 0,256155794
-UCP3 0,256197327
-AU146391 0,25625958
-MMP2 0,256269664
-STXBP2 0,256386629
-TMEM87A 0,2564575
-FXR1 0,256493521
-RDX 0,256507051
-HPS1 0,256516919
-TRAM2 0,256517872
-HYAL2 0,256778041
-TNFRSF14 0,256783849
-NEK7 0,256861333
-AGRN 0,256876471
-SMC4 0,256895131
-GAS7 0,256949822
-PDE4B 0,256950938
-CHD4 0,256970114
-SPP1 0,257084517
-HECA 0,257172806
-NXF2B 0,257181225
-LILRA5 0,257188463
-SCAP 0,257267679
-SNX1 0,257354288
-GIGYF2 0,257400552
-CELF1 0,257407908
-HSD17B14 0,257420303
-DUOX1 0,25770603
-MRM1 0,257826185
-NBR2 0,257852879
-FAM176B 0,257955278
-SYNPO 0,257997864
-GPRIN2 0,258040238
-IER3 0,25816919
-ZNF506 0,258198461
-NM_016414 0,25824817
-VPS53 0,258358594
-PGPEP1 0,258378109
-GNL1 0,25847832
-OGFR 0,258496938
-CXCR2 0,258632799
-C1orf38 0,258857462
-RPL22 0,258901214
-NM_018041 0,259005358
-MYOF 0,259133176
-NGB 0,259197495
-CLIC4 0,259260666
-TBC1D9B 0,259295717
-KCND1 0,259337213
-RNASET2 0,259420675
-EXT1 0,259568659
-AQR 0,259572114
-VWA1 0,259618684
-MUC3A 0,259647513
-CAV1 0,259682957
-IRF4 0,259719685
-OR7C1 0,259728956
-SETDB1 0,259737838
-E2F6 0,259867146
-TFEB 0,259924981
-CPSF3L 0,26005015
-MARCH8 0,260576922
-MFSD11 0,260945964
-ETAA1 0,260954881
-SMARCD2 0,260999203
-RGS12 0,261024661
-CCNG2 0,261112401
-RPS8 0,261183649
-IL17RA 0,261275371
-NUDC 0,261284708
-ZNF133 0,261329337
-ATP13A1 0,261543252
-PICK1 0,26166607
-C20orf117 0,261682534
-GIPR 0,261728602
-HIST2H4B 0,261730186
-S100A11P1 0,261732522
-MARCH3 0,26174629
-ZBED4 0,261794357
-KHK 0,261822851
-SCAMP2 0,26194666
-AF070579 0,261954742
-TECR 0,261998101
-AK024915 0,262016665
-CASP7 0,262240261
-PDK4 0,262293861
-MYO7A 0,262479993
-TUBBP5 0,262483574
-TMEM143 0,262491406
-NAP1L1 0,262524812
-PLEKHB1 0,262542861
-ING1 0,262679424
-SPSB3 0,262786186
-C9orf167 0,262955615
-NTM 0,262977412
-FIP1L1 0,263199662
-FYCO1 0,26321575
-GGT1 0,263227324
-ALG12 0,263240056
-IGL@ 0,263282588
-PPBP 0,263290228
-SNX13 0,263292989
-SRSF4 0,263309909
-CYTH1 0,263721364
-AL050035 0,263831657
-TRMU 0,263920451
-TIMP1 0,263959235
-RFNG 0,263965598
-HIP1R 0,264033626
-NR1H3 0,264039538
-NT5C2 0,264091319
-FNTB 0,264115077
-SAR1B 0,264175117
-GIT1 0,26420824
-RRAGD 0,264311012
-HAP1 0,26435511
-FLT3LG 0,264378926
-NM_018612 0,264421364
-SLC7A9 0,26447762
-GLTSCR2 0,264541217
-SUN1 0,264635751
-CEP152 0,264663399
-MBTD1 0,264688291
-SYT12 0,264690461
-ACTR5 0,264835312
-EIF4A1 0,264933012
-COX7A1 0,26511391
-CMTM6 0,265385079
-FAM102A 0,265449454
-AW970584 0,265532869
-FMO5 0,265619005
-N4BP2L1 0,26587536
-SPAG11A 0,265939376
-TGFBI 0,265987004
-RYK 0,266131346
-SERBP1 0,266135884
-AK021988 0,266152576
-NCAM2 0,266199101
-AK024995 0,266233606
-RAB9A 0,266259326
-SYNJ2 0,266313048
-PHLDB1 0,266315252
-PKN1 0,266439146
-MFAP3L 0,266558078
-PPFIBP2 0,266640652
-WBP5 0,266861878
-TMX1 0,266949292
-SLC6A12 0,267009029
-C3AR1 0,267017849
-CSRP2 0,267020264
-SP3 0,267034674
-ATN1 0,267069634
-GNB3 0,267107148
-TIAL1 0,267113358
-GPATCH8 0,267177985
-PMEPA1 0,267182372
-MAP2K3 0,267199274
-NM_018033 0,267304029
-WWTR1 0,267350058
-SEMA6A 0,267400431
-RBPJ 0,267426168
-AL049279 0,267438916
-IL1RN 0,267473934
-QKI 0,267577841
-SOX15 0,267588393
-DMTF1 0,267672579
-RPL19 0,267821304
-TRIM39R 0,267839755
-SLC26A6 0,267879749
-NM_025056 0,267969441
-BBS9 0,267969882
-M85256 0,26799656
-ADORA3 0,268097905
-TMEM176B 0,268515164
-SECTM1 0,268600799
-ST14 0,268612452
-ARHGEF18 0,268652414
-SIRT5 0,268726991
-MYBPC1 0,268763379
-RPL15P22 0,268793196
-SIGLEC15 0,268860828
-DNAJA1 0,26890035
-LMBR1L 0,269042598
-GIMAP4 0,269074847
-MFAP3 0,269075993
-ABCA6 0,269120338
-AW836210 0,26919833
-LOC100133772 0,269228182
-CHST4 0,269387102
-RNASEH2A 0,269387986
-RPL18 0,269450865
-RPLP2 0,269486597
-MEPE 0,269489799
-FAM106A 0,269545639
-GATAD1 0,269621956
-PPP2R3A 0,269725552
-MASP2 0,269836416
-MYO10 0,26992164
-PIGG 0,269941407
-SMG5 0,269952017
-IFI30 0,269956381
-AK025180 0,269971157
-AMD1 0,269982316
-LMOD1 0,270125966
-SNX15 0,270191178
-SCARB1 0,270338985
-SERTAD3 0,270373355
-MBD5 0,270430073
-SLC2A5 0,270454389
-ITCH 0,270468949
-ADA 0,270490353
-PWP2 0,270541137
-ARHGEF1 0,270572389
-C2CD2 0,270675538
-EIF1 0,27071329
-C1orf35 0,270772513
-IFI16 0,270855012
-LOC285830 0,270905428
-IL10 0,271025993
-MORC4 0,2712707
-CA11 0,271346355
-C5orf54 0,271348162
-C14orf93 0,271428228
-RPL17P7 0,271481741
-TMEM161A 0,271564557
-LRCH3 0,271627825
-DFFB 0,271779652
-BAZ1B 0,271859723
-DKFZp547G183 0,271894591
-RAB11FIP2 0,271895928
-PCK1 0,27194659
-TMPRSS5 0,27195628
-TIPARP 0,272078235
-UBE2L3 0,272125747
-ZNF672 0,272142507
-GALNT10 0,272151507
-EXD2 0,272173543
-KAT2B 0,272322281
-RPS11 0,27237174
-POLR2H 0,272422791
-IGLL3 0,272574443
-AA554430 0,272578205
-DOCK10 0,272578712
-DMC1 0,272606886
-CD40 0,272762332
-CDK11A 0,272811711
-UCKL1 0,272898303
-FAM125B 0,273084179
-UBXN7 0,273084433
-SMA4 0,273204796
-DYNLT1 0,273349219
-CTTNBP2NL 0,273380758
-HSPH1 0,273396703
-CYP39A1 0,273418193
-HOMER3 0,273432217
-RRBP1 0,273480926
-ATAD2B 0,27361049
-LGALS3 0,273847411
-LASS2 0,273913098
-ZNF451 0,273935073
-NXPH4 0,27404559
-C22orf46 0,274118605
-KDM4B 0,27422483
-GPNMB 0,274363725
-CYHR1 0,274415705
-CCDC9 0,274487483
-WWC2 0,274522318
-ZNF652 0,274533788
-ILK 0,274538403
-CTDP1 0,27455992
-LOC51152 0,274810051
-AL442084 0,274963062
-CPNE7 0,275259638
-CENPB 0,275294531
-TCIRG1 0,275300556
-PRPF40A 0,275423637
-ARHGAP17 0,27552534
-LOC100133811 0,275961848
-ADAM17 0,276019886
-CRISPLD2 0,276144309
-IFIH1 0,276175289
-LOC440434 0,276293985
-DCLK2 0,276369722
-MS4A6A 0,276482788
-VASH1 0,276499979
-SRSF7 0,276513035
-B3GAT3 0,276752575
-CALHM2 0,276762436
-MAP4 0,276867434
-DULLARD 0,27687625
-CTSS 0,276943812
-BAG3 0,277040195
-KRT8P12 0,277155277
-POLR2F 0,277193722
-CD14 0,277207134
-SF3B1 0,277255775
-EZH1 0,277320185
-MBD1 0,277342685
-MITF 0,277407356
-BAIAP2 0,277445862
-FCGR2B 0,277531437
-PAQR4 0,277547889
-NFATC2IP 0,277597337
-CAT 0,277600148
-TJP2 0,277610024
-CCNA2 0,277687494
-GEM 0,277887602
-C2orf54 0,277935237
-HIRIP3 0,278018588
-MCM3APAS 0,278082892
-CFB 0,278130274
-TAGLN2 0,278365668
-AK024851 0,278382784
-HGD 0,278585783
-NR2E1 0,278716062
-SEC61A1 0,278797194
-PDE4DIP 0,278806635
-FRMD4A 0,278822955
-RHOC 0,278842121
-UBTF 0,278963815
-NCOR2 0,279024257
-PPP6R3 0,279218049
-ALAS2 0,279327775
-SPSB1 0,279537438
-SGMS1 0,279545277
-TEAD4 0,279565374
-AK024897 0,27961031
-IRS2 0,279708094
-TRIM62 0,279977776
-AF308291 0,279984986
-AK022362 0,280079092
-KIAA0495 0,280115197
-CUL7 0,280170918
-PARD3 0,280192562
-NUP98 0,280376383
-DHRS4L2 0,280391865
-AK024093 0,280444114
-VEGFB 0,280560816
-PTEN 0,280592383
-NBPF10 0,280620974
-CASP1 0,280699269
-AK2 0,280734467
-MLX 0,280792537
-GNG11 0,280826824
-HNRNPM 0,280968313
-IL12RB2 0,28098376
-CDK18 0,28098866
-RARA 0,280998983
-GYPC 0,281028129
-PAK4 0,28104576
-SEMA3F 0,281239182
-BAT2L2 0,281335934
-BRD4 0,28139016
-PAOX 0,281415979
-SMAD3 0,281446531
-PIK3R2 0,281480063
-IFT122 0,281682471
-IRAK4 0,281825175
-RASSF2 0,281825652
-RPL13A 0,282085077
-ZNF22 0,282127023
-KDM4A 0,282136199
-CPM 0,282150511
-EIF2S2 0,282316006
-USP48 0,282335945
-CLCNKB 0,282422648
-C11orf61 0,282474246
-ANKRD11 0,282516441
-PTTG1IP 0,282619596
-SEC14L1 0,282620994
-DOCK6 0,282646645
-CARHSP1 0,28271852
-RRAS 0,282814195
-TRIM38 0,283129972
-PLA1A 0,283206252
-GAB1 0,283220235
-PDLIM1 0,283254227
-SSH3 0,283308195
-KLF9 0,283315657
-N4BP2L2 0,283629404
-TNS4 0,283667599
-C15orf28 0,28383226
-ANXA11 0,283988681
-TAF12 0,283993401
-SLC39A1 0,284190806
-SAP30 0,284320416
-RNASE4 0,284337811
-RPS28P6 0,28438483
-DDR2 0,284449824
-BMP4 0,284614799
-CEPT1 0,284615091
-ITPKB 0,284650775
-PLEKHF2 0,284678379
-AW974812 0,284683098
-PTCRA 0,284827371
-SETMAR 0,2848555
-SOCS3 0,284925858
-NM_014129 0,284930906
-MYO1D 0,285094554
-RBL1 0,28514691
-HN1L 0,285254673
-LASS4 0,285307965
-RPS21 0,285547221
-PPP2R1B 0,285765143
-NEO1 0,285937917
-SEC24C 0,286013109
-BCL3 0,286014454
-KCNMA1 0,286080656
-AL137590 0,286198689
-EDIL3 0,286207431
-ARHGEF16 0,286210956
-HCK 0,286227266
-GSTA1 0,286246055
-SLA 0,286356975
-UNG 0,286379363
-SP100 0,286388329
-PRSS53 0,28642638
-MYL6 0,286728542
-CDH5 0,286728949
-C10orf116 0,286730624
-GTF2IRD1 0,286882519
-POLH 0,286995879
-SFRS16 0,287066034
-TPM4 0,28709233
-ABCD4 0,287100216
-GLT25D2 0,287127854
-COL18A1 0,287131911
-NPIPL3 0,287424398
-C1orf69 0,287453135
-MTF1 0,287488427
-IGF2BP2 0,287555495
-PALLD 0,287872078
-RPS16 0,287887395
-CYP2C9 0,287955438
-SC65 0,288029122
-CRYBG3 0,288096904
-SHC2 0,288312879
-FLNA 0,288339801
-NM_014486 0,288348194
-ISYNA1 0,288383809
-PNO1 0,288506351
-GZMK 0,2886543
-ATG13 0,288748426
-NCOR1 0,288772721
-ZSWIM1 0,288892162
-GPM6B 0,28893274
-SNTA1 0,289049438
-RHOBTB1 0,289064808
-GGA1 0,289073087
-ATXN2L 0,289088819
-FAM46A 0,289172187
-ZNF532 0,289393934
-CD40LG 0,289400418
-ZCCHC11 0,289421485
-WDR5B 0,289498086
-EPN2 0,289629137
-WNK1 0,289684816
-ZNF408 0,289721753
-LHFPL2 0,290003635
-NARG2 0,290029081
-STYXL1 0,29008917
-YY1AP1 0,290249669
-CPOX 0,290281635
-IL11RA 0,290333682
-PAXIP1 0,290387596
-ZNF282 0,290414378
-C11orf95 0,290643441
-MERTK 0,290681835
-VPS13C 0,29069039
-RPS17 0,290756898
-NEIL1 0,290762184
-ZNF292 0,290850132
-NOSIP 0,290873511
-DNAJB2 0,290950763
-INPPL1 0,29102828
-ZFX 0,29106383
-SETX 0,291138151
-SLC25A37 0,291207794
-PCDHGA8 0,291472818
-TXNIP 0,291962928
-DDX27 0,291971417
-BG389073 0,29216848
-JTB 0,292275569
-RBM10 0,292352574
-RASGRF1 0,29242252
-SYNM 0,292474024
-EXPH5 0,292481151
-NPL 0,292494012
-CHKA 0,292519533
-MGA 0,292564204
-SOX10 0,292580481
-AK024185 0,292975066
-FAM120A 0,292996604
-PLXNB1 0,293000141
-BDH2 0,293071563
-JRK 0,293136106
-SLC11A1 0,293139917
-TM4SF1 0,293242649
-EDA 0,293286441
-CDK10 0,293299298
-HLA-E 0,293305618
-LOC642846 0,293349826
-GFPT2 0,293396887
-SENP3 0,293408144
-RPS3AP44 0,293415546
-C16orf88 0,293431615
-FAM60A 0,293472328
-RPL36A 0,293501288
-SERPINA5 0,293547044
-CNOT8 0,293568161
-KDM4C 0,293620372
-POU2F2 0,293815578
-C14orf139 0,293870806
-ZNF217 0,293937173
-NM_025042 0,294034268
-NNMT 0,294200775
-VEZT 0,294224684
-KIAA0754 0,294307773
-RBM28 0,294637248
-ITPR2 0,294711729
-PPPDE1 0,294796015
-KLHL28 0,294874305
-MGP 0,294956866
-LOC729602 0,295016892
-SRSF5 0,295036903
-ROCK1 0,295267164
-SS18L2 0,295271871
-LMNA 0,29532356
-ESRRA 0,295387708
-SNHG3-RCC1 0,295411716
-TAL1 0,295434654
-SQRDL 0,295470062
-TARDBP 0,295665655
-LMAN2L 0,295705138
-RIN3 0,295771443
-PSPH 0,29602696
-DGKD 0,296027908
-WHSC1 0,296067068
-SPRY4 0,296068122
-ADARB2 0,296162399
-ELF3 0,296200778
-TLE1 0,296292637
-ACAN 0,296375799
-AK022038 0,296556116
-IL1RL1 0,296721787
-OR2A9P 0,296898432
-NCRNA00260 0,296954725
-CAD 0,296976627
-PNRC2 0,297129071
-IQCK 0,297134521
-ACOX2 0,297377087
-APOC4 0,297497329
-DGKA 0,297541846
-ZBTB1 0,297547513
-PUS1 0,297622568
-C7orf64 0,297653213
-FBLN1 0,297723957
-SBF1 0,297752819
-TMF1 0,298582891
-IL1R1 0,298701666
-LILRB3 0,298823808
-FLAD1 0,298825369
-CD163 0,299040686
-TCL6 0,299056301
-FADS3 0,299096634
-LBR 0,299180453
-AL162044 0,299184427
-ZNF337 0,299271736
-AHNAK 0,299352615
-YY1 0,299417937
-HIPK2 0,299439852
-NAT15 0,299519834
-ANKZF1 0,299817611
-NECAP2 0,299838267
-MAP3K7 0,299838407
-SAMD4A 0,299863792
-WDR8 0,300094232
-ZNF24 0,300179611
-NR3C1 0,300200063
-FGF1 0,300357727
-NPC1 0,300564708
-LMO4 0,300573598
-TTLL5 0,300853453
-AL050053 0,300945526
-RSU1 0,300958049
-C15orf39 0,301123219
-SLC14A1 0,301147038
-ELAVL1 0,301190126
-SLC17A4 0,301215925
-FANCC 0,301274346
-LRCH4 0,301338927
-EGFL7 0,301340052
-C9orf3 0,301357727
-SRGN 0,301411135
-PLCL1 0,301576339
-MAN1A1 0,301613058
-S100A8 0,301917937
-W86781 0,301984854
-HIP1 0,302012828
-OR7A5 0,302027387
-PPP1CC 0,3020408
-CGGBP1 0,302058231
-CYP3A4 0,302333153
-GALNS 0,302376776
-NR0B1 0,302394827
-SMNDC1 0,302468654
-MGST2 0,302482901
-RPL12 0,302658969
-DMPK 0,302955014
-TNRC6B 0,30299615
-PPM1D 0,303104009
-EED 0,303134999
-STAG3L1 0,3031801
-TMCC1 0,303195736
-RPL13 0,303245467
-RBPMS 0,30326423
-ARHGAP10 0,303298204
-PLCB3 0,303300054
-XPO1 0,303410309
-MYO1F 0,30341788
-SRPK1 0,303531642
-ZCWPW1 0,303562617
-MTHFD2L 0,303678034
-FAM111A 0,303798707
-TTC38 0,304186409
-COL7A1 0,304295553
-C4orf19 0,304312458
-NGLY1 0,304332742
-HTATIP2 0,304339936
-IFNAR2 0,304414877
-CXorf1 0,304737703
-UNC5B 0,304789798
-YAP1 0,30479215
-PHC2 0,30485466
-FBL 0,304914384
-CDH2 0,304939032
-FXYD2 0,304942957
-ANKRD36 0,305000603
-KRT8 0,305028726
-DSCAM 0,30505625
-SMO 0,305151387
-FCGRT 0,305420183
-PAIP2B 0,305483478
-PABPC1 0,305528523
-PIGV 0,305604211
-BACH2 0,305697602
-PLGLA 0,305722503
-MORC3 0,305845022
-DIDO1 0,305996983
-PRPF38B 0,306041882
-TRMT1 0,306054262
-NFATC1 0,306233076
-AK021495 0,306242002
-GPR1 0,306335484
-STARD13 0,306369109
-CELSR2 0,306371185
-ZNF193 0,306396574
-ABHD6 0,306458055
-PLCXD1 0,306486283
-RPAP1 0,306695411
-AL050122 0,306737964
-DHRS3 0,306750918
-C1QA 0,306800137
-AF009267 0,30681596
-SETD2 0,307047565
-STX6 0,307184977
-TMEM204 0,307304516
-SMYD2 0,307490131
-BF942161 0,307560212
-SLC44A1 0,307685609
-ELF2 0,307698089
-AATF 0,307770923
-AV761453 0,307800442
-ACTN1 0,307927265
-AI523613 0,307943372
-SOLH 0,307971092
-ZNF410 0,308222237
-GOLGA4 0,308250269
-FLJ21369 0,308352331
-FCGR2A 0,308469725
-BRD7 0,308638563
-TLR2 0,308769609
-FTHL5 0,308790654
-SPOCK1 0,308861441
-LSM14A 0,308907157
-USF2 0,309161806
-TENC1 0,309220224
-EMP2 0,309252571
-BSDC1 0,309299474
-ZNF701 0,309462113
-PLIN3 0,309516744
-SORBS1 0,309562012
-FTL 0,309588981
-AGFG2 0,309634949
-UBR5 0,309647344
-MMP14 0,30965745
-SFRS8 0,309923113
-ITPR3 0,309975876
-PLK3 0,310097184
-NUP188 0,310124261
-CROCC 0,310245563
-CHSY1 0,310328559
-CTCF 0,310675097
-EDC4 0,310685915
-NFE2L2 0,31069885
-LILRA6 0,311008878
-SATB2 0,311055754
-GTPBP6 0,311254994
-TSPAN14 0,311316513
-C10orf18 0,31133762
-SECISBP2 0,311419174
-DHX34 0,311443077
-LSS 0,311450185
-CHI3L1 0,311532669
-PDGFC 0,311715929
-BMP7 0,311741682
-MBNL1 0,311755686
-DNA2 0,311841432
-COMT 0,312081286
-LOC100133005 0,312165679
-PTOV1 0,312192713
-LCAT 0,312407744
-LRRFIP2 0,312480817
-UCN 0,312589312
-AK024606 0,312655002
-MICAL3 0,312700621
-ROM1 0,31291043
-MED12 0,312925796
-CPNE1 0,313173908
-GBP2 0,313262095
-PELI2 0,313279559
-MLL 0,313398121
-HIF3A 0,313438743
-ST18 0,313449639
-AF131777 0,313643716
-CATSPER2P1 0,313785721
-ZNF302 0,314066212
-APBB2 0,314110219
-KIAA0907 0,31421022
-ZNF592 0,314679884
-HNRNPA1 0,314773035
-TSC2 0,314882123
-SFRS15 0,314884343
-ZNF835 0,314920694
-WDR6 0,314979423
-LOC729143 0,315037798
-PPARD 0,315048839
-U2AF2 0,315118843
-MGAT1 0,315269456
-ZNF44 0,315270856
-RPL36 0,315475789
-GRAMD3 0,315513449
-PTPN2 0,315554784
-AL080072 0,315635626
-C19orf2 0,315918303
-DNAH3 0,315930745
-ZNF146 0,316341954
-SMEK1 0,316538461
-MLXIP 0,31681421
-NMT2 0,316848231
-G3BP1 0,316864559
-DDX3Y 0,316997159
-STEAP1 0,317082981
-BC002629 0,317231764
-KDM2A 0,317406731
-TMEM39A 0,317430306
-C15orf29 0,317437851
-MACF1 0,317513626
-LOC391020 0,317572673
-SETD1A 0,317586539
-KTN1 0,317889697
-RUNX3 0,31809511
-NINJ1 0,318107478
-ARMC7 0,318150459
-BMP1 0,318194029
-DKFZP586I1420 0,318199121
-JARID2 0,318226296
-AW972351 0,318303541
-PAPSS2 0,31841091
-ELTD1 0,31845583
-ETS2 0,318667898
-CREB3L2 0,318705762
-DFNB31 0,31892768
-SERHL2 0,318966243
-C10orf26 0,319058163
-NM_030892 0,319421731
-WRAP53 0,319795295
-UBQLN4 0,319828198
-RALGDS 0,319938162
-PRKCH 0,320101043
-AU146983 0,320105843
-SLC5A3 0,32021553
-DUSP1 0,320239212
-NKX2-2 0,320312108
-C1orf183 0,320387827
-PCM1 0,320482282
-THRA 0,320531901
-NM_025028 0,320726138
-SIVA1 0,320736787
-TTR 0,320757249
-IKBKB 0,320778441
-ARID1A 0,321020715
-HDAC4 0,321059842
-ZFP36L2 0,321167918
-TMEM212 0,321179342
-AA443771 0,321214505
-AGAP5 0,32125931
-PIGA 0,3216713
-SFRS12 0,321704401
-LDLRAP1 0,321832456
-CCDC21 0,321857948
-SSFA2 0,321990716
-RAMP1 0,322050077
-FLJ10357 0,322160744
-LAD1 0,322322766
-RACGAP1 0,322340831
-NPIPL2 0,322616655
-CEP350 0,322648588
-CRLF1 0,322735059
-IGSF9B 0,322744338
-PLXND1 0,322801951
-MCL1 0,322913781
-ALMS1 0,32297709
-ZNF768 0,323059066
-RSL1D1 0,323228527
-C4orf34 0,323582139
-PNPLA6 0,323738553
-MAST4 0,323801655
-NME3 0,323835175
-SNHG3 0,32391938
-S100A12 0,324014586
-PPP4R1 0,32409634
-PLD1 0,324165096
-POLG 0,324186823
-NKTR 0,324203565
-ST3GAL4 0,324231325
-TMEM63A 0,324243134
-ST20 0,32438459
-RNF114 0,324406844
-HYI 0,324468621
-DUSP6 0,324699964
-NR1H2 0,324884332
-DVL2 0,324900869
-SRSF11 0,324979841
-CLK2 0,325170283
-MKLN1 0,325287178
-SCRIB 0,325320413
-KIAA0467 0,325541973
-DMWD 0,325745064
-KLHL23 0,32579572
-RPS6 0,325948088
-ZBTB17 0,326014408
-RAI14 0,326038467
-UBE2G2 0,326143089
-ZNF562 0,326186073
-EZR 0,326282578
-TRPS1 0,326283144
-HFE 0,326390644
-MED23 0,32658232
-DDX11 0,326766632
-SHMT2 0,326784725
-LRP5 0,326954416
-PTH1R 0,327100265
-LOC731602 0,327131294
-AA401963 0,327241371
-CDK5RAP2 0,327276136
-SERP1 0,327279991
-SLC1A5 0,327303416
-BGN 0,327370767
-HSD17B1 0,327475971
-AL390143 0,327497051
-DIAPH2 0,327617697
-PITPNC1 0,327719899
-SPRY2 0,327767132
-FZD7 0,327974293
-MAP4K4 0,328171238
-TNS1 0,328369107
-ZNF783 0,328517049
-M78162 0,328518574
-ADAMTS1 0,32853944
-FKBP5 0,328911405
-AGAP8 0,329115979
-PLEKHF1 0,329179433
-DNAJB1 0,329339376
-RBMS2 0,329438459
-HNRNPH1 0,329454824
-ULK2 0,329496298
-PAPD7 0,329501864
-SURF1 0,329547559
-W61005 0,329673439
-ZNF862 0,330131081
-GNA15 0,330266409
-CHD9 0,330273108
-DLC1 0,330294104
-TMEM2 0,330321664
-AK024879 0,330353812
-N4BP1 0,330435804
-SERF2 0,330633507
-SNRPA 0,330957742
-IRF8 0,33098543
-ABCA2 0,331251046
-NPFF 0,331328402
-CP 0,331565597
-AU144887 0,331713137
-AW851559 0,33185735
-TCF4 0,332062967
-ZNF354A 0,332076549
-TMEM92 0,332352956
-NFATC3 0,332386137
-SSRP1 0,332529738
-TCF7L2 0,332651908
-PIM1 0,332716071
-PIP4K2A 0,332914219
-EIF4EBP1 0,332959146
-LOC100132863 0,333054912
-MMRN2 0,333075923
-AU147295 0,333342973
-VIM 0,333356286
-C2orf67 0,333469715
-DNMT1 0,333550022
-CEP110 0,333679402
-BAZ2B 0,33371151
-KDELR2 0,333939841
-L3MBTL 0,334448273
-CDK19 0,334505985
-CYorf15B 0,334832089
-DDX17 0,334839203
-FKBP4 0,335166906
-STOM 0,335173644
-U82303 0,335241438
-LOC202181 0,335841121
-ATM 0,335893127
-STK3 0,335957389
-MID1 0,336166241
-IGFBP5 0,336454348
-PARP4 0,336459483
-EXOC7 0,336479503
-FANCG 0,336652927
-PHF2 0,336678654
-FBRS 0,33674511
-ANP32B 0,336836072
-NCK2 0,336876937
-CASP6 0,336920233
-ZBTB3 0,337122586
-DHFR 0,337448147
-APOLD1 0,337464001
-STAG1 0,337490482
-NM_024305 0,337551103
-SIGLEC8 0,337608204
-ERLIN1 0,337809212
-POLDIP3 0,337889824
-SPTLC2 0,33799094
-C7orf26 0,338204972
-UBE2D4 0,338265561
-MAP2K7 0,3384787
-MECOM 0,338508564
-DOCK1 0,339029429
-HS1BP3 0,339148762
-PRKY 0,339216015
-GOLGA1 0,33927478
-XPC 0,339433169
-PHF3 0,33953002
-HIC2 0,339768003
-C9orf7 0,340519877
-CTDSPL 0,340591645
-ZNF83 0,34077157
-PHGDH 0,340889735
-TMEM165 0,340978736
-CLN3 0,341078466
-AU147983 0,34113627
-PATZ1 0,341151411
-DIP2C 0,341390806
-RECK 0,341533646
-EWSR1 0,342003886
-SMAD7 0,342182186
-MTRF1L 0,34225773
-TJAP1 0,342452426
-PRKD2 0,342725824
-SPOP 0,343019265
-HLA-J 0,343028528
-PLXNB2 0,343103735
-FBXL14 0,343454364
-LAMA2 0,343637649
-RNF220 0,343845541
-CLK3 0,344164444
-STARD3 0,344187457
-OGT 0,345118989
-IFITM3 0,345141829
-HMOX1 0,345196784
-EIF2C2 0,34557825
-CCND3 0,345663426
-TGFBR3 0,345676022
-POLR2J3 0,345712548
-BCAR3 0,345713549
-C14orf147 0,34610842
-CLDN15 0,34616346
-TOP1 0,346179876
-RASL12 0,346286134
-MED13L 0,346369067
-SOS2 0,346799305
-SERPING1 0,347144597
-IER5 0,347279068
-TLE2 0,347426427
-LLGL2 0,347448236
-TMCC2 0,347500013
-PHF20 0,347602909
-SIRT4 0,347862165
-OSGIN1 0,348060574
-H2BFS 0,348076316
-NM_017756 0,348230007
-NCRNA00115 0,348422218
-MT1E 0,348733923
-NACC2 0,3488369
-NFIB 0,348943619
-AKR1C3 0,349206923
-ARPC1B 0,349407208
-NIPBL 0,349628117
-RPL11 0,349803207
-MSH6 0,350014407
-PTDSS2 0,350073646
-AL050145 0,350120404
-FAM107A 0,350271118
-CHN2 0,350358174
-DAPK2 0,350378033
-DLG5 0,350436992
-OPHN1 0,350596034
-C20orf11 0,351010126
-SLC35D1 0,35135795
-SELL 0,35142274
-FAM193B 0,351790995
-NM_024880 0,352020901
-RASGRP2 0,352114346
-CAPN3 0,352194849
-THOC1 0,352289646
-TAOK3 0,352396226
-FBXO42 0,352613215
-LARP6 0,352692849
-KLKB1 0,352702835
-METTL7A 0,352961228
-STIP1 0,352968743
-WIPF2 0,353085817
-FOXD1 0,353404764
-HSPB2 0,35378232
-ENGASE 0,353978221
-LAT2 0,354239264
-HIST1H2AH 0,354250391
-GSDMD 0,354483715
-TRA2A 0,354674037
-C19orf29 0,354762053
-BRPF1 0,355002213
-NUMA1 0,355146564
-SNW1 0,355320637
-SMARCC1 0,355374541
-ZNF175 0,35555253
-BATF3 0,355680727
-HIST1H2BC 0,35575565
-ERN2 0,356098991
-ZFR 0,356185362
-AW301806 0,356253591
-SMTN 0,356289422
-RPS6KA2 0,356774064
-MIIP 0,35685635
-ARGLU1 0,356919378
-CTNNAL1 0,357152141
-PCDH9 0,357228835
-LAS1L 0,357263917
-DOK1 0,358029668
-AFTPH 0,35852635
-ZNF143 0,358674337
-C11orf71 0,35888557
-MICALL2 0,359221642
-KDM6A 0,359260932
-CFH 0,359284568
-CEBPB 0,359516672
-MTUS1 0,359547348
-AW973791 0,359548173
-SERTAD2 0,359684853
-FGFR1 0,359721729
-KPTN 0,360479451
-NR2F2 0,361169645
-RGL2 0,361384531
-NM_014120 0,361482036
-TAF5 0,361611903
-ZC3HAV1 0,362177526
-BEST1 0,362248528
-TNFRSF1A 0,362724804
-CLIP2 0,363062238
-EHMT2 0,363078239
-IFITM1 0,363162265
-GCFC1 0,363190607
-PECAM1 0,363227012
-YES1 0,363556218
-ZFP36L1 0,363744573
-SBNO2 0,364095165
-RMND5A 0,364201024
-IL10RB 0,364481295
-CBS 0,364486163
-TBC1D2B 0,364503601
-C10orf10 0,36458821
-AU144530 0,365137826
-ZNF500 0,365202134
-ATP6V0E1 0,36527949
-SEPT8 0,365711052
-VCAN 0,365762437
-RPL36AP51 0,366073863
-RPL31 0,36613283
-TAOK1 0,36613666
-GCN1L1 0,366181489
-CALCOCO1 0,366300689
-GNA11 0,366387362
-SH2B2 0,366425408
-RREB1 0,367259867
-SLC35E1 0,3672965
-GPRC5B 0,367311931
-TCF7 0,367371063
-PDIA4 0,367810651
-ZNF34 0,367845233
-MBD3 0,36793004
-CXCR4 0,368041224
-C9orf114 0,368120984
-IFITM2 0,368313531
-ZNF665 0,368328536
-ZCCHC24 0,368368275
-LOC100133944 0,369022431
-CSDA 0,369150342
-AU148255 0,369666508
-CIZ1 0,369704457
-CRTC3 0,369792369
-CTNNA1 0,369962411
-RARRES2 0,37011032
-NM_025033 0,370246707
-VSIG4 0,370274949
-FAM48A 0,370421427
-ZDHHC11 0,370675656
-NPAS2 0,370715345
-ADH1B 0,370935809
-ACSL1 0,371025369
-C1orf63 0,371083889
-TYMP 0,371266716
-LEPREL1 0,371463494
-LAMB2 0,371472469
-MAFB 0,371542293
-AW971248 0,371589606
-BC003629 0,371603781
-FAM63A 0,371786321
-ABCA1 0,371992682
-IGF2R 0,37211512
-SOX13 0,372131188
-WAPAL 0,372391179
-ZFC3H1 0,372437982
-ZNF710 0,372493324
-HSPA6 0,37258644
-CCDC101 0,372823539
-BAZ1A 0,372824952
-AXL 0,372842922
-NPIPL1 0,372916072
-HDGF 0,372923023
-KHDRBS3 0,373093219
-MT1X 0,373144553
-MTMR15 0,373164421
-AF257099 0,373262757
-AEBP1 0,37342966
-KLHL25 0,373672957
-GJB4 0,37372121
-LUC7L3 0,374023648
-U79248 0,374142769
-LOC653562 0,374188384
-RBM4 0,374375075
-ABCC10 0,374890625
-CXorf21 0,374896996
-DAXX 0,374917403
-C1R 0,375063944
-TPST2 0,375279072
-KLHL24 0,375307199
-C7orf68 0,375539219
-ZCCHC8 0,375600764
-CASP4 0,375605037
-ETV1 0,37597402
-BIN1 0,376340315
-RGS19 0,376617752
-PKNOX1 0,377091746
-CTTN 0,377173864
-TRIP10 0,377452782
-ANGEL1 0,377498562
-PLIN2 0,377879768
-NM_025007 0,377942771
-PTMA 0,378229214
-S100A11 0,378255627
-AXIN1 0,378580893
-NPRL3 0,378633074
-PNN 0,378695864
-AV727934 0,378843386
-ANGPT2 0,37912784
-AK023918 0,379250766
-CNPY3 0,37927474
-AF130051 0,37947818
-TLE4 0,379880985
-PAPOLA 0,379974199
-ITGB5 0,380683545
-FAM38B 0,380693638
-PABPN1 0,380909515
-SLC6A8 0,38116858
-RYBP 0,38121367
-NASP 0,381229843
-FGR 0,381246748
-PER1 0,381695992
-CDR2L 0,381867955
-LRRFIP1 0,382075479
-HMHA1 0,382282948
-KIAA0485 0,382313718
-GUSB 0,38235255
-RPS17P5 0,38240934
-FXYD5 0,382563723
-RBL2 0,382697586
-RANBP10 0,382980904
-NEDD9 0,383084673
-MSL2 0,383144236
-FAM50A 0,383317183
-AL080232 0,383323554
-SPG21 0,383712061
-TPD52L1 0,384098652
-H2AFX 0,384141378
-SWAP70 0,384225003
-IVNS1ABP 0,384369268
-KDELC1 0,384542393
-MYL12A 0,384757468
-FOXO3 0,384856157
-MED13 0,385128516
-AL049252 0,38560217
-AF007147 0,385820993
-PAX6 0,385884587
-DNASE2 0,38591545
-SLC12A9 0,386200858
-SIRT1 0,38637719
-ARID5B 0,386492868
-MT2A 0,38656824
-SLC38A2 0,386710042
-GNG5 0,386756333
-SRRM2 0,386841072
-SERPINB6 0,386985458
-CC2D1A 0,387023088
-LRRC37A2 0,387067777
-CSF1 0,387071999
-RPL29P11 0,38708859
-SFRS14 0,387094074
-MYO9B 0,387103012
-AW972855 0,387241981
-TRIP4 0,387728627
-ZBTB40 0,387827711
-STARD8 0,387863703
-WBSCR16 0,387992811
-NXF1 0,388021286
-CTDSP1 0,38803541
-RSAD1 0,388042285
-SUV420H1 0,38833134
-CDKN1C 0,388508896
-NM_016415 0,388588403
-E2F4 0,388673603
-KANK2 0,388702219
-ZC3H7B 0,388980025
-ANGPTL4 0,389035415
-CRY1 0,389801967
-KIAA0556 0,389845114
-TBC1D16 0,390016803
-TCOF1 0,390109025
-ZFYVE26 0,390278079
-IFRD1 0,39034324
-EIF4B 0,390385914
-SMC1A 0,390525141
-SCIN 0,3907272
-MARS 0,391061966
-PTRF 0,391089965
-POLR2J 0,391514571
-APAF1 0,391530483
-ITPK1 0,3915415
-PNRC1 0,392133859
-CLIC2 0,392140808
-KIAA0913 0,392243895
-PRKAR2A 0,392619325
-PRKX 0,392750502
-SYDE1 0,392957216
-ACSL5 0,393140899
-LRP10 0,393162277
-LPP 0,393214983
-SNTB2 0,393383504
-NADK 0,393882671
-PCBP2 0,394206896
-N51370 0,394562467
-CLIC1 0,394663761
-CTBP2 0,394785714
-PHB 0,394929787
-BCL2 0,395102709
-TAF4 0,395492947
-LOC652607 0,395562084
-YBX1 0,396079328
-PRPF3 0,396609142
-SLC38A10 0,396741732
-ERBB2IP 0,396808535
-CFLAR 0,396840203
-TNFRSF10B 0,397091951
-PHC1B 0,397196351
-ARL17A 0,397406114
-ZBTB20 0,397424403
-REPIN1 0,397830532
-BE466926 0,397930108
-MT1P2 0,398055653
-ZNF778 0,398225613
-DICER1 0,398300689
-NM_018603 0,398329284
-RAF1 0,398631868
-MXD4 0,398685167
-FBXL7 0,398770393
-CALD1 0,399121196
-GSDMB 0,399246982
-ZCCHC2 0,399293751
-PODXL 0,399691684
-ACACB 0,400136922
-VEZF1 0,400413083
-PLEKHM1 0,401187317
-CSPG4 0,401646086
-ID3 0,40170175
-RBM41 0,401719975
-KDM6B 0,401885964
-PHF15 0,402522419
-LAMP2 0,402538077
-CDC14B 0,402583482
-HNRNPL 0,403044314
-SLC4A2 0,403448509
-DDX23 0,403953946
-TUBD1 0,40407115
-SLC16A3 0,404204458
-CAPN2 0,405022548
-CBFA2T2 0,40560438
-TCEB2 0,405769952
-HNRNPF 0,406126644
-MORC2 0,406182732
-FOXO1 0,406430281
-AI962978 0,406538883
-HP1BP3 0,406567553
-CBFB 0,406789498
-RBM14 0,406886421
-SFI1 0,407058786
-ZHX3 0,407089165
-KDM3A 0,407233406
-SIRT2 0,407341821
-ANKS1A 0,407373917
-TCF3 0,407442968
-NOTCH2NL 0,407672378
-EEF1D 0,407830724
-SOX12 0,408065349
-SLCO1A2 0,40820492
-HNRNPA3 0,408299868
-GTF2H3 0,408624789
-FZD9 0,408729069
-SAFB2 0,408755308
-APBA3 0,408834306
-ASCL1 0,409161488
-CG012 0,409559201
-WDR59 0,409606436
-LAMA5 0,409632505
-ZNF276 0,409730125
-ZNF395 0,410080702
-TIMM44 0,410223052
-BGLAP 0,410749324
-ZHX2 0,411039562
-CARS2 0,411302016
-SLCO3A1 0,411338796
-LOC442497 0,411765627
-FRYL 0,411842495
-CYP2J2 0,412070197
-ABL1 0,412522321
-INF2 0,412975218
-SGK1 0,413352645
-SFTPB 0,413789208
-TIGD1L 0,41383023
-RBCK1 0,414019825
-TRAPPC10 0,414285862
-DUSP7 0,414641136
-WSCD1 0,415016303
-DCP1A 0,415308358
-LPAR1 0,415365439
-RBBP6 0,415730871
-DONSON 0,416255506
-C16orf5 0,416258918
-NCOA1 0,416350707
-CFHR1 0,416440287
-AA126763 0,416566153
-LRRC32 0,416765832
-CP110 0,41732481
-LTBP3 0,417338221
-TDRD3 0,417356196
-HMG20B 0,417456909
-CDC42EP2 0,417645635
-TAF1C 0,417736819
-NM_013344 0,41778911
-VGLL4 0,417820331
-PHKA2 0,417904785
-KDSR 0,418009802
-RELA 0,418064238
-TBL1X 0,41814877
-SIAH2 0,418727849
-MYO1E 0,418747589
-HIST1H2BD 0,419127582
-AI744451 0,419208355
-PTMAP7 0,419537834
-ARID5A 0,419593497
-CYP27A1 0,420064872
-RAB13 0,420441013
-CPSF7 0,420526378
-CPT1B 0,420770156
-LRDD 0,420794327
-PILRB 0,421599366
-STAB1 0,421733406
-FCHO1 0,422126906
-ZNF32 0,422311821
-TBC1D3H 0,422328806
-C1orf66 0,42292679
-NM_025032 0,423323973
-AI732802 0,423584905
-PCID2 0,423787762
-POGK 0,423912669
-TMEM140 0,424587207
-TMC6 0,424604298
-AL080160 0,42490597
-AK021505 0,425024442
-SCD5 0,425610027
-RAD52 0,425956612
-AF116715 0,425960499
-DCI 0,425967692
-SFRS18 0,426091505
-HCG2P7 0,426136765
-ADORA2A 0,426366158
-NM_021651 0,426442506
-MID1IP1 0,426940092
-HNRNPC 0,427103695
-NM_025024 0,427155973
-AK024315 0,427460397
-AK021514 0,427966252
-SLC29A3 0,428138792
-NSUN5 0,428255135
-PHF10 0,428599049
-DAPP1 0,428626141
-TMEM109 0,428647746
-LOC91316 0,428742129
-ITGB4 0,42956266
-SLC30A1 0,429998682
-AW150065 0,430129937
-ZCCHC6 0,430267528
-ARHGEF2 0,430371137
-AK027193 0,43049002
-TRIM52 0,430535815
-MT1G 0,430767233
-NOTCH1 0,430849119
-ZRSR2 0,43114681
-RPS6KA1 0,43184981
-KANK1 0,432456197
-FURIN 0,432618855
-APOBEC3C 0,432749845
-ANKRD40 0,432772877
-TRIOBP 0,432900403
-ZNF384 0,433116555
-CDKN1A 0,43319672
-BTG1 0,433570541
-EPHX1 0,433658916
-CNOT6 0,434207544
-HSPA1L 0,434322364
-PKD1 0,434547199
-WAS 0,434717417
-RPL23AP32 0,434993767
-P4HA1 0,434997425
-MAX 0,435160002
-UIMC1 0,435278167
-NM_025120 0,435322168
-NCOA6 0,435700178
-TPD52L2 0,435768747
-BCL6 0,435938226
-AK024108 0,436355329
-C7orf23 0,436800978
-CDC42BPA 0,437074951
-CD59 0,437137855
-POLR1B 0,437227618
-TLR5 0,437498143
-HDAC1 0,437993569
-ARHGEF7 0,438071237
-AA045174 0,438161955
-TBC1D17 0,438488128
-PRELP 0,438518539
-GTF2H2B 0,438525643
-HIST1H2BK 0,43866778
-AU147851 0,438979485
-RBM39 0,439661925
-IQGAP1 0,439786742
-RPL18AP3 0,440613252
-LTBR 0,440721546
-RPL35A 0,441136859
-ARAP2 0,441441928
-ARAF 0,441560027
-MT1H 0,441587824
-LOC441258 0,442117007
-ZCCHC14 0,442132801
-IRF7 0,442147625
-NOL12 0,442203671
-PTPLB 0,442541309
-AI683552 0,442752948
-MYST1 0,442881562
-MXI1 0,443040642
-AW974910 0,443299524
-C1orf144 0,443500279
-KRCC1 0,444417306
-PIAS4 0,444438643
-SRSF1 0,444637015
-LRP2 0,444740953
-ZDHHC18 0,445392541
-SPN 0,445443935
-ST13 0,446667878
-PHF17 0,446746739
-NACA2 0,446876872
-SASH1 0,447285208
-CD22 0,44772036
-CSNK1E 0,447902552
-COL5A3 0,447933631
-MAT2A 0,448695587
-EFHD1 0,448820126
-MAP3K3 0,448963961
-BIN3 0,449317201
-LUC7L 0,449469644
-KIF1C 0,449622117
-RNF144A 0,450034368
-TULP3 0,450626451
-CDKN2C 0,450879897
-HSD17B7 0,451226227
-ACIN1 0,451331774
-PABPC3 0,451363083
-PHF21A 0,45139036
-HNRNPH3 0,451480034
-HIST2H2BE 0,452219911
-RRP1B 0,452597128
-SOX2 0,453132172
-ZNF444 0,453296716
-FAM13A 0,453547738
-JUP 0,453753674
-PODNL1 0,453854292
-MAML1 0,453885
-SNRNP70 0,45408945
-SDCCAG3 0,45464357
-PLGLB1 0,454722494
-CDH19 0,454754165
-HSPA1B 0,455063205
-ARHGEF10 0,455229121
-NFIL3 0,455469821
-NFKBIA 0,455577982
-XRCC2 0,455670024
-ACTN4 0,455764555
-PDS5A 0,456071133
-POU2F1 0,456120351
-VPS54 0,456318614
-BANF1 0,456451252
-PGCP 0,456765652
-RPL28 0,456867479
-ICAM2 0,457066169
-SNAP23 0,457069788
-SART1 0,457941993
-AK023891 0,458253977
-BANP 0,458588544
-MAP3K11 0,458968207
-EPOR 0,459463669
-FKSG49 0,459538011
-MT1F 0,459638951
-NM_014128 0,460468204
-AP1G2 0,460676306
-GAS2L1 0,461632768
-PHIP 0,462053958
-NOL8 0,462387404
-NM_017932 0,462395281
-RNF130 0,462894529
-ZMYND8 0,463309493
-AK024525 0,463401166
-TRIM28 0,463454342
-BCAT2 0,463509769
-TYRO3 0,463574548
-PHLPP1 0,463738295
-BST2 0,465024297
-PDGFRB 0,465034704
-AL049987 0,465336929
-AKAP8L 0,466278804
-TGM2 0,467555999
-CREBBP 0,467899354
-KIAA0894 0,468325808
-DDX39 0,468959477
-NCAPD2 0,468959537
-ALPK1 0,469621875
-TGIF1 0,469902489
-PPP1R14B 0,470121069
-PNMT 0,470291567
-NAA16 0,470467422
-ZNF611 0,470526774
-ZRSR1 0,470857426
-NPIP 0,472818474
-RBM38 0,473036567
-USP34 0,473278809
-TGFB3 0,474067001
-ITSN2 0,475328182
-CEBPD 0,475754278
-MCM3AP 0,476296498
-HAPLN2 0,476718109
-POGZ 0,477224004
-NR2F1 0,477556735
-GAS1 0,478628972
-SLTM 0,478903701
-ECE1 0,479007813
-CALCOCO2 0,47910558
-RXRA 0,479821295
-MEIS2 0,480178943
-CLEC2B 0,481843785
-AL049260 0,482481089
-CHST3 0,48259726
-COL16A1 0,483094975
-SLC25A16 0,483255606
-LHPP 0,48421483
-AF010144 0,484619234
-GTSE1 0,484629217
-MUM1 0,484956644
-TNXB 0,485246904
-PRINS 0,486032909
-ANKRD49 0,486282532
-PTPRK 0,486899575
-PPAP2C 0,487395433
-C22orf9 0,488987561
-KHNYN 0,489026627
-RAPGEF3 0,489474077
-AF078844 0,489716822
-MAN2A1 0,489875474
-IFT20 0,490824284
-USP21 0,490859618
-NOP2 0,491526918
-LOC440248 0,491905455
-LOC647070 0,493492979
-MAFF 0,494072026
-BG251521 0,495196452
-C6orf145 0,496322836
-MLL4 0,496324893
-ATF4 0,49676781
-RELN 0,497310216
-PELI1 0,497491599
-P2RX7 0,497499324
-CNOT2 0,498172475
-FAM38A 0,498599859
-DCLRE1C 0,498693515
-INSR 0,502304787
-MAPKAPK2 0,502573806
-NDE1 0,50267356
-MT1M 0,502716901
-CDK5RAP3 0,504041432
-SULT1A4 0,504805398
-NSUN5P2 0,505093708
-ANKRD10 0,505841449
-LOC339047 0,506042447
-LRRC1 0,506594446
-CUX1 0,507257715
-SRRT 0,508240438
-MAF 0,508625791
-EBLN2 0,509549245
-NM_017618 0,510705903
-RBM4B 0,51138423
-FBXW12 0,511744983
-ATP8B1 0,511969804
-NM_024978 0,512045897
-KCNMB4 0,512142959
-CLMN 0,512461537
-LOC100132540 0,512589899
-SERPINH1 0,513136463
-RHBDF2 0,513703735
-PCF11 0,514081494
-HAUS2 0,514694211
-TECPR2 0,514970535
-TNIP2 0,515014912
-AUP1 0,516155581
-KIAA0101 0,516801916
-N35922 0,51703624
-STK38 0,517483454
-AZGP1P1 0,518047589
-C13orf15 0,518310047
-PRR11 0,518691616
-PDCD6 0,51972326
-AFF1 0,520716014
-AF222691 0,521107674
-BE045142 0,521502008
-PACS2 0,521749261
-PSRC1 0,522634606
-ZNF358 0,523463012
-MAPKBP1 0,523696079
-S100A4 0,524041412
-MYO1C 0,524902669
-IRF3 0,52538788
-TOB2 0,526119659
-KLHL21 0,527145117
-PGF 0,527713686
-LOC399491 0,528407104
-ARAP1 0,528556373
-AZGP1 0,528659072
-SIRT7 0,528927974
-C16orf53 0,529668261
-KLHL2 0,533153888
-AK022213 0,533802801
-ANKRD28 0,534099367
-TF 0,536170201
-MAVS 0,53636005
-MSX1 0,536723495
-C12orf35 0,537890473
-AA554945 0,538449904
-SUN2 0,539191173
-RBM6 0,54218394
-AL080112 0,542349721
-SORT1 0,542569398
-AL049285 0,542660805
-FOXO4 0,542834527
-ABCA8 0,543725594
-RING1 0,54468938
-KCNE4 0,546337688
-TAZ 0,546506594
-DIP2A 0,546907877
-CLK4 0,548788669
-ZNF277 0,549312201
-MUS81 0,551193399
-DBT 0,556696292
-EMP3 0,557013195
-DDIT4 0,557077384
-RUFY1 0,557170712
-MYST3 0,559285285
-PRPF4B 0,559881298
-LOC100132247 0,562956585
-HSPB1 0,56508456
-CHD7 0,566776564
-CHORDC1 0,566831861
-COBL 0,569205746
-STAG2 0,569603186
-CTDSP2 0,570069613
-ZNF160 0,572703009
-PDE4C 0,574535337
-WWC3 0,575159977
-BMI1 0,576213767
-CRYAB 0,577245348
-AHCTF1 0,577515066
-ADIPOR2 0,5780263
-CASC3 0,57815663
-MUTYH 0,579456271
-AK023783 0,580340854
-HIGD1B 0,583663012
-PLOD1 0,587347495
-PRR14 0,587364521
-SH3BP4 0,58788373
-C19orf28 0,587956493
-NDRG1 0,588555643
-HIST1H1C 0,591446402
-TCF12 0,592176798
-MPST 0,593408757
-SEPP1 0,593935425
-DNAJB6 0,595685757
-SIRPA 0,596218961
-FLT1 0,597923318
-MYOT 0,598968138
-HIST1H2AC 0,600586387
-HBP1 0,600714263
-KAZ 0,601415288
-PTBP1 0,602313539
-NSUN5P1 0,603090503
-GUSBP3 0,604393039
-KCNJ2 0,616084197
-KAT2A 0,620256502
-MCM7 0,622618327
-FBXW4 0,627081137
-MKNK2 0,628440154
-IL17RB 0,631530593
-CLK1 0,632420317
-LRP4 0,632833859
-FAM53B 0,641895571
-JMJD6 0,64411039
-TYK2 0,644727629
-PLOD3 0,644893842
-CXXC1 0,650530485
-AK024136 0,659066605
-PAN2 0,66036619
-NPTX2 0,665210794
-SPEN 0,669461617
-SETD5 0,670191692
-STX10 0,674048462
-CDK2AP2 0,67411425
-PPM1B 0,68382966
-SLCO4A1 0,685048974
-GLT25D1 0,706365388
-ZC3H11A 0,716021559
-ZBTB16 0,720405109
-ZNF692 0,720940567
-NUPR1 0,724120307
-FLCN 0,747339708
-NFASC 0,755177517
+name value
+GBE1 -0,943978048
+SLC18A2 -0,941309505
+KCNJ6 -0,894120983
+DLK1 -0,887122171
+PTDSS1 -0,851959645
+FGF13 -0,842876271
+PCDH8 -0,83524894
+ZNF226 -0,82900335
+SLC6A3 -0,824713365
+PIP5K1B -0,812285785
+DENR -0,81101551
+TPBG -0,806963209
+PRKAR2B -0,805288865
+OSBPL10 -0,80406299
+ALDH1A1 -0,795042129
+GGCX -0,795035797
+ACP2 -0,794853979
+SLITRK5 -0,793842132
+FAM70A -0,793715412
+HPRT1 -0,792370336
+CCNH -0,790971864
+MYRIP -0,78490295
+TUBB2A -0,783142444
+ACTR10 -0,782043082
+BASP1 -0,778702387
+CADPS2 -0,777552826
+PID1 -0,775106213
+SV2C -0,774895093
+RBM3 -0,77091551
+REEP1 -0,770000111
+RIMBP2 -0,766421185
+CNIH3 -0,765790316
+DMXL2 -0,765309344
+LOC10431 -0,762992699
+SV2B -0,759985564
+AGK -0,756506198
+RCAN2 -0,753762002
+LPPR4 -0,753018962
+RALYL -0,75270126
+L1CAM -0,751978689
+BCAS2 -0,751241508
+LOC100131795 -0,750350108
+TH -0,748260596
+AV756161 -0,747351587
+TRIM36 -0,746057792
+MPPED2 -0,743864716
+NELL2 -0,742513977
+MAGED1 -0,739190733
+LRRC49 -0,738776851
+SYNGR3 -0,734846774
+ERC2 -0,734619705
+VBP1 -0,73223558
+UQCC -0,729749962
+DCLK1 -0,725139215
+GSS -0,724321987
+OPA1 -0,723790592
+PPP2R2B -0,720892147
+COPS4 -0,720599852
+NSF -0,720580224
+DLD -0,72035948
+DYNC1I1 -0,719837984
+GABARAPL3 -0,717235008
+GPRASP1 -0,71302626
+NAP1L2 -0,712876929
+AMPH -0,711957162
+PNMAL1 -0,70952389
+RGS6 -0,706463
+LDB2 -0,704777497
+TTC19 -0,704232585
+SCN3B -0,703738866
+ATPIF1 -0,702603531
+BEX1 -0,700382911
+LMO3 -0,699029823
+TBC1D9 -0,698189481
+NDUFS1 -0,697230219
+INSM1 -0,696524737
+PARL -0,696362568
+MRPL15 -0,688780959
+C3orf14 -0,687875821
+C19orf62 -0,687403479
+PCYOX1L -0,686812669
+VRK1 -0,685016241
+MDH2 -0,684889561
+SMYD3 -0,684642724
+ASAH1 -0,68459801
+GSTA4 -0,684021936
+NDUFA9 -0,683116722
+ATP5C1 -0,682289667
+DDX25 -0,681511867
+GNG3 -0,681122999
+MUDENG -0,67996077
+SCG2 -0,679728044
+MOAP1 -0,679575281
+SYT1 -0,678979261
+ATP6V1H -0,6786546
+SHOC2 -0,677754756
+PCSK1 -0,677441918
+LBH -0,67710638
+HK1 -0,676818391
+KIAA0319 -0,676346138
+SMAP1 -0,67618103
+EHBP1 -0,675429621
+RAP1GAP2 -0,673705297
+FABP7 -0,673485271
+LRRN3 -0,6731503
+AHNAK2 -0,672875949
+DHDDS -0,671959403
+SNAPC5 -0,670824633
+C17orf108 -0,670563093
+AL390170 -0,67026906
+PTS -0,669577055
+NUDT11 -0,668061506
+HMP19 -0,66794356
+IMMT -0,667541939
+RGS4 -0,667109174
+RET -0,667088994
+PBLD -0,666164981
+AP3M2 -0,666056972
+WDR7 -0,665751643
+ATP6V0D1 -0,665487037
+RTF1 -0,664652469
+TUBB3 -0,664644351
+CHCHD2 -0,664529051
+DYNLT3 -0,663584428
+RAB6B -0,662755469
+CHGB -0,661865706
+NGFRAP1 -0,659441958
+AZIN1 -0,659394366
+EN1 -0,659313013
+SNX10 -0,659251628
+MIA3 -0,65882244
+ANK1 -0,657621479
+NR4A2 -0,65598531
+ANAPC13 -0,655864214
+RGS7 -0,654445938
+NME5 -0,652754395
+TXNDC9 -0,652019899
+PPIP5K2 -0,651763237
+RFK -0,651442652
+BE674466 -0,651048329
+PEG10 -0,650932122
+PIAS2 -0,650823358
+CUX2 -0,649970555
+SEPT6 -0,649422911
+FKBP1B -0,649416387
+C12orf10 -0,648407487
+HMGCS1 -0,648164918
+WDR61 -0,648133373
+GFPT1 -0,647751981
+MLLT11 -0,647471245
+AGTR1 -0,645674318
+CSNK1D -0,645408463
+WDR47 -0,64495088
+PSMD14 -0,644669314
+CISD1 -0,643780748
+PSMD11 -0,642982055
+KCNS3 -0,642919136
+TIMM8B -0,642730563
+RUNDC3B -0,641744336
+ANKRD6 -0,640032629
+MDH1 -0,639623665
+STMN2 -0,639070421
+BAI3 -0,638894116
+STX12 -0,638382169
+NECAP1 -0,638376593
+NIT2 -0,638223243
+CIRBP -0,637859912
+XK -0,636787355
+KIAA1797 -0,636384728
+ICMT -0,636379567
+GALT -0,636138691
+SPINT2 -0,635454321
+PAIP1 -0,634724103
+TAGLN3 -0,63459569
+CADPS -0,634245008
+GALNT11 -0,634168707
+SLC9A6 -0,632805526
+ANKRD34C -0,63217094
+COPG2IT1 -0,63213856
+VPS4B -0,63135628
+ATP6V0E2 -0,631164455
+SC5DL -0,631137699
+CNPY2 -0,630875303
+GCC2 -0,630691438
+CRYZL1 -0,63015348
+MOBKL3 -0,630076244
+SNCA -0,629316875
+STAM -0,628134338
+TUBA4A -0,627764216
+MAK16 -0,627148096
+FRY -0,626684765
+UBE2V2 -0,626378865
+RWDD2B -0,626170788
+FBXO9 -0,62572532
+FLJ41278 -0,6251633
+SLC30A9 -0,624759053
+LOC100132015 -0,623179237
+EXOG -0,622056922
+RAP1GAP -0,618803848
+DYNC1LI1 -0,618641756
+HARS -0,618639749
+NDUFA5 -0,618245275
+SPCS1 -0,618130333
+PSMB7 -0,618122572
+NETO2 -0,618103081
+ATP5G3 -0,617855025
+UCHL1 -0,617452524
+FAM127A -0,616124191
+TSSC1 -0,615619431
+CBLN1 -0,615519237
+CYB5R1 -0,615294192
+PSMG1 -0,61487171
+AKAP12 -0,614821543
+CYB561 -0,614281499
+KCND3 -0,613554227
+GABRB1 -0,613364723
+SLIT1 -0,613251897
+HN1 -0,612796898
+F8 -0,612749576
+VSNL1 -0,611517123
+ATP5A1 -0,611141848
+ARMCX5 -0,610703909
+AI097640 -0,610659067
+CERK -0,610508368
+TMX4 -0,610174408
+TSPAN13 -0,609932725
+CAMLG -0,609409157
+NDUFA7 -0,609351405
+STRAP -0,609237631
+RTCD1 -0,607502869
+ORC5L -0,606910471
+SCG5 -0,606870723
+HSPA12A -0,606863939
+VAV3 -0,606070683
+TUBB2C -0,60582666
+DCTN2 -0,605238426
+OCRL -0,604661192
+HPCAL4 -0,604023171
+ARL1 -0,604008234
+CDK14 -0,603712397
+TLK1 -0,603591955
+BLVRA -0,603201697
+NEFL -0,602887281
+SLC25A32 -0,602708801
+ATXN10 -0,602624835
+UQCRC2 -0,601726567
+SLC25A3 -0,601470752
+MYL12B -0,601373186
+CDS2 -0,601292766
+DDC -0,601079077
+BSCL2 -0,6009448
+CACNB3 -0,598982611
+RIMS3 -0,598771066
+LASS6 -0,598387226
+FIBP -0,598382328
+LRPPRC -0,598144321
+PYROXD1 -0,598012671
+MAP3K9 -0,597438703
+CHL1 -0,5969101
+FJX1 -0,596748319
+PFN2 -0,596551333
+ATMIN -0,59649395
+LIN7B -0,596058244
+AV704232 -0,595274626
+PPP2R5C -0,594797769
+SNAP91 -0,59414072
+AKT3 -0,593859242
+NDUFAB1 -0,593111219
+CCDC28A -0,59307395
+GLOD4 -0,592429097
+STXBP1 -0,591440124
+HLTF -0,591296161
+CRMP1 -0,590916915
+KIAA0513 -0,590696005
+GHITM -0,590624599
+ATP6V1B2 -0,590367192
+USP14 -0,589739205
+RNFT2 -0,589705749
+SCG3 -0,589375952
+ATP5B -0,588999541
+FAM136A -0,588982627
+UBE2N -0,588308222
+ANXA6 -0,588071667
+MRTO4 -0,58799806
+SNRK -0,587183425
+CACNA2D2 -0,587134808
+IFT57 -0,586933566
+PPP3CB -0,586906049
+RICH2 -0,586554767
+ME3 -0,586514247
+THOC7 -0,585617181
+FAM188A -0,584083221
+EIF2B3 -0,582997986
+CNTNAP1 -0,582856877
+SCRN1 -0,582791752
+ACAT1 -0,582760841
+IDI1 -0,582694626
+PBX1 -0,582658829
+CDC42 -0,582658446
+NBEA -0,582614884
+PPP1R2 -0,581839918
+ACTR6 -0,581817384
+TAF9 -0,581794162
+NIPSNAP1 -0,581711722
+SEC61A2 -0,58139821
+WDR37 -0,581272248
+VWA5A -0,581248993
+CDC27 -0,580500838
+MYT1L -0,580491453
+PSMC1 -0,580473356
+KATNB1 -0,578133005
+ZWINT -0,577661475
+C12orf24 -0,577181135
+SLC25A46 -0,577144749
+DOLK -0,576794187
+APOO -0,576716633
+GCH1 -0,576494714
+TBC1D30 -0,575582077
+DCTN3 -0,575526778
+FBXL2 -0,575141782
+KIFAP3 -0,574923419
+CMAS -0,574834972
+C18orf10 -0,574780811
+PNMA2 -0,574504978
+PDHX -0,574434123
+SAMM50 -0,574204311
+NDUFA2 -0,574087728
+NPTN -0,573534504
+HIGD1A -0,573110642
+CYC1 -0,573010558
+HMGCR -0,572959475
+TRAPPC2L -0,572517332
+IMPA1 -0,572397104
+IMPACT -0,572070372
+KIAA0802 -0,572067617
+DSTN -0,571964512
+C5orf44 -0,571958339
+CCK -0,571148184
+OGDHL -0,571078621
+TCP11L1 -0,570951095
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+IARS -0,569079443
+CDH8 -0,569072707
+RNF41 -0,568830451
+SCN3A -0,568276898
+PSMD12 -0,567936617
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+FIG4 -0,566751868
+DDX24 -0,566446037
+MARK1 -0,566206858
+ATP8A2 -0,565754513
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+TERF2IP -0,564084181
+VDAC3 -0,563895581
+B3GNT1 -0,563686309
+CHN1 -0,563660153
+GLO1 -0,561564055
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+HRASLS -0,557799459
+TMEM14B -0,557593404
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+AUH -0,55725646
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+ATP5J2 -0,555267292
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+CD2BP2 -0,55167071
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+W88821 -0,551080268
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+ACSL6 -0,549806401
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+PLD3 -0,547495065
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+IPW -0,546596796
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+RFPL1S -0,545994554
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+DRG1 -0,544733954
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+AI263044 -0,544470885
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+ADK -0,540377244
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+ELOVL6 -0,540054201
+FAM189A1 -0,539987546
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+SYNGR1 -0,53757151
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+DEF8 -0,536162488
+PDXK -0,536128962
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+AACS -0,535868362
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+LXN -0,535676847
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+RCN2 -0,535264733
+SDC2 -0,535187449
+NRXN3 -0,534911729
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+PEX11B -0,533915774
+RAP1GDS1 -0,533764019
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+SDHAP1 -0,533209621
+PJA2 -0,532853246
+ACOT7 -0,532662038
+SEZ6L -0,532618647
+CELF2 -0,532603645
+CXorf40A -0,532513065
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+NRG1 -0,532009485
+SEC31B -0,53180843
+ME1 -0,531466374
+PSMD8 -0,531445018
+MSL1 -0,531268404
+PCLO -0,531166247
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+MAGED2 -0,530858407
+EIF3K -0,530846086
+MMD -0,530845303
+MYO5A -0,530805656
+NCRNA00094 -0,530597959
+KIAA1107 -0,53057188
+KIAA0564 -0,530294183
+PSMB2 -0,530140819
+C1orf114 -0,530111522
+GCLM -0,529867963
+NDN -0,529086871
+SRD5A1 -0,528786683
+DNAJB9 -0,528374918
+SLC7A8 -0,528181836
+CLIP3 -0,527794519
+NDUFB1 -0,527724864
+CLSTN2 -0,52726691
+C14orf156 -0,527148764
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+TMEM30A -0,521872901
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+MAPK9 -0,521572661
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+RPS6KA3 -0,520660932
+GNAO1 -0,520506337
+PSMD6 -0,520132666
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+C9orf125 -0,519623009
+MN1 -0,51937171
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+KIF3A -0,518357676
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+QPCT -0,514170797
+ST6GALNAC5 -0,514077764
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+HSD17B12 -0,513489073
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+RUNDC3A -0,511994377
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+PLEKHB2 -0,510964275
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+OPTN -0,509603205
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+STS -0,509361214
+TIMM10 -0,509318807
+C1D -0,509252454
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+CCDC6 -0,509150548
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+VPS35 -0,507278509
+MRPS33 -0,507141908
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+TOMM70A -0,501591565
+STX18 -0,501503813
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+UROS -0,497291028
+OLFM1 -0,496832922
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+B3GALNT1 -0,496135395
+PHLPP2 -0,496077027
+TSPYL1 -0,495383913
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+ITFG1 -0,495195881
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+C7orf43 -0,49286586
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+ASH2L -0,490785052
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+NANS -0,490410248
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+EPB49 -0,489916122
+TUFT1 -0,489843226
+POP4 -0,489594415
+CACNA1G -0,489236615
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+SCAMP1 -0,480275681
+RBKS -0,480222
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+C3orf37 -0,445975885
+RAD17 -0,445659766
+BBS4 -0,445631347
+TBC1D19 -0,445509157
+TSG101 -0,445289202
+DKK3 -0,445181251
+KCNQ2 -0,444911548
+EIF4E -0,44477948
+LOC100134209 -0,444742688
+OSTF1 -0,444651424
+PPCS -0,444330494
+ATP13A2 -0,443924538
+DHRS7B -0,443866868
+TSN -0,443785273
+AI201594 -0,443780197
+UBE2J1 -0,443536878
+C12orf51 -0,443320039
+INPP5F -0,44324612
+KIAA0391 -0,443138749
+NDUFB8 -0,442168118
+COX8A -0,442151263
+PLCB4 -0,442128902
+UQCRC1 -0,442055114
+RNMT -0,442010619
+PSMB4 -0,441631296
+ATP9A -0,441570839
+COMMD8 -0,441419712
+STX7 -0,441415012
+UQCRFS1 -0,441387219
+ARMC8 -0,441335025
+USP33 -0,441131902
+SC4MOL -0,441051846
+AVL9 -0,440604375
+CORO1C -0,440555184
+ATP6V0A1 -0,440500219
+AKTIP -0,440321706
+C11orf49 -0,440065839
+ACCN1 -0,439959618
+DYNC1H1 -0,439954428
+RTN4 -0,439926435
+IFT52 -0,439664934
+ARIH1 -0,439616652
+SLC23A2 -0,439279622
+FDPS -0,439263979
+ZW10 -0,439088192
+C6orf211 -0,438493952
+CAPZA2 -0,438442617
+TRIM9 -0,43841496
+PANK2 -0,438226487
+SLC25A36 -0,437878589
+TM7SF2 -0,437751686
+GPD1L -0,437274057
+TM2D3 -0,437156245
+TBC1D22A -0,436837159
+AFF2 -0,436678505
+PSMA4 -0,43652406
+SCAPER -0,436328183
+KPNB1 -0,43624217
+C8orf33 -0,436164892
+RRAS2 -0,435924543
+PNMA1 -0,435862986
+DRD2 -0,435854058
+CCDC92 -0,435740221
+CYB5B -0,435703661
+DNM1L -0,435497666
+FAM98A -0,435109538
+CYCS -0,43500707
+UBE2B -0,434857087
+DCTPP1 -0,434751269
+ENC1 -0,434576571
+SAP18 -0,434463135
+MED7 -0,43446171
+UBXN6 -0,433506891
+MAEA -0,433493136
+C20orf27 -0,433220759
+ARFGEF2 -0,4331108
+FKBP9 -0,433030189
+COQ10B -0,432955202
+SNRNP25 -0,432902395
+PHKB -0,432809153
+CETN2 -0,432732838
+PIK3R4 -0,432641256
+EFR3A -0,432263211
+FAM162A -0,432255742
+LOC732160 -0,432226821
+SRPK2 -0,432044566
+USP9X -0,431489845
+DENND2A -0,431031563
+PPP2CA -0,430950806
+CHST1 -0,430892555
+OSBPL9 -0,430720865
+TPM3 -0,430527364
+UGP2 -0,430314768
+AL049387 -0,430134526
+ARHGDIG -0,429952838
+GPR161 -0,429932801
+HGSNAT -0,429440496
+TCEAL4 -0,429402449
+KHDC1 -0,429285977
+SPATA7 -0,428924113
+NIPSNAP3B -0,428922472
+NHP2L1 -0,42870798
+BZW2 -0,428685674
+BZW1 -0,428658261
+ABCF3 -0,428526247
+PEX19 -0,428349422
+POLR2K -0,42820853
+FAM134B -0,428156057
+TUBGCP4 -0,428150919
+CSNK2A1 -0,427824997
+PPP2R5D -0,427719013
+CEND1 -0,427667723
+RNF11 -0,427514623
+EBNA1BP2 -0,427275229
+SDHC -0,42690156
+ATP6AP2 -0,426823582
+MAPK1 -0,426681157
+YTHDC2 -0,425950246
+ACTR3B -0,425721173
+LRRC47 -0,424928312
+ANO10 -0,424906321
+MORF4L2 -0,424702281
+NAE1 -0,424669605
+GRSF1 -0,424576498
+UBE3C -0,42455123
+RRM1 -0,424268285
+IARS2 -0,424201991
+HINT1 -0,423973896
+B4GALT7 -0,423964657
+OBSL1 -0,423852756
+RPH3A -0,423713255
+PTPRM -0,423526608
+TRAP1 -0,423405292
+GSTO1 -0,423136683
+PGK1 -0,423107749
+KCTD2 -0,423033005
+AKAP9 -0,423014145
+KIAA0090 -0,422971022
+NIF3L1 -0,422805913
+SAE1 -0,422487927
+TRAPPC4 -0,422454822
+UBE3B -0,422322842
+MRPL13 -0,422291395
+ARF1 -0,422218883
+NCKAP1 -0,421739152
+COX11 -0,421717769
+XPA -0,421552598
+FKBP11 -0,421544606
+ZFAND1 -0,42136139
+RUSC1 -0,421250909
+PSMC2 -0,42099626
+MCM4 -0,420976269
+HEXA -0,420954607
+PDE4A -0,420795908
+VPS45 -0,420785909
+OGFOD1 -0,420640442
+ADPGK -0,420505817
+AP2M1 -0,420467875
+PSMD5 -0,420139323
+PGRMC1 -0,420109613
+CLASP2 -0,419942702
+CAMTA1 -0,419843296
+COX5A -0,419753275
+BCAP29 -0,419678508
+C21orf59 -0,419586484
+INSIG1 -0,419347593
+NDUFAF1 -0,419256514
+SNCG -0,419205938
+NCAN -0,418993508
+SLC24A3 -0,418714364
+MAP2K1 -0,418679322
+BRCC3 -0,418660516
+MYCBP2 -0,418420128
+PREPL -0,41818051
+TUFM -0,418149804
+LYRM2 -0,41810337
+ORC3L -0,417994092
+TSR2 -0,417894679
+SLC41A3 -0,41774061
+DZIP3 -0,417712026
+MRPS11 -0,417644175
+B4GALT6 -0,41761846
+CHD5 -0,417472
+TUBA1C -0,417351982
+OTUB1 -0,41729395
+DCAF6 -0,417154254
+UQCR10 -0,417021115
+BEX4 -0,416948363
+RTN3 -0,416868526
+GOLT1B -0,416408995
+MRPL3 -0,416396676
+DDX19A -0,416375948
+C4orf41 -0,416356919
+SEMA3G -0,416349944
+TUBA3D -0,416216957
+B4GALNT1 -0,415958605
+TOR1A -0,415819164
+SUPT16H -0,415597727
+ACTR3 -0,415469056
+ABCB9 -0,415410201
+SERF1B -0,415262572
+PSMC6 -0,415072747
+GALNT2 -0,414525722
+ARF5 -0,414370994
+TCEB1 -0,414262524
+FEN1 -0,414164817
+HS2ST1 -0,413801139
+FBXL15 -0,413238338
+ANAPC10 -0,413161353
+MAPK10 -0,413048251
+FGF12 -0,412576909
+GTF2B -0,412561968
+CALM3 -0,412474461
+C12orf5 -0,412385409
+BTRC -0,412323302
+UBXN8 -0,411884422
+G6PC3 -0,411853401
+MARK4 -0,411850043
+SDHB -0,411814414
+FXC1 -0,411804756
+KIAA1467 -0,411406746
+COL4A3BP -0,411372338
+MADD -0,411317373
+SLC25A11 -0,411257994
+APBB3 -0,411242683
+LDHB -0,411172229
+ENTPD3 -0,410988615
+CAMK2B -0,410817586
+C15orf24 -0,410807275
+RAB11FIP5 -0,410722406
+C18orf1 -0,410410534
+IL13RA2 -0,410393436
+TMEFF1 -0,40994415
+TAX1BP1 -0,409905258
+ABHD11 -0,409662969
+SETD4 -0,409479623
+NARS -0,409352949
+LOC441259 -0,409193342
+SMAD2 -0,408937637
+MAGEH1 -0,408820062
+LPIN2 -0,408744346
+WRB -0,408371938
+HSPB11 -0,408269901
+COMMD9 -0,407620354
+RMND1 -0,407542555
+RBP1 -0,407484296
+TSPAN7 -0,407465467
+YKT6 -0,407243851
+ATP5L -0,407238078
+STAT1 -0,407123963
+SPTAN1 -0,407085674
+SLBP -0,407034029
+FAM115A -0,407018502
+ATP1B1 -0,407007242
+GIN1 -0,406994648
+SLC25A4 -0,406703055
+RPAP3 -0,40653888
+ELAVL4 -0,406510215
+LDHA -0,406394191
+GABRG2 -0,406143723
+ACOT1 -0,406088493
+LZTFL1 -0,406077259
+LARP4 -0,406073312
+PTPRG -0,405852123
+DIRAS2 -0,405793372
+SNCB -0,405789504
+CDS1 -0,405765281
+ARL2BP -0,405758176
+BCL2L13 -0,405729545
+STAT4 -0,405634359
+C17orf75 -0,405632179
+ELAVL2 -0,405590653
+DNM3 -0,405342092
+SNX16 -0,404866663
+TACO1 -0,40485549
+HPGD -0,404805074
+CHMP2B -0,404775945
+DPP8 -0,404495701
+SYBU -0,403649563
+CHP -0,403478973
+GTF2H5 -0,403475179
+PPP2R5B -0,403191055
+TRAK1 -0,402996995
+ACSL4 -0,402921692
+RABGAP1L -0,402883713
+PSMB3 -0,402864552
+ASTN1 -0,402784524
+TIMM23B -0,402679864
+NDUFC1 -0,402669713
+GPM6A -0,402645229
+NCDN -0,402391637
+TMEM183A -0,402206694
+LACTB2 -0,402125728
+SFPQ -0,401934429
+SLC1A4 -0,401903736
+LOC731884 -0,401617561
+TTC3 -0,401599425
+APBA1 -0,401587582
+FAM20B -0,401527926
+ISOC1 -0,401479145
+TMEM70 -0,401425176
+GLUD1 -0,401204073
+NDUFA4 -0,401152135
+SHANK2 -0,401076931
+NDUFA6 -0,400922451
+FAM128A -0,400907344
+TSNAX -0,400758374
+BLCAP -0,400561763
+WASF3 -0,400514139
+MTMR6 -0,400412018
+CBARA1 -0,399961135
+SMCR7L -0,399645568
+REXO2 -0,399637796
+ASTN2 -0,399013865
+FBXO31 -0,398919379
+MRPS10 -0,398754479
+GNAL -0,398117434
+RDH11 -0,398104472
+ANKH -0,398086916
+EPHA5 -0,397910595
+DPY19L2P2 -0,397861593
+NRXN1 -0,39777997
+FOXA1 -0,397622781
+AGGF1 -0,397583973
+CLCN6 -0,397581706
+PRKAG1 -0,397496639
+GRM5 -0,397456403
+BCAT1 -0,397331444
+MAP1LC3B -0,397317027
+HMGCL -0,397130437
+IFIT5 -0,397045055
+FAM82B -0,397007464
+TMEM189-UBE2V1 -0,39671729
+TMEM160 -0,396535704
+PIGZ -0,396390486
+VDAC2 -0,3962914
+BCAP31 -0,396227306
+CUL2 -0,395939867
+C5orf30 -0,395902062
+VAMP4 -0,395520757
+CLTA -0,395495699
+NOS1AP -0,395452681
+YWHAH -0,395414553
+AGL -0,39537715
+PPIA -0,395286888
+POLR2E -0,395239973
+FAM190B -0,395231307
+CAND1 -0,395218949
+DIABLO -0,395167608
+FAM155A -0,395099838
+FAM174B -0,394929763
+ABCA11P -0,394841999
+LMF1 -0,394801997
+EIF3I -0,394774336
+RRAGA -0,39363313
+SLC25A5 -0,39336993
+BTBD3 -0,393323586
+SLC38A6 -0,393193457
+TSPYL4 -0,39289974
+NDUFA8 -0,392898828
+ERI3 -0,392853573
+CDH11 -0,392815946
+VPS11 -0,392712183
+RPP40 -0,39270293
+SMS -0,392616216
+USP4 -0,39251437
+RAN -0,392486577
+SYT11 -0,392234251
+SEC23IP -0,392233152
+SUPV3L1 -0,392124663
+TOX3 -0,392048323
+OSBPL3 -0,391742979
+ATP5J -0,391738382
+APC -0,391687772
+EIF2AK2 -0,391678642
+MPPE1 -0,391534871
+CHD3 -0,391021702
+BE858194 -0,390954653
+GPN2 -0,390821549
+TMEM97 -0,39059622
+BRF2 -0,390477924
+NSDHL -0,390017568
+LOC654342 -0,389476483
+SATB1 -0,389035394
+RPP14 -0,388984247
+C16orf68 -0,388858051
+PHF14 -0,388842446
+CKAP5 -0,388699527
+MMADHC -0,388406258
+MEST -0,388313548
+UQCRH -0,387974488
+GBAP1 -0,387823169
+PMPCA -0,387778282
+TMEM41B -0,387668262
+SCLY -0,387620138
+OXA1L -0,387520115
+CLPX -0,387517816
+EML1 -0,387443167
+DPP6 -0,387318033
+FBXO3 -0,387294212
+GAPDH -0,386769027
+ATP6V1C1 -0,386766958
+PRAF2 -0,386484628
+NAA35 -0,386425969
+EIF4H -0,386302469
+SGSH -0,386196526
+CLCN3 -0,386084887
+SMARCA1 -0,385880429
+FAM158A -0,385760557
+AP3S2 -0,385712457
+EIF1AX -0,385367803
+RNF115 -0,385287305
+GPI -0,385266179
+SEC62 -0,385020013
+G3BP2 -0,384968143
+NDUFV1 -0,38487232
+C19orf42 -0,384758261
+BEND5 -0,384699839
+KCNAB2 -0,384620267
+EVL -0,384619104
+MTMR9 -0,384460721
+SIRT3 -0,384239932
+CNIH -0,383916854
+TOLLIP -0,383913386
+C11orf2 -0,383735535
+NUDCD3 -0,383703548
+MED4 -0,383545823
+RABGEF1 -0,38353381
+PTN -0,383407974
+GBF1 -0,383365739
+C1orf163 -0,383317238
+LOC100129361 -0,383315417
+CUL4B -0,383032231
+OXR1 -0,382758654
+TRIM33 -0,382726006
+GPC5 -0,382713696
+C11orf51 -0,382673891
+MAN1C1 -0,382595078
+FGF9 -0,382294616
+SPOCK2 -0,382267861
+GLMN -0,382038722
+MPP1 -0,381567886
+KIF21B -0,381555674
+RND1 -0,381481938
+PEX1 -0,381462705
+C2orf34 -0,381417191
+OTUD3 -0,381344145
+MSRB2 -0,381206334
+CCDC85B -0,38118283
+RGS3 -0,380621769
+SERPINI1 -0,380596066
+C14orf2 -0,380470075
+IDH3G -0,380458518
+POLR2C -0,380378788
+CTNNA2 -0,380377628
+XRCC6 -0,380295972
+EIF3A -0,380281294
+CRBN -0,380214781
+RPS6KC1 -0,3801397
+NUDT2 -0,380057201
+GOLPH3L -0,379823471
+CSNK1A1 -0,379812095
+NDUFB2 -0,379757693
+FTO -0,37940886
+SLC6A15 -0,379271656
+PCP4 -0,379256762
+NIT1 -0,37912136
+CCNC -0,378699092
+DGKB -0,378485235
+RANBP6 -0,377965444
+DNAJC8 -0,377764456
+MAPRE2 -0,377675379
+ARFGAP2 -0,377574006
+BDNF -0,377511436
+HSD17B10 -0,376728332
+AKAP7 -0,376531212
+EHD1 -0,376479944
+PSMD10 -0,376243528
+FABP5L2 -0,376090187
+VAMP7 -0,376017526
+WBP4 -0,375749974
+MAP1B -0,375485017
+SMPDL3A -0,375390185
+GPR89C -0,375362209
+SEPT2 -0,37512019
+GPX3 -0,374915078
+AARSD1 -0,374664572
+HSPA9 -0,37466397
+MAP1A -0,374598439
+C16orf62 -0,374459363
+CARKD -0,374388504
+ASS1 -0,374197776
+WDR12 -0,374046313
+ABHD14A -0,37397421
+SPIN2B -0,373568971
+RAB6A -0,373528481
+PTPRF -0,373483075
+RRAGB -0,373427062
+STK39 -0,373365187
+COX7B -0,373307822
+PDCL -0,373110957
+ATP2A2 -0,373066228
+PPM1E -0,37285382
+TRMT61B -0,372798595
+C21orf33 -0,372766056
+MGMT -0,372730061
+LPHN3 -0,372647138
+WBP2 -0,372385809
+ACSBG1 -0,372296169
+PGRMC2 -0,372287654
+LRRC20 -0,372239514
+AGA -0,372171162
+NRCAM -0,372117405
+FUT9 -0,372053568
+C22orf28 -0,371916518
+MRPS15 -0,371914782
+UFM1 -0,371876489
+CAMK2G -0,371790847
+AVPI1 -0,371692415
+MAST2 -0,371637676
+PPP1R7 -0,371553142
+EEF1A2 -0,371514176
+ATP5D -0,371416456
+EEF1E1 -0,37139203
+NLRP1 -0,371368381
+PMS2CL -0,371209965
+CDK5R1 -0,371120209
+C2orf72 -0,371108998
+OAZ2 -0,3710748
+AL109698 -0,37073584
+INPP4A -0,370700597
+ERH -0,370513944
+CAMK1G -0,370474818
+MED24 -0,370430566
+DMXL1 -0,370287216
+COMMD4 -0,370258812
+NOMO3 -0,370043447
+MORF4 -0,369691968
+ZNHIT3 -0,369651044
+GDPD5 -0,369635923
+CUL5 -0,369519961
+AP1B1 -0,369511443
+YARS -0,369387873
+ABHD10 -0,36913324
+KCNB1 -0,369083149
+SKP1 -0,369015624
+FBXO28 -0,368924883
+ATR -0,368436696
+TMED2 -0,368132686
+ARPC1A -0,367983188
+PHYH -0,367958422
+MRPL22 -0,367879083
+SRRD -0,367868238
+WDYHV1 -0,367821841
+EIF3CL -0,367732775
+HMGB3 -0,367450086
+DENND1B -0,36732795
+ALDH5A1 -0,367318431
+CCNA1 -0,367103911
+FAM134A -0,367014983
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+SNX24 -0,365222253
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+AMACR -0,364562114
+TBPL1 -0,364450426
+PTPMT1 -0,364434415
+CANX -0,364232908
+ELAC2 -0,364131757
+EIF2S1 -0,364109368
+AKR1B1 -0,363915593
+ACADM -0,363858719
+RGS16 -0,363795844
+SLC20A1 -0,363602798
+MTUS2 -0,363384151
+ZMIZ2 -0,363364816
+NDUFS4 -0,363146027
+AW242701 -0,363104323
+SNAPC3 -0,363053639
+ENOPH1 -0,362868334
+LYRM1 -0,362706602
+TRMT12 -0,362561085
+BAALC -0,362539013
+CHMP1B -0,362404908
+ATP1A3 -0,362300724
+TOMM20 -0,362192747
+PEX14 -0,362047536
+EIF2AK1 -0,361934247
+CNNM2 -0,361790716
+PPOX -0,361753445
+TAC1 -0,361655557
+GLRX3 -0,361266708
+OBFC1 -0,360197329
+MFN2 -0,360036589
+DGCR14 -0,359808857
+FAM175B -0,359691136
+PARP2 -0,359639462
+GPR107 -0,359495249
+TUBGCP5 -0,35920098
+ENSA -0,359186957
+UMPS -0,358973056
+SSBP1 -0,358916914
+PFDN2 -0,358707301
+IFFO1 -0,35859667
+CCT2 -0,358497035
+PSMA5 -0,358414139
+ZC3H15 -0,358397302
+EPHX2 -0,358269729
+CALB1 -0,358259257
+POP7 -0,358253841
+MRPL12 -0,357874032
+DFNA5 -0,357815106
+PIAS1 -0,357740062
+ARL4C -0,35770713
+HRAS -0,357592893
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+C4orf27 -0,356816465
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+HCCS -0,3526918
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+SLC38A1 -0,283158141
+ACCN2 -0,283147998
+FAM149A -0,283126904
+TIMM22 -0,283102824
+EIF4ENIF1 -0,28310048
+THSD1P1 -0,282819454
+MAGED4 -0,282562753
+CLASP1 -0,282510547
+C1orf61 -0,282424601
+C6orf106 -0,282397365
+WDR44 -0,282155933
+GNL3 -0,282115302
+RCBTB1 -0,28192202
+OSTM1 -0,281535242
+AGPAT5 -0,281510168
+PRNP -0,281405094
+APPBP2 -0,281330465
+GAD1 -0,281295305
+NECAB3 -0,281056363
+ABCF1 -0,280961256
+DNAJC7 -0,280750506
+EPHB1 -0,280596899
+GPRC5A -0,280368026
+HSPA14 -0,280049432
+CLPTM1 -0,280042656
+SGPP1 -0,27999737
+ABCG4 -0,279891909
+GFRA1 -0,279146972
+ATP5SL -0,278849245
+CTSO -0,278677227
+DCTN4 -0,278556645
+MAP2K2 -0,278535478
+ZNF423 -0,278503712
+FUS -0,278285124
+ACTR8 -0,278282163
+PRR13 -0,278189761
+ZNF329 -0,278179162
+RNASEH2B -0,278151755
+LOC284244 -0,278099761
+FAM117A -0,277715513
+MREG -0,277651168
+C2orf18 -0,277609469
+AW612311 -0,277599115
+SYNRG -0,277434047
+SMARCE1 -0,277346186
+DNAJA3 -0,277188103
+PPP2R5E -0,2770317
+TMCO6 -0,276951805
+C6orf35 -0,276886272
+DDX18 -0,276619655
+TTLL1 -0,276373935
+LANCL1 -0,276361838
+SNRPE -0,276287655
+DTX4 -0,276233703
+IDH2 -0,276017451
+SACS -0,275814599
+ABHD2 -0,275491786
+VAMP1 -0,275092752
+AGPAT1 -0,27504004
+TYMS -0,274913065
+ZDHHC3 -0,27479568
+LMO1 -0,274566957
+UVRAG -0,274559415
+HBB -0,274385467
+PSMA2 -0,274273938
+CD24 -0,27422103
+GRAMD1B -0,27394685
+PRC1 -0,27393137
+YARS2 -0,27376193
+SIGMAR1 -0,273597834
+CPEB3 -0,273534888
+ARMC9 -0,273442678
+DNAJC10 -0,273369377
+TM9SF4 -0,27326642
+RBX1 -0,273166064
+C13orf1 -0,273151402
+PDCD4 -0,273130523
+LUZP2 -0,272843047
+APLP2 -0,272609838
+USO1 -0,272598741
+SH3BP5 -0,272512602
+PPP1R11 -0,272494252
+PEMT -0,272485616
+CDC16 -0,272287144
+LCMT2 -0,272235596
+DCX -0,271983078
+DDAH1 -0,271924121
+UBE2D2 -0,271815552
+TANK -0,271664689
+AW974666 -0,271662837
+USH1C -0,271630244
+BDH1 -0,271624449
+B9D1 -0,271589518
+BRD9 -0,271105209
+USP7 -0,271052865
+TRIM2 -0,270764995
+PARK7 -0,270634786
+NSFL1C -0,270597248
+COQ2 -0,269953826
+HNRPDL -0,269787459
+NOV -0,269731303
+SLC25A28 -0,269706278
+EXT2 -0,26958066
+VLDLR -0,269148459
+SLC4A4 -0,268895862
+SMURF1 -0,268798637
+ORC2L -0,268275919
+ZC4H2 -0,268056536
+SDHAF1 -0,267985583
+VDAC1 -0,267895013
+ALDH1A3 -0,267738476
+PNPLA4 -0,267586498
+HAGH -0,267406111
+CNTNAP2 -0,267355858
+KPNA3 -0,267278305
+LRBA -0,267216793
+DPYSL4 -0,267150239
+MCCC2 -0,26714725
+KBTBD4 -0,267031071
+DCTD -0,267005887
+C1orf21 -0,266982234
+C2orf43 -0,26679916
+SF3A3 -0,266732334
+PTPN3 -0,266674559
+FBXO21 -0,26664933
+CCT7 -0,266615147
+CLNS1A -0,266539743
+HAPLN1 -0,266160364
+SYT13 -0,26591944
+SENP5 -0,265695364
+HMGB2 -0,265556554
+CANT1 -0,265168032
+CGREF1 -0,265157579
+GRM1 -0,26510368
+ZFHX4 -0,265049797
+PVRL3 -0,264999073
+ADAR -0,264636454
+TRIM3 -0,264561355
+ANP32E -0,264413865
+PDLIM7 -0,264406742
+MLH1 -0,264377914
+PRKCA -0,264376056
+CYB5R3 -0,264120933
+PDE1A -0,263919942
+LOC100127998 -0,263915362
+WSB2 -0,263691169
+RPF1 -0,263404659
+CXCL12 -0,26333499
+TMEM66 -0,263285506
+EIF6 -0,263232223
+NFE2L1 -0,262789646
+KLHL20 -0,262772392
+PPM1H -0,262689193
+PIN4 -0,262483899
+TUBA4B -0,26241982
+ECT2 -0,262276809
+MGC5566 -0,261888759
+C9orf116 -0,261830489
+ASB1 -0,261751394
+ABCC8 -0,261735107
+ELOVL2 -0,261638578
+PHB2 -0,261466477
+ZNF580 -0,261379751
+DNAJC24 -0,261364702
+PSMB10 -0,261344946
+CSE1L -0,261292597
+ANKRD27 -0,261154598
+TUBG2 -0,261047779
+C6orf162 -0,261001828
+AL034399 -0,260886813
+GLT8D1 -0,26052144
+SRR -0,260520305
+MCC -0,260395686
+COX4I1 -0,260324715
+SEP15 -0,260222524
+RNF103 -0,260210477
+ZNF576 -0,260159221
+MGEA5 -0,260092677
+RSL24D1 -0,259958151
+USP13 -0,25969613
+MLLT3 -0,259631882
+SRI -0,259268888
+NCS1 -0,259133737
+MAPKAPK5 -0,259103348
+IQCG -0,25908825
+FN3KRP -0,258914892
+BCKDHB -0,258870249
+GOLGA5 -0,258736414
+RDBP -0,258483881
+SUPT7L -0,258355414
+METTL1 -0,258206012
+CREB3 -0,258159408
+TMEM111 -0,258136123
+NRSN2 -0,257397396
+CNTN1 -0,257314074
+COX10 -0,257277055
+SERPINB9 -0,257269621
+MTF2 -0,256976969
+EDNRB -0,25676028
+HSF2 -0,25652969
+POLR2L -0,256424652
+TRIM58 -0,256294322
+DACH1 -0,256241463
+UEVLD -0,256239024
+ATP1B3 -0,256215499
+SAP130 -0,256053262
+TRPC6 -0,255890704
+HERC6 -0,255794959
+NAV3 -0,255707496
+GOSR1 -0,25567987
+CNR1 -0,255506006
+PSME4 -0,25522233
+CAMKV -0,254605479
+ADSL -0,254512794
+BCS1L -0,254298738
+CCNB1 -0,253924801
+SNX2 -0,253887319
+ASAP2 -0,25387509
+WDR70 -0,253565737
+PTPRE -0,253309549
+SEPT5 -0,253058348
+SCML1 -0,253051964
+BCR -0,252946659
+MAGOH -0,252829021
+SEMA4F -0,25277628
+CLIP1 -0,252764211
+JMJD4 -0,252747043
+ZMYND11 -0,25273006
+CPSF6 -0,252574141
+PTPRA -0,252430519
+PLA2G12A -0,252393049
+MXRA5 -0,252290125
+RFX5 -0,252264534
+WARS -0,252174212
+HUS1 -0,252166663
+VCAM1 -0,251733145
+CEACAM21 -0,25171453
+RHOT1 -0,251514974
+EMD -0,251327933
+TSPYL2 -0,251307071
+THNSL1 -0,25130438
+NDUFB4 -0,251250318
+CHMP5 -0,251232028
+SKAP2 -0,251185084
+LRPAP1 -0,251070101
+COMMD3 -0,251069448
+ROGDI -0,250917557
+PPAP2B -0,25089017
+ADSS -0,250852878
+LGI2 -0,250809779
+CBX6 -0,250671998
+NELF -0,250584567
+DENND5B -0,250357567
+ATP2C1 -0,239139672
+SUMO2 -0,233193565
+KRAS -0,208565613
+PEX3 -0,200767265
+PRDX2 -0,195371323
+PDCD2 -0,194653063
+TM2D1 -0,189207426
+KHDRBS1 -0,16653347
+KLC1 -0,156510024
+ANK2 -0,155852142
+HBS1L -0,155006259
+NTRK3 -0,121314135
+PTPRO -0,110200451
+PLEKHA5 -0,10184855
+GCOM1 -0,091608137
+TIMM8A -0,084179504
+MKRN1 -0,074942655
+PLA2G4B -0,068760926
+RUFY3 -0,059042335
+RIMS2 -0,057507607
+C21orf2 -0,054091983
+METAP2 -0,053236401
+LRRC40 -0,040678287
+RPL10 -0,034862755
+RIOK3 -0,033313025
+SYNCRIP -0,027340658
+UNC45A -0,021866459
+MPZL1 -0,020796077
+RANBP1 -0,01610173
+ITGB1BP1 -0,011025016
+UBC -0,009666523
+RER1 -0,007044099
+PDS5B -0,005231512
+NCAM1 -0,004638056
+LIMCH1 0,003894784
+VPS13D 0,014841215
+WDFY3 0,017457694
+MRP63 0,023151675
+TSR1 0,064261585
+GRB10 0,066410415
+FAM128B 0,074972161
+PAK2 0,079518764
+PKP4 0,080237181
+TMEM144 0,083124821
+C3orf63 0,086752023
+DDAH2 0,250378216
+AF238870 0,250544885
+PTMS 0,250667518
+JAG1 0,250675664
+RPL32 0,25075902
+UXT 0,250812127
+HSP90B1 0,250888984
+SS18 0,250904748
+RND2 0,250918958
+CLEC4M 0,250931594
+AU147194 0,251115897
+IL1RAPL1 0,251119435
+EPB41L2 0,251131328
+TFDP3 0,251241244
+GAL3ST4 0,251281983
+EDN2 0,251371356
+SFTPC 0,251372616
+TRMT61A 0,251534845
+GPR4 0,251535902
+KEAP1 0,251692277
+RNF122 0,251718243
+NOTCH2 0,251745042
+WDR1 0,251871256
+NFX1 0,252023298
+DOHH 0,252100123
+NES 0,252167647
+SRSF10 0,252172984
+AQP3 0,252182392
+LOC728412 0,252404082
+RCN3 0,252455902
+CSNK1G1 0,252462493
+KCNS1 0,252601737
+CCDC71 0,252614101
+JUND 0,252645305
+LYST 0,252718314
+TPCN1 0,252770336
+MTA1 0,252823052
+RIN1 0,252841454
+ATHL1 0,252944239
+FTSJ3 0,253136044
+SERPINA1 0,253202139
+STARD7 0,2533744
+MRPL34 0,253425868
+PPID 0,25344089
+SH3PXD2A 0,253534644
+UBA7 0,253547625
+RUNX1 0,253686159
+ARNTL 0,253823553
+STAT6 0,253840779
+CASKIN2 0,25393147
+NFATC4 0,253965486
+LILRB2 0,254041373
+PPP1R13L 0,254173566
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+OTUD4 0,254380531
+ZNF516 0,254390037
+ZC3H14 0,254430628
+BTD 0,254441889
+ABHD4 0,254494909
+MT3 0,254554667
+PTCH1 0,254572046
+CDC42EP3 0,254591236
+LOC150776 0,254715807
+PTGES 0,254816225
+TPM2 0,254867646
+TAGLN 0,254960085
+AL050032 0,254984309
+HPN 0,25500915
+FLNC 0,255046574
+GJB3 0,255060346
+RAB40B 0,255071999
+CST1 0,255226531
+FGF21 0,255229382
+AW574933 0,255334628
+FGF5 0,255461872
+CLCN7 0,2555275
+BAHCC1 0,255618646
+FANCA 0,255627746
+CYBA 0,255682121
+TIE1 0,255683605
+ANKHD1-EIF4EBP3 0,255707685
+CDV3 0,255740411
+COL9A1 0,255878907
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+ZIC1 0,256075896
+CCDC121 0,256090992
+FUT4 0,256155794
+UCP3 0,256197327
+AU146391 0,25625958
+MMP2 0,256269664
+STXBP2 0,256386629
+TMEM87A 0,2564575
+FXR1 0,256493521
+RDX 0,256507051
+HPS1 0,256516919
+TRAM2 0,256517872
+HYAL2 0,256778041
+TNFRSF14 0,256783849
+NEK7 0,256861333
+AGRN 0,256876471
+SMC4 0,256895131
+GAS7 0,256949822
+PDE4B 0,256950938
+CHD4 0,256970114
+SPP1 0,257084517
+HECA 0,257172806
+NXF2B 0,257181225
+LILRA5 0,257188463
+SCAP 0,257267679
+SNX1 0,257354288
+GIGYF2 0,257400552
+CELF1 0,257407908
+HSD17B14 0,257420303
+DUOX1 0,25770603
+MRM1 0,257826185
+NBR2 0,257852879
+FAM176B 0,257955278
+SYNPO 0,257997864
+GPRIN2 0,258040238
+IER3 0,25816919
+ZNF506 0,258198461
+NM_016414 0,25824817
+VPS53 0,258358594
+PGPEP1 0,258378109
+GNL1 0,25847832
+OGFR 0,258496938
+CXCR2 0,258632799
+C1orf38 0,258857462
+RPL22 0,258901214
+NM_018041 0,259005358
+MYOF 0,259133176
+NGB 0,259197495
+CLIC4 0,259260666
+TBC1D9B 0,259295717
+KCND1 0,259337213
+RNASET2 0,259420675
+EXT1 0,259568659
+AQR 0,259572114
+VWA1 0,259618684
+MUC3A 0,259647513
+CAV1 0,259682957
+IRF4 0,259719685
+OR7C1 0,259728956
+SETDB1 0,259737838
+E2F6 0,259867146
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+CPSF3L 0,26005015
+MARCH8 0,260576922
+MFSD11 0,260945964
+ETAA1 0,260954881
+SMARCD2 0,260999203
+RGS12 0,261024661
+CCNG2 0,261112401
+RPS8 0,261183649
+IL17RA 0,261275371
+NUDC 0,261284708
+ZNF133 0,261329337
+ATP13A1 0,261543252
+PICK1 0,26166607
+C20orf117 0,261682534
+GIPR 0,261728602
+HIST2H4B 0,261730186
+S100A11P1 0,261732522
+MARCH3 0,26174629
+ZBED4 0,261794357
+KHK 0,261822851
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+AF070579 0,261954742
+TECR 0,261998101
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+CASP7 0,262240261
+PDK4 0,262293861
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+TUBBP5 0,262483574
+TMEM143 0,262491406
+NAP1L1 0,262524812
+PLEKHB1 0,262542861
+ING1 0,262679424
+SPSB3 0,262786186
+C9orf167 0,262955615
+NTM 0,262977412
+FIP1L1 0,263199662
+FYCO1 0,26321575
+GGT1 0,263227324
+ALG12 0,263240056
+IGL@ 0,263282588
+PPBP 0,263290228
+SNX13 0,263292989
+SRSF4 0,263309909
+CYTH1 0,263721364
+AL050035 0,263831657
+TRMU 0,263920451
+TIMP1 0,263959235
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+HIP1R 0,264033626
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+FNTB 0,264115077
+SAR1B 0,264175117
+GIT1 0,26420824
+RRAGD 0,264311012
+HAP1 0,26435511
+FLT3LG 0,264378926
+NM_018612 0,264421364
+SLC7A9 0,26447762
+GLTSCR2 0,264541217
+SUN1 0,264635751
+CEP152 0,264663399
+MBTD1 0,264688291
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+EIF4A1 0,264933012
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+CMTM6 0,265385079
+FAM102A 0,265449454
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+N4BP2L1 0,26587536
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+TGFBI 0,265987004
+RYK 0,266131346
+SERBP1 0,266135884
+AK021988 0,266152576
+NCAM2 0,266199101
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+PHLDB1 0,266315252
+PKN1 0,266439146
+MFAP3L 0,266558078
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+WBP5 0,266861878
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+SLC6A12 0,267009029
+C3AR1 0,267017849
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+ATN1 0,267069634
+GNB3 0,267107148
+TIAL1 0,267113358
+GPATCH8 0,267177985
+PMEPA1 0,267182372
+MAP2K3 0,267199274
+NM_018033 0,267304029
+WWTR1 0,267350058
+SEMA6A 0,267400431
+RBPJ 0,267426168
+AL049279 0,267438916
+IL1RN 0,267473934
+QKI 0,267577841
+SOX15 0,267588393
+DMTF1 0,267672579
+RPL19 0,267821304
+TRIM39R 0,267839755
+SLC26A6 0,267879749
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+BBS9 0,267969882
+M85256 0,26799656
+ADORA3 0,268097905
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+SECTM1 0,268600799
+ST14 0,268612452
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+SIRT5 0,268726991
+MYBPC1 0,268763379
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+DNAJA1 0,26890035
+LMBR1L 0,269042598
+GIMAP4 0,269074847
+MFAP3 0,269075993
+ABCA6 0,269120338
+AW836210 0,26919833
+LOC100133772 0,269228182
+CHST4 0,269387102
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+RPL18 0,269450865
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+MEPE 0,269489799
+FAM106A 0,269545639
+GATAD1 0,269621956
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+PIGG 0,269941407
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+IFI30 0,269956381
+AK025180 0,269971157
+AMD1 0,269982316
+LMOD1 0,270125966
+SNX15 0,270191178
+SCARB1 0,270338985
+SERTAD3 0,270373355
+MBD5 0,270430073
+SLC2A5 0,270454389
+ITCH 0,270468949
+ADA 0,270490353
+PWP2 0,270541137
+ARHGEF1 0,270572389
+C2CD2 0,270675538
+EIF1 0,27071329
+C1orf35 0,270772513
+IFI16 0,270855012
+LOC285830 0,270905428
+IL10 0,271025993
+MORC4 0,2712707
+CA11 0,271346355
+C5orf54 0,271348162
+C14orf93 0,271428228
+RPL17P7 0,271481741
+TMEM161A 0,271564557
+LRCH3 0,271627825
+DFFB 0,271779652
+BAZ1B 0,271859723
+DKFZp547G183 0,271894591
+RAB11FIP2 0,271895928
+PCK1 0,27194659
+TMPRSS5 0,27195628
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+UBE2L3 0,272125747
+ZNF672 0,272142507
+GALNT10 0,272151507
+EXD2 0,272173543
+KAT2B 0,272322281
+RPS11 0,27237174
+POLR2H 0,272422791
+IGLL3 0,272574443
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+DMC1 0,272606886
+CD40 0,272762332
+CDK11A 0,272811711
+UCKL1 0,272898303
+FAM125B 0,273084179
+UBXN7 0,273084433
+SMA4 0,273204796
+DYNLT1 0,273349219
+CTTNBP2NL 0,273380758
+HSPH1 0,273396703
+CYP39A1 0,273418193
+HOMER3 0,273432217
+RRBP1 0,273480926
+ATAD2B 0,27361049
+LGALS3 0,273847411
+LASS2 0,273913098
+ZNF451 0,273935073
+NXPH4 0,27404559
+C22orf46 0,274118605
+KDM4B 0,27422483
+GPNMB 0,274363725
+CYHR1 0,274415705
+CCDC9 0,274487483
+WWC2 0,274522318
+ZNF652 0,274533788
+ILK 0,274538403
+CTDP1 0,27455992
+LOC51152 0,274810051
+AL442084 0,274963062
+CPNE7 0,275259638
+CENPB 0,275294531
+TCIRG1 0,275300556
+PRPF40A 0,275423637
+ARHGAP17 0,27552534
+LOC100133811 0,275961848
+ADAM17 0,276019886
+CRISPLD2 0,276144309
+IFIH1 0,276175289
+LOC440434 0,276293985
+DCLK2 0,276369722
+MS4A6A 0,276482788
+VASH1 0,276499979
+SRSF7 0,276513035
+B3GAT3 0,276752575
+CALHM2 0,276762436
+MAP4 0,276867434
+DULLARD 0,27687625
+CTSS 0,276943812
+BAG3 0,277040195
+KRT8P12 0,277155277
+POLR2F 0,277193722
+CD14 0,277207134
+SF3B1 0,277255775
+EZH1 0,277320185
+MBD1 0,277342685
+MITF 0,277407356
+BAIAP2 0,277445862
+FCGR2B 0,277531437
+PAQR4 0,277547889
+NFATC2IP 0,277597337
+CAT 0,277600148
+TJP2 0,277610024
+CCNA2 0,277687494
+GEM 0,277887602
+C2orf54 0,277935237
+HIRIP3 0,278018588
+MCM3APAS 0,278082892
+CFB 0,278130274
+TAGLN2 0,278365668
+AK024851 0,278382784
+HGD 0,278585783
+NR2E1 0,278716062
+SEC61A1 0,278797194
+PDE4DIP 0,278806635
+FRMD4A 0,278822955
+RHOC 0,278842121
+UBTF 0,278963815
+NCOR2 0,279024257
+PPP6R3 0,279218049
+ALAS2 0,279327775
+SPSB1 0,279537438
+SGMS1 0,279545277
+TEAD4 0,279565374
+AK024897 0,27961031
+IRS2 0,279708094
+TRIM62 0,279977776
+AF308291 0,279984986
+AK022362 0,280079092
+KIAA0495 0,280115197
+CUL7 0,280170918
+PARD3 0,280192562
+NUP98 0,280376383
+DHRS4L2 0,280391865
+AK024093 0,280444114
+VEGFB 0,280560816
+PTEN 0,280592383
+NBPF10 0,280620974
+CASP1 0,280699269
+AK2 0,280734467
+MLX 0,280792537
+GNG11 0,280826824
+HNRNPM 0,280968313
+IL12RB2 0,28098376
+CDK18 0,28098866
+RARA 0,280998983
+GYPC 0,281028129
+PAK4 0,28104576
+SEMA3F 0,281239182
+BAT2L2 0,281335934
+BRD4 0,28139016
+PAOX 0,281415979
+SMAD3 0,281446531
+PIK3R2 0,281480063
+IFT122 0,281682471
+IRAK4 0,281825175
+RASSF2 0,281825652
+RPL13A 0,282085077
+ZNF22 0,282127023
+KDM4A 0,282136199
+CPM 0,282150511
+EIF2S2 0,282316006
+USP48 0,282335945
+CLCNKB 0,282422648
+C11orf61 0,282474246
+ANKRD11 0,282516441
+PTTG1IP 0,282619596
+SEC14L1 0,282620994
+DOCK6 0,282646645
+CARHSP1 0,28271852
+RRAS 0,282814195
+TRIM38 0,283129972
+PLA1A 0,283206252
+GAB1 0,283220235
+PDLIM1 0,283254227
+SSH3 0,283308195
+KLF9 0,283315657
+N4BP2L2 0,283629404
+TNS4 0,283667599
+C15orf28 0,28383226
+ANXA11 0,283988681
+TAF12 0,283993401
+SLC39A1 0,284190806
+SAP30 0,284320416
+RNASE4 0,284337811
+RPS28P6 0,28438483
+DDR2 0,284449824
+BMP4 0,284614799
+CEPT1 0,284615091
+ITPKB 0,284650775
+PLEKHF2 0,284678379
+AW974812 0,284683098
+PTCRA 0,284827371
+SETMAR 0,2848555
+SOCS3 0,284925858
+NM_014129 0,284930906
+MYO1D 0,285094554
+RBL1 0,28514691
+HN1L 0,285254673
+LASS4 0,285307965
+RPS21 0,285547221
+PPP2R1B 0,285765143
+NEO1 0,285937917
+SEC24C 0,286013109
+BCL3 0,286014454
+KCNMA1 0,286080656
+AL137590 0,286198689
+EDIL3 0,286207431
+ARHGEF16 0,286210956
+HCK 0,286227266
+GSTA1 0,286246055
+SLA 0,286356975
+UNG 0,286379363
+SP100 0,286388329
+PRSS53 0,28642638
+MYL6 0,286728542
+CDH5 0,286728949
+C10orf116 0,286730624
+GTF2IRD1 0,286882519
+POLH 0,286995879
+SFRS16 0,287066034
+TPM4 0,28709233
+ABCD4 0,287100216
+GLT25D2 0,287127854
+COL18A1 0,287131911
+NPIPL3 0,287424398
+C1orf69 0,287453135
+MTF1 0,287488427
+IGF2BP2 0,287555495
+PALLD 0,287872078
+RPS16 0,287887395
+CYP2C9 0,287955438
+SC65 0,288029122
+CRYBG3 0,288096904
+SHC2 0,288312879
+FLNA 0,288339801
+NM_014486 0,288348194
+ISYNA1 0,288383809
+PNO1 0,288506351
+GZMK 0,2886543
+ATG13 0,288748426
+NCOR1 0,288772721
+ZSWIM1 0,288892162
+GPM6B 0,28893274
+SNTA1 0,289049438
+RHOBTB1 0,289064808
+GGA1 0,289073087
+ATXN2L 0,289088819
+FAM46A 0,289172187
+ZNF532 0,289393934
+CD40LG 0,289400418
+ZCCHC11 0,289421485
+WDR5B 0,289498086
+EPN2 0,289629137
+WNK1 0,289684816
+ZNF408 0,289721753
+LHFPL2 0,290003635
+NARG2 0,290029081
+STYXL1 0,29008917
+YY1AP1 0,290249669
+CPOX 0,290281635
+IL11RA 0,290333682
+PAXIP1 0,290387596
+ZNF282 0,290414378
+C11orf95 0,290643441
+MERTK 0,290681835
+VPS13C 0,29069039
+RPS17 0,290756898
+NEIL1 0,290762184
+ZNF292 0,290850132
+NOSIP 0,290873511
+DNAJB2 0,290950763
+INPPL1 0,29102828
+ZFX 0,29106383
+SETX 0,291138151
+SLC25A37 0,291207794
+PCDHGA8 0,291472818
+TXNIP 0,291962928
+DDX27 0,291971417
+BG389073 0,29216848
+JTB 0,292275569
+RBM10 0,292352574
+RASGRF1 0,29242252
+SYNM 0,292474024
+EXPH5 0,292481151
+NPL 0,292494012
+CHKA 0,292519533
+MGA 0,292564204
+SOX10 0,292580481
+AK024185 0,292975066
+FAM120A 0,292996604
+PLXNB1 0,293000141
+BDH2 0,293071563
+JRK 0,293136106
+SLC11A1 0,293139917
+TM4SF1 0,293242649
+EDA 0,293286441
+CDK10 0,293299298
+HLA-E 0,293305618
+LOC642846 0,293349826
+GFPT2 0,293396887
+SENP3 0,293408144
+RPS3AP44 0,293415546
+C16orf88 0,293431615
+FAM60A 0,293472328
+RPL36A 0,293501288
+SERPINA5 0,293547044
+CNOT8 0,293568161
+KDM4C 0,293620372
+POU2F2 0,293815578
+C14orf139 0,293870806
+ZNF217 0,293937173
+NM_025042 0,294034268
+NNMT 0,294200775
+VEZT 0,294224684
+KIAA0754 0,294307773
+RBM28 0,294637248
+ITPR2 0,294711729
+PPPDE1 0,294796015
+KLHL28 0,294874305
+MGP 0,294956866
+LOC729602 0,295016892
+SRSF5 0,295036903
+ROCK1 0,295267164
+SS18L2 0,295271871
+LMNA 0,29532356
+ESRRA 0,295387708
+SNHG3-RCC1 0,295411716
+TAL1 0,295434654
+SQRDL 0,295470062
+TARDBP 0,295665655
+LMAN2L 0,295705138
+RIN3 0,295771443
+PSPH 0,29602696
+DGKD 0,296027908
+WHSC1 0,296067068
+SPRY4 0,296068122
+ADARB2 0,296162399
+ELF3 0,296200778
+TLE1 0,296292637
+ACAN 0,296375799
+AK022038 0,296556116
+IL1RL1 0,296721787
+OR2A9P 0,296898432
+NCRNA00260 0,296954725
+CAD 0,296976627
+PNRC2 0,297129071
+IQCK 0,297134521
+ACOX2 0,297377087
+APOC4 0,297497329
+DGKA 0,297541846
+ZBTB1 0,297547513
+PUS1 0,297622568
+C7orf64 0,297653213
+FBLN1 0,297723957
+SBF1 0,297752819
+TMF1 0,298582891
+IL1R1 0,298701666
+LILRB3 0,298823808
+FLAD1 0,298825369
+CD163 0,299040686
+TCL6 0,299056301
+FADS3 0,299096634
+LBR 0,299180453
+AL162044 0,299184427
+ZNF337 0,299271736
+AHNAK 0,299352615
+YY1 0,299417937
+HIPK2 0,299439852
+NAT15 0,299519834
+ANKZF1 0,299817611
+NECAP2 0,299838267
+MAP3K7 0,299838407
+SAMD4A 0,299863792
+WDR8 0,300094232
+ZNF24 0,300179611
+NR3C1 0,300200063
+FGF1 0,300357727
+NPC1 0,300564708
+LMO4 0,300573598
+TTLL5 0,300853453
+AL050053 0,300945526
+RSU1 0,300958049
+C15orf39 0,301123219
+SLC14A1 0,301147038
+ELAVL1 0,301190126
+SLC17A4 0,301215925
+FANCC 0,301274346
+LRCH4 0,301338927
+EGFL7 0,301340052
+C9orf3 0,301357727
+SRGN 0,301411135
+PLCL1 0,301576339
+MAN1A1 0,301613058
+S100A8 0,301917937
+W86781 0,301984854
+HIP1 0,302012828
+OR7A5 0,302027387
+PPP1CC 0,3020408
+CGGBP1 0,302058231
+CYP3A4 0,302333153
+GALNS 0,302376776
+NR0B1 0,302394827
+SMNDC1 0,302468654
+MGST2 0,302482901
+RPL12 0,302658969
+DMPK 0,302955014
+TNRC6B 0,30299615
+PPM1D 0,303104009
+EED 0,303134999
+STAG3L1 0,3031801
+TMCC1 0,303195736
+RPL13 0,303245467
+RBPMS 0,30326423
+ARHGAP10 0,303298204
+PLCB3 0,303300054
+XPO1 0,303410309
+MYO1F 0,30341788
+SRPK1 0,303531642
+ZCWPW1 0,303562617
+MTHFD2L 0,303678034
+FAM111A 0,303798707
+TTC38 0,304186409
+COL7A1 0,304295553
+C4orf19 0,304312458
+NGLY1 0,304332742
+HTATIP2 0,304339936
+IFNAR2 0,304414877
+CXorf1 0,304737703
+UNC5B 0,304789798
+YAP1 0,30479215
+PHC2 0,30485466
+FBL 0,304914384
+CDH2 0,304939032
+FXYD2 0,304942957
+ANKRD36 0,305000603
+KRT8 0,305028726
+DSCAM 0,30505625
+SMO 0,305151387
+FCGRT 0,305420183
+PAIP2B 0,305483478
+PABPC1 0,305528523
+PIGV 0,305604211
+BACH2 0,305697602
+PLGLA 0,305722503
+MORC3 0,305845022
+DIDO1 0,305996983
+PRPF38B 0,306041882
+TRMT1 0,306054262
+NFATC1 0,306233076
+AK021495 0,306242002
+GPR1 0,306335484
+STARD13 0,306369109
+CELSR2 0,306371185
+ZNF193 0,306396574
+ABHD6 0,306458055
+PLCXD1 0,306486283
+RPAP1 0,306695411
+AL050122 0,306737964
+DHRS3 0,306750918
+C1QA 0,306800137
+AF009267 0,30681596
+SETD2 0,307047565
+STX6 0,307184977
+TMEM204 0,307304516
+SMYD2 0,307490131
+BF942161 0,307560212
+SLC44A1 0,307685609
+ELF2 0,307698089
+AATF 0,307770923
+AV761453 0,307800442
+ACTN1 0,307927265
+AI523613 0,307943372
+SOLH 0,307971092
+ZNF410 0,308222237
+GOLGA4 0,308250269
+FLJ21369 0,308352331
+FCGR2A 0,308469725
+BRD7 0,308638563
+TLR2 0,308769609
+FTHL5 0,308790654
+SPOCK1 0,308861441
+LSM14A 0,308907157
+USF2 0,309161806
+TENC1 0,309220224
+EMP2 0,309252571
+BSDC1 0,309299474
+ZNF701 0,309462113
+PLIN3 0,309516744
+SORBS1 0,309562012
+FTL 0,309588981
+AGFG2 0,309634949
+UBR5 0,309647344
+MMP14 0,30965745
+SFRS8 0,309923113
+ITPR3 0,309975876
+PLK3 0,310097184
+NUP188 0,310124261
+CROCC 0,310245563
+CHSY1 0,310328559
+CTCF 0,310675097
+EDC4 0,310685915
+NFE2L2 0,31069885
+LILRA6 0,311008878
+SATB2 0,311055754
+GTPBP6 0,311254994
+TSPAN14 0,311316513
+C10orf18 0,31133762
+SECISBP2 0,311419174
+DHX34 0,311443077
+LSS 0,311450185
+CHI3L1 0,311532669
+PDGFC 0,311715929
+BMP7 0,311741682
+MBNL1 0,311755686
+DNA2 0,311841432
+COMT 0,312081286
+LOC100133005 0,312165679
+PTOV1 0,312192713
+LCAT 0,312407744
+LRRFIP2 0,312480817
+UCN 0,312589312
+AK024606 0,312655002
+MICAL3 0,312700621
+ROM1 0,31291043
+MED12 0,312925796
+CPNE1 0,313173908
+GBP2 0,313262095
+PELI2 0,313279559
+MLL 0,313398121
+HIF3A 0,313438743
+ST18 0,313449639
+AF131777 0,313643716
+CATSPER2P1 0,313785721
+ZNF302 0,314066212
+APBB2 0,314110219
+KIAA0907 0,31421022
+ZNF592 0,314679884
+HNRNPA1 0,314773035
+TSC2 0,314882123
+SFRS15 0,314884343
+ZNF835 0,314920694
+WDR6 0,314979423
+LOC729143 0,315037798
+PPARD 0,315048839
+U2AF2 0,315118843
+MGAT1 0,315269456
+ZNF44 0,315270856
+RPL36 0,315475789
+GRAMD3 0,315513449
+PTPN2 0,315554784
+AL080072 0,315635626
+C19orf2 0,315918303
+DNAH3 0,315930745
+ZNF146 0,316341954
+SMEK1 0,316538461
+MLXIP 0,31681421
+NMT2 0,316848231
+G3BP1 0,316864559
+DDX3Y 0,316997159
+STEAP1 0,317082981
+BC002629 0,317231764
+KDM2A 0,317406731
+TMEM39A 0,317430306
+C15orf29 0,317437851
+MACF1 0,317513626
+LOC391020 0,317572673
+SETD1A 0,317586539
+KTN1 0,317889697
+RUNX3 0,31809511
+NINJ1 0,318107478
+ARMC7 0,318150459
+BMP1 0,318194029
+DKFZP586I1420 0,318199121
+JARID2 0,318226296
+AW972351 0,318303541
+PAPSS2 0,31841091
+ELTD1 0,31845583
+ETS2 0,318667898
+CREB3L2 0,318705762
+DFNB31 0,31892768
+SERHL2 0,318966243
+C10orf26 0,319058163
+NM_030892 0,319421731
+WRAP53 0,319795295
+UBQLN4 0,319828198
+RALGDS 0,319938162
+PRKCH 0,320101043
+AU146983 0,320105843
+SLC5A3 0,32021553
+DUSP1 0,320239212
+NKX2-2 0,320312108
+C1orf183 0,320387827
+PCM1 0,320482282
+THRA 0,320531901
+NM_025028 0,320726138
+SIVA1 0,320736787
+TTR 0,320757249
+IKBKB 0,320778441
+ARID1A 0,321020715
+HDAC4 0,321059842
+ZFP36L2 0,321167918
+TMEM212 0,321179342
+AA443771 0,321214505
+AGAP5 0,32125931
+PIGA 0,3216713
+SFRS12 0,321704401
+LDLRAP1 0,321832456
+CCDC21 0,321857948
+SSFA2 0,321990716
+RAMP1 0,322050077
+FLJ10357 0,322160744
+LAD1 0,322322766
+RACGAP1 0,322340831
+NPIPL2 0,322616655
+CEP350 0,322648588
+CRLF1 0,322735059
+IGSF9B 0,322744338
+PLXND1 0,322801951
+MCL1 0,322913781
+ALMS1 0,32297709
+ZNF768 0,323059066
+RSL1D1 0,323228527
+C4orf34 0,323582139
+PNPLA6 0,323738553
+MAST4 0,323801655
+NME3 0,323835175
+SNHG3 0,32391938
+S100A12 0,324014586
+PPP4R1 0,32409634
+PLD1 0,324165096
+POLG 0,324186823
+NKTR 0,324203565
+ST3GAL4 0,324231325
+TMEM63A 0,324243134
+ST20 0,32438459
+RNF114 0,324406844
+HYI 0,324468621
+DUSP6 0,324699964
+NR1H2 0,324884332
+DVL2 0,324900869
+SRSF11 0,324979841
+CLK2 0,325170283
+MKLN1 0,325287178
+SCRIB 0,325320413
+KIAA0467 0,325541973
+DMWD 0,325745064
+KLHL23 0,32579572
+RPS6 0,325948088
+ZBTB17 0,326014408
+RAI14 0,326038467
+UBE2G2 0,326143089
+ZNF562 0,326186073
+EZR 0,326282578
+TRPS1 0,326283144
+HFE 0,326390644
+MED23 0,32658232
+DDX11 0,326766632
+SHMT2 0,326784725
+LRP5 0,326954416
+PTH1R 0,327100265
+LOC731602 0,327131294
+AA401963 0,327241371
+CDK5RAP2 0,327276136
+SERP1 0,327279991
+SLC1A5 0,327303416
+BGN 0,327370767
+HSD17B1 0,327475971
+AL390143 0,327497051
+DIAPH2 0,327617697
+PITPNC1 0,327719899
+SPRY2 0,327767132
+FZD7 0,327974293
+MAP4K4 0,328171238
+TNS1 0,328369107
+ZNF783 0,328517049
+M78162 0,328518574
+ADAMTS1 0,32853944
+FKBP5 0,328911405
+AGAP8 0,329115979
+PLEKHF1 0,329179433
+DNAJB1 0,329339376
+RBMS2 0,329438459
+HNRNPH1 0,329454824
+ULK2 0,329496298
+PAPD7 0,329501864
+SURF1 0,329547559
+W61005 0,329673439
+ZNF862 0,330131081
+GNA15 0,330266409
+CHD9 0,330273108
+DLC1 0,330294104
+TMEM2 0,330321664
+AK024879 0,330353812
+N4BP1 0,330435804
+SERF2 0,330633507
+SNRPA 0,330957742
+IRF8 0,33098543
+ABCA2 0,331251046
+NPFF 0,331328402
+CP 0,331565597
+AU144887 0,331713137
+AW851559 0,33185735
+TCF4 0,332062967
+ZNF354A 0,332076549
+TMEM92 0,332352956
+NFATC3 0,332386137
+SSRP1 0,332529738
+TCF7L2 0,332651908
+PIM1 0,332716071
+PIP4K2A 0,332914219
+EIF4EBP1 0,332959146
+LOC100132863 0,333054912
+MMRN2 0,333075923
+AU147295 0,333342973
+VIM 0,333356286
+C2orf67 0,333469715
+DNMT1 0,333550022
+CEP110 0,333679402
+BAZ2B 0,33371151
+KDELR2 0,333939841
+L3MBTL 0,334448273
+CDK19 0,334505985
+CYorf15B 0,334832089
+DDX17 0,334839203
+FKBP4 0,335166906
+STOM 0,335173644
+U82303 0,335241438
+LOC202181 0,335841121
+ATM 0,335893127
+STK3 0,335957389
+MID1 0,336166241
+IGFBP5 0,336454348
+PARP4 0,336459483
+EXOC7 0,336479503
+FANCG 0,336652927
+PHF2 0,336678654
+FBRS 0,33674511
+ANP32B 0,336836072
+NCK2 0,336876937
+CASP6 0,336920233
+ZBTB3 0,337122586
+DHFR 0,337448147
+APOLD1 0,337464001
+STAG1 0,337490482
+NM_024305 0,337551103
+SIGLEC8 0,337608204
+ERLIN1 0,337809212
+POLDIP3 0,337889824
+SPTLC2 0,33799094
+C7orf26 0,338204972
+UBE2D4 0,338265561
+MAP2K7 0,3384787
+MECOM 0,338508564
+DOCK1 0,339029429
+HS1BP3 0,339148762
+PRKY 0,339216015
+GOLGA1 0,33927478
+XPC 0,339433169
+PHF3 0,33953002
+HIC2 0,339768003
+C9orf7 0,340519877
+CTDSPL 0,340591645
+ZNF83 0,34077157
+PHGDH 0,340889735
+TMEM165 0,340978736
+CLN3 0,341078466
+AU147983 0,34113627
+PATZ1 0,341151411
+DIP2C 0,341390806
+RECK 0,341533646
+EWSR1 0,342003886
+SMAD7 0,342182186
+MTRF1L 0,34225773
+TJAP1 0,342452426
+PRKD2 0,342725824
+SPOP 0,343019265
+HLA-J 0,343028528
+PLXNB2 0,343103735
+FBXL14 0,343454364
+LAMA2 0,343637649
+RNF220 0,343845541
+CLK3 0,344164444
+STARD3 0,344187457
+OGT 0,345118989
+IFITM3 0,345141829
+HMOX1 0,345196784
+EIF2C2 0,34557825
+CCND3 0,345663426
+TGFBR3 0,345676022
+POLR2J3 0,345712548
+BCAR3 0,345713549
+C14orf147 0,34610842
+CLDN15 0,34616346
+TOP1 0,346179876
+RASL12 0,346286134
+MED13L 0,346369067
+SOS2 0,346799305
+SERPING1 0,347144597
+IER5 0,347279068
+TLE2 0,347426427
+LLGL2 0,347448236
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+PHF20 0,347602909
+SIRT4 0,347862165
+OSGIN1 0,348060574
+H2BFS 0,348076316
+NM_017756 0,348230007
+NCRNA00115 0,348422218
+MT1E 0,348733923
+NACC2 0,3488369
+NFIB 0,348943619
+AKR1C3 0,349206923
+ARPC1B 0,349407208
+NIPBL 0,349628117
+RPL11 0,349803207
+MSH6 0,350014407
+PTDSS2 0,350073646
+AL050145 0,350120404
+FAM107A 0,350271118
+CHN2 0,350358174
+DAPK2 0,350378033
+DLG5 0,350436992
+OPHN1 0,350596034
+C20orf11 0,351010126
+SLC35D1 0,35135795
+SELL 0,35142274
+FAM193B 0,351790995
+NM_024880 0,352020901
+RASGRP2 0,352114346
+CAPN3 0,352194849
+THOC1 0,352289646
+TAOK3 0,352396226
+FBXO42 0,352613215
+LARP6 0,352692849
+KLKB1 0,352702835
+METTL7A 0,352961228
+STIP1 0,352968743
+WIPF2 0,353085817
+FOXD1 0,353404764
+HSPB2 0,35378232
+ENGASE 0,353978221
+LAT2 0,354239264
+HIST1H2AH 0,354250391
+GSDMD 0,354483715
+TRA2A 0,354674037
+C19orf29 0,354762053
+BRPF1 0,355002213
+NUMA1 0,355146564
+SNW1 0,355320637
+SMARCC1 0,355374541
+ZNF175 0,35555253
+BATF3 0,355680727
+HIST1H2BC 0,35575565
+ERN2 0,356098991
+ZFR 0,356185362
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+SMTN 0,356289422
+RPS6KA2 0,356774064
+MIIP 0,35685635
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+CTNNAL1 0,357152141
+PCDH9 0,357228835
+LAS1L 0,357263917
+DOK1 0,358029668
+AFTPH 0,35852635
+ZNF143 0,358674337
+C11orf71 0,35888557
+MICALL2 0,359221642
+KDM6A 0,359260932
+CFH 0,359284568
+CEBPB 0,359516672
+MTUS1 0,359547348
+AW973791 0,359548173
+SERTAD2 0,359684853
+FGFR1 0,359721729
+KPTN 0,360479451
+NR2F2 0,361169645
+RGL2 0,361384531
+NM_014120 0,361482036
+TAF5 0,361611903
+ZC3HAV1 0,362177526
+BEST1 0,362248528
+TNFRSF1A 0,362724804
+CLIP2 0,363062238
+EHMT2 0,363078239
+IFITM1 0,363162265
+GCFC1 0,363190607
+PECAM1 0,363227012
+YES1 0,363556218
+ZFP36L1 0,363744573
+SBNO2 0,364095165
+RMND5A 0,364201024
+IL10RB 0,364481295
+CBS 0,364486163
+TBC1D2B 0,364503601
+C10orf10 0,36458821
+AU144530 0,365137826
+ZNF500 0,365202134
+ATP6V0E1 0,36527949
+SEPT8 0,365711052
+VCAN 0,365762437
+RPL36AP51 0,366073863
+RPL31 0,36613283
+TAOK1 0,36613666
+GCN1L1 0,366181489
+CALCOCO1 0,366300689
+GNA11 0,366387362
+SH2B2 0,366425408
+RREB1 0,367259867
+SLC35E1 0,3672965
+GPRC5B 0,367311931
+TCF7 0,367371063
+PDIA4 0,367810651
+ZNF34 0,367845233
+MBD3 0,36793004
+CXCR4 0,368041224
+C9orf114 0,368120984
+IFITM2 0,368313531
+ZNF665 0,368328536
+ZCCHC24 0,368368275
+LOC100133944 0,369022431
+CSDA 0,369150342
+AU148255 0,369666508
+CIZ1 0,369704457
+CRTC3 0,369792369
+CTNNA1 0,369962411
+RARRES2 0,37011032
+NM_025033 0,370246707
+VSIG4 0,370274949
+FAM48A 0,370421427
+ZDHHC11 0,370675656
+NPAS2 0,370715345
+ADH1B 0,370935809
+ACSL1 0,371025369
+C1orf63 0,371083889
+TYMP 0,371266716
+LEPREL1 0,371463494
+LAMB2 0,371472469
+MAFB 0,371542293
+AW971248 0,371589606
+BC003629 0,371603781
+FAM63A 0,371786321
+ABCA1 0,371992682
+IGF2R 0,37211512
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+WAPAL 0,372391179
+ZFC3H1 0,372437982
+ZNF710 0,372493324
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+CCDC101 0,372823539
+BAZ1A 0,372824952
+AXL 0,372842922
+NPIPL1 0,372916072
+HDGF 0,372923023
+KHDRBS3 0,373093219
+MT1X 0,373144553
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+AF257099 0,373262757
+AEBP1 0,37342966
+KLHL25 0,373672957
+GJB4 0,37372121
+LUC7L3 0,374023648
+U79248 0,374142769
+LOC653562 0,374188384
+RBM4 0,374375075
+ABCC10 0,374890625
+CXorf21 0,374896996
+DAXX 0,374917403
+C1R 0,375063944
+TPST2 0,375279072
+KLHL24 0,375307199
+C7orf68 0,375539219
+ZCCHC8 0,375600764
+CASP4 0,375605037
+ETV1 0,37597402
+BIN1 0,376340315
+RGS19 0,376617752
+PKNOX1 0,377091746
+CTTN 0,377173864
+TRIP10 0,377452782
+ANGEL1 0,377498562
+PLIN2 0,377879768
+NM_025007 0,377942771
+PTMA 0,378229214
+S100A11 0,378255627
+AXIN1 0,378580893
+NPRL3 0,378633074
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+PAPOLA 0,379974199
+ITGB5 0,380683545
+FAM38B 0,380693638
+PABPN1 0,380909515
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+RYBP 0,38121367
+NASP 0,381229843
+FGR 0,381246748
+PER1 0,381695992
+CDR2L 0,381867955
+LRRFIP1 0,382075479
+HMHA1 0,382282948
+KIAA0485 0,382313718
+GUSB 0,38235255
+RPS17P5 0,38240934
+FXYD5 0,382563723
+RBL2 0,382697586
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+SLC38A2 0,386710042
+GNG5 0,386756333
+SRRM2 0,386841072
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+CC2D1A 0,387023088
+LRRC37A2 0,387067777
+CSF1 0,387071999
+RPL29P11 0,38708859
+SFRS14 0,387094074
+MYO9B 0,387103012
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+WBSCR16 0,387992811
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+NM_016415 0,388588403
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+KANK2 0,388702219
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+TBC1D16 0,390016803
+TCOF1 0,390109025
+ZFYVE26 0,390278079
+IFRD1 0,39034324
+EIF4B 0,390385914
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+SCIN 0,3907272
+MARS 0,391061966
+PTRF 0,391089965
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+APAF1 0,391530483
+ITPK1 0,3915415
+PNRC1 0,392133859
+CLIC2 0,392140808
+KIAA0913 0,392243895
+PRKAR2A 0,392619325
+PRKX 0,392750502
+SYDE1 0,392957216
+ACSL5 0,393140899
+LRP10 0,393162277
+LPP 0,393214983
+SNTB2 0,393383504
+NADK 0,393882671
+PCBP2 0,394206896
+N51370 0,394562467
+CLIC1 0,394663761
+CTBP2 0,394785714
+PHB 0,394929787
+BCL2 0,395102709
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+LOC652607 0,395562084
+YBX1 0,396079328
+PRPF3 0,396609142
+SLC38A10 0,396741732
+ERBB2IP 0,396808535
+CFLAR 0,396840203
+TNFRSF10B 0,397091951
+PHC1B 0,397196351
+ARL17A 0,397406114
+ZBTB20 0,397424403
+REPIN1 0,397830532
+BE466926 0,397930108
+MT1P2 0,398055653
+ZNF778 0,398225613
+DICER1 0,398300689
+NM_018603 0,398329284
+RAF1 0,398631868
+MXD4 0,398685167
+FBXL7 0,398770393
+CALD1 0,399121196
+GSDMB 0,399246982
+ZCCHC2 0,399293751
+PODXL 0,399691684
+ACACB 0,400136922
+VEZF1 0,400413083
+PLEKHM1 0,401187317
+CSPG4 0,401646086
+ID3 0,40170175
+RBM41 0,401719975
+KDM6B 0,401885964
+PHF15 0,402522419
+LAMP2 0,402538077
+CDC14B 0,402583482
+HNRNPL 0,403044314
+SLC4A2 0,403448509
+DDX23 0,403953946
+TUBD1 0,40407115
+SLC16A3 0,404204458
+CAPN2 0,405022548
+CBFA2T2 0,40560438
+TCEB2 0,405769952
+HNRNPF 0,406126644
+MORC2 0,406182732
+FOXO1 0,406430281
+AI962978 0,406538883
+HP1BP3 0,406567553
+CBFB 0,406789498
+RBM14 0,406886421
+SFI1 0,407058786
+ZHX3 0,407089165
+KDM3A 0,407233406
+SIRT2 0,407341821
+ANKS1A 0,407373917
+TCF3 0,407442968
+NOTCH2NL 0,407672378
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+SLCO1A2 0,40820492
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+WDR59 0,409606436
+LAMA5 0,409632505
+ZNF276 0,409730125
+ZNF395 0,410080702
+TIMM44 0,410223052
+BGLAP 0,410749324
+ZHX2 0,411039562
+CARS2 0,411302016
+SLCO3A1 0,411338796
+LOC442497 0,411765627
+FRYL 0,411842495
+CYP2J2 0,412070197
+ABL1 0,412522321
+INF2 0,412975218
+SGK1 0,413352645
+SFTPB 0,413789208
+TIGD1L 0,41383023
+RBCK1 0,414019825
+TRAPPC10 0,414285862
+DUSP7 0,414641136
+WSCD1 0,415016303
+DCP1A 0,415308358
+LPAR1 0,415365439
+RBBP6 0,415730871
+DONSON 0,416255506
+C16orf5 0,416258918
+NCOA1 0,416350707
+CFHR1 0,416440287
+AA126763 0,416566153
+LRRC32 0,416765832
+CP110 0,41732481
+LTBP3 0,417338221
+TDRD3 0,417356196
+HMG20B 0,417456909
+CDC42EP2 0,417645635
+TAF1C 0,417736819
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+PHKA2 0,417904785
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+RELA 0,418064238
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+PILRB 0,421599366
+STAB1 0,421733406
+FCHO1 0,422126906
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+C1orf66 0,42292679
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+AI732802 0,423584905
+PCID2 0,423787762
+POGK 0,423912669
+TMEM140 0,424587207
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+AL080160 0,42490597
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+SCD5 0,425610027
+RAD52 0,425956612
+AF116715 0,425960499
+DCI 0,425967692
+SFRS18 0,426091505
+HCG2P7 0,426136765
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+MID1IP1 0,426940092
+HNRNPC 0,427103695
+NM_025024 0,427155973
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+SLC29A3 0,428138792
+NSUN5 0,428255135
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+DAPP1 0,428626141
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+LOC91316 0,428742129
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+TRIM52 0,430535815
+MT1G 0,430767233
+NOTCH1 0,430849119
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+RPS6KA1 0,43184981
+KANK1 0,432456197
+FURIN 0,432618855
+APOBEC3C 0,432749845
+ANKRD40 0,432772877
+TRIOBP 0,432900403
+ZNF384 0,433116555
+CDKN1A 0,43319672
+BTG1 0,433570541
+EPHX1 0,433658916
+CNOT6 0,434207544
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+PKD1 0,434547199
+WAS 0,434717417
+RPL23AP32 0,434993767
+P4HA1 0,434997425
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+UIMC1 0,435278167
+NM_025120 0,435322168
+NCOA6 0,435700178
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+BCL6 0,435938226
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+C7orf23 0,436800978
+CDC42BPA 0,437074951
+CD59 0,437137855
+POLR1B 0,437227618
+TLR5 0,437498143
+HDAC1 0,437993569
+ARHGEF7 0,438071237
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+PRELP 0,438518539
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+RBM39 0,439661925
+IQGAP1 0,439786742
+RPL18AP3 0,440613252
+LTBR 0,440721546
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+ARAP2 0,441441928
+ARAF 0,441560027
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+IRF7 0,442147625
+NOL12 0,442203671
+PTPLB 0,442541309
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+MXI1 0,443040642
+AW974910 0,443299524
+C1orf144 0,443500279
+KRCC1 0,444417306
+PIAS4 0,444438643
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+LRP2 0,444740953
+ZDHHC18 0,445392541
+SPN 0,445443935
+ST13 0,446667878
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+NACA2 0,446876872
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+CD22 0,44772036
+CSNK1E 0,447902552
+COL5A3 0,447933631
+MAT2A 0,448695587
+EFHD1 0,448820126
+MAP3K3 0,448963961
+BIN3 0,449317201
+LUC7L 0,449469644
+KIF1C 0,449622117
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+CDKN2C 0,450879897
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+ZNF444 0,453296716
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+JUP 0,453753674
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+PLGLB1 0,454722494
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+NFIL3 0,455469821
+NFKBIA 0,455577982
+XRCC2 0,455670024
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+POU2F1 0,456120351
+VPS54 0,456318614
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+RPL28 0,456867479
+ICAM2 0,457066169
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+FKSG49 0,459538011
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+NOL8 0,462387404
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+TRIM28 0,463454342
+BCAT2 0,463509769
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+PHLPP1 0,463738295
+BST2 0,465024297
+PDGFRB 0,465034704
+AL049987 0,465336929
+AKAP8L 0,466278804
+TGM2 0,467555999
+CREBBP 0,467899354
+KIAA0894 0,468325808
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+NCAPD2 0,468959537
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+PNMT 0,470291567
+NAA16 0,470467422
+ZNF611 0,470526774
+ZRSR1 0,470857426
+NPIP 0,472818474
+RBM38 0,473036567
+USP34 0,473278809
+TGFB3 0,474067001
+ITSN2 0,475328182
+CEBPD 0,475754278
+MCM3AP 0,476296498
+HAPLN2 0,476718109
+POGZ 0,477224004
+NR2F1 0,477556735
+GAS1 0,478628972
+SLTM 0,478903701
+ECE1 0,479007813
+CALCOCO2 0,47910558
+RXRA 0,479821295
+MEIS2 0,480178943
+CLEC2B 0,481843785
+AL049260 0,482481089
+CHST3 0,48259726
+COL16A1 0,483094975
+SLC25A16 0,483255606
+LHPP 0,48421483
+AF010144 0,484619234
+GTSE1 0,484629217
+MUM1 0,484956644
+TNXB 0,485246904
+PRINS 0,486032909
+ANKRD49 0,486282532
+PTPRK 0,486899575
+PPAP2C 0,487395433
+C22orf9 0,488987561
+KHNYN 0,489026627
+RAPGEF3 0,489474077
+AF078844 0,489716822
+MAN2A1 0,489875474
+IFT20 0,490824284
+USP21 0,490859618
+NOP2 0,491526918
+LOC440248 0,491905455
+LOC647070 0,493492979
+MAFF 0,494072026
+BG251521 0,495196452
+C6orf145 0,496322836
+MLL4 0,496324893
+ATF4 0,49676781
+RELN 0,497310216
+PELI1 0,497491599
+P2RX7 0,497499324
+CNOT2 0,498172475
+FAM38A 0,498599859
+DCLRE1C 0,498693515
+INSR 0,502304787
+MAPKAPK2 0,502573806
+NDE1 0,50267356
+MT1M 0,502716901
+CDK5RAP3 0,504041432
+SULT1A4 0,504805398
+NSUN5P2 0,505093708
+ANKRD10 0,505841449
+LOC339047 0,506042447
+LRRC1 0,506594446
+CUX1 0,507257715
+SRRT 0,508240438
+MAF 0,508625791
+EBLN2 0,509549245
+NM_017618 0,510705903
+RBM4B 0,51138423
+FBXW12 0,511744983
+ATP8B1 0,511969804
+NM_024978 0,512045897
+KCNMB4 0,512142959
+CLMN 0,512461537
+LOC100132540 0,512589899
+SERPINH1 0,513136463
+RHBDF2 0,513703735
+PCF11 0,514081494
+HAUS2 0,514694211
+TECPR2 0,514970535
+TNIP2 0,515014912
+AUP1 0,516155581
+KIAA0101 0,516801916
+N35922 0,51703624
+STK38 0,517483454
+AZGP1P1 0,518047589
+C13orf15 0,518310047
+PRR11 0,518691616
+PDCD6 0,51972326
+AFF1 0,520716014
+AF222691 0,521107674
+BE045142 0,521502008
+PACS2 0,521749261
+PSRC1 0,522634606
+ZNF358 0,523463012
+MAPKBP1 0,523696079
+S100A4 0,524041412
+MYO1C 0,524902669
+IRF3 0,52538788
+TOB2 0,526119659
+KLHL21 0,527145117
+PGF 0,527713686
+LOC399491 0,528407104
+ARAP1 0,528556373
+AZGP1 0,528659072
+SIRT7 0,528927974
+C16orf53 0,529668261
+KLHL2 0,533153888
+AK022213 0,533802801
+ANKRD28 0,534099367
+TF 0,536170201
+MAVS 0,53636005
+MSX1 0,536723495
+C12orf35 0,537890473
+AA554945 0,538449904
+SUN2 0,539191173
+RBM6 0,54218394
+AL080112 0,542349721
+SORT1 0,542569398
+AL049285 0,542660805
+FOXO4 0,542834527
+ABCA8 0,543725594
+RING1 0,54468938
+KCNE4 0,546337688
+TAZ 0,546506594
+DIP2A 0,546907877
+CLK4 0,548788669
+ZNF277 0,549312201
+MUS81 0,551193399
+DBT 0,556696292
+EMP3 0,557013195
+DDIT4 0,557077384
+RUFY1 0,557170712
+MYST3 0,559285285
+PRPF4B 0,559881298
+LOC100132247 0,562956585
+HSPB1 0,56508456
+CHD7 0,566776564
+CHORDC1 0,566831861
+COBL 0,569205746
+STAG2 0,569603186
+CTDSP2 0,570069613
+ZNF160 0,572703009
+PDE4C 0,574535337
+WWC3 0,575159977
+BMI1 0,576213767
+CRYAB 0,577245348
+AHCTF1 0,577515066
+ADIPOR2 0,5780263
+CASC3 0,57815663
+MUTYH 0,579456271
+AK023783 0,580340854
+HIGD1B 0,583663012
+PLOD1 0,587347495
+PRR14 0,587364521
+SH3BP4 0,58788373
+C19orf28 0,587956493
+NDRG1 0,588555643
+HIST1H1C 0,591446402
+TCF12 0,592176798
+MPST 0,593408757
+SEPP1 0,593935425
+DNAJB6 0,595685757
+SIRPA 0,596218961
+FLT1 0,597923318
+MYOT 0,598968138
+HIST1H2AC 0,600586387
+HBP1 0,600714263
+KAZ 0,601415288
+PTBP1 0,602313539
+NSUN5P1 0,603090503
+GUSBP3 0,604393039
+KCNJ2 0,616084197
+KAT2A 0,620256502
+MCM7 0,622618327
+FBXW4 0,627081137
+MKNK2 0,628440154
+IL17RB 0,631530593
+CLK1 0,632420317
+LRP4 0,632833859
+FAM53B 0,641895571
+JMJD6 0,64411039
+TYK2 0,644727629
+PLOD3 0,644893842
+CXXC1 0,650530485
+AK024136 0,659066605
+PAN2 0,66036619
+NPTX2 0,665210794
+SPEN 0,669461617
+SETD5 0,670191692
+STX10 0,674048462
+CDK2AP2 0,67411425
+PPM1B 0,68382966
+SLCO4A1 0,685048974
+GLT25D1 0,706365388
+ZC3H11A 0,716021559
+ZBTB16 0,720405109
+ZNF692 0,720940567
+NUPR1 0,724120307
+FLCN 0,747339708
+NFASC 0,755177517
diff --git a/console/testFiles/pd_full/PD_151217_2/layouts/ageing.txt b/console/testFiles/pd_full/PD_151217_2/layouts/ageing.txt
index 952e851c769c685e0d4eb1f4736e4ac1a49fb5dd..d5c8ec23b48129a18a37c03059aa5a46ad5cea59 100644
--- a/console/testFiles/pd_full/PD_151217_2/layouts/ageing.txt
+++ b/console/testFiles/pd_full/PD_151217_2/layouts/ageing.txt
@@ -1,416 +1,416 @@
-# VERSION=1.0
-# NAME=Ageing brain
+# VERSION=1.0
+# NAME=Ageing brain
# DESCRIPTION=Differential transcriptome expression from post mortem tissue. Source: Allen Brain Atlas datasets, see PMID 25447234.
-name value
-ELMO2 -0.547404913905166
-RGS1 0.664905640201586
-GSTT1 -0.630503181260422
-SDPR 0.576954531502211
-KCNJ2 -0.389733143810031
-DLG2 -0.622560222549952
-C2orf46 0.306481308387015
-YPEL1 -0.110679998012662
-AFF2 -0.580887248407995
-TCP11L2 -0.446138772716671
-TYROBP 0.0965004216809888
-PCK1 0.583148947380073
-C3 -0.229405245486493
-BLOC1S2 -0.501156113973434
-LPAR5 -0.252012578774993
-ACAD11 0.484415314534294
-CALB1 -0.585051808236823
-GNG2 -0.514333881323537
-GRIN3A -0.54737874801763
-BLNK -0.23678687239484
-SMARCD1 -0.480222958914743
-ARMC9 0.512102956486084
-CX3CR1 -0.300766155352383
-SLC31A2 -0.502055753854611
-AGPAT3 -0.413409719893933
-EFNB3 -0.382400551167611
-ELMOD2 0.402518685883201
-PRKCG -0.34345444223993
-LAPTM5 -0.136628457581106
-IQUB 0.562346209462303
-STAM -0.566262263187017
-OR11A1 0.178234692397988
-ZDHHC9 -0.520488129277965
-C11orf9 -0.511135500492906
-KLF4 0.640024343756592
-SYCP2L 0.555576793235834
-C20orf112 -0.63210679508749
-AP3M1 -0.436291767005889
-ALMS1P 0.310301539060874
-GREM1 -0.101042197816266
-HLCS -0.404869146774348
-CARNS1 -0.358503492948689
-TSHZ2 -0.370201532555949
-CDKN1A 0.37878581767329
-CNDP1 -0.387074241865627
-C1orf161 0.408555295769768
-DOK6 -0.552556377657443
-C12orf43 -0.345533858224805
-SIPA1L2 -0.469893969573457
-FLJ40712 0.248899115372987
-TREM2 0.326657235461902
-MS4A6A 0.333196279374371
-RASGRF1 0.18816869654076
-RNF26 -0.576816063125611
-C7orf68 0.551320218061987
-DPP7 0.601525547176648
-OMD 0.556147496355725
-SNAI2 -0.402803074931945
-COL21A1 0.475584827359055
-APBB1IP -0.510593783545533
-PRKCQ -0.625167167620313
-PDGFRA -0.593141766545025
-SLCO2B1 -0.20664851085323
-LPCAT3 -0.457401881600448
-CD37 -0.225548512842192
-IRF8 -0.513003936776053
-CSF1R -0.17710132121375
-CD74 0.0263995452022326
-CHI3L1 0.637898420604861
-SELPLG -0.165789940031603
-CDH8 -0.544872582360693
-CXCL12 -0.350721988871356
-TOPBP1 -0.516846284550731
-SLC16A10 0.372816060474775
-PCDHB9 -0.583344609658305
-HLA-DRA 0.249881965203208
-OLR1 0.105145169714195
-ADORA3 0.352457579745827
-ALOX5AP 0.094898490604102
-HLA-DOA 0.0912244782358314
-ZNF519 0.242878217518759
-FCER1G 0.122597294910367
-MT1H 0.274901514766897
-MFSD2A 0.12726693788776
-AIF1 -0.0853762046815476
-CTSH 0.324179727747488
-C3AR1 0.00893654957093225
-FCGR2A -0.0476956544487118
-CXCL16 0.0931434603948185
-EVI2B -0.236921572611684
-BACE1 -0.616602739604107
-OR1E1 0.491889127463635
-CLK1 0.423619868541565
-FLJ13197 0.340321509869536
-WBP2NL 0.590401706468574
-UGT8 -0.444926073295334
-HSD17B14 0.614959487312916
-GRIK3 -0.628539434045017
-MT1G 0.569589804148072
-BAIAP3 0.50915236570152
-TJAP1 -0.211899568999271
-PIP4K2C -0.546592244445733
-CAMK4 -0.62370886479691
-TMEM63A -0.349108640870675
-CCDC45 0.470491672406875
-ERLIN1 -0.590064605968872
-ATP6V1F 0.31735684237396
-EPHB2 -0.492251103302591
-ANKRD11 -0.576352445468476
-PCDHB2 -0.56247030572076
-ACSL1 -0.580402201513607
-LGR5 -0.49666928921999
-PDE3B 0.561081934872393
-C1orf21 -0.433409479731833
-LRRTM1 -0.430851468978506
-GPR12 -0.285126298493215
-VSTM2A -0.496505850586284
-ODZ1 -0.500803022233123
-CACNG2 -0.568038440978143
-SMPD3 -0.448297258958326
-SORBS2 -0.652515435812272
-DCAF7 -0.561122254419525
-GJD2 -0.500391756170096
-PEG10 -0.529984214958046
-A2M -0.0956498395825097
-THRB -0.278461084991876
-C11orf24 -0.519543924524242
-TFG -0.340307925442264
-MAMLD1 -0.389582104545406
-ASPHD2 -0.44086160208266
-ANKRD37 0.644400268061014
-NCKAP1L -0.38869429192758
-CAPN5 -0.568639095894228
-SERINC3 -0.473478678274642
-CEBPB 0.386715054596765
-PRDM10 -0.575525391963737
-HCN1 -0.384931312491389
-CAMTA1 -0.435666315274373
-KLHDC1 0.27598504319864
-DUSP1 0.576414053338242
-QRICH1 -0.533552393948272
-SH3KBP1 -0.391446975914019
-EBF1 -0.379385913897609
-PPP1R16B -0.356903880861572
-BTBD3 -0.327196312551472
-NRXN2 -0.509283550099326
-KAZ -0.541421535478964
-KIAA0317 -0.636085461640037
-NDST3 -0.426753877235142
-GMCL1 0.45632888308336
-P2RX5 -0.283914132520413
-IGFL3 0.297606727720448
-LOC286161 -0.366837279825892
-PLEKHM1 -0.408702703852517
-RIMS1 -0.372721943202267
-UBE2Q2P1 0.327173892822723
-TTYH2 -0.407525904378876
-DES 0.06209856553185
-DBNDD2 -0.30225683329951
-ENPP2 -0.409429156664166
-NTN4 0.494337823155339
-SUN2 -0.276353435973038
-ACTG2 -0.210220455726459
-CA2 -0.0242596436213912
-THBS1 -0.221580234422776
-LDLRAD3 -0.360622764104025
-SNX1 -0.0377961368749078
-ERBB3 -0.405973590470433
-TTN 0.391623015044573
-ATRN -0.52540142288716
-NPC1 -0.267674240960311
-GNS -0.181466206971045
-KLK6 -0.378431280290618
-FOS 0.360516377902882
-CD69 0.377148542537053
-LYVE1 0.138789282779698
-FTL 0.237591315022414
-JUNB 0.394473562572383
-GSTM5 0.217560993654354
-NR4A1 0.24427289755837
-PGAM2 0.551801840506397
-TMEM176A 0.537931366670412
-EGR1 -0.157019974633097
-GPR183 0.107180842069747
-CXCL11 0.395003724312407
-PLA2G12A -0.18246216314499
-HLA-DMB 0.229795197318716
-CPNE8 0.0508489313725271
-ZFP36 0.42538436064968
-AGPAT4 -0.467855141787709
-HLA-DPA1 0.408536378107808
-PIK3C2B -0.591780318571167
-CPNE6 -0.271576531727541
-PLD3 -0.200022062788495
-PVRL1 -0.555155906198138
-GGCT -0.279243242312552
-P2RY13 -0.360442360434042
-CNTN5 0.00258913839174191
-MCM7 0.195233154899312
-GPR120 -0.199692500084005
-GABRE 0.0682190440098052
-LRRC39 0.498683033772744
-TLR7 -0.164697853025215
-RFC3 -0.486755240432686
-CD33 0.00184280522373291
-CA8 0.363290764959567
-MAS1 -0.492009752548035
-FBLN5 -0.511286958021381
-TMTC1 -0.332133706392934
-C1orf51 0.45497717618641
-RPL35 -0.0899084146126614
-DKK2 -0.38611669080376
-USP53 0.412868805138869
-CD177 -0.217675402988493
-ELAVL1 -0.579547221944692
-AIFM3 0.577935690502709
-ASCL1 0.37568323074867
-EXPH5 -0.575008199569129
-CBWD3 0.283287779368243
-PEPD -0.0553830875558683
-GPNMB 0.364500938005497
-NEDD4L -0.508710397589902
-CALB2 -0.425755713683833
-FAM49A -0.447197463197697
-NT5DC3 -0.265234061560778
-HES6 0.347000889525298
-GDA -0.336613721691585
-RASAL1 -0.344295261121664
-ANO3 -0.518790055621458
-C14orf145 0.508493948450919
-MSRB3 0.374050410076754
-CC2D2B 0.438851338613457
-FAM65B -0.254284575986291
-KIRREL3 -0.539616579176257
-CKLF 0.222793814048359
-DNAJA4 -0.486836211576555
-BCOR -0.579019889055718
-CBLL1 -0.642779519205918
-CACNG3 -0.428582206819538
-GRIN2B -0.577739683994275
-LRRC67 0.341366642004448
-RELL2 0.405916058000189
-NUDT3 -0.340375787654433
-MAST2 -0.541618527665053
-S100A10 -0.105037624066791
-OR13C2 0.379430219617317
-HSPC157 0.570528832119166
-NOP10 0.322245514370384
-C6orf174 -0.338629613564291
-LRRC61 0.0251744454575518
-FOLR2 0.131043427693804
-DYRK2 -0.522163896119695
-CALHM2 0.169628414381558
-CST7 0.313658960797421
-DUSP7 -0.523627393294567
-MTMR10 -0.415446285885383
-PPM1G -0.464776264617981
-ADCY1 -0.454137407761092
-RPL13 0.506459486318965
-RRN3P1 0.525814578931781
-CXCL2 0.3672098081501
-RXRG 0.0402026385616925
-SRGN 0.531671866088554
-HIST1H2AE 0.293542472070096
-CYP2B6 0.275105405791745
-HHIP -0.466578712584274
-KIAA1324L -0.40123393199988
-FLJ90757 -0.507490069062372
-MYT1L -0.584482026813831
-EIF2C2 -0.484852873283777
-NKAIN2 -0.549382635628517
-EIF2AK2 -0.489504988062896
-KIF21A -0.359563932905791
-CCT6A -0.177223944265096
-CDV3 -0.391589063759768
-HIVEP2 -0.600071683037855
-SPATA1 0.543060390879784
-FKBP11 -0.615494036116273
-NDST1 -0.475889745275566
-ARHGEF10 -0.250541551205642
-ZHX1 0.482981433720838
-SLC10A7 -0.337979122832437
-JAKMIP2 -0.415964197082499
-NAV1 -0.510622036406541
-NDUFB2 0.377202661234421
-ZNF507 -0.468104205569414
-MGAT2 0.222876912868186
-TTR 0.346175361449992
-EPB41L3 -0.411485674977879
-CNTNAP2 -0.327376463196595
-HNRNPU -0.346139332150707
-ZNRD1 0.194397447066282
-PMF1 0.232524370350156
-TNFRSF21 -0.387936336469165
-KCNB1 -0.405472129261546
-FOXG1 -0.471157786135538
-S100A13 0.557308910766736
-BRD4 -0.517114201471415
-TIGD6 0.442112009917649
-RSPH9 0.182331610189591
-RGS20 0.417845235693366
-ASAP1 -0.536170937682141
-SLC7A14 -0.280031937135622
-MGAT3 -0.448766981367882
-IFITM4P 0.485622606827836
-SFRS15 -0.542060168583627
-PITPNM3 -0.42639997101521
-PTPRE -0.530218005259195
-ZEB1 -0.477757026844139
-KCNQ3 -0.429926385373833
-CRB1 0.536038063001376
-MAPT -0.50877997133818
-ABCA3 -0.360772553926051
-NPAS2 -0.419863325483148
-CLIC2 0.498878325957547
-LARP1 -0.49884819681315
-NLGN2 -0.429454573027551
-ALS2CR11 0.294226279272528
-NAP1L2 -0.313096105976879
-SLIT1 -0.434411983489453
-PHB 0.00979800238909777
-ZNF587 -0.0136127665384343
-STRN4 -0.576565248356412
-DSCAML1 -0.596992679910324
-MBD2 -0.20298332637123
-CENPQ 0.422898511661338
-PHF10 0.395502631449537
-MAP3K9 -0.405184359146696
-XRCC1 -0.370898065524857
-AKR1C3 0.453192387807177
-TTC29 0.290819126414233
-ISG20L2 -0.428905666986556
-TMEM165 0.492824884935657
-C2CD3 -0.514182826428327
-DPP4 0.23910770529895
-CCDC92 -0.53622071697372
-EXT1 -0.382555479091514
-C1QL2 -0.201706565681442
-ABHD2 -0.301021168563018
-SMURF1 -0.635507196661467
-CSNK1G2 -0.414657842955022
-TSPO 0.312759943492922
-EFEMP1 0.418307207101287
-HIST1H2BC 0.155466056856681
-CACNA1G -0.603776648047605
-FCGRT 0.35186075288181
-OR6N2 0.19188744379883
-LILRA4 0.402116115371683
-GRIA1 -0.509922904695054
-HOXD8 0.311094779788594
-UPP1 0.48025126950744
-C17orf88 0.245494799347336
-MKL2 -0.495926848441475
-TAB3 -0.397855481558619
-KRTAP19-5 0.333726211690568
-PCDHB3 -0.42089893790206
-KLRF1 0.238176912312437
-TLR4 0.293561440425403
-SEPT14 0.268206811480962
-BSN -0.301460000103249
-GRLF1 -0.466342462809911
-C1orf61 0.409705166908955
-GSTM1 0.580671376408388
-SDCCAG3 0.339086319326061
-NHLH2 0.264436125619991
-CRTC1 -0.364358124950179
-ZNF701 0.262422484025346
-FTO -0.484606564596535
-KIAA0430 -0.323429860829196
-HPSE2 0.444523469491999
-AAK1 -0.336960928171931
-ZNF592 -0.459711729876906
-INF2 -0.368727716463355
-UNC80 -0.203435560684691
-KCNJ9 -0.385326074668389
-CREBBP -0.48479916887186
-TMEM187 0.353577074222219
-GIMAP6 0.196334054611495
-MSH4 0.495021650163618
-CYP2F1 -0.202379731783218
-WARS -0.36956071999387
-EIF4H -0.324258084689287
-LMF1 -0.465196534142832
-SLC9A11 0.380530864151023
-RPLP0 0.401187575431913
-SORCS3 -0.524716179920174
-SMPD1 -0.371378049257817
-MLL2 -0.382849048834827
-ACTA2 -0.351473562308814
-CD84 0.0440334284755635
-LRRC57 -0.0868790230732024
-ADAM28 -0.234050278113392
-FLJ37543 0.329929076805089
-NR4A2 -0.525703760298336
-METT11D1 0.315411883405057
-MEX3C -0.570394569556345
-ST8SIA5 -0.525318796364569
-HRH1 -0.276472654345764
-RAB3IP -0.23897971786832
-ETV6 -0.448657117826825
-LUZP2 -0.409590511647277
-TRIM44 -0.386063986999447
-MYH11 -0.280352372336459
-TPK1 0.485143439818794
-C1QC -0.0250872517448672
-A2ML1 0.356485052871728
-ZNF365 0.476040462817264
-CCL2 0.160044975309114
-ADRA2A -0.511689669158592
-TMPRSS5 0.299973105357606
-C5orf53 0.490994640268981
-MORC2 -0.41225212616417
+name value
+ELMO2 -0.547404913905166
+RGS1 0.664905640201586
+GSTT1 -0.630503181260422
+SDPR 0.576954531502211
+KCNJ2 -0.389733143810031
+DLG2 -0.622560222549952
+C2orf46 0.306481308387015
+YPEL1 -0.110679998012662
+AFF2 -0.580887248407995
+TCP11L2 -0.446138772716671
+TYROBP 0.0965004216809888
+PCK1 0.583148947380073
+C3 -0.229405245486493
+BLOC1S2 -0.501156113973434
+LPAR5 -0.252012578774993
+ACAD11 0.484415314534294
+CALB1 -0.585051808236823
+GNG2 -0.514333881323537
+GRIN3A -0.54737874801763
+BLNK -0.23678687239484
+SMARCD1 -0.480222958914743
+ARMC9 0.512102956486084
+CX3CR1 -0.300766155352383
+SLC31A2 -0.502055753854611
+AGPAT3 -0.413409719893933
+EFNB3 -0.382400551167611
+ELMOD2 0.402518685883201
+PRKCG -0.34345444223993
+LAPTM5 -0.136628457581106
+IQUB 0.562346209462303
+STAM -0.566262263187017
+OR11A1 0.178234692397988
+ZDHHC9 -0.520488129277965
+C11orf9 -0.511135500492906
+KLF4 0.640024343756592
+SYCP2L 0.555576793235834
+C20orf112 -0.63210679508749
+AP3M1 -0.436291767005889
+ALMS1P 0.310301539060874
+GREM1 -0.101042197816266
+HLCS -0.404869146774348
+CARNS1 -0.358503492948689
+TSHZ2 -0.370201532555949
+CDKN1A 0.37878581767329
+CNDP1 -0.387074241865627
+C1orf161 0.408555295769768
+DOK6 -0.552556377657443
+C12orf43 -0.345533858224805
+SIPA1L2 -0.469893969573457
+FLJ40712 0.248899115372987
+TREM2 0.326657235461902
+MS4A6A 0.333196279374371
+RASGRF1 0.18816869654076
+RNF26 -0.576816063125611
+C7orf68 0.551320218061987
+DPP7 0.601525547176648
+OMD 0.556147496355725
+SNAI2 -0.402803074931945
+COL21A1 0.475584827359055
+APBB1IP -0.510593783545533
+PRKCQ -0.625167167620313
+PDGFRA -0.593141766545025
+SLCO2B1 -0.20664851085323
+LPCAT3 -0.457401881600448
+CD37 -0.225548512842192
+IRF8 -0.513003936776053
+CSF1R -0.17710132121375
+CD74 0.0263995452022326
+CHI3L1 0.637898420604861
+SELPLG -0.165789940031603
+CDH8 -0.544872582360693
+CXCL12 -0.350721988871356
+TOPBP1 -0.516846284550731
+SLC16A10 0.372816060474775
+PCDHB9 -0.583344609658305
+HLA-DRA 0.249881965203208
+OLR1 0.105145169714195
+ADORA3 0.352457579745827
+ALOX5AP 0.094898490604102
+HLA-DOA 0.0912244782358314
+ZNF519 0.242878217518759
+FCER1G 0.122597294910367
+MT1H 0.274901514766897
+MFSD2A 0.12726693788776
+AIF1 -0.0853762046815476
+CTSH 0.324179727747488
+C3AR1 0.00893654957093225
+FCGR2A -0.0476956544487118
+CXCL16 0.0931434603948185
+EVI2B -0.236921572611684
+BACE1 -0.616602739604107
+OR1E1 0.491889127463635
+CLK1 0.423619868541565
+FLJ13197 0.340321509869536
+WBP2NL 0.590401706468574
+UGT8 -0.444926073295334
+HSD17B14 0.614959487312916
+GRIK3 -0.628539434045017
+MT1G 0.569589804148072
+BAIAP3 0.50915236570152
+TJAP1 -0.211899568999271
+PIP4K2C -0.546592244445733
+CAMK4 -0.62370886479691
+TMEM63A -0.349108640870675
+CCDC45 0.470491672406875
+ERLIN1 -0.590064605968872
+ATP6V1F 0.31735684237396
+EPHB2 -0.492251103302591
+ANKRD11 -0.576352445468476
+PCDHB2 -0.56247030572076
+ACSL1 -0.580402201513607
+LGR5 -0.49666928921999
+PDE3B 0.561081934872393
+C1orf21 -0.433409479731833
+LRRTM1 -0.430851468978506
+GPR12 -0.285126298493215
+VSTM2A -0.496505850586284
+ODZ1 -0.500803022233123
+CACNG2 -0.568038440978143
+SMPD3 -0.448297258958326
+SORBS2 -0.652515435812272
+DCAF7 -0.561122254419525
+GJD2 -0.500391756170096
+PEG10 -0.529984214958046
+A2M -0.0956498395825097
+THRB -0.278461084991876
+C11orf24 -0.519543924524242
+TFG -0.340307925442264
+MAMLD1 -0.389582104545406
+ASPHD2 -0.44086160208266
+ANKRD37 0.644400268061014
+NCKAP1L -0.38869429192758
+CAPN5 -0.568639095894228
+SERINC3 -0.473478678274642
+CEBPB 0.386715054596765
+PRDM10 -0.575525391963737
+HCN1 -0.384931312491389
+CAMTA1 -0.435666315274373
+KLHDC1 0.27598504319864
+DUSP1 0.576414053338242
+QRICH1 -0.533552393948272
+SH3KBP1 -0.391446975914019
+EBF1 -0.379385913897609
+PPP1R16B -0.356903880861572
+BTBD3 -0.327196312551472
+NRXN2 -0.509283550099326
+KAZ -0.541421535478964
+KIAA0317 -0.636085461640037
+NDST3 -0.426753877235142
+GMCL1 0.45632888308336
+P2RX5 -0.283914132520413
+IGFL3 0.297606727720448
+LOC286161 -0.366837279825892
+PLEKHM1 -0.408702703852517
+RIMS1 -0.372721943202267
+UBE2Q2P1 0.327173892822723
+TTYH2 -0.407525904378876
+DES 0.06209856553185
+DBNDD2 -0.30225683329951
+ENPP2 -0.409429156664166
+NTN4 0.494337823155339
+SUN2 -0.276353435973038
+ACTG2 -0.210220455726459
+CA2 -0.0242596436213912
+THBS1 -0.221580234422776
+LDLRAD3 -0.360622764104025
+SNX1 -0.0377961368749078
+ERBB3 -0.405973590470433
+TTN 0.391623015044573
+ATRN -0.52540142288716
+NPC1 -0.267674240960311
+GNS -0.181466206971045
+KLK6 -0.378431280290618
+FOS 0.360516377902882
+CD69 0.377148542537053
+LYVE1 0.138789282779698
+FTL 0.237591315022414
+JUNB 0.394473562572383
+GSTM5 0.217560993654354
+NR4A1 0.24427289755837
+PGAM2 0.551801840506397
+TMEM176A 0.537931366670412
+EGR1 -0.157019974633097
+GPR183 0.107180842069747
+CXCL11 0.395003724312407
+PLA2G12A -0.18246216314499
+HLA-DMB 0.229795197318716
+CPNE8 0.0508489313725271
+ZFP36 0.42538436064968
+AGPAT4 -0.467855141787709
+HLA-DPA1 0.408536378107808
+PIK3C2B -0.591780318571167
+CPNE6 -0.271576531727541
+PLD3 -0.200022062788495
+PVRL1 -0.555155906198138
+GGCT -0.279243242312552
+P2RY13 -0.360442360434042
+CNTN5 0.00258913839174191
+MCM7 0.195233154899312
+GPR120 -0.199692500084005
+GABRE 0.0682190440098052
+LRRC39 0.498683033772744
+TLR7 -0.164697853025215
+RFC3 -0.486755240432686
+CD33 0.00184280522373291
+CA8 0.363290764959567
+MAS1 -0.492009752548035
+FBLN5 -0.511286958021381
+TMTC1 -0.332133706392934
+C1orf51 0.45497717618641
+RPL35 -0.0899084146126614
+DKK2 -0.38611669080376
+USP53 0.412868805138869
+CD177 -0.217675402988493
+ELAVL1 -0.579547221944692
+AIFM3 0.577935690502709
+ASCL1 0.37568323074867
+EXPH5 -0.575008199569129
+CBWD3 0.283287779368243
+PEPD -0.0553830875558683
+GPNMB 0.364500938005497
+NEDD4L -0.508710397589902
+CALB2 -0.425755713683833
+FAM49A -0.447197463197697
+NT5DC3 -0.265234061560778
+HES6 0.347000889525298
+GDA -0.336613721691585
+RASAL1 -0.344295261121664
+ANO3 -0.518790055621458
+C14orf145 0.508493948450919
+MSRB3 0.374050410076754
+CC2D2B 0.438851338613457
+FAM65B -0.254284575986291
+KIRREL3 -0.539616579176257
+CKLF 0.222793814048359
+DNAJA4 -0.486836211576555
+BCOR -0.579019889055718
+CBLL1 -0.642779519205918
+CACNG3 -0.428582206819538
+GRIN2B -0.577739683994275
+LRRC67 0.341366642004448
+RELL2 0.405916058000189
+NUDT3 -0.340375787654433
+MAST2 -0.541618527665053
+S100A10 -0.105037624066791
+OR13C2 0.379430219617317
+HSPC157 0.570528832119166
+NOP10 0.322245514370384
+C6orf174 -0.338629613564291
+LRRC61 0.0251744454575518
+FOLR2 0.131043427693804
+DYRK2 -0.522163896119695
+CALHM2 0.169628414381558
+CST7 0.313658960797421
+DUSP7 -0.523627393294567
+MTMR10 -0.415446285885383
+PPM1G -0.464776264617981
+ADCY1 -0.454137407761092
+RPL13 0.506459486318965
+RRN3P1 0.525814578931781
+CXCL2 0.3672098081501
+RXRG 0.0402026385616925
+SRGN 0.531671866088554
+HIST1H2AE 0.293542472070096
+CYP2B6 0.275105405791745
+HHIP -0.466578712584274
+KIAA1324L -0.40123393199988
+FLJ90757 -0.507490069062372
+MYT1L -0.584482026813831
+EIF2C2 -0.484852873283777
+NKAIN2 -0.549382635628517
+EIF2AK2 -0.489504988062896
+KIF21A -0.359563932905791
+CCT6A -0.177223944265096
+CDV3 -0.391589063759768
+HIVEP2 -0.600071683037855
+SPATA1 0.543060390879784
+FKBP11 -0.615494036116273
+NDST1 -0.475889745275566
+ARHGEF10 -0.250541551205642
+ZHX1 0.482981433720838
+SLC10A7 -0.337979122832437
+JAKMIP2 -0.415964197082499
+NAV1 -0.510622036406541
+NDUFB2 0.377202661234421
+ZNF507 -0.468104205569414
+MGAT2 0.222876912868186
+TTR 0.346175361449992
+EPB41L3 -0.411485674977879
+CNTNAP2 -0.327376463196595
+HNRNPU -0.346139332150707
+ZNRD1 0.194397447066282
+PMF1 0.232524370350156
+TNFRSF21 -0.387936336469165
+KCNB1 -0.405472129261546
+FOXG1 -0.471157786135538
+S100A13 0.557308910766736
+BRD4 -0.517114201471415
+TIGD6 0.442112009917649
+RSPH9 0.182331610189591
+RGS20 0.417845235693366
+ASAP1 -0.536170937682141
+SLC7A14 -0.280031937135622
+MGAT3 -0.448766981367882
+IFITM4P 0.485622606827836
+SFRS15 -0.542060168583627
+PITPNM3 -0.42639997101521
+PTPRE -0.530218005259195
+ZEB1 -0.477757026844139
+KCNQ3 -0.429926385373833
+CRB1 0.536038063001376
+MAPT -0.50877997133818
+ABCA3 -0.360772553926051
+NPAS2 -0.419863325483148
+CLIC2 0.498878325957547
+LARP1 -0.49884819681315
+NLGN2 -0.429454573027551
+ALS2CR11 0.294226279272528
+NAP1L2 -0.313096105976879
+SLIT1 -0.434411983489453
+PHB 0.00979800238909777
+ZNF587 -0.0136127665384343
+STRN4 -0.576565248356412
+DSCAML1 -0.596992679910324
+MBD2 -0.20298332637123
+CENPQ 0.422898511661338
+PHF10 0.395502631449537
+MAP3K9 -0.405184359146696
+XRCC1 -0.370898065524857
+AKR1C3 0.453192387807177
+TTC29 0.290819126414233
+ISG20L2 -0.428905666986556
+TMEM165 0.492824884935657
+C2CD3 -0.514182826428327
+DPP4 0.23910770529895
+CCDC92 -0.53622071697372
+EXT1 -0.382555479091514
+C1QL2 -0.201706565681442
+ABHD2 -0.301021168563018
+SMURF1 -0.635507196661467
+CSNK1G2 -0.414657842955022
+TSPO 0.312759943492922
+EFEMP1 0.418307207101287
+HIST1H2BC 0.155466056856681
+CACNA1G -0.603776648047605
+FCGRT 0.35186075288181
+OR6N2 0.19188744379883
+LILRA4 0.402116115371683
+GRIA1 -0.509922904695054
+HOXD8 0.311094779788594
+UPP1 0.48025126950744
+C17orf88 0.245494799347336
+MKL2 -0.495926848441475
+TAB3 -0.397855481558619
+KRTAP19-5 0.333726211690568
+PCDHB3 -0.42089893790206
+KLRF1 0.238176912312437
+TLR4 0.293561440425403
+SEPT14 0.268206811480962
+BSN -0.301460000103249
+GRLF1 -0.466342462809911
+C1orf61 0.409705166908955
+GSTM1 0.580671376408388
+SDCCAG3 0.339086319326061
+NHLH2 0.264436125619991
+CRTC1 -0.364358124950179
+ZNF701 0.262422484025346
+FTO -0.484606564596535
+KIAA0430 -0.323429860829196
+HPSE2 0.444523469491999
+AAK1 -0.336960928171931
+ZNF592 -0.459711729876906
+INF2 -0.368727716463355
+UNC80 -0.203435560684691
+KCNJ9 -0.385326074668389
+CREBBP -0.48479916887186
+TMEM187 0.353577074222219
+GIMAP6 0.196334054611495
+MSH4 0.495021650163618
+CYP2F1 -0.202379731783218
+WARS -0.36956071999387
+EIF4H -0.324258084689287
+LMF1 -0.465196534142832
+SLC9A11 0.380530864151023
+RPLP0 0.401187575431913
+SORCS3 -0.524716179920174
+SMPD1 -0.371378049257817
+MLL2 -0.382849048834827
+ACTA2 -0.351473562308814
+CD84 0.0440334284755635
+LRRC57 -0.0868790230732024
+ADAM28 -0.234050278113392
+FLJ37543 0.329929076805089
+NR4A2 -0.525703760298336
+METT11D1 0.315411883405057
+MEX3C -0.570394569556345
+ST8SIA5 -0.525318796364569
+HRH1 -0.276472654345764
+RAB3IP -0.23897971786832
+ETV6 -0.448657117826825
+LUZP2 -0.409590511647277
+TRIM44 -0.386063986999447
+MYH11 -0.280352372336459
+TPK1 0.485143439818794
+C1QC -0.0250872517448672
+A2ML1 0.356485052871728
+ZNF365 0.476040462817264
+CCL2 0.160044975309114
+ADRA2A -0.511689669158592
+TMPRSS5 0.299973105357606
+C5orf53 0.490994640268981
+MORC2 -0.41225212616417
diff --git a/console/testFiles/pd_full/PD_160714_2/layouts/PD substantia nigra.txt b/console/testFiles/pd_full/PD_160714_2/layouts/PD substantia nigra.txt
index 8f57d5c9d21132e0b5eebbd5c953a7922f207282..5ed3ee874243594bd2a73e646c0d5cf2d9cc11d2 100644
--- a/console/testFiles/pd_full/PD_160714_2/layouts/PD substantia nigra.txt
+++ b/console/testFiles/pd_full/PD_160714_2/layouts/PD substantia nigra.txt
@@ -1,4342 +1,4342 @@
-# VERSION=1.0
-# NAME=PD substantia nigra
+# VERSION=1.0
+# NAME=PD substantia nigra
# DESCRIPTION=Differential transcriptome expression from post mortem tissue. Meta-analysis from 8 published datasets, FDR = 0.05, see PMIDs 23832570 and 25447234.
-name value
-GBE1 -0,943978048
-SLC18A2 -0,941309505
-KCNJ6 -0,894120983
-DLK1 -0,887122171
-PTDSS1 -0,851959645
-FGF13 -0,842876271
-PCDH8 -0,83524894
-ZNF226 -0,82900335
-SLC6A3 -0,824713365
-PIP5K1B -0,812285785
-DENR -0,81101551
-TPBG -0,806963209
-PRKAR2B -0,805288865
-OSBPL10 -0,80406299
-ALDH1A1 -0,795042129
-GGCX -0,795035797
-ACP2 -0,794853979
-SLITRK5 -0,793842132
-FAM70A -0,793715412
-HPRT1 -0,792370336
-CCNH -0,790971864
-MYRIP -0,78490295
-TUBB2A -0,783142444
-ACTR10 -0,782043082
-BASP1 -0,778702387
-CADPS2 -0,777552826
-PID1 -0,775106213
-SV2C -0,774895093
-RBM3 -0,77091551
-REEP1 -0,770000111
-RIMBP2 -0,766421185
-CNIH3 -0,765790316
-DMXL2 -0,765309344
-LOC10431 -0,762992699
-SV2B -0,759985564
-AGK -0,756506198
-RCAN2 -0,753762002
-LPPR4 -0,753018962
-RALYL -0,75270126
-L1CAM -0,751978689
-BCAS2 -0,751241508
-LOC100131795 -0,750350108
-TH -0,748260596
-AV756161 -0,747351587
-TRIM36 -0,746057792
-MPPED2 -0,743864716
-NELL2 -0,742513977
-MAGED1 -0,739190733
-LRRC49 -0,738776851
-SYNGR3 -0,734846774
-ERC2 -0,734619705
-VBP1 -0,73223558
-UQCC -0,729749962
-DCLK1 -0,725139215
-GSS -0,724321987
-OPA1 -0,723790592
-PPP2R2B -0,720892147
-COPS4 -0,720599852
-NSF -0,720580224
-DLD -0,72035948
-DYNC1I1 -0,719837984
-GABARAPL3 -0,717235008
-GPRASP1 -0,71302626
-NAP1L2 -0,712876929
-AMPH -0,711957162
-PNMAL1 -0,70952389
-RGS6 -0,706463
-LDB2 -0,704777497
-TTC19 -0,704232585
-SCN3B -0,703738866
-ATPIF1 -0,702603531
-BEX1 -0,700382911
-LMO3 -0,699029823
-TBC1D9 -0,698189481
-NDUFS1 -0,697230219
-INSM1 -0,696524737
-PARL -0,696362568
-MRPL15 -0,688780959
-C3orf14 -0,687875821
-C19orf62 -0,687403479
-PCYOX1L -0,686812669
-VRK1 -0,685016241
-MDH2 -0,684889561
-SMYD3 -0,684642724
-ASAH1 -0,68459801
-GSTA4 -0,684021936
-NDUFA9 -0,683116722
-ATP5C1 -0,682289667
-DDX25 -0,681511867
-GNG3 -0,681122999
-MUDENG -0,67996077
-SCG2 -0,679728044
-MOAP1 -0,679575281
-SYT1 -0,678979261
-ATP6V1H -0,6786546
-SHOC2 -0,677754756
-PCSK1 -0,677441918
-LBH -0,67710638
-HK1 -0,676818391
-KIAA0319 -0,676346138
-SMAP1 -0,67618103
-EHBP1 -0,675429621
-RAP1GAP2 -0,673705297
-FABP7 -0,673485271
-LRRN3 -0,6731503
-AHNAK2 -0,672875949
-DHDDS -0,671959403
-SNAPC5 -0,670824633
-C17orf108 -0,670563093
-AL390170 -0,67026906
-PTS -0,669577055
-NUDT11 -0,668061506
-HMP19 -0,66794356
-IMMT -0,667541939
-RGS4 -0,667109174
-RET -0,667088994
-PBLD -0,666164981
-AP3M2 -0,666056972
-WDR7 -0,665751643
-ATP6V0D1 -0,665487037
-RTF1 -0,664652469
-TUBB3 -0,664644351
-CHCHD2 -0,664529051
-DYNLT3 -0,663584428
-RAB6B -0,662755469
-CHGB -0,661865706
-NGFRAP1 -0,659441958
-AZIN1 -0,659394366
-EN1 -0,659313013
-SNX10 -0,659251628
-MIA3 -0,65882244
-ANK1 -0,657621479
-NR4A2 -0,65598531
-ANAPC13 -0,655864214
-RGS7 -0,654445938
-NME5 -0,652754395
-TXNDC9 -0,652019899
-PPIP5K2 -0,651763237
-RFK -0,651442652
-BE674466 -0,651048329
-PEG10 -0,650932122
-PIAS2 -0,650823358
-CUX2 -0,649970555
-SEPT6 -0,649422911
-FKBP1B -0,649416387
-C12orf10 -0,648407487
-HMGCS1 -0,648164918
-WDR61 -0,648133373
-GFPT1 -0,647751981
-MLLT11 -0,647471245
-AGTR1 -0,645674318
-CSNK1D -0,645408463
-WDR47 -0,64495088
-PSMD14 -0,644669314
-CISD1 -0,643780748
-PSMD11 -0,642982055
-KCNS3 -0,642919136
-TIMM8B -0,642730563
-RUNDC3B -0,641744336
-ANKRD6 -0,640032629
-MDH1 -0,639623665
-STMN2 -0,639070421
-BAI3 -0,638894116
-STX12 -0,638382169
-NECAP1 -0,638376593
-NIT2 -0,638223243
-CIRBP -0,637859912
-XK -0,636787355
-KIAA1797 -0,636384728
-ICMT -0,636379567
-GALT -0,636138691
-SPINT2 -0,635454321
-PAIP1 -0,634724103
-TAGLN3 -0,63459569
-CADPS -0,634245008
-GALNT11 -0,634168707
-SLC9A6 -0,632805526
-ANKRD34C -0,63217094
-COPG2IT1 -0,63213856
-VPS4B -0,63135628
-ATP6V0E2 -0,631164455
-SC5DL -0,631137699
-CNPY2 -0,630875303
-GCC2 -0,630691438
-CRYZL1 -0,63015348
-MOBKL3 -0,630076244
-SNCA -0,629316875
-STAM -0,628134338
-TUBA4A -0,627764216
-MAK16 -0,627148096
-FRY -0,626684765
-UBE2V2 -0,626378865
-RWDD2B -0,626170788
-FBXO9 -0,62572532
-FLJ41278 -0,6251633
-SLC30A9 -0,624759053
-LOC100132015 -0,623179237
-EXOG -0,622056922
-RAP1GAP -0,618803848
-DYNC1LI1 -0,618641756
-HARS -0,618639749
-NDUFA5 -0,618245275
-SPCS1 -0,618130333
-PSMB7 -0,618122572
-NETO2 -0,618103081
-ATP5G3 -0,617855025
-UCHL1 -0,617452524
-FAM127A -0,616124191
-TSSC1 -0,615619431
-CBLN1 -0,615519237
-CYB5R1 -0,615294192
-PSMG1 -0,61487171
-AKAP12 -0,614821543
-CYB561 -0,614281499
-KCND3 -0,613554227
-GABRB1 -0,613364723
-SLIT1 -0,613251897
-HN1 -0,612796898
-F8 -0,612749576
-VSNL1 -0,611517123
-ATP5A1 -0,611141848
-ARMCX5 -0,610703909
-AI097640 -0,610659067
-CERK -0,610508368
-TMX4 -0,610174408
-TSPAN13 -0,609932725
-CAMLG -0,609409157
-NDUFA7 -0,609351405
-STRAP -0,609237631
-RTCD1 -0,607502869
-ORC5L -0,606910471
-SCG5 -0,606870723
-HSPA12A -0,606863939
-VAV3 -0,606070683
-TUBB2C -0,60582666
-DCTN2 -0,605238426
-OCRL -0,604661192
-HPCAL4 -0,604023171
-ARL1 -0,604008234
-CDK14 -0,603712397
-TLK1 -0,603591955
-BLVRA -0,603201697
-NEFL -0,602887281
-SLC25A32 -0,602708801
-ATXN10 -0,602624835
-UQCRC2 -0,601726567
-SLC25A3 -0,601470752
-MYL12B -0,601373186
-CDS2 -0,601292766
-DDC -0,601079077
-BSCL2 -0,6009448
-CACNB3 -0,598982611
-RIMS3 -0,598771066
-LASS6 -0,598387226
-FIBP -0,598382328
-LRPPRC -0,598144321
-PYROXD1 -0,598012671
-MAP3K9 -0,597438703
-CHL1 -0,5969101
-FJX1 -0,596748319
-PFN2 -0,596551333
-ATMIN -0,59649395
-LIN7B -0,596058244
-AV704232 -0,595274626
-PPP2R5C -0,594797769
-SNAP91 -0,59414072
-AKT3 -0,593859242
-NDUFAB1 -0,593111219
-CCDC28A -0,59307395
-GLOD4 -0,592429097
-STXBP1 -0,591440124
-HLTF -0,591296161
-CRMP1 -0,590916915
-KIAA0513 -0,590696005
-GHITM -0,590624599
-ATP6V1B2 -0,590367192
-USP14 -0,589739205
-RNFT2 -0,589705749
-SCG3 -0,589375952
-ATP5B -0,588999541
-FAM136A -0,588982627
-UBE2N -0,588308222
-ANXA6 -0,588071667
-MRTO4 -0,58799806
-SNRK -0,587183425
-CACNA2D2 -0,587134808
-IFT57 -0,586933566
-PPP3CB -0,586906049
-RICH2 -0,586554767
-ME3 -0,586514247
-THOC7 -0,585617181
-FAM188A -0,584083221
-EIF2B3 -0,582997986
-CNTNAP1 -0,582856877
-SCRN1 -0,582791752
-ACAT1 -0,582760841
-IDI1 -0,582694626
-PBX1 -0,582658829
-CDC42 -0,582658446
-NBEA -0,582614884
-PPP1R2 -0,581839918
-ACTR6 -0,581817384
-TAF9 -0,581794162
-NIPSNAP1 -0,581711722
-SEC61A2 -0,58139821
-WDR37 -0,581272248
-VWA5A -0,581248993
-CDC27 -0,580500838
-MYT1L -0,580491453
-PSMC1 -0,580473356
-KATNB1 -0,578133005
-ZWINT -0,577661475
-C12orf24 -0,577181135
-SLC25A46 -0,577144749
-DOLK -0,576794187
-APOO -0,576716633
-GCH1 -0,576494714
-TBC1D30 -0,575582077
-DCTN3 -0,575526778
-FBXL2 -0,575141782
-KIFAP3 -0,574923419
-CMAS -0,574834972
-C18orf10 -0,574780811
-PNMA2 -0,574504978
-PDHX -0,574434123
-SAMM50 -0,574204311
-NDUFA2 -0,574087728
-NPTN -0,573534504
-HIGD1A -0,573110642
-CYC1 -0,573010558
-HMGCR -0,572959475
-TRAPPC2L -0,572517332
-IMPA1 -0,572397104
-IMPACT -0,572070372
-KIAA0802 -0,572067617
-DSTN -0,571964512
-C5orf44 -0,571958339
-CCK -0,571148184
-OGDHL -0,571078621
-TCP11L1 -0,570951095
-RNF14 -0,569913578
-IARS -0,569079443
-CDH8 -0,569072707
-RNF41 -0,568830451
-SCN3A -0,568276898
-PSMD12 -0,567936617
-TNFRSF21 -0,567631199
-FIG4 -0,566751868
-DDX24 -0,566446037
-MARK1 -0,566206858
-ATP8A2 -0,565754513
-ACLY -0,565055263
-DDX42 -0,564984354
-KIF3C -0,564949485
-PIN1 -0,564290859
-PSEN2 -0,564206755
-TERF2IP -0,564084181
-VDAC3 -0,563895581
-B3GNT1 -0,563686309
-CHN1 -0,563660153
-GLO1 -0,561564055
-RAB11A -0,561549092
-PRPS1 -0,561391557
-MAP2 -0,561080301
-NHP2 -0,56096586
-DNAJA2 -0,560780556
-NDRG4 -0,560771764
-HNRNPA0 -0,560406816
-NDUFV2 -0,559975953
-ADH5 -0,559909821
-FAM3C -0,559672666
-COPS7A -0,559265307
-SULT4A1 -0,558733244
-MATN3 -0,558346148
-TMEM14A -0,557817575
-HRASLS -0,557799459
-TMEM14B -0,557593404
-TTC1 -0,557573183
-R3HDM1 -0,557428266
-AUH -0,55725646
-C5orf22 -0,55714645
-TUBB -0,557095971
-C5orf13 -0,55663948
-COX7A2L -0,556219721
-POMP -0,556110434
-ATP5J2 -0,555267292
-ZNF204P -0,555121445
-INA -0,554984251
-NUP93 -0,55488654
-STAU2 -0,55454534
-VAT1 -0,554180752
-DDB1 -0,554146967
-THY1 -0,554057809
-SRPRB -0,553818923
-IMP4 -0,553554219
-SRP19 -0,552319097
-FUCA1 -0,551919323
-PRKCZ -0,551777138
-CD2BP2 -0,55167071
-C12orf43 -0,551436389
-SUSD4 -0,55137396
-W88821 -0,551080268
-LSM4 -0,550328209
-SNAP25 -0,550276399
-ACSL6 -0,549806401
-MYH10 -0,549550685
-DDHD2 -0,548942799
-PRKACA -0,548422775
-CHRNB3 -0,547701041
-NEFM -0,547618123
-PLD3 -0,547495065
-GSPT2 -0,547329995
-ATP6V1E1 -0,546911033
-GABBR2 -0,546899558
-IPW -0,546596796
-SCAMP5 -0,546380917
-RFPL1S -0,545994554
-BSN -0,545979557
-MAGI1 -0,54490486
-DRG1 -0,544733954
-PITPNB -0,544704547
-LETMD1 -0,544636809
-AI263044 -0,544470885
-STOML1 -0,544383238
-GBAS -0,544103215
-RAB3GAP1 -0,543092086
-ACTG1 -0,54300405
-PPME1 -0,542943175
-AFG3L2 -0,542490245
-DNAJC6 -0,541912283
-TUBA1B -0,541625287
-ABCE1 -0,541581351
-ARF3 -0,541401116
-SRSF3 -0,54134715
-NEFH -0,540578844
-ADK -0,540377244
-TIMM17A -0,540158649
-ELOVL6 -0,540054201
-FAM189A1 -0,539987546
-ATP6V1A -0,539816156
-OAT -0,53960074
-KIAA0284 -0,539436564
-SLC25A12 -0,538986194
-AP3D1 -0,538816413
-ISCU -0,53848727
-CDH10 -0,538458105
-APEH -0,538385859
-TMEM35 -0,537944022
-NDFIP1 -0,537769873
-U79277 -0,537586945
-SYNGR1 -0,53757151
-MEAF6 -0,537175986
-DNM1 -0,536361784
-DEF8 -0,536162488
-PDXK -0,536128962
-RIT2 -0,536060129
-AACS -0,535868362
-RAB3A -0,535840143
-LXN -0,535676847
-CCBL2 -0,53559953
-ATXN7L3B -0,535570224
-RCN2 -0,535264733
-SDC2 -0,535187449
-NRXN3 -0,534911729
-SDC1 -0,534748047
-PSMD1 -0,534162775
-UBA5 -0,534098166
-PEX11B -0,533915774
-RAP1GDS1 -0,533764019
-NUPL1 -0,533680375
-ARMCX1 -0,533607326
-SDHAP1 -0,533209621
-PJA2 -0,532853246
-ACOT7 -0,532662038
-SEZ6L -0,532618647
-CELF2 -0,532603645
-CXorf40A -0,532513065
-NDUFB5 -0,532279155
-GARS -0,532224902
-NRG1 -0,532009485
-SEC31B -0,53180843
-ME1 -0,531466374
-PSMD8 -0,531445018
-MSL1 -0,531268404
-PCLO -0,531166247
-RAB14 -0,531006634
-MAGED2 -0,530858407
-EIF3K -0,530846086
-MMD -0,530845303
-MYO5A -0,530805656
-NCRNA00094 -0,530597959
-KIAA1107 -0,53057188
-KIAA0564 -0,530294183
-PSMB2 -0,530140819
-C1orf114 -0,530111522
-GCLM -0,529867963
-NDN -0,529086871
-SRD5A1 -0,528786683
-DNAJB9 -0,528374918
-SLC7A8 -0,528181836
-CLIP3 -0,527794519
-NDUFB1 -0,527724864
-CLSTN2 -0,52726691
-C14orf156 -0,527148764
-CIAPIN1 -0,527136633
-ATP5F1 -0,527047789
-PSMB5 -0,526841307
-FAM32A -0,526499611
-KIAA1644 -0,526147045
-RTN1 -0,526062751
-EXOSC9 -0,525622526
-PFKM -0,525053758
-TCF25 -0,524910517
-ATP5O -0,524889972
-PTPRN2 -0,524794642
-SNX4 -0,524373257
-ATP6V1G2 -0,524016622
-SLC35E3 -0,523930118
-SLC2A6 -0,52364368
-SUCLA2 -0,523588063
-PLCB1 -0,523263994
-TMEM30A -0,521872901
-PDE4D -0,521870014
-RAB5A -0,521632556
-MAPK9 -0,521572661
-CAP2 -0,521120749
-RPS6KA3 -0,520660932
-GNAO1 -0,520506337
-PSMD6 -0,520132666
-TBCE -0,519679173
-C9orf125 -0,519623009
-MN1 -0,51937171
-MFSD1 -0,51842841
-KIF3A -0,518357676
-SHFM1 -0,517546292
-NRIP3 -0,516545986
-ANKMY2 -0,516365077
-CDK5 -0,516196782
-REEP5 -0,516165841
-SLC1A1 -0,516141732
-UBE2K -0,516036367
-SMEK2 -0,515537555
-PI4K2A -0,515462049
-TTC39A -0,514924765
-GUCY1B3 -0,514788287
-QPCT -0,514170797
-ST6GALNAC5 -0,514077764
-ATP6V1F -0,513941613
-HSD17B12 -0,513489073
-PPFIA2 -0,51321383
-PLCH1 -0,512855521
-CNTN6 -0,512564243
-ENTPD6 -0,512350634
-ALAS1 -0,512141897
-RUNDC3A -0,511994377
-PCMT1 -0,511547085
-IDS -0,511290223
-PLEKHB2 -0,510964275
-CDO1 -0,510668427
-NDUFB6 -0,510219117
-COX6C -0,509869079
-OPTN -0,509603205
-PSMA1 -0,509510596
-STS -0,509361214
-TIMM10 -0,509318807
-C1D -0,509252454
-GAP43 -0,509215292
-CCDC6 -0,509150548
-TRIM37 -0,509012308
-ATP2B2 -0,508803511
-PGAM1 -0,50863259
-GGNBP2 -0,508616013
-SRP72 -0,508482078
-TCEAL2 -0,508464868
-SV2A -0,508330914
-CDK5R2 -0,508227652
-FHOD3 -0,508155146
-FECH -0,508046235
-ATP2A3 -0,507932978
-SUB1 -0,507787459
-ACO2 -0,507726776
-C20orf3 -0,507526055
-SEC22B -0,507453281
-VPS35 -0,507278509
-MRPS33 -0,507141908
-TXNL4A -0,50704416
-ARHGEF9 -0,506224253
-RBM9 -0,506096633
-TMEM135 -0,506088817
-UHRF1BP1L -0,505757524
-ME2 -0,505446593
-BZRAP1 -0,505378895
-MCAT -0,50534007
-AKAP6 -0,505213579
-COPS3 -0,505110121
-MRPS35 -0,505107922
-YWHAB -0,505015581
-PEX7 -0,504955276
-COPS8 -0,504746043
-OXCT1 -0,504643125
-MAD2L1 -0,504589351
-MCTS1 -0,504510155
-LGALS8 -0,50448664
-ACP1 -0,504339709
-MX1 -0,50393674
-NCALD -0,50389725
-TASP1 -0,503797818
-AGTPBP1 -0,503605082
-RNF128 -0,503554068
-PSMD13 -0,503503704
-TXN -0,50336484
-NHLH2 -0,50325399
-USP12 -0,503149229
-PFDN4 -0,502988386
-NAP1L3 -0,502893901
-MRPL20 -0,502624211
-ACSL3 -0,502355771
-MTPAP -0,502307088
-PMPCB -0,502239978
-SH3GL3 -0,502227406
-API5 -0,502196949
-CAPNS1 -0,5020898
-YWHAZ -0,501747483
-TOMM70A -0,501591565
-STX18 -0,501503813
-HNRNPK -0,501464694
-LRP1B -0,501433491
-CDC123 -0,500993468
-DCTN6 -0,500740808
-VAPB -0,500599356
-CCDC56 -0,499906136
-GOT2 -0,499477446
-RHEB -0,499343134
-PSMD2 -0,499333749
-YPEL5 -0,49910251
-ATP5G1 -0,499077107
-TUBA1A -0,498949544
-GSTM3 -0,498766376
-EPB41L1 -0,498605796
-EPS15 -0,498447403
-ENO2 -0,498261848
-ASMTL -0,498100631
-FH -0,498098378
-CLTC -0,497596743
-PSMA3 -0,497405846
-UROS -0,497291028
-OLFM1 -0,496832922
-ATP6V1G1 -0,496818916
-B3GALNT1 -0,496135395
-PHLPP2 -0,496077027
-TSPYL1 -0,495383913
-SERINC1 -0,49538338
-RPL15 -0,495355843
-ITFG1 -0,495195881
-PDHB -0,494999933
-RABL3 -0,494855325
-TMEM22 -0,49462563
-MCFD2 -0,494506103
-GABARAPL1 -0,494373853
-MAGEL2 -0,493987847
-VPS33B -0,493750355
-CDIPT -0,493440531
-ATP6V0B -0,493438352
-CLGN -0,493358721
-SEC23A -0,493255831
-C7orf43 -0,49286586
-ARL3 -0,492481932
-SLC12A5 -0,492392187
-LAPTM4B -0,492348426
-LOC285359 -0,492290998
-LARP1 -0,49192011
-YME1L1 -0,491725992
-RAB2A -0,491586306
-SPATA20 -0,490991626
-ASH2L -0,490785052
-PTBP2 -0,490747846
-WTAP -0,490599757
-NANS -0,490410248
-SCFD1 -0,490269997
-EPB49 -0,489916122
-TUFT1 -0,489843226
-POP4 -0,489594415
-CACNA1G -0,489236615
-PRPF19 -0,48917604
-NCOA4 -0,488872014
-C1orf216 -0,488856307
-TXNL1 -0,488777426
-AMPD2 -0,48875487
-ASL -0,488300478
-PFDN1 -0,48807629
-EXTL2 -0,488020888
-RPA3 -0,48773487
-ACVR1B -0,487609726
-ANKRD46 -0,487476076
-GRIA1 -0,48726366
-PSMB6 -0,487099126
-CAPRIN2 -0,486969775
-SRGAP3 -0,48684289
-ARPC5L -0,486786621
-PSME3 -0,486309204
-NME2 -0,486066455
-ISCA1 -0,485683262
-ZNF365 -0,485504618
-PINK1 -0,485341061
-RWDD2A -0,48504437
-EXOC1 -0,484927354
-ECE2 -0,484617735
-WDR77 -0,484600271
-AI890972 -0,484490353
-ERBB4 -0,484253264
-PSMD4 -0,483962197
-RAB6C -0,483864006
-CSTF3 -0,483798153
-NIPA2 -0,483638091
-AK5 -0,483482302
-C17orf91 -0,483141592
-INPP4B -0,482534933
-PJA1 -0,482372063
-BE551361 -0,482367089
-B4GALT5 -0,48224903
-MTX2 -0,481915827
-MGST3 -0,481667788
-TRMT11 -0,481613419
-PTPRN -0,481522612
-DNAJC12 -0,48150495
-FTSJ2 -0,481162212
-CCT8 -0,48112028
-PGAP1 -0,481030935
-SLC25A44 -0,480898127
-AMIGO2 -0,480319409
-SCAMP1 -0,480275681
-RBKS -0,480222
-SYN1 -0,48014199
-APEX1 -0,479680328
-AL157484 -0,4790893
-PAK3 -0,479026618
-SLC25A13 -0,478484409
-EIF1B -0,478403329
-DLAT -0,478235597
-AI375694 -0,47804406
-PMS2L1 -0,477748782
-DYNC2LI1 -0,477528415
-RANBP9 -0,477445784
-PTPN20A -0,476653786
-ZMYM4 -0,476508652
-UQCRQ -0,476353248
-EXOSC7 -0,476299374
-NDUFB3 -0,476207507
-LCMT1 -0,476121484
-ZNF547 -0,47597802
-TBCA -0,475802982
-MAPK8IP3 -0,475554385
-N80935 -0,475378775
-SLC4A3 -0,475327531
-AASDHPPT -0,475086681
-CAND2 -0,475049952
-CXorf40B -0,474988185
-FXYD6 -0,47456179
-RNF10 -0,474499733
-ELOVL4 -0,474412575
-AAK1 -0,474378982
-SEH1L -0,474159291
-PTPRU -0,473978747
-LPGAT1 -0,473432618
-VPS24 -0,473360696
-MCF2 -0,473341916
-FAR2 -0,473007144
-CKMT1A -0,472884518
-TMED3 -0,472883274
-RNASEH1 -0,47283341
-NDUFA3 -0,472657747
-GLS -0,472644869
-FAM168A -0,472617309
-KLHDC10 -0,472577269
-GLRX5 -0,472478522
-SYT17 -0,472292582
-PAM -0,472018566
-CLTB -0,471770785
-COPS2 -0,470912718
-DDA1 -0,470419616
-PCSK2 -0,470372976
-SLC25A6 -0,470332168
-TPI1 -0,470300584
-MECR -0,47026417
-ORC4L -0,47025895
-ITPR1 -0,470228063
-HMG20A -0,470060529
-GNB5 -0,470039178
-TMEM208 -0,469963608
-NCAPG -0,469752447
-GLRB -0,469638821
-ATP6V1D -0,469577982
-AKAP11 -0,469501191
-SH3GL2 -0,46948768
-NISCH -0,469445416
-SIPA1L1 -0,469275377
-PFKP -0,469125064
-LYRM4 -0,469088537
-SLC4A1AP -0,46898494
-AP2A2 -0,468669242
-CX3CL1 -0,46850557
-WBP11 -0,468444743
-LASP1 -0,468444317
-GOT1 -0,468375399
-C6orf120 -0,468133996
-SPAG7 -0,468070563
-SERGEF -0,467688975
-TFB2M -0,4675501
-AP3B2 -0,467537408
-PAFAH1B1 -0,467362101
-BPGM -0,467130793
-CRAT -0,466839519
-DDX1 -0,466770911
-ADAM23 -0,46652833
-ASB6 -0,466473575
-PCDHA1 -0,466456945
-TUSC3 -0,465574044
-TCEA2 -0,465512943
-SMARCA4 -0,4653413
-DAPK1 -0,465142929
-DBNDD1 -0,464965333
-NDUFC2 -0,464959656
-IDH3B -0,464778307
-CDC37L1 -0,464692992
-WDR11 -0,464429092
-CD200 -0,464378251
-TUSC2 -0,464289641
-IRGQ -0,464009317
-CALY -0,463919598
-NNT -0,463872117
-MSH2 -0,463745236
-GYG1 -0,463657489
-FAM134C -0,463380379
-RTN2 -0,463379977
-RBM12 -0,463289569
-SYNJ1 -0,463207762
-ABCA5 -0,462881594
-ENTPD4 -0,462777994
-MAP2K4 -0,462732144
-AIMP2 -0,46256199
-PITPNA -0,462484131
-BNIP3 -0,461982272
-COPS5 -0,461956463
-BRE -0,461910476
-MIR21 -0,461667267
-ATP5S -0,46152488
-SIN3B -0,461515059
-NAT10 -0,461457105
-MTCH2 -0,461117099
-ACHE -0,461032229
-PSD3 -0,46079613
-UCHL3 -0,460466303
-SMPX -0,459975528
-USP11 -0,459753441
-RNF187 -0,459566796
-AAGAB -0,458932639
-ENY2 -0,458770966
-NDEL1 -0,458614173
-FAM184A -0,458384449
-TOX4 -0,458204483
-SLC25A15 -0,458110832
-SACM1L -0,458050139
-ADARB1 -0,458034616
-SPHK2 -0,457781426
-CES2 -0,457687554
-CYFIP2 -0,457201169
-KPNA2 -0,457034156
-ACTR1A -0,456856222
-SLC25A22 -0,456321526
-DPYSL3 -0,456025294
-PRKAR1A -0,455984698
-SIDT1 -0,455560984
-TIPRL -0,455474112
-EIF5 -0,455347544
-C16orf58 -0,455176502
-RAB7A -0,454946879
-MFSD6 -0,454914435
-NDUFS2 -0,454605666
-APOOL -0,454580027
-GNB1 -0,454284789
-SARS -0,454282127
-PIK3R3 -0,454240907
-SERINC3 -0,454097365
-ST3GAL5 -0,45407104
-DHRS11 -0,453695947
-NEDD8 -0,45367218
-RAB15 -0,453664346
-HSPA13 -0,453577406
-OLA1 -0,453153228
-C3orf18 -0,45312023
-AF131844 -0,453027105
-C12orf52 -0,452914604
-ACBD3 -0,452894377
-PCIF1 -0,452240197
-BMP2K -0,451224584
-TSPYL5 -0,450674174
-SEC63 -0,450642641
-C7orf44 -0,450408444
-PWP1 -0,450360796
-SLC25A14 -0,45012674
-SYP -0,449768016
-PRKCB -0,449564151
-KIF2A -0,449276369
-PEX26 -0,449100108
-SDHA -0,448617251
-PITRM1 -0,448602767
-PPA2 -0,448269554
-MAN2A2 -0,448177121
-FAM49A -0,448170721
-KCTD9 -0,448062861
-REEP2 -0,44801948
-NDUFS3 -0,447803075
-CHGA -0,447356315
-UBE2E3 -0,447311178
-LOC595101 -0,447006376
-RNF170 -0,446698112
-TMCO1 -0,446651514
-PCCB -0,446640741
-RAB1A -0,44645249
-ATP1A1 -0,446309137
-KIAA1045 -0,446174802
-CASD1 -0,445992918
-C3orf37 -0,445975885
-RAD17 -0,445659766
-BBS4 -0,445631347
-TBC1D19 -0,445509157
-TSG101 -0,445289202
-DKK3 -0,445181251
-KCNQ2 -0,444911548
-EIF4E -0,44477948
-LOC100134209 -0,444742688
-OSTF1 -0,444651424
-PPCS -0,444330494
-ATP13A2 -0,443924538
-DHRS7B -0,443866868
-TSN -0,443785273
-AI201594 -0,443780197
-UBE2J1 -0,443536878
-C12orf51 -0,443320039
-INPP5F -0,44324612
-KIAA0391 -0,443138749
-NDUFB8 -0,442168118
-COX8A -0,442151263
-PLCB4 -0,442128902
-UQCRC1 -0,442055114
-RNMT -0,442010619
-PSMB4 -0,441631296
-ATP9A -0,441570839
-COMMD8 -0,441419712
-STX7 -0,441415012
-UQCRFS1 -0,441387219
-ARMC8 -0,441335025
-USP33 -0,441131902
-SC4MOL -0,441051846
-AVL9 -0,440604375
-CORO1C -0,440555184
-ATP6V0A1 -0,440500219
-AKTIP -0,440321706
-C11orf49 -0,440065839
-ACCN1 -0,439959618
-DYNC1H1 -0,439954428
-RTN4 -0,439926435
-IFT52 -0,439664934
-ARIH1 -0,439616652
-SLC23A2 -0,439279622
-FDPS -0,439263979
-ZW10 -0,439088192
-C6orf211 -0,438493952
-CAPZA2 -0,438442617
-TRIM9 -0,43841496
-PANK2 -0,438226487
-SLC25A36 -0,437878589
-TM7SF2 -0,437751686
-GPD1L -0,437274057
-TM2D3 -0,437156245
-TBC1D22A -0,436837159
-AFF2 -0,436678505
-PSMA4 -0,43652406
-SCAPER -0,436328183
-KPNB1 -0,43624217
-C8orf33 -0,436164892
-RRAS2 -0,435924543
-PNMA1 -0,435862986
-DRD2 -0,435854058
-CCDC92 -0,435740221
-CYB5B -0,435703661
-DNM1L -0,435497666
-FAM98A -0,435109538
-CYCS -0,43500707
-UBE2B -0,434857087
-DCTPP1 -0,434751269
-ENC1 -0,434576571
-SAP18 -0,434463135
-MED7 -0,43446171
-UBXN6 -0,433506891
-MAEA -0,433493136
-C20orf27 -0,433220759
-ARFGEF2 -0,4331108
-FKBP9 -0,433030189
-COQ10B -0,432955202
-SNRNP25 -0,432902395
-PHKB -0,432809153
-CETN2 -0,432732838
-PIK3R4 -0,432641256
-EFR3A -0,432263211
-FAM162A -0,432255742
-LOC732160 -0,432226821
-SRPK2 -0,432044566
-USP9X -0,431489845
-DENND2A -0,431031563
-PPP2CA -0,430950806
-CHST1 -0,430892555
-OSBPL9 -0,430720865
-TPM3 -0,430527364
-UGP2 -0,430314768
-AL049387 -0,430134526
-ARHGDIG -0,429952838
-GPR161 -0,429932801
-HGSNAT -0,429440496
-TCEAL4 -0,429402449
-KHDC1 -0,429285977
-SPATA7 -0,428924113
-NIPSNAP3B -0,428922472
-NHP2L1 -0,42870798
-BZW2 -0,428685674
-BZW1 -0,428658261
-ABCF3 -0,428526247
-PEX19 -0,428349422
-POLR2K -0,42820853
-FAM134B -0,428156057
-TUBGCP4 -0,428150919
-CSNK2A1 -0,427824997
-PPP2R5D -0,427719013
-CEND1 -0,427667723
-RNF11 -0,427514623
-EBNA1BP2 -0,427275229
-SDHC -0,42690156
-ATP6AP2 -0,426823582
-MAPK1 -0,426681157
-YTHDC2 -0,425950246
-ACTR3B -0,425721173
-LRRC47 -0,424928312
-ANO10 -0,424906321
-MORF4L2 -0,424702281
-NAE1 -0,424669605
-GRSF1 -0,424576498
-UBE3C -0,42455123
-RRM1 -0,424268285
-IARS2 -0,424201991
-HINT1 -0,423973896
-B4GALT7 -0,423964657
-OBSL1 -0,423852756
-RPH3A -0,423713255
-PTPRM -0,423526608
-TRAP1 -0,423405292
-GSTO1 -0,423136683
-PGK1 -0,423107749
-KCTD2 -0,423033005
-AKAP9 -0,423014145
-KIAA0090 -0,422971022
-NIF3L1 -0,422805913
-SAE1 -0,422487927
-TRAPPC4 -0,422454822
-UBE3B -0,422322842
-MRPL13 -0,422291395
-ARF1 -0,422218883
-NCKAP1 -0,421739152
-COX11 -0,421717769
-XPA -0,421552598
-FKBP11 -0,421544606
-ZFAND1 -0,42136139
-RUSC1 -0,421250909
-PSMC2 -0,42099626
-MCM4 -0,420976269
-HEXA -0,420954607
-PDE4A -0,420795908
-VPS45 -0,420785909
-OGFOD1 -0,420640442
-ADPGK -0,420505817
-AP2M1 -0,420467875
-PSMD5 -0,420139323
-PGRMC1 -0,420109613
-CLASP2 -0,419942702
-CAMTA1 -0,419843296
-COX5A -0,419753275
-BCAP29 -0,419678508
-C21orf59 -0,419586484
-INSIG1 -0,419347593
-NDUFAF1 -0,419256514
-SNCG -0,419205938
-NCAN -0,418993508
-SLC24A3 -0,418714364
-MAP2K1 -0,418679322
-BRCC3 -0,418660516
-MYCBP2 -0,418420128
-PREPL -0,41818051
-TUFM -0,418149804
-LYRM2 -0,41810337
-ORC3L -0,417994092
-TSR2 -0,417894679
-SLC41A3 -0,41774061
-DZIP3 -0,417712026
-MRPS11 -0,417644175
-B4GALT6 -0,41761846
-CHD5 -0,417472
-TUBA1C -0,417351982
-OTUB1 -0,41729395
-DCAF6 -0,417154254
-UQCR10 -0,417021115
-BEX4 -0,416948363
-RTN3 -0,416868526
-GOLT1B -0,416408995
-MRPL3 -0,416396676
-DDX19A -0,416375948
-C4orf41 -0,416356919
-SEMA3G -0,416349944
-TUBA3D -0,416216957
-B4GALNT1 -0,415958605
-TOR1A -0,415819164
-SUPT16H -0,415597727
-ACTR3 -0,415469056
-ABCB9 -0,415410201
-SERF1B -0,415262572
-PSMC6 -0,415072747
-GALNT2 -0,414525722
-ARF5 -0,414370994
-TCEB1 -0,414262524
-FEN1 -0,414164817
-HS2ST1 -0,413801139
-FBXL15 -0,413238338
-ANAPC10 -0,413161353
-MAPK10 -0,413048251
-FGF12 -0,412576909
-GTF2B -0,412561968
-CALM3 -0,412474461
-C12orf5 -0,412385409
-BTRC -0,412323302
-UBXN8 -0,411884422
-G6PC3 -0,411853401
-MARK4 -0,411850043
-SDHB -0,411814414
-FXC1 -0,411804756
-KIAA1467 -0,411406746
-COL4A3BP -0,411372338
-MADD -0,411317373
-SLC25A11 -0,411257994
-APBB3 -0,411242683
-LDHB -0,411172229
-ENTPD3 -0,410988615
-CAMK2B -0,410817586
-C15orf24 -0,410807275
-RAB11FIP5 -0,410722406
-C18orf1 -0,410410534
-IL13RA2 -0,410393436
-TMEFF1 -0,40994415
-TAX1BP1 -0,409905258
-ABHD11 -0,409662969
-SETD4 -0,409479623
-NARS -0,409352949
-LOC441259 -0,409193342
-SMAD2 -0,408937637
-MAGEH1 -0,408820062
-LPIN2 -0,408744346
-WRB -0,408371938
-HSPB11 -0,408269901
-COMMD9 -0,407620354
-RMND1 -0,407542555
-RBP1 -0,407484296
-TSPAN7 -0,407465467
-YKT6 -0,407243851
-ATP5L -0,407238078
-STAT1 -0,407123963
-SPTAN1 -0,407085674
-SLBP -0,407034029
-FAM115A -0,407018502
-ATP1B1 -0,407007242
-GIN1 -0,406994648
-SLC25A4 -0,406703055
-RPAP3 -0,40653888
-ELAVL4 -0,406510215
-LDHA -0,406394191
-GABRG2 -0,406143723
-ACOT1 -0,406088493
-LZTFL1 -0,406077259
-LARP4 -0,406073312
-PTPRG -0,405852123
-DIRAS2 -0,405793372
-SNCB -0,405789504
-CDS1 -0,405765281
-ARL2BP -0,405758176
-BCL2L13 -0,405729545
-STAT4 -0,405634359
-C17orf75 -0,405632179
-ELAVL2 -0,405590653
-DNM3 -0,405342092
-SNX16 -0,404866663
-TACO1 -0,40485549
-HPGD -0,404805074
-CHMP2B -0,404775945
-DPP8 -0,404495701
-SYBU -0,403649563
-CHP -0,403478973
-GTF2H5 -0,403475179
-PPP2R5B -0,403191055
-TRAK1 -0,402996995
-ACSL4 -0,402921692
-RABGAP1L -0,402883713
-PSMB3 -0,402864552
-ASTN1 -0,402784524
-TIMM23B -0,402679864
-NDUFC1 -0,402669713
-GPM6A -0,402645229
-NCDN -0,402391637
-TMEM183A -0,402206694
-LACTB2 -0,402125728
-SFPQ -0,401934429
-SLC1A4 -0,401903736
-LOC731884 -0,401617561
-TTC3 -0,401599425
-APBA1 -0,401587582
-FAM20B -0,401527926
-ISOC1 -0,401479145
-TMEM70 -0,401425176
-GLUD1 -0,401204073
-NDUFA4 -0,401152135
-SHANK2 -0,401076931
-NDUFA6 -0,400922451
-FAM128A -0,400907344
-TSNAX -0,400758374
-BLCAP -0,400561763
-WASF3 -0,400514139
-MTMR6 -0,400412018
-CBARA1 -0,399961135
-SMCR7L -0,399645568
-REXO2 -0,399637796
-ASTN2 -0,399013865
-FBXO31 -0,398919379
-MRPS10 -0,398754479
-GNAL -0,398117434
-RDH11 -0,398104472
-ANKH -0,398086916
-EPHA5 -0,397910595
-DPY19L2P2 -0,397861593
-NRXN1 -0,39777997
-FOXA1 -0,397622781
-AGGF1 -0,397583973
-CLCN6 -0,397581706
-PRKAG1 -0,397496639
-GRM5 -0,397456403
-BCAT1 -0,397331444
-MAP1LC3B -0,397317027
-HMGCL -0,397130437
-IFIT5 -0,397045055
-FAM82B -0,397007464
-TMEM189-UBE2V1 -0,39671729
-TMEM160 -0,396535704
-PIGZ -0,396390486
-VDAC2 -0,3962914
-BCAP31 -0,396227306
-CUL2 -0,395939867
-C5orf30 -0,395902062
-VAMP4 -0,395520757
-CLTA -0,395495699
-NOS1AP -0,395452681
-YWHAH -0,395414553
-AGL -0,39537715
-PPIA -0,395286888
-POLR2E -0,395239973
-FAM190B -0,395231307
-CAND1 -0,395218949
-DIABLO -0,395167608
-FAM155A -0,395099838
-FAM174B -0,394929763
-ABCA11P -0,394841999
-LMF1 -0,394801997
-EIF3I -0,394774336
-RRAGA -0,39363313
-SLC25A5 -0,39336993
-BTBD3 -0,393323586
-SLC38A6 -0,393193457
-TSPYL4 -0,39289974
-NDUFA8 -0,392898828
-ERI3 -0,392853573
-CDH11 -0,392815946
-VPS11 -0,392712183
-RPP40 -0,39270293
-SMS -0,392616216
-USP4 -0,39251437
-RAN -0,392486577
-SYT11 -0,392234251
-SEC23IP -0,392233152
-SUPV3L1 -0,392124663
-TOX3 -0,392048323
-OSBPL3 -0,391742979
-ATP5J -0,391738382
-APC -0,391687772
-EIF2AK2 -0,391678642
-MPPE1 -0,391534871
-CHD3 -0,391021702
-BE858194 -0,390954653
-GPN2 -0,390821549
-TMEM97 -0,39059622
-BRF2 -0,390477924
-NSDHL -0,390017568
-LOC654342 -0,389476483
-SATB1 -0,389035394
-RPP14 -0,388984247
-C16orf68 -0,388858051
-PHF14 -0,388842446
-CKAP5 -0,388699527
-MMADHC -0,388406258
-MEST -0,388313548
-UQCRH -0,387974488
-GBAP1 -0,387823169
-PMPCA -0,387778282
-TMEM41B -0,387668262
-SCLY -0,387620138
-OXA1L -0,387520115
-CLPX -0,387517816
-EML1 -0,387443167
-DPP6 -0,387318033
-FBXO3 -0,387294212
-GAPDH -0,386769027
-ATP6V1C1 -0,386766958
-PRAF2 -0,386484628
-NAA35 -0,386425969
-EIF4H -0,386302469
-SGSH -0,386196526
-CLCN3 -0,386084887
-SMARCA1 -0,385880429
-FAM158A -0,385760557
-AP3S2 -0,385712457
-EIF1AX -0,385367803
-RNF115 -0,385287305
-GPI -0,385266179
-SEC62 -0,385020013
-G3BP2 -0,384968143
-NDUFV1 -0,38487232
-C19orf42 -0,384758261
-BEND5 -0,384699839
-KCNAB2 -0,384620267
-EVL -0,384619104
-MTMR9 -0,384460721
-SIRT3 -0,384239932
-CNIH -0,383916854
-TOLLIP -0,383913386
-C11orf2 -0,383735535
-NUDCD3 -0,383703548
-MED4 -0,383545823
-RABGEF1 -0,38353381
-PTN -0,383407974
-GBF1 -0,383365739
-C1orf163 -0,383317238
-LOC100129361 -0,383315417
-CUL4B -0,383032231
-OXR1 -0,382758654
-TRIM33 -0,382726006
-GPC5 -0,382713696
-C11orf51 -0,382673891
-MAN1C1 -0,382595078
-FGF9 -0,382294616
-SPOCK2 -0,382267861
-GLMN -0,382038722
-MPP1 -0,381567886
-KIF21B -0,381555674
-RND1 -0,381481938
-PEX1 -0,381462705
-C2orf34 -0,381417191
-OTUD3 -0,381344145
-MSRB2 -0,381206334
-CCDC85B -0,38118283
-RGS3 -0,380621769
-SERPINI1 -0,380596066
-C14orf2 -0,380470075
-IDH3G -0,380458518
-POLR2C -0,380378788
-CTNNA2 -0,380377628
-XRCC6 -0,380295972
-EIF3A -0,380281294
-CRBN -0,380214781
-RPS6KC1 -0,3801397
-NUDT2 -0,380057201
-GOLPH3L -0,379823471
-CSNK1A1 -0,379812095
-NDUFB2 -0,379757693
-FTO -0,37940886
-SLC6A15 -0,379271656
-PCP4 -0,379256762
-NIT1 -0,37912136
-CCNC -0,378699092
-DGKB -0,378485235
-RANBP6 -0,377965444
-DNAJC8 -0,377764456
-MAPRE2 -0,377675379
-ARFGAP2 -0,377574006
-BDNF -0,377511436
-HSD17B10 -0,376728332
-AKAP7 -0,376531212
-EHD1 -0,376479944
-PSMD10 -0,376243528
-FABP5L2 -0,376090187
-VAMP7 -0,376017526
-WBP4 -0,375749974
-MAP1B -0,375485017
-SMPDL3A -0,375390185
-GPR89C -0,375362209
-SEPT2 -0,37512019
-GPX3 -0,374915078
-AARSD1 -0,374664572
-HSPA9 -0,37466397
-MAP1A -0,374598439
-C16orf62 -0,374459363
-CARKD -0,374388504
-ASS1 -0,374197776
-WDR12 -0,374046313
-ABHD14A -0,37397421
-SPIN2B -0,373568971
-RAB6A -0,373528481
-PTPRF -0,373483075
-RRAGB -0,373427062
-STK39 -0,373365187
-COX7B -0,373307822
-PDCL -0,373110957
-ATP2A2 -0,373066228
-PPM1E -0,37285382
-TRMT61B -0,372798595
-C21orf33 -0,372766056
-MGMT -0,372730061
-LPHN3 -0,372647138
-WBP2 -0,372385809
-ACSBG1 -0,372296169
-PGRMC2 -0,372287654
-LRRC20 -0,372239514
-AGA -0,372171162
-NRCAM -0,372117405
-FUT9 -0,372053568
-C22orf28 -0,371916518
-MRPS15 -0,371914782
-UFM1 -0,371876489
-CAMK2G -0,371790847
-AVPI1 -0,371692415
-MAST2 -0,371637676
-PPP1R7 -0,371553142
-EEF1A2 -0,371514176
-ATP5D -0,371416456
-EEF1E1 -0,37139203
-NLRP1 -0,371368381
-PMS2CL -0,371209965
-CDK5R1 -0,371120209
-C2orf72 -0,371108998
-OAZ2 -0,3710748
-AL109698 -0,37073584
-INPP4A -0,370700597
-ERH -0,370513944
-CAMK1G -0,370474818
-MED24 -0,370430566
-DMXL1 -0,370287216
-COMMD4 -0,370258812
-NOMO3 -0,370043447
-MORF4 -0,369691968
-ZNHIT3 -0,369651044
-GDPD5 -0,369635923
-CUL5 -0,369519961
-AP1B1 -0,369511443
-YARS -0,369387873
-ABHD10 -0,36913324
-KCNB1 -0,369083149
-SKP1 -0,369015624
-FBXO28 -0,368924883
-ATR -0,368436696
-TMED2 -0,368132686
-ARPC1A -0,367983188
-PHYH -0,367958422
-MRPL22 -0,367879083
-SRRD -0,367868238
-WDYHV1 -0,367821841
-EIF3CL -0,367732775
-HMGB3 -0,367450086
-DENND1B -0,36732795
-ALDH5A1 -0,367318431
-CCNA1 -0,367103911
-FAM134A -0,367014983
-DZIP1 -0,366778091
-WASF1 -0,366602553
-ATXN3 -0,366426778
-CCDC25 -0,3658102
-ERP29 -0,365799413
-IVD -0,365499555
-SNX24 -0,365222253
-CDK20 -0,365176415
-TTC9 -0,365148586
-RBM8A -0,36488846
-AMACR -0,364562114
-TBPL1 -0,364450426
-PTPMT1 -0,364434415
-CANX -0,364232908
-ELAC2 -0,364131757
-EIF2S1 -0,364109368
-AKR1B1 -0,363915593
-ACADM -0,363858719
-RGS16 -0,363795844
-SLC20A1 -0,363602798
-MTUS2 -0,363384151
-ZMIZ2 -0,363364816
-NDUFS4 -0,363146027
-AW242701 -0,363104323
-SNAPC3 -0,363053639
-ENOPH1 -0,362868334
-LYRM1 -0,362706602
-TRMT12 -0,362561085
-BAALC -0,362539013
-CHMP1B -0,362404908
-ATP1A3 -0,362300724
-TOMM20 -0,362192747
-PEX14 -0,362047536
-EIF2AK1 -0,361934247
-CNNM2 -0,361790716
-PPOX -0,361753445
-TAC1 -0,361655557
-GLRX3 -0,361266708
-OBFC1 -0,360197329
-MFN2 -0,360036589
-DGCR14 -0,359808857
-FAM175B -0,359691136
-PARP2 -0,359639462
-GPR107 -0,359495249
-TUBGCP5 -0,35920098
-ENSA -0,359186957
-UMPS -0,358973056
-SSBP1 -0,358916914
-PFDN2 -0,358707301
-IFFO1 -0,35859667
-CCT2 -0,358497035
-PSMA5 -0,358414139
-ZC3H15 -0,358397302
-EPHX2 -0,358269729
-CALB1 -0,358259257
-POP7 -0,358253841
-MRPL12 -0,357874032
-DFNA5 -0,357815106
-PIAS1 -0,357740062
-ARL4C -0,35770713
-HRAS -0,357592893
-CEP68 -0,35754909
-SNRPA1 -0,357535253
-SCP2 -0,357518758
-C4orf27 -0,356816465
-TMEM185B -0,35662055
-SPAG16 -0,356585241
-ESYT1 -0,356493695
-PTP4A1 -0,356347412
-PDLIM2 -0,356333479
-MSRA -0,355999453
-UAP1 -0,355870622
-CDK16 -0,355785531
-MBOAT7 -0,355761708
-FARSA -0,355610517
-MRPS7 -0,355424517
-EPHB2 -0,355389176
-LOC729991-MEF2B -0,355378273
-PDHA1 -0,355252318
-ACTL6B -0,355166654
-SAR1A -0,355144478
-KDM1A -0,355067715
-PRDX3 -0,354963773
-ETF1 -0,354759299
-ARMCX2 -0,354758912
-IQSEC1 -0,35395949
-TIMM13 -0,353925241
-AP2B1 -0,353904118
-STYK1 -0,353863363
-CDK7 -0,353806664
-DLG3 -0,353783905
-SEPHS2 -0,353722454
-MTOR -0,353463273
-PPIH -0,353351383
-GRPEL1 -0,353254529
-C9orf91 -0,353075824
-RGS17 -0,353023569
-NTSR1 -0,352789658
-HNRNPH2 -0,352751195
-HCCS -0,3526918
-C2orf3 -0,352661516
-TFDP2 -0,352647453
-GOSR2 -0,352396188
-PSMB1 -0,352279045
-MPI -0,35224609
-DUSP26 -0,351953212
-HERC1 -0,351631367
-SORD -0,351295095
-TUBB2B -0,351140866
-LPCAT4 -0,351128323
-CFL1 -0,351124653
-ARPP19 -0,350935095
-MTMR4 -0,350923479
-COX7A2 -0,350878835
-PGM1 -0,350865278
-RHOQ -0,350802567
-CCDC53 -0,350756677
-UQCRB -0,350742301
-NAPA -0,350657124
-CSDC2 -0,35061274
-BECN1 -0,350596093
-GYG2 -0,350535323
-GPKOW -0,35045328
-FXYD7 -0,350387292
-CYLD -0,349973469
-CSPG5 -0,349825086
-TTC15 -0,349816074
-ILF2 -0,349761198
-STOML2 -0,349586681
-CACNB2 -0,349516102
-VARS -0,349372141
-ZSCAN18 -0,349241937
-PTRH2 -0,349224021
-P2RX5 -0,349175679
-RALB -0,349042784
-NUBPL -0,348899542
-NCBP2 -0,348786336
-DKFZp434H1419 -0,348772873
-UFSP2 -0,348370783
-ARHGEF17 -0,348050229
-FXR2 -0,34801331
-INSIG2 -0,347755165
-XRCC5 -0,347746659
-CLTCL1 -0,34759935
-TMEM177 -0,347585446
-VAMP2 -0,347189398
-EML2 -0,347084746
-SNUPN -0,346850632
-GPX4 -0,346688538
-RASA1 -0,346685342
-USP46 -0,346590476
-LSM5 -0,346546029
-SEC31A -0,34652486
-PALM2-AKAP2 -0,346447335
-CKAP2 -0,346385113
-ELOVL5 -0,346375127
-PMS2L3 -0,346133275
-PAQR3 -0,346117871
-ST8SIA3 -0,34604187
-FDX1 -0,34603415
-C12orf4 -0,345989709
-COQ7 -0,345988262
-UROD -0,345987158
-RPE65 -0,345902642
-DCK -0,345889475
-RARS -0,345819092
-CAPZA1 -0,345775372
-NRN1 -0,345693574
-RNF7 -0,345545425
-ABAT -0,345474072
-CRY2 -0,345467057
-HR -0,345290796
-CACNA2D3 -0,345213407
-TWIST1 -0,345148814
-P4HTM -0,345112277
-GDI1 -0,344731063
-GRIA3 -0,344721718
-D4S234E -0,344715573
-TMEM151B -0,344385728
-MPHOSPH6 -0,344298044
-PYGB -0,344201683
-MARCH6 -0,344086188
-AL050136 -0,343680587
-NDUFS6 -0,343667551
-TRAPPC9 -0,343555476
-PYGL -0,343533875
-EFNB3 -0,343417492
-SCD -0,343398039
-TFG -0,342863204
-PPFIA3 -0,342761025
-SENP6 -0,342750174
-KCMF1 -0,342689973
-GNAS -0,342684217
-MAPK6 -0,342588157
-PRMT5 -0,34246621
-SEPT11 -0,342460355
-MEIS3P1 -0,342265108
-FABP3 -0,3421554
-YIPF6 -0,3420929
-FABP6 -0,342074193
-SRSF9 -0,341825092
-AP1AR -0,341737984
-PKNOX2 -0,341609179
-PAK6 -0,341535575
-PRKAA1 -0,341378959
-UBA3 -0,34130955
-OAZ1 -0,341251276
-EID1 -0,340941987
-MRPS28 -0,340842312
-AA890010 -0,340724739
-OSBP -0,340497775
-ATP6V0C -0,34047911
-ARHGAP24 -0,340414643
-PNKP -0,340118439
-PSMD7 -0,340085658
-IPO9 -0,340071575
-ARF4 -0,339993296
-TERF2 -0,339818219
-SRSF2 -0,339525933
-PSMC5 -0,33950993
-TM9SF1 -0,339389717
-ACAT2 -0,339093022
-CDK8 -0,33909169
-KIAA0196 -0,338987444
-TFPT -0,338941882
-TRPC4AP -0,338718194
-TUBG1 -0,338211067
-SCN2B -0,338080627
-MTHFD1 -0,338071854
-ATPAF2 -0,338050158
-IGSF1 -0,337997383
-RGPD6 -0,337877048
-C16orf45 -0,33773508
-C10orf76 -0,337659307
-UBE2A -0,33762595
-PQLC1 -0,337612976
-SOD1 -0,337454918
-ARPC2 -0,337418781
-MEMO1 -0,33728488
-CSDE1 -0,337036578
-PHYHIP -0,336992273
-LYPLA1 -0,33698776
-NDUFA1 -0,336883322
-MARCKSL1 -0,336747008
-DCTN1 -0,336745427
-COX6A1 -0,336728807
-DPM1 -0,336614034
-ELP3 -0,336602956
-LOC653566 -0,336555692
-COX7BP1 -0,336528019
-CAPZB -0,336348777
-DCUN1D4 -0,335942405
-UCHL5 -0,335933871
-PSIP1 -0,335684272
-MRS2 -0,335589123
-RABGAP1 -0,335570544
-KCNA6 -0,335454989
-RAC1 -0,335429141
-ZMYM2 -0,33542626
-MRPL17 -0,335371398
-MLF1 -0,335274724
-RFC3 -0,33507418
-ARMCX3 -0,335005795
-GMDS -0,334931775
-KIAA0317 -0,334922749
-CAMSAP1 -0,334678333
-LSG1 -0,334628714
-PNPO -0,334625052
-THOC5 -0,334532053
-C11orf58 -0,334154436
-MTCH1 -0,334038037
-KAL1 -0,333848755
-OMG -0,333590731
-KLHL7 -0,333537148
-TTPAL -0,333489991
-GLA -0,333336937
-SEZ6L2 -0,333262252
-SNURF -0,333035272
-ARL6IP1 -0,332988884
-BFSP1 -0,332976059
-MAPKSP1 -0,332894473
-HABP4 -0,332672498
-SLC8A2 -0,332645114
-CKAP4 -0,332543738
-NPM1 -0,332250102
-CLSTN3 -0,332157745
-RUSC2 -0,33210981
-RCHY1 -0,331805148
-CACNA1D -0,331681156
-ZFAND5 -0,331302172
-TACC2 -0,331046487
-CHCHD3 -0,331008486
-RGS2 -0,330792786
-LDOC1 -0,330775706
-BTN2A1 -0,33075204
-WDR45 -0,330593865
-W87688 -0,330499179
-YWHAQ -0,330473094
-RAB3GAP2 -0,33029144
-HTRA2 -0,330240669
-SNRPD1 -0,330240562
-ANXA7 -0,330030639
-KIAA1024 -0,329770804
-RAD51C -0,329735785
-PRPF18 -0,329474331
-CCT6B -0,329361737
-ABCD3 -0,329205796
-PARN -0,329139621
-APOL2 -0,328983174
-MRPS18A -0,32863432
-RASL10A -0,328581006
-COG8 -0,328398026
-ZNF512B -0,327877848
-ATP5H -0,327758416
-PRDM4 -0,327710757
-TSPAN3 -0,327644045
-EPB41L3 -0,327416874
-APLNR -0,327394979
-TFR2 -0,327337619
-GADD45A -0,327012981
-POLR3F -0,326871651
-FASTKD3 -0,326789822
-TCERG1 -0,326746174
-VPS41 -0,326459968
-C17orf101 -0,325979143
-EXOC3 -0,325763291
-SLC25A17 -0,325666279
-GDAP1L1 -0,325526797
-HCFC1R1 -0,325022815
-SF3B5 -0,324878766
-TEX10 -0,324812522
-PSMA7 -0,324673715
-TCTN3 -0,324389244
-NOVA1 -0,32437578
-RABEPK -0,324366299
-ALG5 -0,324335095
-ENOSF1 -0,32427768
-SH3BGRL3 -0,32409913
-CTNND2 -0,324002004
-NKRF -0,323983769
-SLC6A1 -0,323833407
-MAPK1IP1L -0,323722226
-RAB22A -0,323713658
-GRP -0,323354345
-SDS -0,323335387
-IBTK -0,323304602
-CARS -0,322679359
-WWP1 -0,322463311
-ARL8B -0,322442301
-SLC19A2 -0,322361872
-F8A3 -0,322202521
-LPHN1 -0,322183082
-SMARCD3 -0,322148361
-GPN1 -0,322024809
-FAF2 -0,322014431
-SLC35B1 -0,321878066
-MPV17 -0,321698226
-TOM1 -0,321634922
-NEDD4L -0,321518057
-MRFAP1L1 -0,321393672
-C6orf62 -0,321303598
-POLR3B -0,321247444
-HTR2A -0,321189596
-CUL3 -0,321141566
-PSMD9 -0,321108014
-LRP3 -0,32099653
-TMEM62 -0,320873847
-PLS3 -0,320803014
-SUMO1 -0,32076762
-DLG4 -0,320617015
-ANKRD17 -0,320557554
-ARFIP2 -0,320500236
-HMGN4 -0,320196335
-PRKAG2 -0,319945607
-STAR -0,319749743
-NF1 -0,319726773
-ATOX1 -0,31967306
-UBE2M -0,319629201
-NDRG3 -0,319446308
-SNPH -0,319396594
-TPD52 -0,319178712
-PLK2 -0,319120325
-C1QBP -0,318975829
-SRSF8 -0,318843616
-USP22 -0,318806098
-GPD1 -0,318728943
-MAPK8IP2 -0,318691894
-USP20 -0,318610382
-RPA2 -0,31845096
-CCPG1 -0,318358561
-NQO2 -0,318256129
-POLR3C -0,318231923
-HBXIP -0,318079181
-MRPS31 -0,318018334
-SNRPB2 -0,31801084
-CACNG3 -0,317104885
-CCNE1 -0,316783937
-NDUFAF4 -0,316755785
-GRK6 -0,316405946
-ZER1 -0,316363024
-CHCHD7 -0,316179658
-C20orf29 -0,315860291
-AI693193 -0,315746456
-TPMT -0,315745725
-TPPP3 -0,315557058
-CTH -0,315210231
-HSDL2 -0,31516145
-MAPRE3 -0,314964867
-NLE1 -0,314918022
-ARHGEF4 -0,314777145
-STK19 -0,314737564
-AW503390 -0,314280211
-KIAA1279 -0,314104435
-CA14 -0,313849822
-CYP2E1 -0,313441486
-FHL1 -0,313417456
-MYL6B -0,313075964
-PACRG -0,3129322
-SCN2A -0,312912414
-POLR3G -0,312898745
-MED6 -0,312862133
-PCSK1N -0,312861133
-FLJ10038 -0,312756044
-PHTF1 -0,312716368
-PRPF4 -0,312654478
-RPRD1A -0,312642779
-HLF -0,312545473
-MTMR1 -0,312535102
-MFN1 -0,312461722
-C1orf50 -0,312398425
-QPRT -0,312349796
-ZDHHC6 -0,31229266
-ITGAE -0,311863717
-SLC18A1 -0,311739998
-CD83 -0,311711539
-GGCT -0,311631664
-KIAA0100 -0,311503156
-OPN3 -0,311374884
-SSX2IP -0,311111099
-NUCB2 -0,31105706
-UTP11L -0,311015852
-GOLGA8B -0,310924837
-UST -0,310734373
-PRKCI -0,310493775
-AP2S1 -0,310480065
-WBSCR22 -0,310476192
-PPP3CA -0,310434457
-PDSS2 -0,310396648
-PEG3 -0,310335546
-ATP5E -0,310319916
-GABRA5 -0,310200087
-AGPAT4 -0,310173061
-PDCD10 -0,310157516
-DDOST -0,310094837
-RPL23 -0,309992315
-HOMER1 -0,309485866
-C1orf123 -0,309187816
-POLE3 -0,309012195
-DDX41 -0,308923345
-HSD17B8 -0,308824584
-GMPR2 -0,308792858
-SCARB2 -0,308695909
-DGUOK -0,308606021
-MAGEF1 -0,308535371
-FOXA2 -0,308348483
-GLS2 -0,308287643
-TBCC -0,308286536
-FBXO41 -0,308255485
-SLC12A1 -0,308214984
-PELO -0,308137793
-KCNE1L -0,30811412
-RBBP4 -0,308007454
-UBL5 -0,307720013
-KLHL12 -0,307571676
-FTSJ1 -0,307464516
-ZFYVE16 -0,307366442
-PPT1 -0,3073579
-ZC3H13 -0,307293327
-DYRK1A -0,307183877
-PHACTR2 -0,306935621
-SLITRK3 -0,306872073
-PI4KA -0,306770561
-RNPS1 -0,306364972
-RALGAPB -0,306086767
-BRP44 -0,305953308
-BNIP1 -0,305883874
-SUPT4H1 -0,305675152
-BCKDK -0,30566687
-PLAA -0,305619464
-ACTR2 -0,305363631
-PION -0,305054773
-NFU1 -0,305010295
-CCT6A -0,304801168
-KIAA0427 -0,304585348
-EHD3 -0,304533089
-FAM63B -0,304437794
-STK25 -0,304425083
-POLB -0,304419007
-MRPL35 -0,304416576
-UBE2Z -0,3043165
-GSTZ1 -0,304133065
-AP3S1 -0,30395899
-SPATS2L -0,303776395
-LOC729580 -0,303766036
-RALGAPA1 -0,303697943
-PUF60 -0,303647762
-DAP3 -0,303640732
-AHI1 -0,303570806
-UBE2NL -0,303361552
-TMEM164 -0,303165514
-DOCK3 -0,303099341
-CADM3 -0,303050893
-ZNF219 -0,302968533
-PRKAR1B -0,302898104
-DOK5 -0,302798088
-ORMDL2 -0,302372011
-ACVR2A -0,302331205
-ALDOA -0,30171568
-ATRN -0,301666345
-COX7C -0,301597748
-PRKDC -0,301229867
-GNG10 -0,300757182
-SNX17 -0,300752701
-RBMS1 -0,300466996
-AJAP1 -0,300458474
-PREP -0,300414848
-ALDOC -0,300361514
-LAMA4 -0,300246196
-PI4KAP1 -0,300223018
-TMEM222 -0,30010369
-PIGB -0,299980372
-SSSCA1 -0,29997354
-DCUN1D1 -0,299517655
-DLSTP1 -0,299414392
-ITM2B -0,299325985
-AK025651 -0,299260618
-ACOT13 -0,299073057
-ZNF593 -0,298588283
-LOC100129250 -0,298385026
-H2AFY -0,298292243
-IGF1 -0,298232454
-KIAA0368 -0,29819687
-FKBP3 -0,298122528
-C12orf49 -0,297820161
-PRKRIR -0,297808472
-GLUD2 -0,297805688
-NBL1 -0,297799978
-PTPN4 -0,297657679
-LOC644617 -0,297586698
-IL33 -0,297538719
-CUL4A -0,29730361
-SIP1 -0,297199387
-POLDIP2 -0,297140479
-EBP -0,297109427
-FASTKD2 -0,296665172
-SMPD1 -0,296658212
-FAM55C -0,296650198
-TRPV2 -0,296465177
-DOPEY1 -0,29633822
-SCYL3 -0,296201386
-UBL3 -0,296188632
-STK38L -0,296164266
-APITD1 -0,296017845
-SFXN1 -0,295918484
-CPT1A -0,295754312
-USP8 -0,29570338
-MRPS30 -0,295702739
-ATG7 -0,295335659
-C10orf88 -0,29514056
-PIPOX -0,295018193
-RAC3 -0,294600261
-CIAO1 -0,294564961
-KLC2 -0,294523931
-LEPROTL1 -0,29448316
-ENDOD1 -0,294147277
-FEM1B -0,294007766
-IRS1 -0,293342341
-CYP51A1 -0,293155923
-DYNLRB1 -0,292974645
-TOM1L2 -0,292906836
-TDP2 -0,292808809
-MRPL49 -0,292778686
-LRP8 -0,292767989
-MOSPD1 -0,292730297
-C6orf134 -0,29255632
-TRPC1 -0,29249815
-RASL11B -0,292459191
-AL109671 -0,292334441
-TTC37 -0,292136499
-ODZ4 -0,292070818
-KIN -0,291741417
-KPNA1 -0,291721639
-CAST -0,291558763
-NDUFA13 -0,291524477
-AKR1A1 -0,29149158
-QARS -0,29146477
-MRPS22 -0,29145846
-MMACHC -0,291414294
-UBQLN2 -0,291358191
-PIK3CB -0,291242041
-COX6B1 -0,291081182
-PDK2 -0,290962723
-RABGGTB -0,290962562
-SR140 -0,290943983
-ATF2 -0,290881352
-FADS1 -0,290820194
-SRP14 -0,290691218
-RAD23B -0,290632171
-AHCY -0,290521401
-RINT1 -0,290502144
-SRP54 -0,290224786
-COX5B -0,289972152
-NBN -0,289962803
-DDX50 -0,289845246
-NUFIP1 -0,289611609
-HDGFRP3 -0,289540354
-HBA2 -0,289412602
-SRP9L1 -0,289377441
-ARFGEF1 -0,289327503
-FAM13B -0,289118442
-DIMT1L -0,288943725
-LPO -0,28888192
-VPS28 -0,288730564
-SSR3 -0,28867602
-SEPT7 -0,288663677
-NARS2 -0,288651232
-EMG1 -0,288493971
-HSPA8 -0,288488899
-TBC1D13 -0,288209587
-TTC35 -0,288076299
-GTPBP4 -0,287916733
-SPG7 -0,287774853
-PAFAH1B3 -0,28772138
-MAPT -0,28765216
-RERGL -0,287509361
-HNRNPD -0,287438947
-PLCL2 -0,287391702
-HLA-DPA1 -0,287200849
-CD55 -0,286966384
-IDH3A -0,286870398
-STXBP5L -0,286801199
-MAP3K12 -0,286334641
-PPP2R1A -0,286259611
-TMEM126B -0,286136364
-CDKN3 -0,286064506
-ABCC5 -0,286013319
-TMEM127 -0,285913561
-DNAJC2 -0,285585137
-SEC61G -0,285583827
-SSR1 -0,285489405
-AIMP1 -0,285281231
-YTHDF2 -0,285194578
-FAM86B1 -0,285046154
-CTBP1 -0,285027477
-CHRFAM7A -0,285001423
-SSBP3 -0,284934817
-MRPL46 -0,284930449
-TSPAN6 -0,284861931
-MYST2 -0,284824247
-GGH -0,284817124
-PRKACB -0,2847024
-C2orf47 -0,284692381
-NLK -0,284579832
-ASNS -0,28445955
-EXOC5 -0,28439526
-OAZ3 -0,284379411
-CTNNBIP1 -0,284364924
-PVR -0,284070802
-C16orf80 -0,284019987
-UBE3A -0,283816198
-EAPP -0,28376748
-IGSF3 -0,283764031
-KCND2 -0,283569047
-FOXK2 -0,283286684
-SLC35A2 -0,283204451
-TBCB -0,283168385
-SLC38A1 -0,283158141
-ACCN2 -0,283147998
-FAM149A -0,283126904
-TIMM22 -0,283102824
-EIF4ENIF1 -0,28310048
-THSD1P1 -0,282819454
-MAGED4 -0,282562753
-CLASP1 -0,282510547
-C1orf61 -0,282424601
-C6orf106 -0,282397365
-WDR44 -0,282155933
-GNL3 -0,282115302
-RCBTB1 -0,28192202
-OSTM1 -0,281535242
-AGPAT5 -0,281510168
-PRNP -0,281405094
-APPBP2 -0,281330465
-GAD1 -0,281295305
-NECAB3 -0,281056363
-ABCF1 -0,280961256
-DNAJC7 -0,280750506
-EPHB1 -0,280596899
-GPRC5A -0,280368026
-HSPA14 -0,280049432
-CLPTM1 -0,280042656
-SGPP1 -0,27999737
-ABCG4 -0,279891909
-GFRA1 -0,279146972
-ATP5SL -0,278849245
-CTSO -0,278677227
-DCTN4 -0,278556645
-MAP2K2 -0,278535478
-ZNF423 -0,278503712
-FUS -0,278285124
-ACTR8 -0,278282163
-PRR13 -0,278189761
-ZNF329 -0,278179162
-RNASEH2B -0,278151755
-LOC284244 -0,278099761
-FAM117A -0,277715513
-MREG -0,277651168
-C2orf18 -0,277609469
-AW612311 -0,277599115
-SYNRG -0,277434047
-SMARCE1 -0,277346186
-DNAJA3 -0,277188103
-PPP2R5E -0,2770317
-TMCO6 -0,276951805
-C6orf35 -0,276886272
-DDX18 -0,276619655
-TTLL1 -0,276373935
-LANCL1 -0,276361838
-SNRPE -0,276287655
-DTX4 -0,276233703
-IDH2 -0,276017451
-SACS -0,275814599
-ABHD2 -0,275491786
-VAMP1 -0,275092752
-AGPAT1 -0,27504004
-TYMS -0,274913065
-ZDHHC3 -0,27479568
-LMO1 -0,274566957
-UVRAG -0,274559415
-HBB -0,274385467
-PSMA2 -0,274273938
-CD24 -0,27422103
-GRAMD1B -0,27394685
-PRC1 -0,27393137
-YARS2 -0,27376193
-SIGMAR1 -0,273597834
-CPEB3 -0,273534888
-ARMC9 -0,273442678
-DNAJC10 -0,273369377
-TM9SF4 -0,27326642
-RBX1 -0,273166064
-C13orf1 -0,273151402
-PDCD4 -0,273130523
-LUZP2 -0,272843047
-APLP2 -0,272609838
-USO1 -0,272598741
-SH3BP5 -0,272512602
-PPP1R11 -0,272494252
-PEMT -0,272485616
-CDC16 -0,272287144
-LCMT2 -0,272235596
-DCX -0,271983078
-DDAH1 -0,271924121
-UBE2D2 -0,271815552
-TANK -0,271664689
-AW974666 -0,271662837
-USH1C -0,271630244
-BDH1 -0,271624449
-B9D1 -0,271589518
-BRD9 -0,271105209
-USP7 -0,271052865
-TRIM2 -0,270764995
-PARK7 -0,270634786
-NSFL1C -0,270597248
-COQ2 -0,269953826
-HNRPDL -0,269787459
-NOV -0,269731303
-SLC25A28 -0,269706278
-EXT2 -0,26958066
-VLDLR -0,269148459
-SLC4A4 -0,268895862
-SMURF1 -0,268798637
-ORC2L -0,268275919
-ZC4H2 -0,268056536
-SDHAF1 -0,267985583
-VDAC1 -0,267895013
-ALDH1A3 -0,267738476
-PNPLA4 -0,267586498
-HAGH -0,267406111
-CNTNAP2 -0,267355858
-KPNA3 -0,267278305
-LRBA -0,267216793
-DPYSL4 -0,267150239
-MCCC2 -0,26714725
-KBTBD4 -0,267031071
-DCTD -0,267005887
-C1orf21 -0,266982234
-C2orf43 -0,26679916
-SF3A3 -0,266732334
-PTPN3 -0,266674559
-FBXO21 -0,26664933
-CCT7 -0,266615147
-CLNS1A -0,266539743
-HAPLN1 -0,266160364
-SYT13 -0,26591944
-SENP5 -0,265695364
-HMGB2 -0,265556554
-CANT1 -0,265168032
-CGREF1 -0,265157579
-GRM1 -0,26510368
-ZFHX4 -0,265049797
-PVRL3 -0,264999073
-ADAR -0,264636454
-TRIM3 -0,264561355
-ANP32E -0,264413865
-PDLIM7 -0,264406742
-MLH1 -0,264377914
-PRKCA -0,264376056
-CYB5R3 -0,264120933
-PDE1A -0,263919942
-LOC100127998 -0,263915362
-WSB2 -0,263691169
-RPF1 -0,263404659
-CXCL12 -0,26333499
-TMEM66 -0,263285506
-EIF6 -0,263232223
-NFE2L1 -0,262789646
-KLHL20 -0,262772392
-PPM1H -0,262689193
-PIN4 -0,262483899
-TUBA4B -0,26241982
-ECT2 -0,262276809
-MGC5566 -0,261888759
-C9orf116 -0,261830489
-ASB1 -0,261751394
-ABCC8 -0,261735107
-ELOVL2 -0,261638578
-PHB2 -0,261466477
-ZNF580 -0,261379751
-DNAJC24 -0,261364702
-PSMB10 -0,261344946
-CSE1L -0,261292597
-ANKRD27 -0,261154598
-TUBG2 -0,261047779
-C6orf162 -0,261001828
-AL034399 -0,260886813
-GLT8D1 -0,26052144
-SRR -0,260520305
-MCC -0,260395686
-COX4I1 -0,260324715
-SEP15 -0,260222524
-RNF103 -0,260210477
-ZNF576 -0,260159221
-MGEA5 -0,260092677
-RSL24D1 -0,259958151
-USP13 -0,25969613
-MLLT3 -0,259631882
-SRI -0,259268888
-NCS1 -0,259133737
-MAPKAPK5 -0,259103348
-IQCG -0,25908825
-FN3KRP -0,258914892
-BCKDHB -0,258870249
-GOLGA5 -0,258736414
-RDBP -0,258483881
-SUPT7L -0,258355414
-METTL1 -0,258206012
-CREB3 -0,258159408
-TMEM111 -0,258136123
-NRSN2 -0,257397396
-CNTN1 -0,257314074
-COX10 -0,257277055
-SERPINB9 -0,257269621
-MTF2 -0,256976969
-EDNRB -0,25676028
-HSF2 -0,25652969
-POLR2L -0,256424652
-TRIM58 -0,256294322
-DACH1 -0,256241463
-UEVLD -0,256239024
-ATP1B3 -0,256215499
-SAP130 -0,256053262
-TRPC6 -0,255890704
-HERC6 -0,255794959
-NAV3 -0,255707496
-GOSR1 -0,25567987
-CNR1 -0,255506006
-PSME4 -0,25522233
-CAMKV -0,254605479
-ADSL -0,254512794
-BCS1L -0,254298738
-CCNB1 -0,253924801
-SNX2 -0,253887319
-ASAP2 -0,25387509
-WDR70 -0,253565737
-PTPRE -0,253309549
-SEPT5 -0,253058348
-SCML1 -0,253051964
-BCR -0,252946659
-MAGOH -0,252829021
-SEMA4F -0,25277628
-CLIP1 -0,252764211
-JMJD4 -0,252747043
-ZMYND11 -0,25273006
-CPSF6 -0,252574141
-PTPRA -0,252430519
-PLA2G12A -0,252393049
-MXRA5 -0,252290125
-RFX5 -0,252264534
-WARS -0,252174212
-HUS1 -0,252166663
-VCAM1 -0,251733145
-CEACAM21 -0,25171453
-RHOT1 -0,251514974
-EMD -0,251327933
-TSPYL2 -0,251307071
-THNSL1 -0,25130438
-NDUFB4 -0,251250318
-CHMP5 -0,251232028
-SKAP2 -0,251185084
-LRPAP1 -0,251070101
-COMMD3 -0,251069448
-ROGDI -0,250917557
-PPAP2B -0,25089017
-ADSS -0,250852878
-LGI2 -0,250809779
-CBX6 -0,250671998
-NELF -0,250584567
-DENND5B -0,250357567
-ATP2C1 -0,239139672
-SUMO2 -0,233193565
-KRAS -0,208565613
-PEX3 -0,200767265
-PRDX2 -0,195371323
-PDCD2 -0,194653063
-TM2D1 -0,189207426
-KHDRBS1 -0,16653347
-KLC1 -0,156510024
-ANK2 -0,155852142
-HBS1L -0,155006259
-NTRK3 -0,121314135
-PTPRO -0,110200451
-PLEKHA5 -0,10184855
-GCOM1 -0,091608137
-TIMM8A -0,084179504
-MKRN1 -0,074942655
-PLA2G4B -0,068760926
-RUFY3 -0,059042335
-RIMS2 -0,057507607
-C21orf2 -0,054091983
-METAP2 -0,053236401
-LRRC40 -0,040678287
-RPL10 -0,034862755
-RIOK3 -0,033313025
-SYNCRIP -0,027340658
-UNC45A -0,021866459
-MPZL1 -0,020796077
-RANBP1 -0,01610173
-ITGB1BP1 -0,011025016
-UBC -0,009666523
-RER1 -0,007044099
-PDS5B -0,005231512
-NCAM1 -0,004638056
-LIMCH1 0,003894784
-VPS13D 0,014841215
-WDFY3 0,017457694
-MRP63 0,023151675
-TSR1 0,064261585
-GRB10 0,066410415
-FAM128B 0,074972161
-PAK2 0,079518764
-PKP4 0,080237181
-TMEM144 0,083124821
-C3orf63 0,086752023
-DDAH2 0,250378216
-AF238870 0,250544885
-PTMS 0,250667518
-JAG1 0,250675664
-RPL32 0,25075902
-UXT 0,250812127
-HSP90B1 0,250888984
-SS18 0,250904748
-RND2 0,250918958
-CLEC4M 0,250931594
-AU147194 0,251115897
-IL1RAPL1 0,251119435
-EPB41L2 0,251131328
-TFDP3 0,251241244
-GAL3ST4 0,251281983
-EDN2 0,251371356
-SFTPC 0,251372616
-TRMT61A 0,251534845
-GPR4 0,251535902
-KEAP1 0,251692277
-RNF122 0,251718243
-NOTCH2 0,251745042
-WDR1 0,251871256
-NFX1 0,252023298
-DOHH 0,252100123
-NES 0,252167647
-SRSF10 0,252172984
-AQP3 0,252182392
-LOC728412 0,252404082
-RCN3 0,252455902
-CSNK1G1 0,252462493
-KCNS1 0,252601737
-CCDC71 0,252614101
-JUND 0,252645305
-LYST 0,252718314
-TPCN1 0,252770336
-MTA1 0,252823052
-RIN1 0,252841454
-ATHL1 0,252944239
-FTSJ3 0,253136044
-SERPINA1 0,253202139
-STARD7 0,2533744
-MRPL34 0,253425868
-PPID 0,25344089
-SH3PXD2A 0,253534644
-UBA7 0,253547625
-RUNX1 0,253686159
-ARNTL 0,253823553
-STAT6 0,253840779
-CASKIN2 0,25393147
-NFATC4 0,253965486
-LILRB2 0,254041373
-PPP1R13L 0,254173566
-RAP1A 0,254249533
-OTUD4 0,254380531
-ZNF516 0,254390037
-ZC3H14 0,254430628
-BTD 0,254441889
-ABHD4 0,254494909
-MT3 0,254554667
-PTCH1 0,254572046
-CDC42EP3 0,254591236
-LOC150776 0,254715807
-PTGES 0,254816225
-TPM2 0,254867646
-TAGLN 0,254960085
-AL050032 0,254984309
-HPN 0,25500915
-FLNC 0,255046574
-GJB3 0,255060346
-RAB40B 0,255071999
-CST1 0,255226531
-FGF21 0,255229382
-AW574933 0,255334628
-FGF5 0,255461872
-CLCN7 0,2555275
-BAHCC1 0,255618646
-FANCA 0,255627746
-CYBA 0,255682121
-TIE1 0,255683605
-ANKHD1-EIF4EBP3 0,255707685
-CDV3 0,255740411
-COL9A1 0,255878907
-TTC31 0,256049153
-ZIC1 0,256075896
-CCDC121 0,256090992
-FUT4 0,256155794
-UCP3 0,256197327
-AU146391 0,25625958
-MMP2 0,256269664
-STXBP2 0,256386629
-TMEM87A 0,2564575
-FXR1 0,256493521
-RDX 0,256507051
-HPS1 0,256516919
-TRAM2 0,256517872
-HYAL2 0,256778041
-TNFRSF14 0,256783849
-NEK7 0,256861333
-AGRN 0,256876471
-SMC4 0,256895131
-GAS7 0,256949822
-PDE4B 0,256950938
-CHD4 0,256970114
-SPP1 0,257084517
-HECA 0,257172806
-NXF2B 0,257181225
-LILRA5 0,257188463
-SCAP 0,257267679
-SNX1 0,257354288
-GIGYF2 0,257400552
-CELF1 0,257407908
-HSD17B14 0,257420303
-DUOX1 0,25770603
-MRM1 0,257826185
-NBR2 0,257852879
-FAM176B 0,257955278
-SYNPO 0,257997864
-GPRIN2 0,258040238
-IER3 0,25816919
-ZNF506 0,258198461
-NM_016414 0,25824817
-VPS53 0,258358594
-PGPEP1 0,258378109
-GNL1 0,25847832
-OGFR 0,258496938
-CXCR2 0,258632799
-C1orf38 0,258857462
-RPL22 0,258901214
-NM_018041 0,259005358
-MYOF 0,259133176
-NGB 0,259197495
-CLIC4 0,259260666
-TBC1D9B 0,259295717
-KCND1 0,259337213
-RNASET2 0,259420675
-EXT1 0,259568659
-AQR 0,259572114
-VWA1 0,259618684
-MUC3A 0,259647513
-CAV1 0,259682957
-IRF4 0,259719685
-OR7C1 0,259728956
-SETDB1 0,259737838
-E2F6 0,259867146
-TFEB 0,259924981
-CPSF3L 0,26005015
-MARCH8 0,260576922
-MFSD11 0,260945964
-ETAA1 0,260954881
-SMARCD2 0,260999203
-RGS12 0,261024661
-CCNG2 0,261112401
-RPS8 0,261183649
-IL17RA 0,261275371
-NUDC 0,261284708
-ZNF133 0,261329337
-ATP13A1 0,261543252
-PICK1 0,26166607
-C20orf117 0,261682534
-GIPR 0,261728602
-HIST2H4B 0,261730186
-S100A11P1 0,261732522
-MARCH3 0,26174629
-ZBED4 0,261794357
-KHK 0,261822851
-SCAMP2 0,26194666
-AF070579 0,261954742
-TECR 0,261998101
-AK024915 0,262016665
-CASP7 0,262240261
-PDK4 0,262293861
-MYO7A 0,262479993
-TUBBP5 0,262483574
-TMEM143 0,262491406
-NAP1L1 0,262524812
-PLEKHB1 0,262542861
-ING1 0,262679424
-SPSB3 0,262786186
-C9orf167 0,262955615
-NTM 0,262977412
-FIP1L1 0,263199662
-FYCO1 0,26321575
-GGT1 0,263227324
-ALG12 0,263240056
-IGL@ 0,263282588
-PPBP 0,263290228
-SNX13 0,263292989
-SRSF4 0,263309909
-CYTH1 0,263721364
-AL050035 0,263831657
-TRMU 0,263920451
-TIMP1 0,263959235
-RFNG 0,263965598
-HIP1R 0,264033626
-NR1H3 0,264039538
-NT5C2 0,264091319
-FNTB 0,264115077
-SAR1B 0,264175117
-GIT1 0,26420824
-RRAGD 0,264311012
-HAP1 0,26435511
-FLT3LG 0,264378926
-NM_018612 0,264421364
-SLC7A9 0,26447762
-GLTSCR2 0,264541217
-SUN1 0,264635751
-CEP152 0,264663399
-MBTD1 0,264688291
-SYT12 0,264690461
-ACTR5 0,264835312
-EIF4A1 0,264933012
-COX7A1 0,26511391
-CMTM6 0,265385079
-FAM102A 0,265449454
-AW970584 0,265532869
-FMO5 0,265619005
-N4BP2L1 0,26587536
-SPAG11A 0,265939376
-TGFBI 0,265987004
-RYK 0,266131346
-SERBP1 0,266135884
-AK021988 0,266152576
-NCAM2 0,266199101
-AK024995 0,266233606
-RAB9A 0,266259326
-SYNJ2 0,266313048
-PHLDB1 0,266315252
-PKN1 0,266439146
-MFAP3L 0,266558078
-PPFIBP2 0,266640652
-WBP5 0,266861878
-TMX1 0,266949292
-SLC6A12 0,267009029
-C3AR1 0,267017849
-CSRP2 0,267020264
-SP3 0,267034674
-ATN1 0,267069634
-GNB3 0,267107148
-TIAL1 0,267113358
-GPATCH8 0,267177985
-PMEPA1 0,267182372
-MAP2K3 0,267199274
-NM_018033 0,267304029
-WWTR1 0,267350058
-SEMA6A 0,267400431
-RBPJ 0,267426168
-AL049279 0,267438916
-IL1RN 0,267473934
-QKI 0,267577841
-SOX15 0,267588393
-DMTF1 0,267672579
-RPL19 0,267821304
-TRIM39R 0,267839755
-SLC26A6 0,267879749
-NM_025056 0,267969441
-BBS9 0,267969882
-M85256 0,26799656
-ADORA3 0,268097905
-TMEM176B 0,268515164
-SECTM1 0,268600799
-ST14 0,268612452
-ARHGEF18 0,268652414
-SIRT5 0,268726991
-MYBPC1 0,268763379
-RPL15P22 0,268793196
-SIGLEC15 0,268860828
-DNAJA1 0,26890035
-LMBR1L 0,269042598
-GIMAP4 0,269074847
-MFAP3 0,269075993
-ABCA6 0,269120338
-AW836210 0,26919833
-LOC100133772 0,269228182
-CHST4 0,269387102
-RNASEH2A 0,269387986
-RPL18 0,269450865
-RPLP2 0,269486597
-MEPE 0,269489799
-FAM106A 0,269545639
-GATAD1 0,269621956
-PPP2R3A 0,269725552
-MASP2 0,269836416
-MYO10 0,26992164
-PIGG 0,269941407
-SMG5 0,269952017
-IFI30 0,269956381
-AK025180 0,269971157
-AMD1 0,269982316
-LMOD1 0,270125966
-SNX15 0,270191178
-SCARB1 0,270338985
-SERTAD3 0,270373355
-MBD5 0,270430073
-SLC2A5 0,270454389
-ITCH 0,270468949
-ADA 0,270490353
-PWP2 0,270541137
-ARHGEF1 0,270572389
-C2CD2 0,270675538
-EIF1 0,27071329
-C1orf35 0,270772513
-IFI16 0,270855012
-LOC285830 0,270905428
-IL10 0,271025993
-MORC4 0,2712707
-CA11 0,271346355
-C5orf54 0,271348162
-C14orf93 0,271428228
-RPL17P7 0,271481741
-TMEM161A 0,271564557
-LRCH3 0,271627825
-DFFB 0,271779652
-BAZ1B 0,271859723
-DKFZp547G183 0,271894591
-RAB11FIP2 0,271895928
-PCK1 0,27194659
-TMPRSS5 0,27195628
-TIPARP 0,272078235
-UBE2L3 0,272125747
-ZNF672 0,272142507
-GALNT10 0,272151507
-EXD2 0,272173543
-KAT2B 0,272322281
-RPS11 0,27237174
-POLR2H 0,272422791
-IGLL3 0,272574443
-AA554430 0,272578205
-DOCK10 0,272578712
-DMC1 0,272606886
-CD40 0,272762332
-CDK11A 0,272811711
-UCKL1 0,272898303
-FAM125B 0,273084179
-UBXN7 0,273084433
-SMA4 0,273204796
-DYNLT1 0,273349219
-CTTNBP2NL 0,273380758
-HSPH1 0,273396703
-CYP39A1 0,273418193
-HOMER3 0,273432217
-RRBP1 0,273480926
-ATAD2B 0,27361049
-LGALS3 0,273847411
-LASS2 0,273913098
-ZNF451 0,273935073
-NXPH4 0,27404559
-C22orf46 0,274118605
-KDM4B 0,27422483
-GPNMB 0,274363725
-CYHR1 0,274415705
-CCDC9 0,274487483
-WWC2 0,274522318
-ZNF652 0,274533788
-ILK 0,274538403
-CTDP1 0,27455992
-LOC51152 0,274810051
-AL442084 0,274963062
-CPNE7 0,275259638
-CENPB 0,275294531
-TCIRG1 0,275300556
-PRPF40A 0,275423637
-ARHGAP17 0,27552534
-LOC100133811 0,275961848
-ADAM17 0,276019886
-CRISPLD2 0,276144309
-IFIH1 0,276175289
-LOC440434 0,276293985
-DCLK2 0,276369722
-MS4A6A 0,276482788
-VASH1 0,276499979
-SRSF7 0,276513035
-B3GAT3 0,276752575
-CALHM2 0,276762436
-MAP4 0,276867434
-DULLARD 0,27687625
-CTSS 0,276943812
-BAG3 0,277040195
-KRT8P12 0,277155277
-POLR2F 0,277193722
-CD14 0,277207134
-SF3B1 0,277255775
-EZH1 0,277320185
-MBD1 0,277342685
-MITF 0,277407356
-BAIAP2 0,277445862
-FCGR2B 0,277531437
-PAQR4 0,277547889
-NFATC2IP 0,277597337
-CAT 0,277600148
-TJP2 0,277610024
-CCNA2 0,277687494
-GEM 0,277887602
-C2orf54 0,277935237
-HIRIP3 0,278018588
-MCM3APAS 0,278082892
-CFB 0,278130274
-TAGLN2 0,278365668
-AK024851 0,278382784
-HGD 0,278585783
-NR2E1 0,278716062
-SEC61A1 0,278797194
-PDE4DIP 0,278806635
-FRMD4A 0,278822955
-RHOC 0,278842121
-UBTF 0,278963815
-NCOR2 0,279024257
-PPP6R3 0,279218049
-ALAS2 0,279327775
-SPSB1 0,279537438
-SGMS1 0,279545277
-TEAD4 0,279565374
-AK024897 0,27961031
-IRS2 0,279708094
-TRIM62 0,279977776
-AF308291 0,279984986
-AK022362 0,280079092
-KIAA0495 0,280115197
-CUL7 0,280170918
-PARD3 0,280192562
-NUP98 0,280376383
-DHRS4L2 0,280391865
-AK024093 0,280444114
-VEGFB 0,280560816
-PTEN 0,280592383
-NBPF10 0,280620974
-CASP1 0,280699269
-AK2 0,280734467
-MLX 0,280792537
-GNG11 0,280826824
-HNRNPM 0,280968313
-IL12RB2 0,28098376
-CDK18 0,28098866
-RARA 0,280998983
-GYPC 0,281028129
-PAK4 0,28104576
-SEMA3F 0,281239182
-BAT2L2 0,281335934
-BRD4 0,28139016
-PAOX 0,281415979
-SMAD3 0,281446531
-PIK3R2 0,281480063
-IFT122 0,281682471
-IRAK4 0,281825175
-RASSF2 0,281825652
-RPL13A 0,282085077
-ZNF22 0,282127023
-KDM4A 0,282136199
-CPM 0,282150511
-EIF2S2 0,282316006
-USP48 0,282335945
-CLCNKB 0,282422648
-C11orf61 0,282474246
-ANKRD11 0,282516441
-PTTG1IP 0,282619596
-SEC14L1 0,282620994
-DOCK6 0,282646645
-CARHSP1 0,28271852
-RRAS 0,282814195
-TRIM38 0,283129972
-PLA1A 0,283206252
-GAB1 0,283220235
-PDLIM1 0,283254227
-SSH3 0,283308195
-KLF9 0,283315657
-N4BP2L2 0,283629404
-TNS4 0,283667599
-C15orf28 0,28383226
-ANXA11 0,283988681
-TAF12 0,283993401
-SLC39A1 0,284190806
-SAP30 0,284320416
-RNASE4 0,284337811
-RPS28P6 0,28438483
-DDR2 0,284449824
-BMP4 0,284614799
-CEPT1 0,284615091
-ITPKB 0,284650775
-PLEKHF2 0,284678379
-AW974812 0,284683098
-PTCRA 0,284827371
-SETMAR 0,2848555
-SOCS3 0,284925858
-NM_014129 0,284930906
-MYO1D 0,285094554
-RBL1 0,28514691
-HN1L 0,285254673
-LASS4 0,285307965
-RPS21 0,285547221
-PPP2R1B 0,285765143
-NEO1 0,285937917
-SEC24C 0,286013109
-BCL3 0,286014454
-KCNMA1 0,286080656
-AL137590 0,286198689
-EDIL3 0,286207431
-ARHGEF16 0,286210956
-HCK 0,286227266
-GSTA1 0,286246055
-SLA 0,286356975
-UNG 0,286379363
-SP100 0,286388329
-PRSS53 0,28642638
-MYL6 0,286728542
-CDH5 0,286728949
-C10orf116 0,286730624
-GTF2IRD1 0,286882519
-POLH 0,286995879
-SFRS16 0,287066034
-TPM4 0,28709233
-ABCD4 0,287100216
-GLT25D2 0,287127854
-COL18A1 0,287131911
-NPIPL3 0,287424398
-C1orf69 0,287453135
-MTF1 0,287488427
-IGF2BP2 0,287555495
-PALLD 0,287872078
-RPS16 0,287887395
-CYP2C9 0,287955438
-SC65 0,288029122
-CRYBG3 0,288096904
-SHC2 0,288312879
-FLNA 0,288339801
-NM_014486 0,288348194
-ISYNA1 0,288383809
-PNO1 0,288506351
-GZMK 0,2886543
-ATG13 0,288748426
-NCOR1 0,288772721
-ZSWIM1 0,288892162
-GPM6B 0,28893274
-SNTA1 0,289049438
-RHOBTB1 0,289064808
-GGA1 0,289073087
-ATXN2L 0,289088819
-FAM46A 0,289172187
-ZNF532 0,289393934
-CD40LG 0,289400418
-ZCCHC11 0,289421485
-WDR5B 0,289498086
-EPN2 0,289629137
-WNK1 0,289684816
-ZNF408 0,289721753
-LHFPL2 0,290003635
-NARG2 0,290029081
-STYXL1 0,29008917
-YY1AP1 0,290249669
-CPOX 0,290281635
-IL11RA 0,290333682
-PAXIP1 0,290387596
-ZNF282 0,290414378
-C11orf95 0,290643441
-MERTK 0,290681835
-VPS13C 0,29069039
-RPS17 0,290756898
-NEIL1 0,290762184
-ZNF292 0,290850132
-NOSIP 0,290873511
-DNAJB2 0,290950763
-INPPL1 0,29102828
-ZFX 0,29106383
-SETX 0,291138151
-SLC25A37 0,291207794
-PCDHGA8 0,291472818
-TXNIP 0,291962928
-DDX27 0,291971417
-BG389073 0,29216848
-JTB 0,292275569
-RBM10 0,292352574
-RASGRF1 0,29242252
-SYNM 0,292474024
-EXPH5 0,292481151
-NPL 0,292494012
-CHKA 0,292519533
-MGA 0,292564204
-SOX10 0,292580481
-AK024185 0,292975066
-FAM120A 0,292996604
-PLXNB1 0,293000141
-BDH2 0,293071563
-JRK 0,293136106
-SLC11A1 0,293139917
-TM4SF1 0,293242649
-EDA 0,293286441
-CDK10 0,293299298
-HLA-E 0,293305618
-LOC642846 0,293349826
-GFPT2 0,293396887
-SENP3 0,293408144
-RPS3AP44 0,293415546
-C16orf88 0,293431615
-FAM60A 0,293472328
-RPL36A 0,293501288
-SERPINA5 0,293547044
-CNOT8 0,293568161
-KDM4C 0,293620372
-POU2F2 0,293815578
-C14orf139 0,293870806
-ZNF217 0,293937173
-NM_025042 0,294034268
-NNMT 0,294200775
-VEZT 0,294224684
-KIAA0754 0,294307773
-RBM28 0,294637248
-ITPR2 0,294711729
-PPPDE1 0,294796015
-KLHL28 0,294874305
-MGP 0,294956866
-LOC729602 0,295016892
-SRSF5 0,295036903
-ROCK1 0,295267164
-SS18L2 0,295271871
-LMNA 0,29532356
-ESRRA 0,295387708
-SNHG3-RCC1 0,295411716
-TAL1 0,295434654
-SQRDL 0,295470062
-TARDBP 0,295665655
-LMAN2L 0,295705138
-RIN3 0,295771443
-PSPH 0,29602696
-DGKD 0,296027908
-WHSC1 0,296067068
-SPRY4 0,296068122
-ADARB2 0,296162399
-ELF3 0,296200778
-TLE1 0,296292637
-ACAN 0,296375799
-AK022038 0,296556116
-IL1RL1 0,296721787
-OR2A9P 0,296898432
-NCRNA00260 0,296954725
-CAD 0,296976627
-PNRC2 0,297129071
-IQCK 0,297134521
-ACOX2 0,297377087
-APOC4 0,297497329
-DGKA 0,297541846
-ZBTB1 0,297547513
-PUS1 0,297622568
-C7orf64 0,297653213
-FBLN1 0,297723957
-SBF1 0,297752819
-TMF1 0,298582891
-IL1R1 0,298701666
-LILRB3 0,298823808
-FLAD1 0,298825369
-CD163 0,299040686
-TCL6 0,299056301
-FADS3 0,299096634
-LBR 0,299180453
-AL162044 0,299184427
-ZNF337 0,299271736
-AHNAK 0,299352615
-YY1 0,299417937
-HIPK2 0,299439852
-NAT15 0,299519834
-ANKZF1 0,299817611
-NECAP2 0,299838267
-MAP3K7 0,299838407
-SAMD4A 0,299863792
-WDR8 0,300094232
-ZNF24 0,300179611
-NR3C1 0,300200063
-FGF1 0,300357727
-NPC1 0,300564708
-LMO4 0,300573598
-TTLL5 0,300853453
-AL050053 0,300945526
-RSU1 0,300958049
-C15orf39 0,301123219
-SLC14A1 0,301147038
-ELAVL1 0,301190126
-SLC17A4 0,301215925
-FANCC 0,301274346
-LRCH4 0,301338927
-EGFL7 0,301340052
-C9orf3 0,301357727
-SRGN 0,301411135
-PLCL1 0,301576339
-MAN1A1 0,301613058
-S100A8 0,301917937
-W86781 0,301984854
-HIP1 0,302012828
-OR7A5 0,302027387
-PPP1CC 0,3020408
-CGGBP1 0,302058231
-CYP3A4 0,302333153
-GALNS 0,302376776
-NR0B1 0,302394827
-SMNDC1 0,302468654
-MGST2 0,302482901
-RPL12 0,302658969
-DMPK 0,302955014
-TNRC6B 0,30299615
-PPM1D 0,303104009
-EED 0,303134999
-STAG3L1 0,3031801
-TMCC1 0,303195736
-RPL13 0,303245467
-RBPMS 0,30326423
-ARHGAP10 0,303298204
-PLCB3 0,303300054
-XPO1 0,303410309
-MYO1F 0,30341788
-SRPK1 0,303531642
-ZCWPW1 0,303562617
-MTHFD2L 0,303678034
-FAM111A 0,303798707
-TTC38 0,304186409
-COL7A1 0,304295553
-C4orf19 0,304312458
-NGLY1 0,304332742
-HTATIP2 0,304339936
-IFNAR2 0,304414877
-CXorf1 0,304737703
-UNC5B 0,304789798
-YAP1 0,30479215
-PHC2 0,30485466
-FBL 0,304914384
-CDH2 0,304939032
-FXYD2 0,304942957
-ANKRD36 0,305000603
-KRT8 0,305028726
-DSCAM 0,30505625
-SMO 0,305151387
-FCGRT 0,305420183
-PAIP2B 0,305483478
-PABPC1 0,305528523
-PIGV 0,305604211
-BACH2 0,305697602
-PLGLA 0,305722503
-MORC3 0,305845022
-DIDO1 0,305996983
-PRPF38B 0,306041882
-TRMT1 0,306054262
-NFATC1 0,306233076
-AK021495 0,306242002
-GPR1 0,306335484
-STARD13 0,306369109
-CELSR2 0,306371185
-ZNF193 0,306396574
-ABHD6 0,306458055
-PLCXD1 0,306486283
-RPAP1 0,306695411
-AL050122 0,306737964
-DHRS3 0,306750918
-C1QA 0,306800137
-AF009267 0,30681596
-SETD2 0,307047565
-STX6 0,307184977
-TMEM204 0,307304516
-SMYD2 0,307490131
-BF942161 0,307560212
-SLC44A1 0,307685609
-ELF2 0,307698089
-AATF 0,307770923
-AV761453 0,307800442
-ACTN1 0,307927265
-AI523613 0,307943372
-SOLH 0,307971092
-ZNF410 0,308222237
-GOLGA4 0,308250269
-FLJ21369 0,308352331
-FCGR2A 0,308469725
-BRD7 0,308638563
-TLR2 0,308769609
-FTHL5 0,308790654
-SPOCK1 0,308861441
-LSM14A 0,308907157
-USF2 0,309161806
-TENC1 0,309220224
-EMP2 0,309252571
-BSDC1 0,309299474
-ZNF701 0,309462113
-PLIN3 0,309516744
-SORBS1 0,309562012
-FTL 0,309588981
-AGFG2 0,309634949
-UBR5 0,309647344
-MMP14 0,30965745
-SFRS8 0,309923113
-ITPR3 0,309975876
-PLK3 0,310097184
-NUP188 0,310124261
-CROCC 0,310245563
-CHSY1 0,310328559
-CTCF 0,310675097
-EDC4 0,310685915
-NFE2L2 0,31069885
-LILRA6 0,311008878
-SATB2 0,311055754
-GTPBP6 0,311254994
-TSPAN14 0,311316513
-C10orf18 0,31133762
-SECISBP2 0,311419174
-DHX34 0,311443077
-LSS 0,311450185
-CHI3L1 0,311532669
-PDGFC 0,311715929
-BMP7 0,311741682
-MBNL1 0,311755686
-DNA2 0,311841432
-COMT 0,312081286
-LOC100133005 0,312165679
-PTOV1 0,312192713
-LCAT 0,312407744
-LRRFIP2 0,312480817
-UCN 0,312589312
-AK024606 0,312655002
-MICAL3 0,312700621
-ROM1 0,31291043
-MED12 0,312925796
-CPNE1 0,313173908
-GBP2 0,313262095
-PELI2 0,313279559
-MLL 0,313398121
-HIF3A 0,313438743
-ST18 0,313449639
-AF131777 0,313643716
-CATSPER2P1 0,313785721
-ZNF302 0,314066212
-APBB2 0,314110219
-KIAA0907 0,31421022
-ZNF592 0,314679884
-HNRNPA1 0,314773035
-TSC2 0,314882123
-SFRS15 0,314884343
-ZNF835 0,314920694
-WDR6 0,314979423
-LOC729143 0,315037798
-PPARD 0,315048839
-U2AF2 0,315118843
-MGAT1 0,315269456
-ZNF44 0,315270856
-RPL36 0,315475789
-GRAMD3 0,315513449
-PTPN2 0,315554784
-AL080072 0,315635626
-C19orf2 0,315918303
-DNAH3 0,315930745
-ZNF146 0,316341954
-SMEK1 0,316538461
-MLXIP 0,31681421
-NMT2 0,316848231
-G3BP1 0,316864559
-DDX3Y 0,316997159
-STEAP1 0,317082981
-BC002629 0,317231764
-KDM2A 0,317406731
-TMEM39A 0,317430306
-C15orf29 0,317437851
-MACF1 0,317513626
-LOC391020 0,317572673
-SETD1A 0,317586539
-KTN1 0,317889697
-RUNX3 0,31809511
-NINJ1 0,318107478
-ARMC7 0,318150459
-BMP1 0,318194029
-DKFZP586I1420 0,318199121
-JARID2 0,318226296
-AW972351 0,318303541
-PAPSS2 0,31841091
-ELTD1 0,31845583
-ETS2 0,318667898
-CREB3L2 0,318705762
-DFNB31 0,31892768
-SERHL2 0,318966243
-C10orf26 0,319058163
-NM_030892 0,319421731
-WRAP53 0,319795295
-UBQLN4 0,319828198
-RALGDS 0,319938162
-PRKCH 0,320101043
-AU146983 0,320105843
-SLC5A3 0,32021553
-DUSP1 0,320239212
-NKX2-2 0,320312108
-C1orf183 0,320387827
-PCM1 0,320482282
-THRA 0,320531901
-NM_025028 0,320726138
-SIVA1 0,320736787
-TTR 0,320757249
-IKBKB 0,320778441
-ARID1A 0,321020715
-HDAC4 0,321059842
-ZFP36L2 0,321167918
-TMEM212 0,321179342
-AA443771 0,321214505
-AGAP5 0,32125931
-PIGA 0,3216713
-SFRS12 0,321704401
-LDLRAP1 0,321832456
-CCDC21 0,321857948
-SSFA2 0,321990716
-RAMP1 0,322050077
-FLJ10357 0,322160744
-LAD1 0,322322766
-RACGAP1 0,322340831
-NPIPL2 0,322616655
-CEP350 0,322648588
-CRLF1 0,322735059
-IGSF9B 0,322744338
-PLXND1 0,322801951
-MCL1 0,322913781
-ALMS1 0,32297709
-ZNF768 0,323059066
-RSL1D1 0,323228527
-C4orf34 0,323582139
-PNPLA6 0,323738553
-MAST4 0,323801655
-NME3 0,323835175
-SNHG3 0,32391938
-S100A12 0,324014586
-PPP4R1 0,32409634
-PLD1 0,324165096
-POLG 0,324186823
-NKTR 0,324203565
-ST3GAL4 0,324231325
-TMEM63A 0,324243134
-ST20 0,32438459
-RNF114 0,324406844
-HYI 0,324468621
-DUSP6 0,324699964
-NR1H2 0,324884332
-DVL2 0,324900869
-SRSF11 0,324979841
-CLK2 0,325170283
-MKLN1 0,325287178
-SCRIB 0,325320413
-KIAA0467 0,325541973
-DMWD 0,325745064
-KLHL23 0,32579572
-RPS6 0,325948088
-ZBTB17 0,326014408
-RAI14 0,326038467
-UBE2G2 0,326143089
-ZNF562 0,326186073
-EZR 0,326282578
-TRPS1 0,326283144
-HFE 0,326390644
-MED23 0,32658232
-DDX11 0,326766632
-SHMT2 0,326784725
-LRP5 0,326954416
-PTH1R 0,327100265
-LOC731602 0,327131294
-AA401963 0,327241371
-CDK5RAP2 0,327276136
-SERP1 0,327279991
-SLC1A5 0,327303416
-BGN 0,327370767
-HSD17B1 0,327475971
-AL390143 0,327497051
-DIAPH2 0,327617697
-PITPNC1 0,327719899
-SPRY2 0,327767132
-FZD7 0,327974293
-MAP4K4 0,328171238
-TNS1 0,328369107
-ZNF783 0,328517049
-M78162 0,328518574
-ADAMTS1 0,32853944
-FKBP5 0,328911405
-AGAP8 0,329115979
-PLEKHF1 0,329179433
-DNAJB1 0,329339376
-RBMS2 0,329438459
-HNRNPH1 0,329454824
-ULK2 0,329496298
-PAPD7 0,329501864
-SURF1 0,329547559
-W61005 0,329673439
-ZNF862 0,330131081
-GNA15 0,330266409
-CHD9 0,330273108
-DLC1 0,330294104
-TMEM2 0,330321664
-AK024879 0,330353812
-N4BP1 0,330435804
-SERF2 0,330633507
-SNRPA 0,330957742
-IRF8 0,33098543
-ABCA2 0,331251046
-NPFF 0,331328402
-CP 0,331565597
-AU144887 0,331713137
-AW851559 0,33185735
-TCF4 0,332062967
-ZNF354A 0,332076549
-TMEM92 0,332352956
-NFATC3 0,332386137
-SSRP1 0,332529738
-TCF7L2 0,332651908
-PIM1 0,332716071
-PIP4K2A 0,332914219
-EIF4EBP1 0,332959146
-LOC100132863 0,333054912
-MMRN2 0,333075923
-AU147295 0,333342973
-VIM 0,333356286
-C2orf67 0,333469715
-DNMT1 0,333550022
-CEP110 0,333679402
-BAZ2B 0,33371151
-KDELR2 0,333939841
-L3MBTL 0,334448273
-CDK19 0,334505985
-CYorf15B 0,334832089
-DDX17 0,334839203
-FKBP4 0,335166906
-STOM 0,335173644
-U82303 0,335241438
-LOC202181 0,335841121
-ATM 0,335893127
-STK3 0,335957389
-MID1 0,336166241
-IGFBP5 0,336454348
-PARP4 0,336459483
-EXOC7 0,336479503
-FANCG 0,336652927
-PHF2 0,336678654
-FBRS 0,33674511
-ANP32B 0,336836072
-NCK2 0,336876937
-CASP6 0,336920233
-ZBTB3 0,337122586
-DHFR 0,337448147
-APOLD1 0,337464001
-STAG1 0,337490482
-NM_024305 0,337551103
-SIGLEC8 0,337608204
-ERLIN1 0,337809212
-POLDIP3 0,337889824
-SPTLC2 0,33799094
-C7orf26 0,338204972
-UBE2D4 0,338265561
-MAP2K7 0,3384787
-MECOM 0,338508564
-DOCK1 0,339029429
-HS1BP3 0,339148762
-PRKY 0,339216015
-GOLGA1 0,33927478
-XPC 0,339433169
-PHF3 0,33953002
-HIC2 0,339768003
-C9orf7 0,340519877
-CTDSPL 0,340591645
-ZNF83 0,34077157
-PHGDH 0,340889735
-TMEM165 0,340978736
-CLN3 0,341078466
-AU147983 0,34113627
-PATZ1 0,341151411
-DIP2C 0,341390806
-RECK 0,341533646
-EWSR1 0,342003886
-SMAD7 0,342182186
-MTRF1L 0,34225773
-TJAP1 0,342452426
-PRKD2 0,342725824
-SPOP 0,343019265
-HLA-J 0,343028528
-PLXNB2 0,343103735
-FBXL14 0,343454364
-LAMA2 0,343637649
-RNF220 0,343845541
-CLK3 0,344164444
-STARD3 0,344187457
-OGT 0,345118989
-IFITM3 0,345141829
-HMOX1 0,345196784
-EIF2C2 0,34557825
-CCND3 0,345663426
-TGFBR3 0,345676022
-POLR2J3 0,345712548
-BCAR3 0,345713549
-C14orf147 0,34610842
-CLDN15 0,34616346
-TOP1 0,346179876
-RASL12 0,346286134
-MED13L 0,346369067
-SOS2 0,346799305
-SERPING1 0,347144597
-IER5 0,347279068
-TLE2 0,347426427
-LLGL2 0,347448236
-TMCC2 0,347500013
-PHF20 0,347602909
-SIRT4 0,347862165
-OSGIN1 0,348060574
-H2BFS 0,348076316
-NM_017756 0,348230007
-NCRNA00115 0,348422218
-MT1E 0,348733923
-NACC2 0,3488369
-NFIB 0,348943619
-AKR1C3 0,349206923
-ARPC1B 0,349407208
-NIPBL 0,349628117
-RPL11 0,349803207
-MSH6 0,350014407
-PTDSS2 0,350073646
-AL050145 0,350120404
-FAM107A 0,350271118
-CHN2 0,350358174
-DAPK2 0,350378033
-DLG5 0,350436992
-OPHN1 0,350596034
-C20orf11 0,351010126
-SLC35D1 0,35135795
-SELL 0,35142274
-FAM193B 0,351790995
-NM_024880 0,352020901
-RASGRP2 0,352114346
-CAPN3 0,352194849
-THOC1 0,352289646
-TAOK3 0,352396226
-FBXO42 0,352613215
-LARP6 0,352692849
-KLKB1 0,352702835
-METTL7A 0,352961228
-STIP1 0,352968743
-WIPF2 0,353085817
-FOXD1 0,353404764
-HSPB2 0,35378232
-ENGASE 0,353978221
-LAT2 0,354239264
-HIST1H2AH 0,354250391
-GSDMD 0,354483715
-TRA2A 0,354674037
-C19orf29 0,354762053
-BRPF1 0,355002213
-NUMA1 0,355146564
-SNW1 0,355320637
-SMARCC1 0,355374541
-ZNF175 0,35555253
-BATF3 0,355680727
-HIST1H2BC 0,35575565
-ERN2 0,356098991
-ZFR 0,356185362
-AW301806 0,356253591
-SMTN 0,356289422
-RPS6KA2 0,356774064
-MIIP 0,35685635
-ARGLU1 0,356919378
-CTNNAL1 0,357152141
-PCDH9 0,357228835
-LAS1L 0,357263917
-DOK1 0,358029668
-AFTPH 0,35852635
-ZNF143 0,358674337
-C11orf71 0,35888557
-MICALL2 0,359221642
-KDM6A 0,359260932
-CFH 0,359284568
-CEBPB 0,359516672
-MTUS1 0,359547348
-AW973791 0,359548173
-SERTAD2 0,359684853
-FGFR1 0,359721729
-KPTN 0,360479451
-NR2F2 0,361169645
-RGL2 0,361384531
-NM_014120 0,361482036
-TAF5 0,361611903
-ZC3HAV1 0,362177526
-BEST1 0,362248528
-TNFRSF1A 0,362724804
-CLIP2 0,363062238
-EHMT2 0,363078239
-IFITM1 0,363162265
-GCFC1 0,363190607
-PECAM1 0,363227012
-YES1 0,363556218
-ZFP36L1 0,363744573
-SBNO2 0,364095165
-RMND5A 0,364201024
-IL10RB 0,364481295
-CBS 0,364486163
-TBC1D2B 0,364503601
-C10orf10 0,36458821
-AU144530 0,365137826
-ZNF500 0,365202134
-ATP6V0E1 0,36527949
-SEPT8 0,365711052
-VCAN 0,365762437
-RPL36AP51 0,366073863
-RPL31 0,36613283
-TAOK1 0,36613666
-GCN1L1 0,366181489
-CALCOCO1 0,366300689
-GNA11 0,366387362
-SH2B2 0,366425408
-RREB1 0,367259867
-SLC35E1 0,3672965
-GPRC5B 0,367311931
-TCF7 0,367371063
-PDIA4 0,367810651
-ZNF34 0,367845233
-MBD3 0,36793004
-CXCR4 0,368041224
-C9orf114 0,368120984
-IFITM2 0,368313531
-ZNF665 0,368328536
-ZCCHC24 0,368368275
-LOC100133944 0,369022431
-CSDA 0,369150342
-AU148255 0,369666508
-CIZ1 0,369704457
-CRTC3 0,369792369
-CTNNA1 0,369962411
-RARRES2 0,37011032
-NM_025033 0,370246707
-VSIG4 0,370274949
-FAM48A 0,370421427
-ZDHHC11 0,370675656
-NPAS2 0,370715345
-ADH1B 0,370935809
-ACSL1 0,371025369
-C1orf63 0,371083889
-TYMP 0,371266716
-LEPREL1 0,371463494
-LAMB2 0,371472469
-MAFB 0,371542293
-AW971248 0,371589606
-BC003629 0,371603781
-FAM63A 0,371786321
-ABCA1 0,371992682
-IGF2R 0,37211512
-SOX13 0,372131188
-WAPAL 0,372391179
-ZFC3H1 0,372437982
-ZNF710 0,372493324
-HSPA6 0,37258644
-CCDC101 0,372823539
-BAZ1A 0,372824952
-AXL 0,372842922
-NPIPL1 0,372916072
-HDGF 0,372923023
-KHDRBS3 0,373093219
-MT1X 0,373144553
-MTMR15 0,373164421
-AF257099 0,373262757
-AEBP1 0,37342966
-KLHL25 0,373672957
-GJB4 0,37372121
-LUC7L3 0,374023648
-U79248 0,374142769
-LOC653562 0,374188384
-RBM4 0,374375075
-ABCC10 0,374890625
-CXorf21 0,374896996
-DAXX 0,374917403
-C1R 0,375063944
-TPST2 0,375279072
-KLHL24 0,375307199
-C7orf68 0,375539219
-ZCCHC8 0,375600764
-CASP4 0,375605037
-ETV1 0,37597402
-BIN1 0,376340315
-RGS19 0,376617752
-PKNOX1 0,377091746
-CTTN 0,377173864
-TRIP10 0,377452782
-ANGEL1 0,377498562
-PLIN2 0,377879768
-NM_025007 0,377942771
-PTMA 0,378229214
-S100A11 0,378255627
-AXIN1 0,378580893
-NPRL3 0,378633074
-PNN 0,378695864
-AV727934 0,378843386
-ANGPT2 0,37912784
-AK023918 0,379250766
-CNPY3 0,37927474
-AF130051 0,37947818
-TLE4 0,379880985
-PAPOLA 0,379974199
-ITGB5 0,380683545
-FAM38B 0,380693638
-PABPN1 0,380909515
-SLC6A8 0,38116858
-RYBP 0,38121367
-NASP 0,381229843
-FGR 0,381246748
-PER1 0,381695992
-CDR2L 0,381867955
-LRRFIP1 0,382075479
-HMHA1 0,382282948
-KIAA0485 0,382313718
-GUSB 0,38235255
-RPS17P5 0,38240934
-FXYD5 0,382563723
-RBL2 0,382697586
-RANBP10 0,382980904
-NEDD9 0,383084673
-MSL2 0,383144236
-FAM50A 0,383317183
-AL080232 0,383323554
-SPG21 0,383712061
-TPD52L1 0,384098652
-H2AFX 0,384141378
-SWAP70 0,384225003
-IVNS1ABP 0,384369268
-KDELC1 0,384542393
-MYL12A 0,384757468
-FOXO3 0,384856157
-MED13 0,385128516
-AL049252 0,38560217
-AF007147 0,385820993
-PAX6 0,385884587
-DNASE2 0,38591545
-SLC12A9 0,386200858
-SIRT1 0,38637719
-ARID5B 0,386492868
-MT2A 0,38656824
-SLC38A2 0,386710042
-GNG5 0,386756333
-SRRM2 0,386841072
-SERPINB6 0,386985458
-CC2D1A 0,387023088
-LRRC37A2 0,387067777
-CSF1 0,387071999
-RPL29P11 0,38708859
-SFRS14 0,387094074
-MYO9B 0,387103012
-AW972855 0,387241981
-TRIP4 0,387728627
-ZBTB40 0,387827711
-STARD8 0,387863703
-WBSCR16 0,387992811
-NXF1 0,388021286
-CTDSP1 0,38803541
-RSAD1 0,388042285
-SUV420H1 0,38833134
-CDKN1C 0,388508896
-NM_016415 0,388588403
-E2F4 0,388673603
-KANK2 0,388702219
-ZC3H7B 0,388980025
-ANGPTL4 0,389035415
-CRY1 0,389801967
-KIAA0556 0,389845114
-TBC1D16 0,390016803
-TCOF1 0,390109025
-ZFYVE26 0,390278079
-IFRD1 0,39034324
-EIF4B 0,390385914
-SMC1A 0,390525141
-SCIN 0,3907272
-MARS 0,391061966
-PTRF 0,391089965
-POLR2J 0,391514571
-APAF1 0,391530483
-ITPK1 0,3915415
-PNRC1 0,392133859
-CLIC2 0,392140808
-KIAA0913 0,392243895
-PRKAR2A 0,392619325
-PRKX 0,392750502
-SYDE1 0,392957216
-ACSL5 0,393140899
-LRP10 0,393162277
-LPP 0,393214983
-SNTB2 0,393383504
-NADK 0,393882671
-PCBP2 0,394206896
-N51370 0,394562467
-CLIC1 0,394663761
-CTBP2 0,394785714
-PHB 0,394929787
-BCL2 0,395102709
-TAF4 0,395492947
-LOC652607 0,395562084
-YBX1 0,396079328
-PRPF3 0,396609142
-SLC38A10 0,396741732
-ERBB2IP 0,396808535
-CFLAR 0,396840203
-TNFRSF10B 0,397091951
-PHC1B 0,397196351
-ARL17A 0,397406114
-ZBTB20 0,397424403
-REPIN1 0,397830532
-BE466926 0,397930108
-MT1P2 0,398055653
-ZNF778 0,398225613
-DICER1 0,398300689
-NM_018603 0,398329284
-RAF1 0,398631868
-MXD4 0,398685167
-FBXL7 0,398770393
-CALD1 0,399121196
-GSDMB 0,399246982
-ZCCHC2 0,399293751
-PODXL 0,399691684
-ACACB 0,400136922
-VEZF1 0,400413083
-PLEKHM1 0,401187317
-CSPG4 0,401646086
-ID3 0,40170175
-RBM41 0,401719975
-KDM6B 0,401885964
-PHF15 0,402522419
-LAMP2 0,402538077
-CDC14B 0,402583482
-HNRNPL 0,403044314
-SLC4A2 0,403448509
-DDX23 0,403953946
-TUBD1 0,40407115
-SLC16A3 0,404204458
-CAPN2 0,405022548
-CBFA2T2 0,40560438
-TCEB2 0,405769952
-HNRNPF 0,406126644
-MORC2 0,406182732
-FOXO1 0,406430281
-AI962978 0,406538883
-HP1BP3 0,406567553
-CBFB 0,406789498
-RBM14 0,406886421
-SFI1 0,407058786
-ZHX3 0,407089165
-KDM3A 0,407233406
-SIRT2 0,407341821
-ANKS1A 0,407373917
-TCF3 0,407442968
-NOTCH2NL 0,407672378
-EEF1D 0,407830724
-SOX12 0,408065349
-SLCO1A2 0,40820492
-HNRNPA3 0,408299868
-GTF2H3 0,408624789
-FZD9 0,408729069
-SAFB2 0,408755308
-APBA3 0,408834306
-ASCL1 0,409161488
-CG012 0,409559201
-WDR59 0,409606436
-LAMA5 0,409632505
-ZNF276 0,409730125
-ZNF395 0,410080702
-TIMM44 0,410223052
-BGLAP 0,410749324
-ZHX2 0,411039562
-CARS2 0,411302016
-SLCO3A1 0,411338796
-LOC442497 0,411765627
-FRYL 0,411842495
-CYP2J2 0,412070197
-ABL1 0,412522321
-INF2 0,412975218
-SGK1 0,413352645
-SFTPB 0,413789208
-TIGD1L 0,41383023
-RBCK1 0,414019825
-TRAPPC10 0,414285862
-DUSP7 0,414641136
-WSCD1 0,415016303
-DCP1A 0,415308358
-LPAR1 0,415365439
-RBBP6 0,415730871
-DONSON 0,416255506
-C16orf5 0,416258918
-NCOA1 0,416350707
-CFHR1 0,416440287
-AA126763 0,416566153
-LRRC32 0,416765832
-CP110 0,41732481
-LTBP3 0,417338221
-TDRD3 0,417356196
-HMG20B 0,417456909
-CDC42EP2 0,417645635
-TAF1C 0,417736819
-NM_013344 0,41778911
-VGLL4 0,417820331
-PHKA2 0,417904785
-KDSR 0,418009802
-RELA 0,418064238
-TBL1X 0,41814877
-SIAH2 0,418727849
-MYO1E 0,418747589
-HIST1H2BD 0,419127582
-AI744451 0,419208355
-PTMAP7 0,419537834
-ARID5A 0,419593497
-CYP27A1 0,420064872
-RAB13 0,420441013
-CPSF7 0,420526378
-CPT1B 0,420770156
-LRDD 0,420794327
-PILRB 0,421599366
-STAB1 0,421733406
-FCHO1 0,422126906
-ZNF32 0,422311821
-TBC1D3H 0,422328806
-C1orf66 0,42292679
-NM_025032 0,423323973
-AI732802 0,423584905
-PCID2 0,423787762
-POGK 0,423912669
-TMEM140 0,424587207
-TMC6 0,424604298
-AL080160 0,42490597
-AK021505 0,425024442
-SCD5 0,425610027
-RAD52 0,425956612
-AF116715 0,425960499
-DCI 0,425967692
-SFRS18 0,426091505
-HCG2P7 0,426136765
-ADORA2A 0,426366158
-NM_021651 0,426442506
-MID1IP1 0,426940092
-HNRNPC 0,427103695
-NM_025024 0,427155973
-AK024315 0,427460397
-AK021514 0,427966252
-SLC29A3 0,428138792
-NSUN5 0,428255135
-PHF10 0,428599049
-DAPP1 0,428626141
-TMEM109 0,428647746
-LOC91316 0,428742129
-ITGB4 0,42956266
-SLC30A1 0,429998682
-AW150065 0,430129937
-ZCCHC6 0,430267528
-ARHGEF2 0,430371137
-AK027193 0,43049002
-TRIM52 0,430535815
-MT1G 0,430767233
-NOTCH1 0,430849119
-ZRSR2 0,43114681
-RPS6KA1 0,43184981
-KANK1 0,432456197
-FURIN 0,432618855
-APOBEC3C 0,432749845
-ANKRD40 0,432772877
-TRIOBP 0,432900403
-ZNF384 0,433116555
-CDKN1A 0,43319672
-BTG1 0,433570541
-EPHX1 0,433658916
-CNOT6 0,434207544
-HSPA1L 0,434322364
-PKD1 0,434547199
-WAS 0,434717417
-RPL23AP32 0,434993767
-P4HA1 0,434997425
-MAX 0,435160002
-UIMC1 0,435278167
-NM_025120 0,435322168
-NCOA6 0,435700178
-TPD52L2 0,435768747
-BCL6 0,435938226
-AK024108 0,436355329
-C7orf23 0,436800978
-CDC42BPA 0,437074951
-CD59 0,437137855
-POLR1B 0,437227618
-TLR5 0,437498143
-HDAC1 0,437993569
-ARHGEF7 0,438071237
-AA045174 0,438161955
-TBC1D17 0,438488128
-PRELP 0,438518539
-GTF2H2B 0,438525643
-HIST1H2BK 0,43866778
-AU147851 0,438979485
-RBM39 0,439661925
-IQGAP1 0,439786742
-RPL18AP3 0,440613252
-LTBR 0,440721546
-RPL35A 0,441136859
-ARAP2 0,441441928
-ARAF 0,441560027
-MT1H 0,441587824
-LOC441258 0,442117007
-ZCCHC14 0,442132801
-IRF7 0,442147625
-NOL12 0,442203671
-PTPLB 0,442541309
-AI683552 0,442752948
-MYST1 0,442881562
-MXI1 0,443040642
-AW974910 0,443299524
-C1orf144 0,443500279
-KRCC1 0,444417306
-PIAS4 0,444438643
-SRSF1 0,444637015
-LRP2 0,444740953
-ZDHHC18 0,445392541
-SPN 0,445443935
-ST13 0,446667878
-PHF17 0,446746739
-NACA2 0,446876872
-SASH1 0,447285208
-CD22 0,44772036
-CSNK1E 0,447902552
-COL5A3 0,447933631
-MAT2A 0,448695587
-EFHD1 0,448820126
-MAP3K3 0,448963961
-BIN3 0,449317201
-LUC7L 0,449469644
-KIF1C 0,449622117
-RNF144A 0,450034368
-TULP3 0,450626451
-CDKN2C 0,450879897
-HSD17B7 0,451226227
-ACIN1 0,451331774
-PABPC3 0,451363083
-PHF21A 0,45139036
-HNRNPH3 0,451480034
-HIST2H2BE 0,452219911
-RRP1B 0,452597128
-SOX2 0,453132172
-ZNF444 0,453296716
-FAM13A 0,453547738
-JUP 0,453753674
-PODNL1 0,453854292
-MAML1 0,453885
-SNRNP70 0,45408945
-SDCCAG3 0,45464357
-PLGLB1 0,454722494
-CDH19 0,454754165
-HSPA1B 0,455063205
-ARHGEF10 0,455229121
-NFIL3 0,455469821
-NFKBIA 0,455577982
-XRCC2 0,455670024
-ACTN4 0,455764555
-PDS5A 0,456071133
-POU2F1 0,456120351
-VPS54 0,456318614
-BANF1 0,456451252
-PGCP 0,456765652
-RPL28 0,456867479
-ICAM2 0,457066169
-SNAP23 0,457069788
-SART1 0,457941993
-AK023891 0,458253977
-BANP 0,458588544
-MAP3K11 0,458968207
-EPOR 0,459463669
-FKSG49 0,459538011
-MT1F 0,459638951
-NM_014128 0,460468204
-AP1G2 0,460676306
-GAS2L1 0,461632768
-PHIP 0,462053958
-NOL8 0,462387404
-NM_017932 0,462395281
-RNF130 0,462894529
-ZMYND8 0,463309493
-AK024525 0,463401166
-TRIM28 0,463454342
-BCAT2 0,463509769
-TYRO3 0,463574548
-PHLPP1 0,463738295
-BST2 0,465024297
-PDGFRB 0,465034704
-AL049987 0,465336929
-AKAP8L 0,466278804
-TGM2 0,467555999
-CREBBP 0,467899354
-KIAA0894 0,468325808
-DDX39 0,468959477
-NCAPD2 0,468959537
-ALPK1 0,469621875
-TGIF1 0,469902489
-PPP1R14B 0,470121069
-PNMT 0,470291567
-NAA16 0,470467422
-ZNF611 0,470526774
-ZRSR1 0,470857426
-NPIP 0,472818474
-RBM38 0,473036567
-USP34 0,473278809
-TGFB3 0,474067001
-ITSN2 0,475328182
-CEBPD 0,475754278
-MCM3AP 0,476296498
-HAPLN2 0,476718109
-POGZ 0,477224004
-NR2F1 0,477556735
-GAS1 0,478628972
-SLTM 0,478903701
-ECE1 0,479007813
-CALCOCO2 0,47910558
-RXRA 0,479821295
-MEIS2 0,480178943
-CLEC2B 0,481843785
-AL049260 0,482481089
-CHST3 0,48259726
-COL16A1 0,483094975
-SLC25A16 0,483255606
-LHPP 0,48421483
-AF010144 0,484619234
-GTSE1 0,484629217
-MUM1 0,484956644
-TNXB 0,485246904
-PRINS 0,486032909
-ANKRD49 0,486282532
-PTPRK 0,486899575
-PPAP2C 0,487395433
-C22orf9 0,488987561
-KHNYN 0,489026627
-RAPGEF3 0,489474077
-AF078844 0,489716822
-MAN2A1 0,489875474
-IFT20 0,490824284
-USP21 0,490859618
-NOP2 0,491526918
-LOC440248 0,491905455
-LOC647070 0,493492979
-MAFF 0,494072026
-BG251521 0,495196452
-C6orf145 0,496322836
-MLL4 0,496324893
-ATF4 0,49676781
-RELN 0,497310216
-PELI1 0,497491599
-P2RX7 0,497499324
-CNOT2 0,498172475
-FAM38A 0,498599859
-DCLRE1C 0,498693515
-INSR 0,502304787
-MAPKAPK2 0,502573806
-NDE1 0,50267356
-MT1M 0,502716901
-CDK5RAP3 0,504041432
-SULT1A4 0,504805398
-NSUN5P2 0,505093708
-ANKRD10 0,505841449
-LOC339047 0,506042447
-LRRC1 0,506594446
-CUX1 0,507257715
-SRRT 0,508240438
-MAF 0,508625791
-EBLN2 0,509549245
-NM_017618 0,510705903
-RBM4B 0,51138423
-FBXW12 0,511744983
-ATP8B1 0,511969804
-NM_024978 0,512045897
-KCNMB4 0,512142959
-CLMN 0,512461537
-LOC100132540 0,512589899
-SERPINH1 0,513136463
-RHBDF2 0,513703735
-PCF11 0,514081494
-HAUS2 0,514694211
-TECPR2 0,514970535
-TNIP2 0,515014912
-AUP1 0,516155581
-KIAA0101 0,516801916
-N35922 0,51703624
-STK38 0,517483454
-AZGP1P1 0,518047589
-C13orf15 0,518310047
-PRR11 0,518691616
-PDCD6 0,51972326
-AFF1 0,520716014
-AF222691 0,521107674
-BE045142 0,521502008
-PACS2 0,521749261
-PSRC1 0,522634606
-ZNF358 0,523463012
-MAPKBP1 0,523696079
-S100A4 0,524041412
-MYO1C 0,524902669
-IRF3 0,52538788
-TOB2 0,526119659
-KLHL21 0,527145117
-PGF 0,527713686
-LOC399491 0,528407104
-ARAP1 0,528556373
-AZGP1 0,528659072
-SIRT7 0,528927974
-C16orf53 0,529668261
-KLHL2 0,533153888
-AK022213 0,533802801
-ANKRD28 0,534099367
-TF 0,536170201
-MAVS 0,53636005
-MSX1 0,536723495
-C12orf35 0,537890473
-AA554945 0,538449904
-SUN2 0,539191173
-RBM6 0,54218394
-AL080112 0,542349721
-SORT1 0,542569398
-AL049285 0,542660805
-FOXO4 0,542834527
-ABCA8 0,543725594
-RING1 0,54468938
-KCNE4 0,546337688
-TAZ 0,546506594
-DIP2A 0,546907877
-CLK4 0,548788669
-ZNF277 0,549312201
-MUS81 0,551193399
-DBT 0,556696292
-EMP3 0,557013195
-DDIT4 0,557077384
-RUFY1 0,557170712
-MYST3 0,559285285
-PRPF4B 0,559881298
-LOC100132247 0,562956585
-HSPB1 0,56508456
-CHD7 0,566776564
-CHORDC1 0,566831861
-COBL 0,569205746
-STAG2 0,569603186
-CTDSP2 0,570069613
-ZNF160 0,572703009
-PDE4C 0,574535337
-WWC3 0,575159977
-BMI1 0,576213767
-CRYAB 0,577245348
-AHCTF1 0,577515066
-ADIPOR2 0,5780263
-CASC3 0,57815663
-MUTYH 0,579456271
-AK023783 0,580340854
-HIGD1B 0,583663012
-PLOD1 0,587347495
-PRR14 0,587364521
-SH3BP4 0,58788373
-C19orf28 0,587956493
-NDRG1 0,588555643
-HIST1H1C 0,591446402
-TCF12 0,592176798
-MPST 0,593408757
-SEPP1 0,593935425
-DNAJB6 0,595685757
-SIRPA 0,596218961
-FLT1 0,597923318
-MYOT 0,598968138
-HIST1H2AC 0,600586387
-HBP1 0,600714263
-KAZ 0,601415288
-PTBP1 0,602313539
-NSUN5P1 0,603090503
-GUSBP3 0,604393039
-KCNJ2 0,616084197
-KAT2A 0,620256502
-MCM7 0,622618327
-FBXW4 0,627081137
-MKNK2 0,628440154
-IL17RB 0,631530593
-CLK1 0,632420317
-LRP4 0,632833859
-FAM53B 0,641895571
-JMJD6 0,64411039
-TYK2 0,644727629
-PLOD3 0,644893842
-CXXC1 0,650530485
-AK024136 0,659066605
-PAN2 0,66036619
-NPTX2 0,665210794
-SPEN 0,669461617
-SETD5 0,670191692
-STX10 0,674048462
-CDK2AP2 0,67411425
-PPM1B 0,68382966
-SLCO4A1 0,685048974
-GLT25D1 0,706365388
-ZC3H11A 0,716021559
-ZBTB16 0,720405109
-ZNF692 0,720940567
-NUPR1 0,724120307
-FLCN 0,747339708
-NFASC 0,755177517
+name value
+GBE1 -0,943978048
+SLC18A2 -0,941309505
+KCNJ6 -0,894120983
+DLK1 -0,887122171
+PTDSS1 -0,851959645
+FGF13 -0,842876271
+PCDH8 -0,83524894
+ZNF226 -0,82900335
+SLC6A3 -0,824713365
+PIP5K1B -0,812285785
+DENR -0,81101551
+TPBG -0,806963209
+PRKAR2B -0,805288865
+OSBPL10 -0,80406299
+ALDH1A1 -0,795042129
+GGCX -0,795035797
+ACP2 -0,794853979
+SLITRK5 -0,793842132
+FAM70A -0,793715412
+HPRT1 -0,792370336
+CCNH -0,790971864
+MYRIP -0,78490295
+TUBB2A -0,783142444
+ACTR10 -0,782043082
+BASP1 -0,778702387
+CADPS2 -0,777552826
+PID1 -0,775106213
+SV2C -0,774895093
+RBM3 -0,77091551
+REEP1 -0,770000111
+RIMBP2 -0,766421185
+CNIH3 -0,765790316
+DMXL2 -0,765309344
+LOC10431 -0,762992699
+SV2B -0,759985564
+AGK -0,756506198
+RCAN2 -0,753762002
+LPPR4 -0,753018962
+RALYL -0,75270126
+L1CAM -0,751978689
+BCAS2 -0,751241508
+LOC100131795 -0,750350108
+TH -0,748260596
+AV756161 -0,747351587
+TRIM36 -0,746057792
+MPPED2 -0,743864716
+NELL2 -0,742513977
+MAGED1 -0,739190733
+LRRC49 -0,738776851
+SYNGR3 -0,734846774
+ERC2 -0,734619705
+VBP1 -0,73223558
+UQCC -0,729749962
+DCLK1 -0,725139215
+GSS -0,724321987
+OPA1 -0,723790592
+PPP2R2B -0,720892147
+COPS4 -0,720599852
+NSF -0,720580224
+DLD -0,72035948
+DYNC1I1 -0,719837984
+GABARAPL3 -0,717235008
+GPRASP1 -0,71302626
+NAP1L2 -0,712876929
+AMPH -0,711957162
+PNMAL1 -0,70952389
+RGS6 -0,706463
+LDB2 -0,704777497
+TTC19 -0,704232585
+SCN3B -0,703738866
+ATPIF1 -0,702603531
+BEX1 -0,700382911
+LMO3 -0,699029823
+TBC1D9 -0,698189481
+NDUFS1 -0,697230219
+INSM1 -0,696524737
+PARL -0,696362568
+MRPL15 -0,688780959
+C3orf14 -0,687875821
+C19orf62 -0,687403479
+PCYOX1L -0,686812669
+VRK1 -0,685016241
+MDH2 -0,684889561
+SMYD3 -0,684642724
+ASAH1 -0,68459801
+GSTA4 -0,684021936
+NDUFA9 -0,683116722
+ATP5C1 -0,682289667
+DDX25 -0,681511867
+GNG3 -0,681122999
+MUDENG -0,67996077
+SCG2 -0,679728044
+MOAP1 -0,679575281
+SYT1 -0,678979261
+ATP6V1H -0,6786546
+SHOC2 -0,677754756
+PCSK1 -0,677441918
+LBH -0,67710638
+HK1 -0,676818391
+KIAA0319 -0,676346138
+SMAP1 -0,67618103
+EHBP1 -0,675429621
+RAP1GAP2 -0,673705297
+FABP7 -0,673485271
+LRRN3 -0,6731503
+AHNAK2 -0,672875949
+DHDDS -0,671959403
+SNAPC5 -0,670824633
+C17orf108 -0,670563093
+AL390170 -0,67026906
+PTS -0,669577055
+NUDT11 -0,668061506
+HMP19 -0,66794356
+IMMT -0,667541939
+RGS4 -0,667109174
+RET -0,667088994
+PBLD -0,666164981
+AP3M2 -0,666056972
+WDR7 -0,665751643
+ATP6V0D1 -0,665487037
+RTF1 -0,664652469
+TUBB3 -0,664644351
+CHCHD2 -0,664529051
+DYNLT3 -0,663584428
+RAB6B -0,662755469
+CHGB -0,661865706
+NGFRAP1 -0,659441958
+AZIN1 -0,659394366
+EN1 -0,659313013
+SNX10 -0,659251628
+MIA3 -0,65882244
+ANK1 -0,657621479
+NR4A2 -0,65598531
+ANAPC13 -0,655864214
+RGS7 -0,654445938
+NME5 -0,652754395
+TXNDC9 -0,652019899
+PPIP5K2 -0,651763237
+RFK -0,651442652
+BE674466 -0,651048329
+PEG10 -0,650932122
+PIAS2 -0,650823358
+CUX2 -0,649970555
+SEPT6 -0,649422911
+FKBP1B -0,649416387
+C12orf10 -0,648407487
+HMGCS1 -0,648164918
+WDR61 -0,648133373
+GFPT1 -0,647751981
+MLLT11 -0,647471245
+AGTR1 -0,645674318
+CSNK1D -0,645408463
+WDR47 -0,64495088
+PSMD14 -0,644669314
+CISD1 -0,643780748
+PSMD11 -0,642982055
+KCNS3 -0,642919136
+TIMM8B -0,642730563
+RUNDC3B -0,641744336
+ANKRD6 -0,640032629
+MDH1 -0,639623665
+STMN2 -0,639070421
+BAI3 -0,638894116
+STX12 -0,638382169
+NECAP1 -0,638376593
+NIT2 -0,638223243
+CIRBP -0,637859912
+XK -0,636787355
+KIAA1797 -0,636384728
+ICMT -0,636379567
+GALT -0,636138691
+SPINT2 -0,635454321
+PAIP1 -0,634724103
+TAGLN3 -0,63459569
+CADPS -0,634245008
+GALNT11 -0,634168707
+SLC9A6 -0,632805526
+ANKRD34C -0,63217094
+COPG2IT1 -0,63213856
+VPS4B -0,63135628
+ATP6V0E2 -0,631164455
+SC5DL -0,631137699
+CNPY2 -0,630875303
+GCC2 -0,630691438
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+FBXO9 -0,62572532
+FLJ41278 -0,6251633
+SLC30A9 -0,624759053
+LOC100132015 -0,623179237
+EXOG -0,622056922
+RAP1GAP -0,618803848
+DYNC1LI1 -0,618641756
+HARS -0,618639749
+NDUFA5 -0,618245275
+SPCS1 -0,618130333
+PSMB7 -0,618122572
+NETO2 -0,618103081
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+HN1 -0,612796898
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+ATP5A1 -0,611141848
+ARMCX5 -0,610703909
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+CERK -0,610508368
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+STRAP -0,609237631
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+ZWINT -0,577661475
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+FBXL2 -0,575141782
+KIFAP3 -0,574923419
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+TCP11L1 -0,570951095
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+IARS -0,569079443
+CDH8 -0,569072707
+RNF41 -0,568830451
+SCN3A -0,568276898
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+FIG4 -0,566751868
+DDX24 -0,566446037
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+VDAC3 -0,563895581
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+CCT8 -0,48112028
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+SLC4A1AP -0,46898494
+AP2A2 -0,468669242
+CX3CL1 -0,46850557
+WBP11 -0,468444743
+LASP1 -0,468444317
+GOT1 -0,468375399
+C6orf120 -0,468133996
+SPAG7 -0,468070563
+SERGEF -0,467688975
+TFB2M -0,4675501
+AP3B2 -0,467537408
+PAFAH1B1 -0,467362101
+BPGM -0,467130793
+CRAT -0,466839519
+DDX1 -0,466770911
+ADAM23 -0,46652833
+ASB6 -0,466473575
+PCDHA1 -0,466456945
+TUSC3 -0,465574044
+TCEA2 -0,465512943
+SMARCA4 -0,4653413
+DAPK1 -0,465142929
+DBNDD1 -0,464965333
+NDUFC2 -0,464959656
+IDH3B -0,464778307
+CDC37L1 -0,464692992
+WDR11 -0,464429092
+CD200 -0,464378251
+TUSC2 -0,464289641
+IRGQ -0,464009317
+CALY -0,463919598
+NNT -0,463872117
+MSH2 -0,463745236
+GYG1 -0,463657489
+FAM134C -0,463380379
+RTN2 -0,463379977
+RBM12 -0,463289569
+SYNJ1 -0,463207762
+ABCA5 -0,462881594
+ENTPD4 -0,462777994
+MAP2K4 -0,462732144
+AIMP2 -0,46256199
+PITPNA -0,462484131
+BNIP3 -0,461982272
+COPS5 -0,461956463
+BRE -0,461910476
+MIR21 -0,461667267
+ATP5S -0,46152488
+SIN3B -0,461515059
+NAT10 -0,461457105
+MTCH2 -0,461117099
+ACHE -0,461032229
+PSD3 -0,46079613
+UCHL3 -0,460466303
+SMPX -0,459975528
+USP11 -0,459753441
+RNF187 -0,459566796
+AAGAB -0,458932639
+ENY2 -0,458770966
+NDEL1 -0,458614173
+FAM184A -0,458384449
+TOX4 -0,458204483
+SLC25A15 -0,458110832
+SACM1L -0,458050139
+ADARB1 -0,458034616
+SPHK2 -0,457781426
+CES2 -0,457687554
+CYFIP2 -0,457201169
+KPNA2 -0,457034156
+ACTR1A -0,456856222
+SLC25A22 -0,456321526
+DPYSL3 -0,456025294
+PRKAR1A -0,455984698
+SIDT1 -0,455560984
+TIPRL -0,455474112
+EIF5 -0,455347544
+C16orf58 -0,455176502
+RAB7A -0,454946879
+MFSD6 -0,454914435
+NDUFS2 -0,454605666
+APOOL -0,454580027
+GNB1 -0,454284789
+SARS -0,454282127
+PIK3R3 -0,454240907
+SERINC3 -0,454097365
+ST3GAL5 -0,45407104
+DHRS11 -0,453695947
+NEDD8 -0,45367218
+RAB15 -0,453664346
+HSPA13 -0,453577406
+OLA1 -0,453153228
+C3orf18 -0,45312023
+AF131844 -0,453027105
+C12orf52 -0,452914604
+ACBD3 -0,452894377
+PCIF1 -0,452240197
+BMP2K -0,451224584
+TSPYL5 -0,450674174
+SEC63 -0,450642641
+C7orf44 -0,450408444
+PWP1 -0,450360796
+SLC25A14 -0,45012674
+SYP -0,449768016
+PRKCB -0,449564151
+KIF2A -0,449276369
+PEX26 -0,449100108
+SDHA -0,448617251
+PITRM1 -0,448602767
+PPA2 -0,448269554
+MAN2A2 -0,448177121
+FAM49A -0,448170721
+KCTD9 -0,448062861
+REEP2 -0,44801948
+NDUFS3 -0,447803075
+CHGA -0,447356315
+UBE2E3 -0,447311178
+LOC595101 -0,447006376
+RNF170 -0,446698112
+TMCO1 -0,446651514
+PCCB -0,446640741
+RAB1A -0,44645249
+ATP1A1 -0,446309137
+KIAA1045 -0,446174802
+CASD1 -0,445992918
+C3orf37 -0,445975885
+RAD17 -0,445659766
+BBS4 -0,445631347
+TBC1D19 -0,445509157
+TSG101 -0,445289202
+DKK3 -0,445181251
+KCNQ2 -0,444911548
+EIF4E -0,44477948
+LOC100134209 -0,444742688
+OSTF1 -0,444651424
+PPCS -0,444330494
+ATP13A2 -0,443924538
+DHRS7B -0,443866868
+TSN -0,443785273
+AI201594 -0,443780197
+UBE2J1 -0,443536878
+C12orf51 -0,443320039
+INPP5F -0,44324612
+KIAA0391 -0,443138749
+NDUFB8 -0,442168118
+COX8A -0,442151263
+PLCB4 -0,442128902
+UQCRC1 -0,442055114
+RNMT -0,442010619
+PSMB4 -0,441631296
+ATP9A -0,441570839
+COMMD8 -0,441419712
+STX7 -0,441415012
+UQCRFS1 -0,441387219
+ARMC8 -0,441335025
+USP33 -0,441131902
+SC4MOL -0,441051846
+AVL9 -0,440604375
+CORO1C -0,440555184
+ATP6V0A1 -0,440500219
+AKTIP -0,440321706
+C11orf49 -0,440065839
+ACCN1 -0,439959618
+DYNC1H1 -0,439954428
+RTN4 -0,439926435
+IFT52 -0,439664934
+ARIH1 -0,439616652
+SLC23A2 -0,439279622
+FDPS -0,439263979
+ZW10 -0,439088192
+C6orf211 -0,438493952
+CAPZA2 -0,438442617
+TRIM9 -0,43841496
+PANK2 -0,438226487
+SLC25A36 -0,437878589
+TM7SF2 -0,437751686
+GPD1L -0,437274057
+TM2D3 -0,437156245
+TBC1D22A -0,436837159
+AFF2 -0,436678505
+PSMA4 -0,43652406
+SCAPER -0,436328183
+KPNB1 -0,43624217
+C8orf33 -0,436164892
+RRAS2 -0,435924543
+PNMA1 -0,435862986
+DRD2 -0,435854058
+CCDC92 -0,435740221
+CYB5B -0,435703661
+DNM1L -0,435497666
+FAM98A -0,435109538
+CYCS -0,43500707
+UBE2B -0,434857087
+DCTPP1 -0,434751269
+ENC1 -0,434576571
+SAP18 -0,434463135
+MED7 -0,43446171
+UBXN6 -0,433506891
+MAEA -0,433493136
+C20orf27 -0,433220759
+ARFGEF2 -0,4331108
+FKBP9 -0,433030189
+COQ10B -0,432955202
+SNRNP25 -0,432902395
+PHKB -0,432809153
+CETN2 -0,432732838
+PIK3R4 -0,432641256
+EFR3A -0,432263211
+FAM162A -0,432255742
+LOC732160 -0,432226821
+SRPK2 -0,432044566
+USP9X -0,431489845
+DENND2A -0,431031563
+PPP2CA -0,430950806
+CHST1 -0,430892555
+OSBPL9 -0,430720865
+TPM3 -0,430527364
+UGP2 -0,430314768
+AL049387 -0,430134526
+ARHGDIG -0,429952838
+GPR161 -0,429932801
+HGSNAT -0,429440496
+TCEAL4 -0,429402449
+KHDC1 -0,429285977
+SPATA7 -0,428924113
+NIPSNAP3B -0,428922472
+NHP2L1 -0,42870798
+BZW2 -0,428685674
+BZW1 -0,428658261
+ABCF3 -0,428526247
+PEX19 -0,428349422
+POLR2K -0,42820853
+FAM134B -0,428156057
+TUBGCP4 -0,428150919
+CSNK2A1 -0,427824997
+PPP2R5D -0,427719013
+CEND1 -0,427667723
+RNF11 -0,427514623
+EBNA1BP2 -0,427275229
+SDHC -0,42690156
+ATP6AP2 -0,426823582
+MAPK1 -0,426681157
+YTHDC2 -0,425950246
+ACTR3B -0,425721173
+LRRC47 -0,424928312
+ANO10 -0,424906321
+MORF4L2 -0,424702281
+NAE1 -0,424669605
+GRSF1 -0,424576498
+UBE3C -0,42455123
+RRM1 -0,424268285
+IARS2 -0,424201991
+HINT1 -0,423973896
+B4GALT7 -0,423964657
+OBSL1 -0,423852756
+RPH3A -0,423713255
+PTPRM -0,423526608
+TRAP1 -0,423405292
+GSTO1 -0,423136683
+PGK1 -0,423107749
+KCTD2 -0,423033005
+AKAP9 -0,423014145
+KIAA0090 -0,422971022
+NIF3L1 -0,422805913
+SAE1 -0,422487927
+TRAPPC4 -0,422454822
+UBE3B -0,422322842
+MRPL13 -0,422291395
+ARF1 -0,422218883
+NCKAP1 -0,421739152
+COX11 -0,421717769
+XPA -0,421552598
+FKBP11 -0,421544606
+ZFAND1 -0,42136139
+RUSC1 -0,421250909
+PSMC2 -0,42099626
+MCM4 -0,420976269
+HEXA -0,420954607
+PDE4A -0,420795908
+VPS45 -0,420785909
+OGFOD1 -0,420640442
+ADPGK -0,420505817
+AP2M1 -0,420467875
+PSMD5 -0,420139323
+PGRMC1 -0,420109613
+CLASP2 -0,419942702
+CAMTA1 -0,419843296
+COX5A -0,419753275
+BCAP29 -0,419678508
+C21orf59 -0,419586484
+INSIG1 -0,419347593
+NDUFAF1 -0,419256514
+SNCG -0,419205938
+NCAN -0,418993508
+SLC24A3 -0,418714364
+MAP2K1 -0,418679322
+BRCC3 -0,418660516
+MYCBP2 -0,418420128
+PREPL -0,41818051
+TUFM -0,418149804
+LYRM2 -0,41810337
+ORC3L -0,417994092
+TSR2 -0,417894679
+SLC41A3 -0,41774061
+DZIP3 -0,417712026
+MRPS11 -0,417644175
+B4GALT6 -0,41761846
+CHD5 -0,417472
+TUBA1C -0,417351982
+OTUB1 -0,41729395
+DCAF6 -0,417154254
+UQCR10 -0,417021115
+BEX4 -0,416948363
+RTN3 -0,416868526
+GOLT1B -0,416408995
+MRPL3 -0,416396676
+DDX19A -0,416375948
+C4orf41 -0,416356919
+SEMA3G -0,416349944
+TUBA3D -0,416216957
+B4GALNT1 -0,415958605
+TOR1A -0,415819164
+SUPT16H -0,415597727
+ACTR3 -0,415469056
+ABCB9 -0,415410201
+SERF1B -0,415262572
+PSMC6 -0,415072747
+GALNT2 -0,414525722
+ARF5 -0,414370994
+TCEB1 -0,414262524
+FEN1 -0,414164817
+HS2ST1 -0,413801139
+FBXL15 -0,413238338
+ANAPC10 -0,413161353
+MAPK10 -0,413048251
+FGF12 -0,412576909
+GTF2B -0,412561968
+CALM3 -0,412474461
+C12orf5 -0,412385409
+BTRC -0,412323302
+UBXN8 -0,411884422
+G6PC3 -0,411853401
+MARK4 -0,411850043
+SDHB -0,411814414
+FXC1 -0,411804756
+KIAA1467 -0,411406746
+COL4A3BP -0,411372338
+MADD -0,411317373
+SLC25A11 -0,411257994
+APBB3 -0,411242683
+LDHB -0,411172229
+ENTPD3 -0,410988615
+CAMK2B -0,410817586
+C15orf24 -0,410807275
+RAB11FIP5 -0,410722406
+C18orf1 -0,410410534
+IL13RA2 -0,410393436
+TMEFF1 -0,40994415
+TAX1BP1 -0,409905258
+ABHD11 -0,409662969
+SETD4 -0,409479623
+NARS -0,409352949
+LOC441259 -0,409193342
+SMAD2 -0,408937637
+MAGEH1 -0,408820062
+LPIN2 -0,408744346
+WRB -0,408371938
+HSPB11 -0,408269901
+COMMD9 -0,407620354
+RMND1 -0,407542555
+RBP1 -0,407484296
+TSPAN7 -0,407465467
+YKT6 -0,407243851
+ATP5L -0,407238078
+STAT1 -0,407123963
+SPTAN1 -0,407085674
+SLBP -0,407034029
+FAM115A -0,407018502
+ATP1B1 -0,407007242
+GIN1 -0,406994648
+SLC25A4 -0,406703055
+RPAP3 -0,40653888
+ELAVL4 -0,406510215
+LDHA -0,406394191
+GABRG2 -0,406143723
+ACOT1 -0,406088493
+LZTFL1 -0,406077259
+LARP4 -0,406073312
+PTPRG -0,405852123
+DIRAS2 -0,405793372
+SNCB -0,405789504
+CDS1 -0,405765281
+ARL2BP -0,405758176
+BCL2L13 -0,405729545
+STAT4 -0,405634359
+C17orf75 -0,405632179
+ELAVL2 -0,405590653
+DNM3 -0,405342092
+SNX16 -0,404866663
+TACO1 -0,40485549
+HPGD -0,404805074
+CHMP2B -0,404775945
+DPP8 -0,404495701
+SYBU -0,403649563
+CHP -0,403478973
+GTF2H5 -0,403475179
+PPP2R5B -0,403191055
+TRAK1 -0,402996995
+ACSL4 -0,402921692
+RABGAP1L -0,402883713
+PSMB3 -0,402864552
+ASTN1 -0,402784524
+TIMM23B -0,402679864
+NDUFC1 -0,402669713
+GPM6A -0,402645229
+NCDN -0,402391637
+TMEM183A -0,402206694
+LACTB2 -0,402125728
+SFPQ -0,401934429
+SLC1A4 -0,401903736
+LOC731884 -0,401617561
+TTC3 -0,401599425
+APBA1 -0,401587582
+FAM20B -0,401527926
+ISOC1 -0,401479145
+TMEM70 -0,401425176
+GLUD1 -0,401204073
+NDUFA4 -0,401152135
+SHANK2 -0,401076931
+NDUFA6 -0,400922451
+FAM128A -0,400907344
+TSNAX -0,400758374
+BLCAP -0,400561763
+WASF3 -0,400514139
+MTMR6 -0,400412018
+CBARA1 -0,399961135
+SMCR7L -0,399645568
+REXO2 -0,399637796
+ASTN2 -0,399013865
+FBXO31 -0,398919379
+MRPS10 -0,398754479
+GNAL -0,398117434
+RDH11 -0,398104472
+ANKH -0,398086916
+EPHA5 -0,397910595
+DPY19L2P2 -0,397861593
+NRXN1 -0,39777997
+FOXA1 -0,397622781
+AGGF1 -0,397583973
+CLCN6 -0,397581706
+PRKAG1 -0,397496639
+GRM5 -0,397456403
+BCAT1 -0,397331444
+MAP1LC3B -0,397317027
+HMGCL -0,397130437
+IFIT5 -0,397045055
+FAM82B -0,397007464
+TMEM189-UBE2V1 -0,39671729
+TMEM160 -0,396535704
+PIGZ -0,396390486
+VDAC2 -0,3962914
+BCAP31 -0,396227306
+CUL2 -0,395939867
+C5orf30 -0,395902062
+VAMP4 -0,395520757
+CLTA -0,395495699
+NOS1AP -0,395452681
+YWHAH -0,395414553
+AGL -0,39537715
+PPIA -0,395286888
+POLR2E -0,395239973
+FAM190B -0,395231307
+CAND1 -0,395218949
+DIABLO -0,395167608
+FAM155A -0,395099838
+FAM174B -0,394929763
+ABCA11P -0,394841999
+LMF1 -0,394801997
+EIF3I -0,394774336
+RRAGA -0,39363313
+SLC25A5 -0,39336993
+BTBD3 -0,393323586
+SLC38A6 -0,393193457
+TSPYL4 -0,39289974
+NDUFA8 -0,392898828
+ERI3 -0,392853573
+CDH11 -0,392815946
+VPS11 -0,392712183
+RPP40 -0,39270293
+SMS -0,392616216
+USP4 -0,39251437
+RAN -0,392486577
+SYT11 -0,392234251
+SEC23IP -0,392233152
+SUPV3L1 -0,392124663
+TOX3 -0,392048323
+OSBPL3 -0,391742979
+ATP5J -0,391738382
+APC -0,391687772
+EIF2AK2 -0,391678642
+MPPE1 -0,391534871
+CHD3 -0,391021702
+BE858194 -0,390954653
+GPN2 -0,390821549
+TMEM97 -0,39059622
+BRF2 -0,390477924
+NSDHL -0,390017568
+LOC654342 -0,389476483
+SATB1 -0,389035394
+RPP14 -0,388984247
+C16orf68 -0,388858051
+PHF14 -0,388842446
+CKAP5 -0,388699527
+MMADHC -0,388406258
+MEST -0,388313548
+UQCRH -0,387974488
+GBAP1 -0,387823169
+PMPCA -0,387778282
+TMEM41B -0,387668262
+SCLY -0,387620138
+OXA1L -0,387520115
+CLPX -0,387517816
+EML1 -0,387443167
+DPP6 -0,387318033
+FBXO3 -0,387294212
+GAPDH -0,386769027
+ATP6V1C1 -0,386766958
+PRAF2 -0,386484628
+NAA35 -0,386425969
+EIF4H -0,386302469
+SGSH -0,386196526
+CLCN3 -0,386084887
+SMARCA1 -0,385880429
+FAM158A -0,385760557
+AP3S2 -0,385712457
+EIF1AX -0,385367803
+RNF115 -0,385287305
+GPI -0,385266179
+SEC62 -0,385020013
+G3BP2 -0,384968143
+NDUFV1 -0,38487232
+C19orf42 -0,384758261
+BEND5 -0,384699839
+KCNAB2 -0,384620267
+EVL -0,384619104
+MTMR9 -0,384460721
+SIRT3 -0,384239932
+CNIH -0,383916854
+TOLLIP -0,383913386
+C11orf2 -0,383735535
+NUDCD3 -0,383703548
+MED4 -0,383545823
+RABGEF1 -0,38353381
+PTN -0,383407974
+GBF1 -0,383365739
+C1orf163 -0,383317238
+LOC100129361 -0,383315417
+CUL4B -0,383032231
+OXR1 -0,382758654
+TRIM33 -0,382726006
+GPC5 -0,382713696
+C11orf51 -0,382673891
+MAN1C1 -0,382595078
+FGF9 -0,382294616
+SPOCK2 -0,382267861
+GLMN -0,382038722
+MPP1 -0,381567886
+KIF21B -0,381555674
+RND1 -0,381481938
+PEX1 -0,381462705
+C2orf34 -0,381417191
+OTUD3 -0,381344145
+MSRB2 -0,381206334
+CCDC85B -0,38118283
+RGS3 -0,380621769
+SERPINI1 -0,380596066
+C14orf2 -0,380470075
+IDH3G -0,380458518
+POLR2C -0,380378788
+CTNNA2 -0,380377628
+XRCC6 -0,380295972
+EIF3A -0,380281294
+CRBN -0,380214781
+RPS6KC1 -0,3801397
+NUDT2 -0,380057201
+GOLPH3L -0,379823471
+CSNK1A1 -0,379812095
+NDUFB2 -0,379757693
+FTO -0,37940886
+SLC6A15 -0,379271656
+PCP4 -0,379256762
+NIT1 -0,37912136
+CCNC -0,378699092
+DGKB -0,378485235
+RANBP6 -0,377965444
+DNAJC8 -0,377764456
+MAPRE2 -0,377675379
+ARFGAP2 -0,377574006
+BDNF -0,377511436
+HSD17B10 -0,376728332
+AKAP7 -0,376531212
+EHD1 -0,376479944
+PSMD10 -0,376243528
+FABP5L2 -0,376090187
+VAMP7 -0,376017526
+WBP4 -0,375749974
+MAP1B -0,375485017
+SMPDL3A -0,375390185
+GPR89C -0,375362209
+SEPT2 -0,37512019
+GPX3 -0,374915078
+AARSD1 -0,374664572
+HSPA9 -0,37466397
+MAP1A -0,374598439
+C16orf62 -0,374459363
+CARKD -0,374388504
+ASS1 -0,374197776
+WDR12 -0,374046313
+ABHD14A -0,37397421
+SPIN2B -0,373568971
+RAB6A -0,373528481
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+PDCL -0,373110957
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+PPM1E -0,37285382
+TRMT61B -0,372798595
+C21orf33 -0,372766056
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+WBP2 -0,372385809
+ACSBG1 -0,372296169
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+LRRC20 -0,372239514
+AGA -0,372171162
+NRCAM -0,372117405
+FUT9 -0,372053568
+C22orf28 -0,371916518
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+UFM1 -0,371876489
+CAMK2G -0,371790847
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+EEF1E1 -0,37139203
+NLRP1 -0,371368381
+PMS2CL -0,371209965
+CDK5R1 -0,371120209
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+AL109698 -0,37073584
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+COMMD4 -0,370258812
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+ZNHIT3 -0,369651044
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+HNRNPH2 -0,352751195
+HCCS -0,3526918
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+POLDIP2 -0,297140479
+EBP -0,297109427
+FASTKD2 -0,296665172
+SMPD1 -0,296658212
+FAM55C -0,296650198
+TRPV2 -0,296465177
+DOPEY1 -0,29633822
+SCYL3 -0,296201386
+UBL3 -0,296188632
+STK38L -0,296164266
+APITD1 -0,296017845
+SFXN1 -0,295918484
+CPT1A -0,295754312
+USP8 -0,29570338
+MRPS30 -0,295702739
+ATG7 -0,295335659
+C10orf88 -0,29514056
+PIPOX -0,295018193
+RAC3 -0,294600261
+CIAO1 -0,294564961
+KLC2 -0,294523931
+LEPROTL1 -0,29448316
+ENDOD1 -0,294147277
+FEM1B -0,294007766
+IRS1 -0,293342341
+CYP51A1 -0,293155923
+DYNLRB1 -0,292974645
+TOM1L2 -0,292906836
+TDP2 -0,292808809
+MRPL49 -0,292778686
+LRP8 -0,292767989
+MOSPD1 -0,292730297
+C6orf134 -0,29255632
+TRPC1 -0,29249815
+RASL11B -0,292459191
+AL109671 -0,292334441
+TTC37 -0,292136499
+ODZ4 -0,292070818
+KIN -0,291741417
+KPNA1 -0,291721639
+CAST -0,291558763
+NDUFA13 -0,291524477
+AKR1A1 -0,29149158
+QARS -0,29146477
+MRPS22 -0,29145846
+MMACHC -0,291414294
+UBQLN2 -0,291358191
+PIK3CB -0,291242041
+COX6B1 -0,291081182
+PDK2 -0,290962723
+RABGGTB -0,290962562
+SR140 -0,290943983
+ATF2 -0,290881352
+FADS1 -0,290820194
+SRP14 -0,290691218
+RAD23B -0,290632171
+AHCY -0,290521401
+RINT1 -0,290502144
+SRP54 -0,290224786
+COX5B -0,289972152
+NBN -0,289962803
+DDX50 -0,289845246
+NUFIP1 -0,289611609
+HDGFRP3 -0,289540354
+HBA2 -0,289412602
+SRP9L1 -0,289377441
+ARFGEF1 -0,289327503
+FAM13B -0,289118442
+DIMT1L -0,288943725
+LPO -0,28888192
+VPS28 -0,288730564
+SSR3 -0,28867602
+SEPT7 -0,288663677
+NARS2 -0,288651232
+EMG1 -0,288493971
+HSPA8 -0,288488899
+TBC1D13 -0,288209587
+TTC35 -0,288076299
+GTPBP4 -0,287916733
+SPG7 -0,287774853
+PAFAH1B3 -0,28772138
+MAPT -0,28765216
+RERGL -0,287509361
+HNRNPD -0,287438947
+PLCL2 -0,287391702
+HLA-DPA1 -0,287200849
+CD55 -0,286966384
+IDH3A -0,286870398
+STXBP5L -0,286801199
+MAP3K12 -0,286334641
+PPP2R1A -0,286259611
+TMEM126B -0,286136364
+CDKN3 -0,286064506
+ABCC5 -0,286013319
+TMEM127 -0,285913561
+DNAJC2 -0,285585137
+SEC61G -0,285583827
+SSR1 -0,285489405
+AIMP1 -0,285281231
+YTHDF2 -0,285194578
+FAM86B1 -0,285046154
+CTBP1 -0,285027477
+CHRFAM7A -0,285001423
+SSBP3 -0,284934817
+MRPL46 -0,284930449
+TSPAN6 -0,284861931
+MYST2 -0,284824247
+GGH -0,284817124
+PRKACB -0,2847024
+C2orf47 -0,284692381
+NLK -0,284579832
+ASNS -0,28445955
+EXOC5 -0,28439526
+OAZ3 -0,284379411
+CTNNBIP1 -0,284364924
+PVR -0,284070802
+C16orf80 -0,284019987
+UBE3A -0,283816198
+EAPP -0,28376748
+IGSF3 -0,283764031
+KCND2 -0,283569047
+FOXK2 -0,283286684
+SLC35A2 -0,283204451
+TBCB -0,283168385
+SLC38A1 -0,283158141
+ACCN2 -0,283147998
+FAM149A -0,283126904
+TIMM22 -0,283102824
+EIF4ENIF1 -0,28310048
+THSD1P1 -0,282819454
+MAGED4 -0,282562753
+CLASP1 -0,282510547
+C1orf61 -0,282424601
+C6orf106 -0,282397365
+WDR44 -0,282155933
+GNL3 -0,282115302
+RCBTB1 -0,28192202
+OSTM1 -0,281535242
+AGPAT5 -0,281510168
+PRNP -0,281405094
+APPBP2 -0,281330465
+GAD1 -0,281295305
+NECAB3 -0,281056363
+ABCF1 -0,280961256
+DNAJC7 -0,280750506
+EPHB1 -0,280596899
+GPRC5A -0,280368026
+HSPA14 -0,280049432
+CLPTM1 -0,280042656
+SGPP1 -0,27999737
+ABCG4 -0,279891909
+GFRA1 -0,279146972
+ATP5SL -0,278849245
+CTSO -0,278677227
+DCTN4 -0,278556645
+MAP2K2 -0,278535478
+ZNF423 -0,278503712
+FUS -0,278285124
+ACTR8 -0,278282163
+PRR13 -0,278189761
+ZNF329 -0,278179162
+RNASEH2B -0,278151755
+LOC284244 -0,278099761
+FAM117A -0,277715513
+MREG -0,277651168
+C2orf18 -0,277609469
+AW612311 -0,277599115
+SYNRG -0,277434047
+SMARCE1 -0,277346186
+DNAJA3 -0,277188103
+PPP2R5E -0,2770317
+TMCO6 -0,276951805
+C6orf35 -0,276886272
+DDX18 -0,276619655
+TTLL1 -0,276373935
+LANCL1 -0,276361838
+SNRPE -0,276287655
+DTX4 -0,276233703
+IDH2 -0,276017451
+SACS -0,275814599
+ABHD2 -0,275491786
+VAMP1 -0,275092752
+AGPAT1 -0,27504004
+TYMS -0,274913065
+ZDHHC3 -0,27479568
+LMO1 -0,274566957
+UVRAG -0,274559415
+HBB -0,274385467
+PSMA2 -0,274273938
+CD24 -0,27422103
+GRAMD1B -0,27394685
+PRC1 -0,27393137
+YARS2 -0,27376193
+SIGMAR1 -0,273597834
+CPEB3 -0,273534888
+ARMC9 -0,273442678
+DNAJC10 -0,273369377
+TM9SF4 -0,27326642
+RBX1 -0,273166064
+C13orf1 -0,273151402
+PDCD4 -0,273130523
+LUZP2 -0,272843047
+APLP2 -0,272609838
+USO1 -0,272598741
+SH3BP5 -0,272512602
+PPP1R11 -0,272494252
+PEMT -0,272485616
+CDC16 -0,272287144
+LCMT2 -0,272235596
+DCX -0,271983078
+DDAH1 -0,271924121
+UBE2D2 -0,271815552
+TANK -0,271664689
+AW974666 -0,271662837
+USH1C -0,271630244
+BDH1 -0,271624449
+B9D1 -0,271589518
+BRD9 -0,271105209
+USP7 -0,271052865
+TRIM2 -0,270764995
+PARK7 -0,270634786
+NSFL1C -0,270597248
+COQ2 -0,269953826
+HNRPDL -0,269787459
+NOV -0,269731303
+SLC25A28 -0,269706278
+EXT2 -0,26958066
+VLDLR -0,269148459
+SLC4A4 -0,268895862
+SMURF1 -0,268798637
+ORC2L -0,268275919
+ZC4H2 -0,268056536
+SDHAF1 -0,267985583
+VDAC1 -0,267895013
+ALDH1A3 -0,267738476
+PNPLA4 -0,267586498
+HAGH -0,267406111
+CNTNAP2 -0,267355858
+KPNA3 -0,267278305
+LRBA -0,267216793
+DPYSL4 -0,267150239
+MCCC2 -0,26714725
+KBTBD4 -0,267031071
+DCTD -0,267005887
+C1orf21 -0,266982234
+C2orf43 -0,26679916
+SF3A3 -0,266732334
+PTPN3 -0,266674559
+FBXO21 -0,26664933
+CCT7 -0,266615147
+CLNS1A -0,266539743
+HAPLN1 -0,266160364
+SYT13 -0,26591944
+SENP5 -0,265695364
+HMGB2 -0,265556554
+CANT1 -0,265168032
+CGREF1 -0,265157579
+GRM1 -0,26510368
+ZFHX4 -0,265049797
+PVRL3 -0,264999073
+ADAR -0,264636454
+TRIM3 -0,264561355
+ANP32E -0,264413865
+PDLIM7 -0,264406742
+MLH1 -0,264377914
+PRKCA -0,264376056
+CYB5R3 -0,264120933
+PDE1A -0,263919942
+LOC100127998 -0,263915362
+WSB2 -0,263691169
+RPF1 -0,263404659
+CXCL12 -0,26333499
+TMEM66 -0,263285506
+EIF6 -0,263232223
+NFE2L1 -0,262789646
+KLHL20 -0,262772392
+PPM1H -0,262689193
+PIN4 -0,262483899
+TUBA4B -0,26241982
+ECT2 -0,262276809
+MGC5566 -0,261888759
+C9orf116 -0,261830489
+ASB1 -0,261751394
+ABCC8 -0,261735107
+ELOVL2 -0,261638578
+PHB2 -0,261466477
+ZNF580 -0,261379751
+DNAJC24 -0,261364702
+PSMB10 -0,261344946
+CSE1L -0,261292597
+ANKRD27 -0,261154598
+TUBG2 -0,261047779
+C6orf162 -0,261001828
+AL034399 -0,260886813
+GLT8D1 -0,26052144
+SRR -0,260520305
+MCC -0,260395686
+COX4I1 -0,260324715
+SEP15 -0,260222524
+RNF103 -0,260210477
+ZNF576 -0,260159221
+MGEA5 -0,260092677
+RSL24D1 -0,259958151
+USP13 -0,25969613
+MLLT3 -0,259631882
+SRI -0,259268888
+NCS1 -0,259133737
+MAPKAPK5 -0,259103348
+IQCG -0,25908825
+FN3KRP -0,258914892
+BCKDHB -0,258870249
+GOLGA5 -0,258736414
+RDBP -0,258483881
+SUPT7L -0,258355414
+METTL1 -0,258206012
+CREB3 -0,258159408
+TMEM111 -0,258136123
+NRSN2 -0,257397396
+CNTN1 -0,257314074
+COX10 -0,257277055
+SERPINB9 -0,257269621
+MTF2 -0,256976969
+EDNRB -0,25676028
+HSF2 -0,25652969
+POLR2L -0,256424652
+TRIM58 -0,256294322
+DACH1 -0,256241463
+UEVLD -0,256239024
+ATP1B3 -0,256215499
+SAP130 -0,256053262
+TRPC6 -0,255890704
+HERC6 -0,255794959
+NAV3 -0,255707496
+GOSR1 -0,25567987
+CNR1 -0,255506006
+PSME4 -0,25522233
+CAMKV -0,254605479
+ADSL -0,254512794
+BCS1L -0,254298738
+CCNB1 -0,253924801
+SNX2 -0,253887319
+ASAP2 -0,25387509
+WDR70 -0,253565737
+PTPRE -0,253309549
+SEPT5 -0,253058348
+SCML1 -0,253051964
+BCR -0,252946659
+MAGOH -0,252829021
+SEMA4F -0,25277628
+CLIP1 -0,252764211
+JMJD4 -0,252747043
+ZMYND11 -0,25273006
+CPSF6 -0,252574141
+PTPRA -0,252430519
+PLA2G12A -0,252393049
+MXRA5 -0,252290125
+RFX5 -0,252264534
+WARS -0,252174212
+HUS1 -0,252166663
+VCAM1 -0,251733145
+CEACAM21 -0,25171453
+RHOT1 -0,251514974
+EMD -0,251327933
+TSPYL2 -0,251307071
+THNSL1 -0,25130438
+NDUFB4 -0,251250318
+CHMP5 -0,251232028
+SKAP2 -0,251185084
+LRPAP1 -0,251070101
+COMMD3 -0,251069448
+ROGDI -0,250917557
+PPAP2B -0,25089017
+ADSS -0,250852878
+LGI2 -0,250809779
+CBX6 -0,250671998
+NELF -0,250584567
+DENND5B -0,250357567
+ATP2C1 -0,239139672
+SUMO2 -0,233193565
+KRAS -0,208565613
+PEX3 -0,200767265
+PRDX2 -0,195371323
+PDCD2 -0,194653063
+TM2D1 -0,189207426
+KHDRBS1 -0,16653347
+KLC1 -0,156510024
+ANK2 -0,155852142
+HBS1L -0,155006259
+NTRK3 -0,121314135
+PTPRO -0,110200451
+PLEKHA5 -0,10184855
+GCOM1 -0,091608137
+TIMM8A -0,084179504
+MKRN1 -0,074942655
+PLA2G4B -0,068760926
+RUFY3 -0,059042335
+RIMS2 -0,057507607
+C21orf2 -0,054091983
+METAP2 -0,053236401
+LRRC40 -0,040678287
+RPL10 -0,034862755
+RIOK3 -0,033313025
+SYNCRIP -0,027340658
+UNC45A -0,021866459
+MPZL1 -0,020796077
+RANBP1 -0,01610173
+ITGB1BP1 -0,011025016
+UBC -0,009666523
+RER1 -0,007044099
+PDS5B -0,005231512
+NCAM1 -0,004638056
+LIMCH1 0,003894784
+VPS13D 0,014841215
+WDFY3 0,017457694
+MRP63 0,023151675
+TSR1 0,064261585
+GRB10 0,066410415
+FAM128B 0,074972161
+PAK2 0,079518764
+PKP4 0,080237181
+TMEM144 0,083124821
+C3orf63 0,086752023
+DDAH2 0,250378216
+AF238870 0,250544885
+PTMS 0,250667518
+JAG1 0,250675664
+RPL32 0,25075902
+UXT 0,250812127
+HSP90B1 0,250888984
+SS18 0,250904748
+RND2 0,250918958
+CLEC4M 0,250931594
+AU147194 0,251115897
+IL1RAPL1 0,251119435
+EPB41L2 0,251131328
+TFDP3 0,251241244
+GAL3ST4 0,251281983
+EDN2 0,251371356
+SFTPC 0,251372616
+TRMT61A 0,251534845
+GPR4 0,251535902
+KEAP1 0,251692277
+RNF122 0,251718243
+NOTCH2 0,251745042
+WDR1 0,251871256
+NFX1 0,252023298
+DOHH 0,252100123
+NES 0,252167647
+SRSF10 0,252172984
+AQP3 0,252182392
+LOC728412 0,252404082
+RCN3 0,252455902
+CSNK1G1 0,252462493
+KCNS1 0,252601737
+CCDC71 0,252614101
+JUND 0,252645305
+LYST 0,252718314
+TPCN1 0,252770336
+MTA1 0,252823052
+RIN1 0,252841454
+ATHL1 0,252944239
+FTSJ3 0,253136044
+SERPINA1 0,253202139
+STARD7 0,2533744
+MRPL34 0,253425868
+PPID 0,25344089
+SH3PXD2A 0,253534644
+UBA7 0,253547625
+RUNX1 0,253686159
+ARNTL 0,253823553
+STAT6 0,253840779
+CASKIN2 0,25393147
+NFATC4 0,253965486
+LILRB2 0,254041373
+PPP1R13L 0,254173566
+RAP1A 0,254249533
+OTUD4 0,254380531
+ZNF516 0,254390037
+ZC3H14 0,254430628
+BTD 0,254441889
+ABHD4 0,254494909
+MT3 0,254554667
+PTCH1 0,254572046
+CDC42EP3 0,254591236
+LOC150776 0,254715807
+PTGES 0,254816225
+TPM2 0,254867646
+TAGLN 0,254960085
+AL050032 0,254984309
+HPN 0,25500915
+FLNC 0,255046574
+GJB3 0,255060346
+RAB40B 0,255071999
+CST1 0,255226531
+FGF21 0,255229382
+AW574933 0,255334628
+FGF5 0,255461872
+CLCN7 0,2555275
+BAHCC1 0,255618646
+FANCA 0,255627746
+CYBA 0,255682121
+TIE1 0,255683605
+ANKHD1-EIF4EBP3 0,255707685
+CDV3 0,255740411
+COL9A1 0,255878907
+TTC31 0,256049153
+ZIC1 0,256075896
+CCDC121 0,256090992
+FUT4 0,256155794
+UCP3 0,256197327
+AU146391 0,25625958
+MMP2 0,256269664
+STXBP2 0,256386629
+TMEM87A 0,2564575
+FXR1 0,256493521
+RDX 0,256507051
+HPS1 0,256516919
+TRAM2 0,256517872
+HYAL2 0,256778041
+TNFRSF14 0,256783849
+NEK7 0,256861333
+AGRN 0,256876471
+SMC4 0,256895131
+GAS7 0,256949822
+PDE4B 0,256950938
+CHD4 0,256970114
+SPP1 0,257084517
+HECA 0,257172806
+NXF2B 0,257181225
+LILRA5 0,257188463
+SCAP 0,257267679
+SNX1 0,257354288
+GIGYF2 0,257400552
+CELF1 0,257407908
+HSD17B14 0,257420303
+DUOX1 0,25770603
+MRM1 0,257826185
+NBR2 0,257852879
+FAM176B 0,257955278
+SYNPO 0,257997864
+GPRIN2 0,258040238
+IER3 0,25816919
+ZNF506 0,258198461
+NM_016414 0,25824817
+VPS53 0,258358594
+PGPEP1 0,258378109
+GNL1 0,25847832
+OGFR 0,258496938
+CXCR2 0,258632799
+C1orf38 0,258857462
+RPL22 0,258901214
+NM_018041 0,259005358
+MYOF 0,259133176
+NGB 0,259197495
+CLIC4 0,259260666
+TBC1D9B 0,259295717
+KCND1 0,259337213
+RNASET2 0,259420675
+EXT1 0,259568659
+AQR 0,259572114
+VWA1 0,259618684
+MUC3A 0,259647513
+CAV1 0,259682957
+IRF4 0,259719685
+OR7C1 0,259728956
+SETDB1 0,259737838
+E2F6 0,259867146
+TFEB 0,259924981
+CPSF3L 0,26005015
+MARCH8 0,260576922
+MFSD11 0,260945964
+ETAA1 0,260954881
+SMARCD2 0,260999203
+RGS12 0,261024661
+CCNG2 0,261112401
+RPS8 0,261183649
+IL17RA 0,261275371
+NUDC 0,261284708
+ZNF133 0,261329337
+ATP13A1 0,261543252
+PICK1 0,26166607
+C20orf117 0,261682534
+GIPR 0,261728602
+HIST2H4B 0,261730186
+S100A11P1 0,261732522
+MARCH3 0,26174629
+ZBED4 0,261794357
+KHK 0,261822851
+SCAMP2 0,26194666
+AF070579 0,261954742
+TECR 0,261998101
+AK024915 0,262016665
+CASP7 0,262240261
+PDK4 0,262293861
+MYO7A 0,262479993
+TUBBP5 0,262483574
+TMEM143 0,262491406
+NAP1L1 0,262524812
+PLEKHB1 0,262542861
+ING1 0,262679424
+SPSB3 0,262786186
+C9orf167 0,262955615
+NTM 0,262977412
+FIP1L1 0,263199662
+FYCO1 0,26321575
+GGT1 0,263227324
+ALG12 0,263240056
+IGL@ 0,263282588
+PPBP 0,263290228
+SNX13 0,263292989
+SRSF4 0,263309909
+CYTH1 0,263721364
+AL050035 0,263831657
+TRMU 0,263920451
+TIMP1 0,263959235
+RFNG 0,263965598
+HIP1R 0,264033626
+NR1H3 0,264039538
+NT5C2 0,264091319
+FNTB 0,264115077
+SAR1B 0,264175117
+GIT1 0,26420824
+RRAGD 0,264311012
+HAP1 0,26435511
+FLT3LG 0,264378926
+NM_018612 0,264421364
+SLC7A9 0,26447762
+GLTSCR2 0,264541217
+SUN1 0,264635751
+CEP152 0,264663399
+MBTD1 0,264688291
+SYT12 0,264690461
+ACTR5 0,264835312
+EIF4A1 0,264933012
+COX7A1 0,26511391
+CMTM6 0,265385079
+FAM102A 0,265449454
+AW970584 0,265532869
+FMO5 0,265619005
+N4BP2L1 0,26587536
+SPAG11A 0,265939376
+TGFBI 0,265987004
+RYK 0,266131346
+SERBP1 0,266135884
+AK021988 0,266152576
+NCAM2 0,266199101
+AK024995 0,266233606
+RAB9A 0,266259326
+SYNJ2 0,266313048
+PHLDB1 0,266315252
+PKN1 0,266439146
+MFAP3L 0,266558078
+PPFIBP2 0,266640652
+WBP5 0,266861878
+TMX1 0,266949292
+SLC6A12 0,267009029
+C3AR1 0,267017849
+CSRP2 0,267020264
+SP3 0,267034674
+ATN1 0,267069634
+GNB3 0,267107148
+TIAL1 0,267113358
+GPATCH8 0,267177985
+PMEPA1 0,267182372
+MAP2K3 0,267199274
+NM_018033 0,267304029
+WWTR1 0,267350058
+SEMA6A 0,267400431
+RBPJ 0,267426168
+AL049279 0,267438916
+IL1RN 0,267473934
+QKI 0,267577841
+SOX15 0,267588393
+DMTF1 0,267672579
+RPL19 0,267821304
+TRIM39R 0,267839755
+SLC26A6 0,267879749
+NM_025056 0,267969441
+BBS9 0,267969882
+M85256 0,26799656
+ADORA3 0,268097905
+TMEM176B 0,268515164
+SECTM1 0,268600799
+ST14 0,268612452
+ARHGEF18 0,268652414
+SIRT5 0,268726991
+MYBPC1 0,268763379
+RPL15P22 0,268793196
+SIGLEC15 0,268860828
+DNAJA1 0,26890035
+LMBR1L 0,269042598
+GIMAP4 0,269074847
+MFAP3 0,269075993
+ABCA6 0,269120338
+AW836210 0,26919833
+LOC100133772 0,269228182
+CHST4 0,269387102
+RNASEH2A 0,269387986
+RPL18 0,269450865
+RPLP2 0,269486597
+MEPE 0,269489799
+FAM106A 0,269545639
+GATAD1 0,269621956
+PPP2R3A 0,269725552
+MASP2 0,269836416
+MYO10 0,26992164
+PIGG 0,269941407
+SMG5 0,269952017
+IFI30 0,269956381
+AK025180 0,269971157
+AMD1 0,269982316
+LMOD1 0,270125966
+SNX15 0,270191178
+SCARB1 0,270338985
+SERTAD3 0,270373355
+MBD5 0,270430073
+SLC2A5 0,270454389
+ITCH 0,270468949
+ADA 0,270490353
+PWP2 0,270541137
+ARHGEF1 0,270572389
+C2CD2 0,270675538
+EIF1 0,27071329
+C1orf35 0,270772513
+IFI16 0,270855012
+LOC285830 0,270905428
+IL10 0,271025993
+MORC4 0,2712707
+CA11 0,271346355
+C5orf54 0,271348162
+C14orf93 0,271428228
+RPL17P7 0,271481741
+TMEM161A 0,271564557
+LRCH3 0,271627825
+DFFB 0,271779652
+BAZ1B 0,271859723
+DKFZp547G183 0,271894591
+RAB11FIP2 0,271895928
+PCK1 0,27194659
+TMPRSS5 0,27195628
+TIPARP 0,272078235
+UBE2L3 0,272125747
+ZNF672 0,272142507
+GALNT10 0,272151507
+EXD2 0,272173543
+KAT2B 0,272322281
+RPS11 0,27237174
+POLR2H 0,272422791
+IGLL3 0,272574443
+AA554430 0,272578205
+DOCK10 0,272578712
+DMC1 0,272606886
+CD40 0,272762332
+CDK11A 0,272811711
+UCKL1 0,272898303
+FAM125B 0,273084179
+UBXN7 0,273084433
+SMA4 0,273204796
+DYNLT1 0,273349219
+CTTNBP2NL 0,273380758
+HSPH1 0,273396703
+CYP39A1 0,273418193
+HOMER3 0,273432217
+RRBP1 0,273480926
+ATAD2B 0,27361049
+LGALS3 0,273847411
+LASS2 0,273913098
+ZNF451 0,273935073
+NXPH4 0,27404559
+C22orf46 0,274118605
+KDM4B 0,27422483
+GPNMB 0,274363725
+CYHR1 0,274415705
+CCDC9 0,274487483
+WWC2 0,274522318
+ZNF652 0,274533788
+ILK 0,274538403
+CTDP1 0,27455992
+LOC51152 0,274810051
+AL442084 0,274963062
+CPNE7 0,275259638
+CENPB 0,275294531
+TCIRG1 0,275300556
+PRPF40A 0,275423637
+ARHGAP17 0,27552534
+LOC100133811 0,275961848
+ADAM17 0,276019886
+CRISPLD2 0,276144309
+IFIH1 0,276175289
+LOC440434 0,276293985
+DCLK2 0,276369722
+MS4A6A 0,276482788
+VASH1 0,276499979
+SRSF7 0,276513035
+B3GAT3 0,276752575
+CALHM2 0,276762436
+MAP4 0,276867434
+DULLARD 0,27687625
+CTSS 0,276943812
+BAG3 0,277040195
+KRT8P12 0,277155277
+POLR2F 0,277193722
+CD14 0,277207134
+SF3B1 0,277255775
+EZH1 0,277320185
+MBD1 0,277342685
+MITF 0,277407356
+BAIAP2 0,277445862
+FCGR2B 0,277531437
+PAQR4 0,277547889
+NFATC2IP 0,277597337
+CAT 0,277600148
+TJP2 0,277610024
+CCNA2 0,277687494
+GEM 0,277887602
+C2orf54 0,277935237
+HIRIP3 0,278018588
+MCM3APAS 0,278082892
+CFB 0,278130274
+TAGLN2 0,278365668
+AK024851 0,278382784
+HGD 0,278585783
+NR2E1 0,278716062
+SEC61A1 0,278797194
+PDE4DIP 0,278806635
+FRMD4A 0,278822955
+RHOC 0,278842121
+UBTF 0,278963815
+NCOR2 0,279024257
+PPP6R3 0,279218049
+ALAS2 0,279327775
+SPSB1 0,279537438
+SGMS1 0,279545277
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+AK024897 0,27961031
+IRS2 0,279708094
+TRIM62 0,279977776
+AF308291 0,279984986
+AK022362 0,280079092
+KIAA0495 0,280115197
+CUL7 0,280170918
+PARD3 0,280192562
+NUP98 0,280376383
+DHRS4L2 0,280391865
+AK024093 0,280444114
+VEGFB 0,280560816
+PTEN 0,280592383
+NBPF10 0,280620974
+CASP1 0,280699269
+AK2 0,280734467
+MLX 0,280792537
+GNG11 0,280826824
+HNRNPM 0,280968313
+IL12RB2 0,28098376
+CDK18 0,28098866
+RARA 0,280998983
+GYPC 0,281028129
+PAK4 0,28104576
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+BAT2L2 0,281335934
+BRD4 0,28139016
+PAOX 0,281415979
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+PIK3R2 0,281480063
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+RPL13A 0,282085077
+ZNF22 0,282127023
+KDM4A 0,282136199
+CPM 0,282150511
+EIF2S2 0,282316006
+USP48 0,282335945
+CLCNKB 0,282422648
+C11orf61 0,282474246
+ANKRD11 0,282516441
+PTTG1IP 0,282619596
+SEC14L1 0,282620994
+DOCK6 0,282646645
+CARHSP1 0,28271852
+RRAS 0,282814195
+TRIM38 0,283129972
+PLA1A 0,283206252
+GAB1 0,283220235
+PDLIM1 0,283254227
+SSH3 0,283308195
+KLF9 0,283315657
+N4BP2L2 0,283629404
+TNS4 0,283667599
+C15orf28 0,28383226
+ANXA11 0,283988681
+TAF12 0,283993401
+SLC39A1 0,284190806
+SAP30 0,284320416
+RNASE4 0,284337811
+RPS28P6 0,28438483
+DDR2 0,284449824
+BMP4 0,284614799
+CEPT1 0,284615091
+ITPKB 0,284650775
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+AW974812 0,284683098
+PTCRA 0,284827371
+SETMAR 0,2848555
+SOCS3 0,284925858
+NM_014129 0,284930906
+MYO1D 0,285094554
+RBL1 0,28514691
+HN1L 0,285254673
+LASS4 0,285307965
+RPS21 0,285547221
+PPP2R1B 0,285765143
+NEO1 0,285937917
+SEC24C 0,286013109
+BCL3 0,286014454
+KCNMA1 0,286080656
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+EDIL3 0,286207431
+ARHGEF16 0,286210956
+HCK 0,286227266
+GSTA1 0,286246055
+SLA 0,286356975
+UNG 0,286379363
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+PRSS53 0,28642638
+MYL6 0,286728542
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+SFRS16 0,287066034
+TPM4 0,28709233
+ABCD4 0,287100216
+GLT25D2 0,287127854
+COL18A1 0,287131911
+NPIPL3 0,287424398
+C1orf69 0,287453135
+MTF1 0,287488427
+IGF2BP2 0,287555495
+PALLD 0,287872078
+RPS16 0,287887395
+CYP2C9 0,287955438
+SC65 0,288029122
+CRYBG3 0,288096904
+SHC2 0,288312879
+FLNA 0,288339801
+NM_014486 0,288348194
+ISYNA1 0,288383809
+PNO1 0,288506351
+GZMK 0,2886543
+ATG13 0,288748426
+NCOR1 0,288772721
+ZSWIM1 0,288892162
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+SNTA1 0,289049438
+RHOBTB1 0,289064808
+GGA1 0,289073087
+ATXN2L 0,289088819
+FAM46A 0,289172187
+ZNF532 0,289393934
+CD40LG 0,289400418
+ZCCHC11 0,289421485
+WDR5B 0,289498086
+EPN2 0,289629137
+WNK1 0,289684816
+ZNF408 0,289721753
+LHFPL2 0,290003635
+NARG2 0,290029081
+STYXL1 0,29008917
+YY1AP1 0,290249669
+CPOX 0,290281635
+IL11RA 0,290333682
+PAXIP1 0,290387596
+ZNF282 0,290414378
+C11orf95 0,290643441
+MERTK 0,290681835
+VPS13C 0,29069039
+RPS17 0,290756898
+NEIL1 0,290762184
+ZNF292 0,290850132
+NOSIP 0,290873511
+DNAJB2 0,290950763
+INPPL1 0,29102828
+ZFX 0,29106383
+SETX 0,291138151
+SLC25A37 0,291207794
+PCDHGA8 0,291472818
+TXNIP 0,291962928
+DDX27 0,291971417
+BG389073 0,29216848
+JTB 0,292275569
+RBM10 0,292352574
+RASGRF1 0,29242252
+SYNM 0,292474024
+EXPH5 0,292481151
+NPL 0,292494012
+CHKA 0,292519533
+MGA 0,292564204
+SOX10 0,292580481
+AK024185 0,292975066
+FAM120A 0,292996604
+PLXNB1 0,293000141
+BDH2 0,293071563
+JRK 0,293136106
+SLC11A1 0,293139917
+TM4SF1 0,293242649
+EDA 0,293286441
+CDK10 0,293299298
+HLA-E 0,293305618
+LOC642846 0,293349826
+GFPT2 0,293396887
+SENP3 0,293408144
+RPS3AP44 0,293415546
+C16orf88 0,293431615
+FAM60A 0,293472328
+RPL36A 0,293501288
+SERPINA5 0,293547044
+CNOT8 0,293568161
+KDM4C 0,293620372
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+C14orf139 0,293870806
+ZNF217 0,293937173
+NM_025042 0,294034268
+NNMT 0,294200775
+VEZT 0,294224684
+KIAA0754 0,294307773
+RBM28 0,294637248
+ITPR2 0,294711729
+PPPDE1 0,294796015
+KLHL28 0,294874305
+MGP 0,294956866
+LOC729602 0,295016892
+SRSF5 0,295036903
+ROCK1 0,295267164
+SS18L2 0,295271871
+LMNA 0,29532356
+ESRRA 0,295387708
+SNHG3-RCC1 0,295411716
+TAL1 0,295434654
+SQRDL 0,295470062
+TARDBP 0,295665655
+LMAN2L 0,295705138
+RIN3 0,295771443
+PSPH 0,29602696
+DGKD 0,296027908
+WHSC1 0,296067068
+SPRY4 0,296068122
+ADARB2 0,296162399
+ELF3 0,296200778
+TLE1 0,296292637
+ACAN 0,296375799
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+IL1RL1 0,296721787
+OR2A9P 0,296898432
+NCRNA00260 0,296954725
+CAD 0,296976627
+PNRC2 0,297129071
+IQCK 0,297134521
+ACOX2 0,297377087
+APOC4 0,297497329
+DGKA 0,297541846
+ZBTB1 0,297547513
+PUS1 0,297622568
+C7orf64 0,297653213
+FBLN1 0,297723957
+SBF1 0,297752819
+TMF1 0,298582891
+IL1R1 0,298701666
+LILRB3 0,298823808
+FLAD1 0,298825369
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+TCL6 0,299056301
+FADS3 0,299096634
+LBR 0,299180453
+AL162044 0,299184427
+ZNF337 0,299271736
+AHNAK 0,299352615
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+AL050053 0,300945526
+RSU1 0,300958049
+C15orf39 0,301123219
+SLC14A1 0,301147038
+ELAVL1 0,301190126
+SLC17A4 0,301215925
+FANCC 0,301274346
+LRCH4 0,301338927
+EGFL7 0,301340052
+C9orf3 0,301357727
+SRGN 0,301411135
+PLCL1 0,301576339
+MAN1A1 0,301613058
+S100A8 0,301917937
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+HIP1 0,302012828
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+PPP1CC 0,3020408
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+GALNS 0,302376776
+NR0B1 0,302394827
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+MGST2 0,302482901
+RPL12 0,302658969
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+STAG3L1 0,3031801
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+RPL13 0,303245467
+RBPMS 0,30326423
+ARHGAP10 0,303298204
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+ZCWPW1 0,303562617
+MTHFD2L 0,303678034
+FAM111A 0,303798707
+TTC38 0,304186409
+COL7A1 0,304295553
+C4orf19 0,304312458
+NGLY1 0,304332742
+HTATIP2 0,304339936
+IFNAR2 0,304414877
+CXorf1 0,304737703
+UNC5B 0,304789798
+YAP1 0,30479215
+PHC2 0,30485466
+FBL 0,304914384
+CDH2 0,304939032
+FXYD2 0,304942957
+ANKRD36 0,305000603
+KRT8 0,305028726
+DSCAM 0,30505625
+SMO 0,305151387
+FCGRT 0,305420183
+PAIP2B 0,305483478
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+PIGV 0,305604211
+BACH2 0,305697602
+PLGLA 0,305722503
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+DIDO1 0,305996983
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+TRMT1 0,306054262
+NFATC1 0,306233076
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+GPR1 0,306335484
+STARD13 0,306369109
+CELSR2 0,306371185
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+ABHD6 0,306458055
+PLCXD1 0,306486283
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+DHRS3 0,306750918
+C1QA 0,306800137
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+SETD2 0,307047565
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+SMYD2 0,307490131
+BF942161 0,307560212
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+AATF 0,307770923
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+ACTN1 0,307927265
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+SOLH 0,307971092
+ZNF410 0,308222237
+GOLGA4 0,308250269
+FLJ21369 0,308352331
+FCGR2A 0,308469725
+BRD7 0,308638563
+TLR2 0,308769609
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+LSM14A 0,308907157
+USF2 0,309161806
+TENC1 0,309220224
+EMP2 0,309252571
+BSDC1 0,309299474
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+SORBS1 0,309562012
+FTL 0,309588981
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+UBR5 0,309647344
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+ITPR3 0,309975876
+PLK3 0,310097184
+NUP188 0,310124261
+CROCC 0,310245563
+CHSY1 0,310328559
+CTCF 0,310675097
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+LILRA6 0,311008878
+SATB2 0,311055754
+GTPBP6 0,311254994
+TSPAN14 0,311316513
+C10orf18 0,31133762
+SECISBP2 0,311419174
+DHX34 0,311443077
+LSS 0,311450185
+CHI3L1 0,311532669
+PDGFC 0,311715929
+BMP7 0,311741682
+MBNL1 0,311755686
+DNA2 0,311841432
+COMT 0,312081286
+LOC100133005 0,312165679
+PTOV1 0,312192713
+LCAT 0,312407744
+LRRFIP2 0,312480817
+UCN 0,312589312
+AK024606 0,312655002
+MICAL3 0,312700621
+ROM1 0,31291043
+MED12 0,312925796
+CPNE1 0,313173908
+GBP2 0,313262095
+PELI2 0,313279559
+MLL 0,313398121
+HIF3A 0,313438743
+ST18 0,313449639
+AF131777 0,313643716
+CATSPER2P1 0,313785721
+ZNF302 0,314066212
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+TSC2 0,314882123
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+ZNF835 0,314920694
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+LOC729143 0,315037798
+PPARD 0,315048839
+U2AF2 0,315118843
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+ZNF44 0,315270856
+RPL36 0,315475789
+GRAMD3 0,315513449
+PTPN2 0,315554784
+AL080072 0,315635626
+C19orf2 0,315918303
+DNAH3 0,315930745
+ZNF146 0,316341954
+SMEK1 0,316538461
+MLXIP 0,31681421
+NMT2 0,316848231
+G3BP1 0,316864559
+DDX3Y 0,316997159
+STEAP1 0,317082981
+BC002629 0,317231764
+KDM2A 0,317406731
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+C15orf29 0,317437851
+MACF1 0,317513626
+LOC391020 0,317572673
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+KTN1 0,317889697
+RUNX3 0,31809511
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+BMP1 0,318194029
+DKFZP586I1420 0,318199121
+JARID2 0,318226296
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+PAPSS2 0,31841091
+ELTD1 0,31845583
+ETS2 0,318667898
+CREB3L2 0,318705762
+DFNB31 0,31892768
+SERHL2 0,318966243
+C10orf26 0,319058163
+NM_030892 0,319421731
+WRAP53 0,319795295
+UBQLN4 0,319828198
+RALGDS 0,319938162
+PRKCH 0,320101043
+AU146983 0,320105843
+SLC5A3 0,32021553
+DUSP1 0,320239212
+NKX2-2 0,320312108
+C1orf183 0,320387827
+PCM1 0,320482282
+THRA 0,320531901
+NM_025028 0,320726138
+SIVA1 0,320736787
+TTR 0,320757249
+IKBKB 0,320778441
+ARID1A 0,321020715
+HDAC4 0,321059842
+ZFP36L2 0,321167918
+TMEM212 0,321179342
+AA443771 0,321214505
+AGAP5 0,32125931
+PIGA 0,3216713
+SFRS12 0,321704401
+LDLRAP1 0,321832456
+CCDC21 0,321857948
+SSFA2 0,321990716
+RAMP1 0,322050077
+FLJ10357 0,322160744
+LAD1 0,322322766
+RACGAP1 0,322340831
+NPIPL2 0,322616655
+CEP350 0,322648588
+CRLF1 0,322735059
+IGSF9B 0,322744338
+PLXND1 0,322801951
+MCL1 0,322913781
+ALMS1 0,32297709
+ZNF768 0,323059066
+RSL1D1 0,323228527
+C4orf34 0,323582139
+PNPLA6 0,323738553
+MAST4 0,323801655
+NME3 0,323835175
+SNHG3 0,32391938
+S100A12 0,324014586
+PPP4R1 0,32409634
+PLD1 0,324165096
+POLG 0,324186823
+NKTR 0,324203565
+ST3GAL4 0,324231325
+TMEM63A 0,324243134
+ST20 0,32438459
+RNF114 0,324406844
+HYI 0,324468621
+DUSP6 0,324699964
+NR1H2 0,324884332
+DVL2 0,324900869
+SRSF11 0,324979841
+CLK2 0,325170283
+MKLN1 0,325287178
+SCRIB 0,325320413
+KIAA0467 0,325541973
+DMWD 0,325745064
+KLHL23 0,32579572
+RPS6 0,325948088
+ZBTB17 0,326014408
+RAI14 0,326038467
+UBE2G2 0,326143089
+ZNF562 0,326186073
+EZR 0,326282578
+TRPS1 0,326283144
+HFE 0,326390644
+MED23 0,32658232
+DDX11 0,326766632
+SHMT2 0,326784725
+LRP5 0,326954416
+PTH1R 0,327100265
+LOC731602 0,327131294
+AA401963 0,327241371
+CDK5RAP2 0,327276136
+SERP1 0,327279991
+SLC1A5 0,327303416
+BGN 0,327370767
+HSD17B1 0,327475971
+AL390143 0,327497051
+DIAPH2 0,327617697
+PITPNC1 0,327719899
+SPRY2 0,327767132
+FZD7 0,327974293
+MAP4K4 0,328171238
+TNS1 0,328369107
+ZNF783 0,328517049
+M78162 0,328518574
+ADAMTS1 0,32853944
+FKBP5 0,328911405
+AGAP8 0,329115979
+PLEKHF1 0,329179433
+DNAJB1 0,329339376
+RBMS2 0,329438459
+HNRNPH1 0,329454824
+ULK2 0,329496298
+PAPD7 0,329501864
+SURF1 0,329547559
+W61005 0,329673439
+ZNF862 0,330131081
+GNA15 0,330266409
+CHD9 0,330273108
+DLC1 0,330294104
+TMEM2 0,330321664
+AK024879 0,330353812
+N4BP1 0,330435804
+SERF2 0,330633507
+SNRPA 0,330957742
+IRF8 0,33098543
+ABCA2 0,331251046
+NPFF 0,331328402
+CP 0,331565597
+AU144887 0,331713137
+AW851559 0,33185735
+TCF4 0,332062967
+ZNF354A 0,332076549
+TMEM92 0,332352956
+NFATC3 0,332386137
+SSRP1 0,332529738
+TCF7L2 0,332651908
+PIM1 0,332716071
+PIP4K2A 0,332914219
+EIF4EBP1 0,332959146
+LOC100132863 0,333054912
+MMRN2 0,333075923
+AU147295 0,333342973
+VIM 0,333356286
+C2orf67 0,333469715
+DNMT1 0,333550022
+CEP110 0,333679402
+BAZ2B 0,33371151
+KDELR2 0,333939841
+L3MBTL 0,334448273
+CDK19 0,334505985
+CYorf15B 0,334832089
+DDX17 0,334839203
+FKBP4 0,335166906
+STOM 0,335173644
+U82303 0,335241438
+LOC202181 0,335841121
+ATM 0,335893127
+STK3 0,335957389
+MID1 0,336166241
+IGFBP5 0,336454348
+PARP4 0,336459483
+EXOC7 0,336479503
+FANCG 0,336652927
+PHF2 0,336678654
+FBRS 0,33674511
+ANP32B 0,336836072
+NCK2 0,336876937
+CASP6 0,336920233
+ZBTB3 0,337122586
+DHFR 0,337448147
+APOLD1 0,337464001
+STAG1 0,337490482
+NM_024305 0,337551103
+SIGLEC8 0,337608204
+ERLIN1 0,337809212
+POLDIP3 0,337889824
+SPTLC2 0,33799094
+C7orf26 0,338204972
+UBE2D4 0,338265561
+MAP2K7 0,3384787
+MECOM 0,338508564
+DOCK1 0,339029429
+HS1BP3 0,339148762
+PRKY 0,339216015
+GOLGA1 0,33927478
+XPC 0,339433169
+PHF3 0,33953002
+HIC2 0,339768003
+C9orf7 0,340519877
+CTDSPL 0,340591645
+ZNF83 0,34077157
+PHGDH 0,340889735
+TMEM165 0,340978736
+CLN3 0,341078466
+AU147983 0,34113627
+PATZ1 0,341151411
+DIP2C 0,341390806
+RECK 0,341533646
+EWSR1 0,342003886
+SMAD7 0,342182186
+MTRF1L 0,34225773
+TJAP1 0,342452426
+PRKD2 0,342725824
+SPOP 0,343019265
+HLA-J 0,343028528
+PLXNB2 0,343103735
+FBXL14 0,343454364
+LAMA2 0,343637649
+RNF220 0,343845541
+CLK3 0,344164444
+STARD3 0,344187457
+OGT 0,345118989
+IFITM3 0,345141829
+HMOX1 0,345196784
+EIF2C2 0,34557825
+CCND3 0,345663426
+TGFBR3 0,345676022
+POLR2J3 0,345712548
+BCAR3 0,345713549
+C14orf147 0,34610842
+CLDN15 0,34616346
+TOP1 0,346179876
+RASL12 0,346286134
+MED13L 0,346369067
+SOS2 0,346799305
+SERPING1 0,347144597
+IER5 0,347279068
+TLE2 0,347426427
+LLGL2 0,347448236
+TMCC2 0,347500013
+PHF20 0,347602909
+SIRT4 0,347862165
+OSGIN1 0,348060574
+H2BFS 0,348076316
+NM_017756 0,348230007
+NCRNA00115 0,348422218
+MT1E 0,348733923
+NACC2 0,3488369
+NFIB 0,348943619
+AKR1C3 0,349206923
+ARPC1B 0,349407208
+NIPBL 0,349628117
+RPL11 0,349803207
+MSH6 0,350014407
+PTDSS2 0,350073646
+AL050145 0,350120404
+FAM107A 0,350271118
+CHN2 0,350358174
+DAPK2 0,350378033
+DLG5 0,350436992
+OPHN1 0,350596034
+C20orf11 0,351010126
+SLC35D1 0,35135795
+SELL 0,35142274
+FAM193B 0,351790995
+NM_024880 0,352020901
+RASGRP2 0,352114346
+CAPN3 0,352194849
+THOC1 0,352289646
+TAOK3 0,352396226
+FBXO42 0,352613215
+LARP6 0,352692849
+KLKB1 0,352702835
+METTL7A 0,352961228
+STIP1 0,352968743
+WIPF2 0,353085817
+FOXD1 0,353404764
+HSPB2 0,35378232
+ENGASE 0,353978221
+LAT2 0,354239264
+HIST1H2AH 0,354250391
+GSDMD 0,354483715
+TRA2A 0,354674037
+C19orf29 0,354762053
+BRPF1 0,355002213
+NUMA1 0,355146564
+SNW1 0,355320637
+SMARCC1 0,355374541
+ZNF175 0,35555253
+BATF3 0,355680727
+HIST1H2BC 0,35575565
+ERN2 0,356098991
+ZFR 0,356185362
+AW301806 0,356253591
+SMTN 0,356289422
+RPS6KA2 0,356774064
+MIIP 0,35685635
+ARGLU1 0,356919378
+CTNNAL1 0,357152141
+PCDH9 0,357228835
+LAS1L 0,357263917
+DOK1 0,358029668
+AFTPH 0,35852635
+ZNF143 0,358674337
+C11orf71 0,35888557
+MICALL2 0,359221642
+KDM6A 0,359260932
+CFH 0,359284568
+CEBPB 0,359516672
+MTUS1 0,359547348
+AW973791 0,359548173
+SERTAD2 0,359684853
+FGFR1 0,359721729
+KPTN 0,360479451
+NR2F2 0,361169645
+RGL2 0,361384531
+NM_014120 0,361482036
+TAF5 0,361611903
+ZC3HAV1 0,362177526
+BEST1 0,362248528
+TNFRSF1A 0,362724804
+CLIP2 0,363062238
+EHMT2 0,363078239
+IFITM1 0,363162265
+GCFC1 0,363190607
+PECAM1 0,363227012
+YES1 0,363556218
+ZFP36L1 0,363744573
+SBNO2 0,364095165
+RMND5A 0,364201024
+IL10RB 0,364481295
+CBS 0,364486163
+TBC1D2B 0,364503601
+C10orf10 0,36458821
+AU144530 0,365137826
+ZNF500 0,365202134
+ATP6V0E1 0,36527949
+SEPT8 0,365711052
+VCAN 0,365762437
+RPL36AP51 0,366073863
+RPL31 0,36613283
+TAOK1 0,36613666
+GCN1L1 0,366181489
+CALCOCO1 0,366300689
+GNA11 0,366387362
+SH2B2 0,366425408
+RREB1 0,367259867
+SLC35E1 0,3672965
+GPRC5B 0,367311931
+TCF7 0,367371063
+PDIA4 0,367810651
+ZNF34 0,367845233
+MBD3 0,36793004
+CXCR4 0,368041224
+C9orf114 0,368120984
+IFITM2 0,368313531
+ZNF665 0,368328536
+ZCCHC24 0,368368275
+LOC100133944 0,369022431
+CSDA 0,369150342
+AU148255 0,369666508
+CIZ1 0,369704457
+CRTC3 0,369792369
+CTNNA1 0,369962411
+RARRES2 0,37011032
+NM_025033 0,370246707
+VSIG4 0,370274949
+FAM48A 0,370421427
+ZDHHC11 0,370675656
+NPAS2 0,370715345
+ADH1B 0,370935809
+ACSL1 0,371025369
+C1orf63 0,371083889
+TYMP 0,371266716
+LEPREL1 0,371463494
+LAMB2 0,371472469
+MAFB 0,371542293
+AW971248 0,371589606
+BC003629 0,371603781
+FAM63A 0,371786321
+ABCA1 0,371992682
+IGF2R 0,37211512
+SOX13 0,372131188
+WAPAL 0,372391179
+ZFC3H1 0,372437982
+ZNF710 0,372493324
+HSPA6 0,37258644
+CCDC101 0,372823539
+BAZ1A 0,372824952
+AXL 0,372842922
+NPIPL1 0,372916072
+HDGF 0,372923023
+KHDRBS3 0,373093219
+MT1X 0,373144553
+MTMR15 0,373164421
+AF257099 0,373262757
+AEBP1 0,37342966
+KLHL25 0,373672957
+GJB4 0,37372121
+LUC7L3 0,374023648
+U79248 0,374142769
+LOC653562 0,374188384
+RBM4 0,374375075
+ABCC10 0,374890625
+CXorf21 0,374896996
+DAXX 0,374917403
+C1R 0,375063944
+TPST2 0,375279072
+KLHL24 0,375307199
+C7orf68 0,375539219
+ZCCHC8 0,375600764
+CASP4 0,375605037
+ETV1 0,37597402
+BIN1 0,376340315
+RGS19 0,376617752
+PKNOX1 0,377091746
+CTTN 0,377173864
+TRIP10 0,377452782
+ANGEL1 0,377498562
+PLIN2 0,377879768
+NM_025007 0,377942771
+PTMA 0,378229214
+S100A11 0,378255627
+AXIN1 0,378580893
+NPRL3 0,378633074
+PNN 0,378695864
+AV727934 0,378843386
+ANGPT2 0,37912784
+AK023918 0,379250766
+CNPY3 0,37927474
+AF130051 0,37947818
+TLE4 0,379880985
+PAPOLA 0,379974199
+ITGB5 0,380683545
+FAM38B 0,380693638
+PABPN1 0,380909515
+SLC6A8 0,38116858
+RYBP 0,38121367
+NASP 0,381229843
+FGR 0,381246748
+PER1 0,381695992
+CDR2L 0,381867955
+LRRFIP1 0,382075479
+HMHA1 0,382282948
+KIAA0485 0,382313718
+GUSB 0,38235255
+RPS17P5 0,38240934
+FXYD5 0,382563723
+RBL2 0,382697586
+RANBP10 0,382980904
+NEDD9 0,383084673
+MSL2 0,383144236
+FAM50A 0,383317183
+AL080232 0,383323554
+SPG21 0,383712061
+TPD52L1 0,384098652
+H2AFX 0,384141378
+SWAP70 0,384225003
+IVNS1ABP 0,384369268
+KDELC1 0,384542393
+MYL12A 0,384757468
+FOXO3 0,384856157
+MED13 0,385128516
+AL049252 0,38560217
+AF007147 0,385820993
+PAX6 0,385884587
+DNASE2 0,38591545
+SLC12A9 0,386200858
+SIRT1 0,38637719
+ARID5B 0,386492868
+MT2A 0,38656824
+SLC38A2 0,386710042
+GNG5 0,386756333
+SRRM2 0,386841072
+SERPINB6 0,386985458
+CC2D1A 0,387023088
+LRRC37A2 0,387067777
+CSF1 0,387071999
+RPL29P11 0,38708859
+SFRS14 0,387094074
+MYO9B 0,387103012
+AW972855 0,387241981
+TRIP4 0,387728627
+ZBTB40 0,387827711
+STARD8 0,387863703
+WBSCR16 0,387992811
+NXF1 0,388021286
+CTDSP1 0,38803541
+RSAD1 0,388042285
+SUV420H1 0,38833134
+CDKN1C 0,388508896
+NM_016415 0,388588403
+E2F4 0,388673603
+KANK2 0,388702219
+ZC3H7B 0,388980025
+ANGPTL4 0,389035415
+CRY1 0,389801967
+KIAA0556 0,389845114
+TBC1D16 0,390016803
+TCOF1 0,390109025
+ZFYVE26 0,390278079
+IFRD1 0,39034324
+EIF4B 0,390385914
+SMC1A 0,390525141
+SCIN 0,3907272
+MARS 0,391061966
+PTRF 0,391089965
+POLR2J 0,391514571
+APAF1 0,391530483
+ITPK1 0,3915415
+PNRC1 0,392133859
+CLIC2 0,392140808
+KIAA0913 0,392243895
+PRKAR2A 0,392619325
+PRKX 0,392750502
+SYDE1 0,392957216
+ACSL5 0,393140899
+LRP10 0,393162277
+LPP 0,393214983
+SNTB2 0,393383504
+NADK 0,393882671
+PCBP2 0,394206896
+N51370 0,394562467
+CLIC1 0,394663761
+CTBP2 0,394785714
+PHB 0,394929787
+BCL2 0,395102709
+TAF4 0,395492947
+LOC652607 0,395562084
+YBX1 0,396079328
+PRPF3 0,396609142
+SLC38A10 0,396741732
+ERBB2IP 0,396808535
+CFLAR 0,396840203
+TNFRSF10B 0,397091951
+PHC1B 0,397196351
+ARL17A 0,397406114
+ZBTB20 0,397424403
+REPIN1 0,397830532
+BE466926 0,397930108
+MT1P2 0,398055653
+ZNF778 0,398225613
+DICER1 0,398300689
+NM_018603 0,398329284
+RAF1 0,398631868
+MXD4 0,398685167
+FBXL7 0,398770393
+CALD1 0,399121196
+GSDMB 0,399246982
+ZCCHC2 0,399293751
+PODXL 0,399691684
+ACACB 0,400136922
+VEZF1 0,400413083
+PLEKHM1 0,401187317
+CSPG4 0,401646086
+ID3 0,40170175
+RBM41 0,401719975
+KDM6B 0,401885964
+PHF15 0,402522419
+LAMP2 0,402538077
+CDC14B 0,402583482
+HNRNPL 0,403044314
+SLC4A2 0,403448509
+DDX23 0,403953946
+TUBD1 0,40407115
+SLC16A3 0,404204458
+CAPN2 0,405022548
+CBFA2T2 0,40560438
+TCEB2 0,405769952
+HNRNPF 0,406126644
+MORC2 0,406182732
+FOXO1 0,406430281
+AI962978 0,406538883
+HP1BP3 0,406567553
+CBFB 0,406789498
+RBM14 0,406886421
+SFI1 0,407058786
+ZHX3 0,407089165
+KDM3A 0,407233406
+SIRT2 0,407341821
+ANKS1A 0,407373917
+TCF3 0,407442968
+NOTCH2NL 0,407672378
+EEF1D 0,407830724
+SOX12 0,408065349
+SLCO1A2 0,40820492
+HNRNPA3 0,408299868
+GTF2H3 0,408624789
+FZD9 0,408729069
+SAFB2 0,408755308
+APBA3 0,408834306
+ASCL1 0,409161488
+CG012 0,409559201
+WDR59 0,409606436
+LAMA5 0,409632505
+ZNF276 0,409730125
+ZNF395 0,410080702
+TIMM44 0,410223052
+BGLAP 0,410749324
+ZHX2 0,411039562
+CARS2 0,411302016
+SLCO3A1 0,411338796
+LOC442497 0,411765627
+FRYL 0,411842495
+CYP2J2 0,412070197
+ABL1 0,412522321
+INF2 0,412975218
+SGK1 0,413352645
+SFTPB 0,413789208
+TIGD1L 0,41383023
+RBCK1 0,414019825
+TRAPPC10 0,414285862
+DUSP7 0,414641136
+WSCD1 0,415016303
+DCP1A 0,415308358
+LPAR1 0,415365439
+RBBP6 0,415730871
+DONSON 0,416255506
+C16orf5 0,416258918
+NCOA1 0,416350707
+CFHR1 0,416440287
+AA126763 0,416566153
+LRRC32 0,416765832
+CP110 0,41732481
+LTBP3 0,417338221
+TDRD3 0,417356196
+HMG20B 0,417456909
+CDC42EP2 0,417645635
+TAF1C 0,417736819
+NM_013344 0,41778911
+VGLL4 0,417820331
+PHKA2 0,417904785
+KDSR 0,418009802
+RELA 0,418064238
+TBL1X 0,41814877
+SIAH2 0,418727849
+MYO1E 0,418747589
+HIST1H2BD 0,419127582
+AI744451 0,419208355
+PTMAP7 0,419537834
+ARID5A 0,419593497
+CYP27A1 0,420064872
+RAB13 0,420441013
+CPSF7 0,420526378
+CPT1B 0,420770156
+LRDD 0,420794327
+PILRB 0,421599366
+STAB1 0,421733406
+FCHO1 0,422126906
+ZNF32 0,422311821
+TBC1D3H 0,422328806
+C1orf66 0,42292679
+NM_025032 0,423323973
+AI732802 0,423584905
+PCID2 0,423787762
+POGK 0,423912669
+TMEM140 0,424587207
+TMC6 0,424604298
+AL080160 0,42490597
+AK021505 0,425024442
+SCD5 0,425610027
+RAD52 0,425956612
+AF116715 0,425960499
+DCI 0,425967692
+SFRS18 0,426091505
+HCG2P7 0,426136765
+ADORA2A 0,426366158
+NM_021651 0,426442506
+MID1IP1 0,426940092
+HNRNPC 0,427103695
+NM_025024 0,427155973
+AK024315 0,427460397
+AK021514 0,427966252
+SLC29A3 0,428138792
+NSUN5 0,428255135
+PHF10 0,428599049
+DAPP1 0,428626141
+TMEM109 0,428647746
+LOC91316 0,428742129
+ITGB4 0,42956266
+SLC30A1 0,429998682
+AW150065 0,430129937
+ZCCHC6 0,430267528
+ARHGEF2 0,430371137
+AK027193 0,43049002
+TRIM52 0,430535815
+MT1G 0,430767233
+NOTCH1 0,430849119
+ZRSR2 0,43114681
+RPS6KA1 0,43184981
+KANK1 0,432456197
+FURIN 0,432618855
+APOBEC3C 0,432749845
+ANKRD40 0,432772877
+TRIOBP 0,432900403
+ZNF384 0,433116555
+CDKN1A 0,43319672
+BTG1 0,433570541
+EPHX1 0,433658916
+CNOT6 0,434207544
+HSPA1L 0,434322364
+PKD1 0,434547199
+WAS 0,434717417
+RPL23AP32 0,434993767
+P4HA1 0,434997425
+MAX 0,435160002
+UIMC1 0,435278167
+NM_025120 0,435322168
+NCOA6 0,435700178
+TPD52L2 0,435768747
+BCL6 0,435938226
+AK024108 0,436355329
+C7orf23 0,436800978
+CDC42BPA 0,437074951
+CD59 0,437137855
+POLR1B 0,437227618
+TLR5 0,437498143
+HDAC1 0,437993569
+ARHGEF7 0,438071237
+AA045174 0,438161955
+TBC1D17 0,438488128
+PRELP 0,438518539
+GTF2H2B 0,438525643
+HIST1H2BK 0,43866778
+AU147851 0,438979485
+RBM39 0,439661925
+IQGAP1 0,439786742
+RPL18AP3 0,440613252
+LTBR 0,440721546
+RPL35A 0,441136859
+ARAP2 0,441441928
+ARAF 0,441560027
+MT1H 0,441587824
+LOC441258 0,442117007
+ZCCHC14 0,442132801
+IRF7 0,442147625
+NOL12 0,442203671
+PTPLB 0,442541309
+AI683552 0,442752948
+MYST1 0,442881562
+MXI1 0,443040642
+AW974910 0,443299524
+C1orf144 0,443500279
+KRCC1 0,444417306
+PIAS4 0,444438643
+SRSF1 0,444637015
+LRP2 0,444740953
+ZDHHC18 0,445392541
+SPN 0,445443935
+ST13 0,446667878
+PHF17 0,446746739
+NACA2 0,446876872
+SASH1 0,447285208
+CD22 0,44772036
+CSNK1E 0,447902552
+COL5A3 0,447933631
+MAT2A 0,448695587
+EFHD1 0,448820126
+MAP3K3 0,448963961
+BIN3 0,449317201
+LUC7L 0,449469644
+KIF1C 0,449622117
+RNF144A 0,450034368
+TULP3 0,450626451
+CDKN2C 0,450879897
+HSD17B7 0,451226227
+ACIN1 0,451331774
+PABPC3 0,451363083
+PHF21A 0,45139036
+HNRNPH3 0,451480034
+HIST2H2BE 0,452219911
+RRP1B 0,452597128
+SOX2 0,453132172
+ZNF444 0,453296716
+FAM13A 0,453547738
+JUP 0,453753674
+PODNL1 0,453854292
+MAML1 0,453885
+SNRNP70 0,45408945
+SDCCAG3 0,45464357
+PLGLB1 0,454722494
+CDH19 0,454754165
+HSPA1B 0,455063205
+ARHGEF10 0,455229121
+NFIL3 0,455469821
+NFKBIA 0,455577982
+XRCC2 0,455670024
+ACTN4 0,455764555
+PDS5A 0,456071133
+POU2F1 0,456120351
+VPS54 0,456318614
+BANF1 0,456451252
+PGCP 0,456765652
+RPL28 0,456867479
+ICAM2 0,457066169
+SNAP23 0,457069788
+SART1 0,457941993
+AK023891 0,458253977
+BANP 0,458588544
+MAP3K11 0,458968207
+EPOR 0,459463669
+FKSG49 0,459538011
+MT1F 0,459638951
+NM_014128 0,460468204
+AP1G2 0,460676306
+GAS2L1 0,461632768
+PHIP 0,462053958
+NOL8 0,462387404
+NM_017932 0,462395281
+RNF130 0,462894529
+ZMYND8 0,463309493
+AK024525 0,463401166
+TRIM28 0,463454342
+BCAT2 0,463509769
+TYRO3 0,463574548
+PHLPP1 0,463738295
+BST2 0,465024297
+PDGFRB 0,465034704
+AL049987 0,465336929
+AKAP8L 0,466278804
+TGM2 0,467555999
+CREBBP 0,467899354
+KIAA0894 0,468325808
+DDX39 0,468959477
+NCAPD2 0,468959537
+ALPK1 0,469621875
+TGIF1 0,469902489
+PPP1R14B 0,470121069
+PNMT 0,470291567
+NAA16 0,470467422
+ZNF611 0,470526774
+ZRSR1 0,470857426
+NPIP 0,472818474
+RBM38 0,473036567
+USP34 0,473278809
+TGFB3 0,474067001
+ITSN2 0,475328182
+CEBPD 0,475754278
+MCM3AP 0,476296498
+HAPLN2 0,476718109
+POGZ 0,477224004
+NR2F1 0,477556735
+GAS1 0,478628972
+SLTM 0,478903701
+ECE1 0,479007813
+CALCOCO2 0,47910558
+RXRA 0,479821295
+MEIS2 0,480178943
+CLEC2B 0,481843785
+AL049260 0,482481089
+CHST3 0,48259726
+COL16A1 0,483094975
+SLC25A16 0,483255606
+LHPP 0,48421483
+AF010144 0,484619234
+GTSE1 0,484629217
+MUM1 0,484956644
+TNXB 0,485246904
+PRINS 0,486032909
+ANKRD49 0,486282532
+PTPRK 0,486899575
+PPAP2C 0,487395433
+C22orf9 0,488987561
+KHNYN 0,489026627
+RAPGEF3 0,489474077
+AF078844 0,489716822
+MAN2A1 0,489875474
+IFT20 0,490824284
+USP21 0,490859618
+NOP2 0,491526918
+LOC440248 0,491905455
+LOC647070 0,493492979
+MAFF 0,494072026
+BG251521 0,495196452
+C6orf145 0,496322836
+MLL4 0,496324893
+ATF4 0,49676781
+RELN 0,497310216
+PELI1 0,497491599
+P2RX7 0,497499324
+CNOT2 0,498172475
+FAM38A 0,498599859
+DCLRE1C 0,498693515
+INSR 0,502304787
+MAPKAPK2 0,502573806
+NDE1 0,50267356
+MT1M 0,502716901
+CDK5RAP3 0,504041432
+SULT1A4 0,504805398
+NSUN5P2 0,505093708
+ANKRD10 0,505841449
+LOC339047 0,506042447
+LRRC1 0,506594446
+CUX1 0,507257715
+SRRT 0,508240438
+MAF 0,508625791
+EBLN2 0,509549245
+NM_017618 0,510705903
+RBM4B 0,51138423
+FBXW12 0,511744983
+ATP8B1 0,511969804
+NM_024978 0,512045897
+KCNMB4 0,512142959
+CLMN 0,512461537
+LOC100132540 0,512589899
+SERPINH1 0,513136463
+RHBDF2 0,513703735
+PCF11 0,514081494
+HAUS2 0,514694211
+TECPR2 0,514970535
+TNIP2 0,515014912
+AUP1 0,516155581
+KIAA0101 0,516801916
+N35922 0,51703624
+STK38 0,517483454
+AZGP1P1 0,518047589
+C13orf15 0,518310047
+PRR11 0,518691616
+PDCD6 0,51972326
+AFF1 0,520716014
+AF222691 0,521107674
+BE045142 0,521502008
+PACS2 0,521749261
+PSRC1 0,522634606
+ZNF358 0,523463012
+MAPKBP1 0,523696079
+S100A4 0,524041412
+MYO1C 0,524902669
+IRF3 0,52538788
+TOB2 0,526119659
+KLHL21 0,527145117
+PGF 0,527713686
+LOC399491 0,528407104
+ARAP1 0,528556373
+AZGP1 0,528659072
+SIRT7 0,528927974
+C16orf53 0,529668261
+KLHL2 0,533153888
+AK022213 0,533802801
+ANKRD28 0,534099367
+TF 0,536170201
+MAVS 0,53636005
+MSX1 0,536723495
+C12orf35 0,537890473
+AA554945 0,538449904
+SUN2 0,539191173
+RBM6 0,54218394
+AL080112 0,542349721
+SORT1 0,542569398
+AL049285 0,542660805
+FOXO4 0,542834527
+ABCA8 0,543725594
+RING1 0,54468938
+KCNE4 0,546337688
+TAZ 0,546506594
+DIP2A 0,546907877
+CLK4 0,548788669
+ZNF277 0,549312201
+MUS81 0,551193399
+DBT 0,556696292
+EMP3 0,557013195
+DDIT4 0,557077384
+RUFY1 0,557170712
+MYST3 0,559285285
+PRPF4B 0,559881298
+LOC100132247 0,562956585
+HSPB1 0,56508456
+CHD7 0,566776564
+CHORDC1 0,566831861
+COBL 0,569205746
+STAG2 0,569603186
+CTDSP2 0,570069613
+ZNF160 0,572703009
+PDE4C 0,574535337
+WWC3 0,575159977
+BMI1 0,576213767
+CRYAB 0,577245348
+AHCTF1 0,577515066
+ADIPOR2 0,5780263
+CASC3 0,57815663
+MUTYH 0,579456271
+AK023783 0,580340854
+HIGD1B 0,583663012
+PLOD1 0,587347495
+PRR14 0,587364521
+SH3BP4 0,58788373
+C19orf28 0,587956493
+NDRG1 0,588555643
+HIST1H1C 0,591446402
+TCF12 0,592176798
+MPST 0,593408757
+SEPP1 0,593935425
+DNAJB6 0,595685757
+SIRPA 0,596218961
+FLT1 0,597923318
+MYOT 0,598968138
+HIST1H2AC 0,600586387
+HBP1 0,600714263
+KAZ 0,601415288
+PTBP1 0,602313539
+NSUN5P1 0,603090503
+GUSBP3 0,604393039
+KCNJ2 0,616084197
+KAT2A 0,620256502
+MCM7 0,622618327
+FBXW4 0,627081137
+MKNK2 0,628440154
+IL17RB 0,631530593
+CLK1 0,632420317
+LRP4 0,632833859
+FAM53B 0,641895571
+JMJD6 0,64411039
+TYK2 0,644727629
+PLOD3 0,644893842
+CXXC1 0,650530485
+AK024136 0,659066605
+PAN2 0,66036619
+NPTX2 0,665210794
+SPEN 0,669461617
+SETD5 0,670191692
+STX10 0,674048462
+CDK2AP2 0,67411425
+PPM1B 0,68382966
+SLCO4A1 0,685048974
+GLT25D1 0,706365388
+ZC3H11A 0,716021559
+ZBTB16 0,720405109
+ZNF692 0,720940567
+NUPR1 0,724120307
+FLCN 0,747339708
+NFASC 0,755177517
diff --git a/console/testFiles/pd_full/PD_160714_2/layouts/ageing.txt b/console/testFiles/pd_full/PD_160714_2/layouts/ageing.txt
index 952e851c769c685e0d4eb1f4736e4ac1a49fb5dd..d5c8ec23b48129a18a37c03059aa5a46ad5cea59 100644
--- a/console/testFiles/pd_full/PD_160714_2/layouts/ageing.txt
+++ b/console/testFiles/pd_full/PD_160714_2/layouts/ageing.txt
@@ -1,416 +1,416 @@
-# VERSION=1.0
-# NAME=Ageing brain
+# VERSION=1.0
+# NAME=Ageing brain
# DESCRIPTION=Differential transcriptome expression from post mortem tissue. Source: Allen Brain Atlas datasets, see PMID 25447234.
-name value
-ELMO2 -0.547404913905166
-RGS1 0.664905640201586
-GSTT1 -0.630503181260422
-SDPR 0.576954531502211
-KCNJ2 -0.389733143810031
-DLG2 -0.622560222549952
-C2orf46 0.306481308387015
-YPEL1 -0.110679998012662
-AFF2 -0.580887248407995
-TCP11L2 -0.446138772716671
-TYROBP 0.0965004216809888
-PCK1 0.583148947380073
-C3 -0.229405245486493
-BLOC1S2 -0.501156113973434
-LPAR5 -0.252012578774993
-ACAD11 0.484415314534294
-CALB1 -0.585051808236823
-GNG2 -0.514333881323537
-GRIN3A -0.54737874801763
-BLNK -0.23678687239484
-SMARCD1 -0.480222958914743
-ARMC9 0.512102956486084
-CX3CR1 -0.300766155352383
-SLC31A2 -0.502055753854611
-AGPAT3 -0.413409719893933
-EFNB3 -0.382400551167611
-ELMOD2 0.402518685883201
-PRKCG -0.34345444223993
-LAPTM5 -0.136628457581106
-IQUB 0.562346209462303
-STAM -0.566262263187017
-OR11A1 0.178234692397988
-ZDHHC9 -0.520488129277965
-C11orf9 -0.511135500492906
-KLF4 0.640024343756592
-SYCP2L 0.555576793235834
-C20orf112 -0.63210679508749
-AP3M1 -0.436291767005889
-ALMS1P 0.310301539060874
-GREM1 -0.101042197816266
-HLCS -0.404869146774348
-CARNS1 -0.358503492948689
-TSHZ2 -0.370201532555949
-CDKN1A 0.37878581767329
-CNDP1 -0.387074241865627
-C1orf161 0.408555295769768
-DOK6 -0.552556377657443
-C12orf43 -0.345533858224805
-SIPA1L2 -0.469893969573457
-FLJ40712 0.248899115372987
-TREM2 0.326657235461902
-MS4A6A 0.333196279374371
-RASGRF1 0.18816869654076
-RNF26 -0.576816063125611
-C7orf68 0.551320218061987
-DPP7 0.601525547176648
-OMD 0.556147496355725
-SNAI2 -0.402803074931945
-COL21A1 0.475584827359055
-APBB1IP -0.510593783545533
-PRKCQ -0.625167167620313
-PDGFRA -0.593141766545025
-SLCO2B1 -0.20664851085323
-LPCAT3 -0.457401881600448
-CD37 -0.225548512842192
-IRF8 -0.513003936776053
-CSF1R -0.17710132121375
-CD74 0.0263995452022326
-CHI3L1 0.637898420604861
-SELPLG -0.165789940031603
-CDH8 -0.544872582360693
-CXCL12 -0.350721988871356
-TOPBP1 -0.516846284550731
-SLC16A10 0.372816060474775
-PCDHB9 -0.583344609658305
-HLA-DRA 0.249881965203208
-OLR1 0.105145169714195
-ADORA3 0.352457579745827
-ALOX5AP 0.094898490604102
-HLA-DOA 0.0912244782358314
-ZNF519 0.242878217518759
-FCER1G 0.122597294910367
-MT1H 0.274901514766897
-MFSD2A 0.12726693788776
-AIF1 -0.0853762046815476
-CTSH 0.324179727747488
-C3AR1 0.00893654957093225
-FCGR2A -0.0476956544487118
-CXCL16 0.0931434603948185
-EVI2B -0.236921572611684
-BACE1 -0.616602739604107
-OR1E1 0.491889127463635
-CLK1 0.423619868541565
-FLJ13197 0.340321509869536
-WBP2NL 0.590401706468574
-UGT8 -0.444926073295334
-HSD17B14 0.614959487312916
-GRIK3 -0.628539434045017
-MT1G 0.569589804148072
-BAIAP3 0.50915236570152
-TJAP1 -0.211899568999271
-PIP4K2C -0.546592244445733
-CAMK4 -0.62370886479691
-TMEM63A -0.349108640870675
-CCDC45 0.470491672406875
-ERLIN1 -0.590064605968872
-ATP6V1F 0.31735684237396
-EPHB2 -0.492251103302591
-ANKRD11 -0.576352445468476
-PCDHB2 -0.56247030572076
-ACSL1 -0.580402201513607
-LGR5 -0.49666928921999
-PDE3B 0.561081934872393
-C1orf21 -0.433409479731833
-LRRTM1 -0.430851468978506
-GPR12 -0.285126298493215
-VSTM2A -0.496505850586284
-ODZ1 -0.500803022233123
-CACNG2 -0.568038440978143
-SMPD3 -0.448297258958326
-SORBS2 -0.652515435812272
-DCAF7 -0.561122254419525
-GJD2 -0.500391756170096
-PEG10 -0.529984214958046
-A2M -0.0956498395825097
-THRB -0.278461084991876
-C11orf24 -0.519543924524242
-TFG -0.340307925442264
-MAMLD1 -0.389582104545406
-ASPHD2 -0.44086160208266
-ANKRD37 0.644400268061014
-NCKAP1L -0.38869429192758
-CAPN5 -0.568639095894228
-SERINC3 -0.473478678274642
-CEBPB 0.386715054596765
-PRDM10 -0.575525391963737
-HCN1 -0.384931312491389
-CAMTA1 -0.435666315274373
-KLHDC1 0.27598504319864
-DUSP1 0.576414053338242
-QRICH1 -0.533552393948272
-SH3KBP1 -0.391446975914019
-EBF1 -0.379385913897609
-PPP1R16B -0.356903880861572
-BTBD3 -0.327196312551472
-NRXN2 -0.509283550099326
-KAZ -0.541421535478964
-KIAA0317 -0.636085461640037
-NDST3 -0.426753877235142
-GMCL1 0.45632888308336
-P2RX5 -0.283914132520413
-IGFL3 0.297606727720448
-LOC286161 -0.366837279825892
-PLEKHM1 -0.408702703852517
-RIMS1 -0.372721943202267
-UBE2Q2P1 0.327173892822723
-TTYH2 -0.407525904378876
-DES 0.06209856553185
-DBNDD2 -0.30225683329951
-ENPP2 -0.409429156664166
-NTN4 0.494337823155339
-SUN2 -0.276353435973038
-ACTG2 -0.210220455726459
-CA2 -0.0242596436213912
-THBS1 -0.221580234422776
-LDLRAD3 -0.360622764104025
-SNX1 -0.0377961368749078
-ERBB3 -0.405973590470433
-TTN 0.391623015044573
-ATRN -0.52540142288716
-NPC1 -0.267674240960311
-GNS -0.181466206971045
-KLK6 -0.378431280290618
-FOS 0.360516377902882
-CD69 0.377148542537053
-LYVE1 0.138789282779698
-FTL 0.237591315022414
-JUNB 0.394473562572383
-GSTM5 0.217560993654354
-NR4A1 0.24427289755837
-PGAM2 0.551801840506397
-TMEM176A 0.537931366670412
-EGR1 -0.157019974633097
-GPR183 0.107180842069747
-CXCL11 0.395003724312407
-PLA2G12A -0.18246216314499
-HLA-DMB 0.229795197318716
-CPNE8 0.0508489313725271
-ZFP36 0.42538436064968
-AGPAT4 -0.467855141787709
-HLA-DPA1 0.408536378107808
-PIK3C2B -0.591780318571167
-CPNE6 -0.271576531727541
-PLD3 -0.200022062788495
-PVRL1 -0.555155906198138
-GGCT -0.279243242312552
-P2RY13 -0.360442360434042
-CNTN5 0.00258913839174191
-MCM7 0.195233154899312
-GPR120 -0.199692500084005
-GABRE 0.0682190440098052
-LRRC39 0.498683033772744
-TLR7 -0.164697853025215
-RFC3 -0.486755240432686
-CD33 0.00184280522373291
-CA8 0.363290764959567
-MAS1 -0.492009752548035
-FBLN5 -0.511286958021381
-TMTC1 -0.332133706392934
-C1orf51 0.45497717618641
-RPL35 -0.0899084146126614
-DKK2 -0.38611669080376
-USP53 0.412868805138869
-CD177 -0.217675402988493
-ELAVL1 -0.579547221944692
-AIFM3 0.577935690502709
-ASCL1 0.37568323074867
-EXPH5 -0.575008199569129
-CBWD3 0.283287779368243
-PEPD -0.0553830875558683
-GPNMB 0.364500938005497
-NEDD4L -0.508710397589902
-CALB2 -0.425755713683833
-FAM49A -0.447197463197697
-NT5DC3 -0.265234061560778
-HES6 0.347000889525298
-GDA -0.336613721691585
-RASAL1 -0.344295261121664
-ANO3 -0.518790055621458
-C14orf145 0.508493948450919
-MSRB3 0.374050410076754
-CC2D2B 0.438851338613457
-FAM65B -0.254284575986291
-KIRREL3 -0.539616579176257
-CKLF 0.222793814048359
-DNAJA4 -0.486836211576555
-BCOR -0.579019889055718
-CBLL1 -0.642779519205918
-CACNG3 -0.428582206819538
-GRIN2B -0.577739683994275
-LRRC67 0.341366642004448
-RELL2 0.405916058000189
-NUDT3 -0.340375787654433
-MAST2 -0.541618527665053
-S100A10 -0.105037624066791
-OR13C2 0.379430219617317
-HSPC157 0.570528832119166
-NOP10 0.322245514370384
-C6orf174 -0.338629613564291
-LRRC61 0.0251744454575518
-FOLR2 0.131043427693804
-DYRK2 -0.522163896119695
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+name value
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+FTO -0.484606564596535
+KIAA0430 -0.323429860829196
+HPSE2 0.444523469491999
+AAK1 -0.336960928171931
+ZNF592 -0.459711729876906
+INF2 -0.368727716463355
+UNC80 -0.203435560684691
+KCNJ9 -0.385326074668389
+CREBBP -0.48479916887186
+TMEM187 0.353577074222219
+GIMAP6 0.196334054611495
+MSH4 0.495021650163618
+CYP2F1 -0.202379731783218
+WARS -0.36956071999387
+EIF4H -0.324258084689287
+LMF1 -0.465196534142832
+SLC9A11 0.380530864151023
+RPLP0 0.401187575431913
+SORCS3 -0.524716179920174
+SMPD1 -0.371378049257817
+MLL2 -0.382849048834827
+ACTA2 -0.351473562308814
+CD84 0.0440334284755635
+LRRC57 -0.0868790230732024
+ADAM28 -0.234050278113392
+FLJ37543 0.329929076805089
+NR4A2 -0.525703760298336
+METT11D1 0.315411883405057
+MEX3C -0.570394569556345
+ST8SIA5 -0.525318796364569
+HRH1 -0.276472654345764
+RAB3IP -0.23897971786832
+ETV6 -0.448657117826825
+LUZP2 -0.409590511647277
+TRIM44 -0.386063986999447
+MYH11 -0.280352372336459
+TPK1 0.485143439818794
+C1QC -0.0250872517448672
+A2ML1 0.356485052871728
+ZNF365 0.476040462817264
+CCL2 0.160044975309114
+ADRA2A -0.511689669158592
+TMPRSS5 0.299973105357606
+C5orf53 0.490994640268981
+MORC2 -0.41225212616417
diff --git a/converter-CellDesigner/src/test/resources/log4j.properties b/converter-CellDesigner/src/test/resources/log4j.properties
index c749802b0ebb078e88e6f597b17936a60b4b0020..28f78fc1879d9160da5c708db9b99a2049d7dc34 100644
--- a/converter-CellDesigner/src/test/resources/log4j.properties
+++ b/converter-CellDesigner/src/test/resources/log4j.properties
@@ -1,21 +1,21 @@
-#Set root logger 's level and its appender to an appender called CONSOLE which is defined below.
-log4j.rootLogger=info, CONSOLE, R
-
-#Set the behavior of the CONSOLE appender
-log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
-log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
-log4j.appender.CONSOLE.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
-#log4j.appender.CONSOLE.layout.ConversionPattern=%m%n
-
-
-#Set the behavior of the FILE appender
-log4j.appender.R=org.apache.log4j.FileAppender
-log4j.appender.R.File=${catalina.home}/logs/MapViewer.log
-log4j.appender.R.layout=org.apache.log4j.PatternLayout
-log4j.appender.R.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
-
-
-log4j.logger.org.springframework=warn
-log4j.logger.org.hibernate=warn
-log4j.logger.lcsb=debug
-log4j.logger.lcsb.mapviewer.common.comparator=info
+#Set root logger 's level and its appender to an appender called CONSOLE which is defined below.
+log4j.rootLogger=info, CONSOLE, R
+
+#Set the behavior of the CONSOLE appender
+log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
+log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
+log4j.appender.CONSOLE.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
+#log4j.appender.CONSOLE.layout.ConversionPattern=%m%n
+
+
+#Set the behavior of the FILE appender
+log4j.appender.R=org.apache.log4j.FileAppender
+log4j.appender.R.File=${catalina.home}/logs/MapViewer.log
+log4j.appender.R.layout=org.apache.log4j.PatternLayout
+log4j.appender.R.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
+
+
+log4j.logger.org.springframework=warn
+log4j.logger.org.hibernate=warn
+log4j.logger.lcsb=debug
+log4j.logger.lcsb.mapviewer.common.comparator=info
diff --git a/converter-CellDesigner/testFiles/annotation/invalid_rdf.xml b/converter-CellDesigner/testFiles/annotation/invalid_rdf.xml
index 11bcfac12978c081dffe93c0a39448315950dbfd..b2e5fb5e7d4486441b4712953439cae65e6d53ea 100644
--- a/converter-CellDesigner/testFiles/annotation/invalid_rdf.xml
+++ b/converter-CellDesigner/testFiles/annotation/invalid_rdf.xml
@@ -1,2 +1,2 @@
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
</rdf:RDF>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/annotation/invalid_rdf2.xml b/converter-CellDesigner/testFiles/annotation/invalid_rdf2.xml
index df2d68b495bb70503d72f3c14fd28ae3ab9da1c0..5e21af6c7de77f09c88421788d873e822b95a979 100644
--- a/converter-CellDesigner/testFiles/annotation/invalid_rdf2.xml
+++ b/converter-CellDesigner/testFiles/annotation/invalid_rdf2.xml
@@ -1,10 +1,10 @@
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#re836">
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li/>
-<rdf:li rdf:resource="urn:miriam:pubmed:15639314"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-</rdf:Description>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#re836">
+<bqbiol:isVersionOf>
+<rdf:Bag>
+<rdf:li/>
+<rdf:li rdf:resource="urn:miriam:pubmed:15639314"/>
+</rdf:Bag>
+</bqbiol:isVersionOf>
+</rdf:Description>
</rdf:RDF>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/annotation/invalid_rdf3.xml b/converter-CellDesigner/testFiles/annotation/invalid_rdf3.xml
index 6e67e05da32bb726739ef34236caaf28364c3fa6..225ad4bb56e14f08d859dba9135ed4c893690a83 100644
--- a/converter-CellDesigner/testFiles/annotation/invalid_rdf3.xml
+++ b/converter-CellDesigner/testFiles/annotation/invalid_rdf3.xml
@@ -1,10 +1,10 @@
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#re836">
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li rdf:resource="urn"/>
-<rdf:li rdf:resource="urn:miriam:pubmed:15639314"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-</rdf:Description>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#re836">
+<bqbiol:isVersionOf>
+<rdf:Bag>
+<rdf:li rdf:resource="urn"/>
+<rdf:li rdf:resource="urn:miriam:pubmed:15639314"/>
+</rdf:Bag>
+</bqbiol:isVersionOf>
+</rdf:Description>
</rdf:RDF>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/annotation/invalid_rdf4.xml b/converter-CellDesigner/testFiles/annotation/invalid_rdf4.xml
index cbdc94e696e54fe33eb2a3bbe6401e3dccb26de1..b94751fdf0ec47ece3df40991bafd857eca52edb 100644
--- a/converter-CellDesigner/testFiles/annotation/invalid_rdf4.xml
+++ b/converter-CellDesigner/testFiles/annotation/invalid_rdf4.xml
@@ -1,9 +1,9 @@
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#re836">
-<bqbiol:unk>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A28870"/>
-</rdf:Bag>
-</bqbiol:unk>
-</rdf:Description>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#re836">
+<bqbiol:unk>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A28870"/>
+</rdf:Bag>
+</bqbiol:unk>
+</rdf:Description>
</rdf:RDF>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/antisense_rna.xml b/converter-CellDesigner/testFiles/invalid/antisense_rna.xml
index a8bbcd098cd47633063cc49d32d12f4227780ca7..16ee1973b9443567aa5485b3a0fd0945d6a77635 100644
--- a/converter-CellDesigner/testFiles/invalid/antisense_rna.xml
+++ b/converter-CellDesigner/testFiles/invalid/antisense_rna.xml
@@ -1,16 +1,16 @@
-<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-some notes
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfRegions>
-<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="CodingRegion"/>
-<unk/>
-</celldesigner:listOfRegions>
+<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+some notes
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="CodingRegion"/>
+<unk/>
+</celldesigner:listOfRegions>
</celldesigner:AntisenseRNA>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/antisense_rna2.xml b/converter-CellDesigner/testFiles/invalid/antisense_rna2.xml
index 5bed846e3d441a93d703b67f01aa946596e43261..8911982737e363a51e83d5918d5656f076b2bc94 100644
--- a/converter-CellDesigner/testFiles/invalid/antisense_rna2.xml
+++ b/converter-CellDesigner/testFiles/invalid/antisense_rna2.xml
@@ -1,16 +1,16 @@
-<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
-<unk/>
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-some notes
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfRegions>
-<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="CodingRegion"/>
-</celldesigner:listOfRegions>
+<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
+<unk/>
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+some notes
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="CodingRegion"/>
+</celldesigner:listOfRegions>
</celldesigner:AntisenseRNA>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/antisense_rna3.xml b/converter-CellDesigner/testFiles/invalid/antisense_rna3.xml
index 75a9bab43457da579ca40c1b29322aa3858f2566..6bf281a7fb03dc4184d13f5052772cacc726d9e6 100644
--- a/converter-CellDesigner/testFiles/invalid/antisense_rna3.xml
+++ b/converter-CellDesigner/testFiles/invalid/antisense_rna3.xml
@@ -1,15 +1,15 @@
-<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-some notes
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfRegions>
-<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="unkBlaType"/>
-</celldesigner:listOfRegions>
+<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+some notes
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="unkBlaType"/>
+</celldesigner:listOfRegions>
</celldesigner:AntisenseRNA>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/antisense_rna4.xml b/converter-CellDesigner/testFiles/invalid/antisense_rna4.xml
index 310a5b13d51220756ba7d66c78f4fc43e3ce958e..81c4083034dee65c91594e83c81a2a48e6ad629d 100644
--- a/converter-CellDesigner/testFiles/invalid/antisense_rna4.xml
+++ b/converter-CellDesigner/testFiles/invalid/antisense_rna4.xml
@@ -1,17 +1,17 @@
-<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-some notes
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfRegions>
-<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="CodingRegion">
-<unk/>
-</celldesigner:region>
-</celldesigner:listOfRegions>
+<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+some notes
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="CodingRegion">
+<unk/>
+</celldesigner:region>
+</celldesigner:listOfRegions>
</celldesigner:AntisenseRNA>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/antisense_rna_collection.xml b/converter-CellDesigner/testFiles/invalid/antisense_rna_collection.xml
index fe47951f2675ab7ea6b1ab94370971a1a5b55a8f..ad061bc48c8b51e326e9e9106d7186c25df574de 100644
--- a/converter-CellDesigner/testFiles/invalid/antisense_rna_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/antisense_rna_collection.xml
@@ -1,3 +1,3 @@
-<celldesigner:listOfAntisenseRNAs>
-<unknoen/>
+<celldesigner:listOfAntisenseRNAs>
+<unknoen/>
</celldesigner:listOfAntisenseRNAs>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/block_diagrams.xml b/converter-CellDesigner/testFiles/invalid/block_diagrams.xml
index 8cbe9778aba8c8a1390f66e28f74499697c89f62..53f93e7b14cb34ebb8db4d3635380ac7027ee5da 100644
--- a/converter-CellDesigner/testFiles/invalid/block_diagrams.xml
+++ b/converter-CellDesigner/testFiles/invalid/block_diagrams.xml
@@ -1,3 +1,3 @@
-<celldesigner:listOfBlockDiagrams>
-<unk_block/>
-</celldesigner:listOfBlockDiagrams>
+<celldesigner:listOfBlockDiagrams>
+<unk_block/>
+</celldesigner:listOfBlockDiagrams>
diff --git a/converter-CellDesigner/testFiles/invalid/compartment.xml b/converter-CellDesigner/testFiles/invalid/compartment.xml
index da48b5c4e51519400141cf138dce0451d102ccad..d13281799973d670e2917c82e0b12d79073cd90c 100644
--- a/converter-CellDesigner/testFiles/invalid/compartment.xml
+++ b/converter-CellDesigner/testFiles/invalid/compartment.xml
@@ -1,4 +1,4 @@
-<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
-<annotation_inv>
-</annotation_inv>
-</compartment>
+<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
+<annotation_inv>
+</annotation_inv>
+</compartment>
diff --git a/converter-CellDesigner/testFiles/invalid/compartment2.xml b/converter-CellDesigner/testFiles/invalid/compartment2.xml
index 81ee8645d50af8c233ace38f57fa9a5215fbe8a5..b161a3d10ce5702159ba96a157c499591374e671 100644
--- a/converter-CellDesigner/testFiles/invalid/compartment2.xml
+++ b/converter-CellDesigner/testFiles/invalid/compartment2.xml
@@ -1,8 +1,8 @@
-<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
-<annotation>
-<celldesigner:extension>
-<celldesigner:name>c1</celldesigner:name>
-</celldesigner:extension>
-<ins_inv/>
-</annotation>
-</compartment>
+<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c1</celldesigner:name>
+</celldesigner:extension>
+<ins_inv/>
+</annotation>
+</compartment>
diff --git a/converter-CellDesigner/testFiles/invalid/compartment3.xml b/converter-CellDesigner/testFiles/invalid/compartment3.xml
index 8b5b409563d186f6847fc0351299e0cd1f48c167..438e87b6bd68f6dff3833d61f587253a5f9416f5 100644
--- a/converter-CellDesigner/testFiles/invalid/compartment3.xml
+++ b/converter-CellDesigner/testFiles/invalid/compartment3.xml
@@ -1,8 +1,8 @@
-<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
-<annotation>
-<celldesigner:extension>
-<celldesigner:name>c1</celldesigner:name>
-<ext_inv/>
-</celldesigner:extension>
-</annotation>
-</compartment>
+<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c1</celldesigner:name>
+<ext_inv/>
+</celldesigner:extension>
+</annotation>
+</compartment>
diff --git a/converter-CellDesigner/testFiles/invalid/compartment_alias.xml b/converter-CellDesigner/testFiles/invalid/compartment_alias.xml
index e65eee095ad67152dfd53d9366faa073860952c7..1d050e6d795d2f2eccfa826b6ec6e9d24ad8dd59 100644
--- a/converter-CellDesigner/testFiles/invalid/compartment_alias.xml
+++ b/converter-CellDesigner/testFiles/invalid/compartment_alias.xml
@@ -1,8 +1,8 @@
-<celldesigner:compartmentAlias id="ca1" compartment="c1">
-<celldesigner:class>UNKNOWN_TYPE_BLA</celldesigner:class>
-<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
-<celldesigner:namePoint x="392.5" y="196.5"/>
-<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
-<celldesigner:paint color="ffcccc00" scheme="Color"/>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>UNKNOWN_TYPE_BLA</celldesigner:class>
+<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
+<celldesigner:namePoint x="392.5" y="196.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:compartmentAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/compartment_alias2.xml b/converter-CellDesigner/testFiles/invalid/compartment_alias2.xml
index 24ad80ce5f9e633b056a0fe7e125503a347fdbd7..ee09c1e2e05a046937aa0b36add552a43d5bdd5d 100644
--- a/converter-CellDesigner/testFiles/invalid/compartment_alias2.xml
+++ b/converter-CellDesigner/testFiles/invalid/compartment_alias2.xml
@@ -1,9 +1,9 @@
-<celldesigner:compartmentAlias id="ca1" compartment="c1">
-<celldesigner:class>SQUARE</celldesigner:class>
-<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
-<celldesigner:namePoint x="392.5" y="196.5"/>
-<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
-<celldesigner:paint color="ffcccc00" scheme="Color"/>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-<celldesigner:point/>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
+<celldesigner:namePoint x="392.5" y="196.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:point/>
</celldesigner:compartmentAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/compartment_alias3.xml b/converter-CellDesigner/testFiles/invalid/compartment_alias3.xml
index 3a9634e0949d80885502a36940e0182f6ccda406..3d56061e24a3bf20c5315676639863c9a72e1fb9 100644
--- a/converter-CellDesigner/testFiles/invalid/compartment_alias3.xml
+++ b/converter-CellDesigner/testFiles/invalid/compartment_alias3.xml
@@ -1,9 +1,9 @@
-<celldesigner:compartmentAlias id="ca1" compartment="c1">
-<unk_tag/>
-<celldesigner:class>SQUARE</celldesigner:class>
-<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
-<celldesigner:namePoint x="392.5" y="196.5"/>
-<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
-<celldesigner:paint color="ffcccc00" scheme="Color"/>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<unk_tag/>
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
+<celldesigner:namePoint x="392.5" y="196.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:compartmentAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/compartment_alias_collection.xml b/converter-CellDesigner/testFiles/invalid/compartment_alias_collection.xml
index 9d475028ce3f8923c6799885dca22f1c68fa4733..09ceb78c358a7ab4c68651f5e3f9da25feab277d 100644
--- a/converter-CellDesigner/testFiles/invalid/compartment_alias_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/compartment_alias_collection.xml
@@ -1,27 +1,27 @@
-<celldesigner:listOfCompartmentAliases>
-<unk/>
-<celldesigner:compartmentAlias id="ca1" compartment="c1">
-<celldesigner:class>SQUARE</celldesigner:class>
-<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
-<celldesigner:namePoint x="392.5" y="196.5"/>
-<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
-<celldesigner:paint color="ffcccc00" scheme="Color"/>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:compartmentAlias>
-<celldesigner:compartmentAlias id="ca2" compartment="c2">
-<celldesigner:class>SQUARE</celldesigner:class>
-<celldesigner:bounds x="707.0" y="187.0" w="118.0" h="73.0"/>
-<celldesigner:namePoint x="758.5" y="223.5"/>
-<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
-<celldesigner:paint color="ffcccc00" scheme="Color"/>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:compartmentAlias>
-<celldesigner:compartmentAlias id="ca3" compartment="c3">
-<celldesigner:class>OVAL</celldesigner:class>
-<celldesigner:bounds x="185.0" y="143.0" w="86.0" h="50.0"/>
-<celldesigner:namePoint x="220.5" y="156.11618483532334"/>
-<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
-<celldesigner:paint color="ffcccc00" scheme="Color"/>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:compartmentAlias>
-</celldesigner:listOfCompartmentAliases>
+<celldesigner:listOfCompartmentAliases>
+<unk/>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
+<celldesigner:namePoint x="392.5" y="196.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+<celldesigner:compartmentAlias id="ca2" compartment="c2">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="707.0" y="187.0" w="118.0" h="73.0"/>
+<celldesigner:namePoint x="758.5" y="223.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+<celldesigner:compartmentAlias id="ca3" compartment="c3">
+<celldesigner:class>OVAL</celldesigner:class>
+<celldesigner:bounds x="185.0" y="143.0" w="86.0" h="50.0"/>
+<celldesigner:namePoint x="220.5" y="156.11618483532334"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+</celldesigner:listOfCompartmentAliases>
diff --git a/converter-CellDesigner/testFiles/invalid/complex_alias_collection.xml b/converter-CellDesigner/testFiles/invalid/complex_alias_collection.xml
index 9ee6cee1ef17ab0954c83cd48058301051056982..4fbc36c28497cd8691190f7d910d2454d7930101 100644
--- a/converter-CellDesigner/testFiles/invalid/complex_alias_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/complex_alias_collection.xml
@@ -1,66 +1,66 @@
-<celldesigner:listOfComplexSpeciesAliases>
-<unk/>
-<celldesigner:complexSpeciesAlias id="csa1" species="s2597">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="744.0" y="0.0" w="100.0" h="120.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="100.0" height="120.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
-<celldesigner:complexSpeciesAlias id="csa2" species="s2598">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="863.0" y="35.0" w="100.0" h="120.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="100.0" height="120.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
-<celldesigner:complexSpeciesAlias id="csa3" species="s2599" complexSpeciesAlias="csa1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="767.0" y="15.0" w="61.0" h="87.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="23.0" y="15.0"/>
-<celldesigner:boxSize width="61.0" height="87.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
-</celldesigner:listOfComplexSpeciesAliases>
+<celldesigner:listOfComplexSpeciesAliases>
+<unk/>
+<celldesigner:complexSpeciesAlias id="csa1" species="s2597">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="744.0" y="0.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa2" species="s2598">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="863.0" y="35.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa3" species="s2599" complexSpeciesAlias="csa1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="767.0" y="15.0" w="61.0" h="87.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="23.0" y="15.0"/>
+<celldesigner:boxSize width="61.0" height="87.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+</celldesigner:listOfComplexSpeciesAliases>
diff --git a/converter-CellDesigner/testFiles/invalid/gene_collection.xml b/converter-CellDesigner/testFiles/invalid/gene_collection.xml
index 4633a9e50e6c8072ebe5f836dda7e1512cd7668d..bc790db2e564923358f58e73a126d4451f201700 100644
--- a/converter-CellDesigner/testFiles/invalid/gene_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/gene_collection.xml
@@ -1,3 +1,3 @@
-<celldesigner:listOfGenes>
-<unkgenenode/>
+<celldesigner:listOfGenes>
+<unkgenenode/>
</celldesigner:listOfGenes>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/group_collection.xml b/converter-CellDesigner/testFiles/invalid/group_collection.xml
index e9107f1b2f58bd43ac37fb27d94470487d7a9c0f..27ec8b138ab10dde4e4ab79b6874e53d3c9b56b5 100644
--- a/converter-CellDesigner/testFiles/invalid/group_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/group_collection.xml
@@ -1,4 +1,4 @@
-<celldesigner:listOfGroups>
-<invalid/>
-<celldesigner:group id="g1" members="sa1,sa2,sa3"/>
-</celldesigner:listOfGroups>
+<celldesigner:listOfGroups>
+<invalid/>
+<celldesigner:group id="g1" members="sa1,sa2,sa3"/>
+</celldesigner:listOfGroups>
diff --git a/converter-CellDesigner/testFiles/invalid/group_collection2.xml b/converter-CellDesigner/testFiles/invalid/group_collection2.xml
index 38bc03af6392d0bb64b0ab8233cdfe31dc35ff73..85276ccffbc56fc1b95348af23f8e4beacf1e77e 100644
--- a/converter-CellDesigner/testFiles/invalid/group_collection2.xml
+++ b/converter-CellDesigner/testFiles/invalid/group_collection2.xml
@@ -1,3 +1,3 @@
-<celldesigner:listOfGroups>
-<celldesigner:group id="g1" members="sa1,sa2,sa3"/>
-</celldesigner:listOfGroups>
+<celldesigner:listOfGroups>
+<celldesigner:group id="g1" members="sa1,sa2,sa3"/>
+</celldesigner:listOfGroups>
diff --git a/converter-CellDesigner/testFiles/invalid/group_collection3.xml b/converter-CellDesigner/testFiles/invalid/group_collection3.xml
index 26d55307ddb9125e6938035936a25ca8a2e8f379..ccbce7c5e709fba78eac2d5fa806faea7993f573 100644
--- a/converter-CellDesigner/testFiles/invalid/group_collection3.xml
+++ b/converter-CellDesigner/testFiles/invalid/group_collection3.xml
@@ -1,5 +1,5 @@
-<celldesigner:listOfGroups>
-<celldesigner:group id="g1" members="sa1">
-<x/>
-</celldesigner:group>
-</celldesigner:listOfGroups>
+<celldesigner:listOfGroups>
+<celldesigner:group id="g1" members="sa1">
+<x/>
+</celldesigner:group>
+</celldesigner:listOfGroups>
diff --git a/converter-CellDesigner/testFiles/invalid/included_species_collection.xml b/converter-CellDesigner/testFiles/invalid/included_species_collection.xml
index d070c64ad5f25fbd7a0f1ba3fc9738cf4b6eff63..341460a27e4559a0663e048dfdb1943cb766ee7a 100644
--- a/converter-CellDesigner/testFiles/invalid/included_species_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/included_species_collection.xml
@@ -1,53 +1,53 @@
-<celldesigner:listOfIncludedSpecies>
-<celldesigner:species name="s10">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>COMPLEX</celldesigner:class>
-<celldesigner:name>s10</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
-<celldesigner:species id="s11" name="s11">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
-<celldesigner:species id="s12" name="s12">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s10</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species name="s10">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s10</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s11" name="s11">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s12" name="s12">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s10</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
</celldesigner:listOfIncludedSpecies>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/included_species_collection2.xml b/converter-CellDesigner/testFiles/invalid/included_species_collection2.xml
index 046af22cb25b8374a5020a43c498806dd9f49a1e..8c53aac2aae95355fb466068f0a6121f65fa176f 100644
--- a/converter-CellDesigner/testFiles/invalid/included_species_collection2.xml
+++ b/converter-CellDesigner/testFiles/invalid/included_species_collection2.xml
@@ -1,46 +1,46 @@
-<celldesigner:listOfIncludedSpecies>
-<celldesigner:species id="s10" name="s10">
-<unk/>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>COMPLEX</celldesigner:class>
-<celldesigner:name>s10</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
-<celldesigner:species id="s11" name="s11">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
-<celldesigner:species id="s12" name="s12">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s10</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species id="s10" name="s10">
+<unk/>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s10</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s11" name="s11">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s12" name="s12">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s10</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
</celldesigner:listOfIncludedSpecies>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/included_species_collection3.xml b/converter-CellDesigner/testFiles/invalid/included_species_collection3.xml
index 05595cc967f108826a277baf9a3c44c391015700..02212bf749642e3bca9a8941a975a699900fb629 100644
--- a/converter-CellDesigner/testFiles/invalid/included_species_collection3.xml
+++ b/converter-CellDesigner/testFiles/invalid/included_species_collection3.xml
@@ -1,46 +1,46 @@
-<celldesigner:listOfIncludedSpecies>
-<celldesigner:species id="s10" name="s10">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-</celldesigner:species>
-<celldesigner:species id="s11" name="s11">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
-<celldesigner:species id="s12" name="s12">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s10</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species id="s10" name="s10">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+</celldesigner:species>
+<celldesigner:species id="s11" name="s11">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s12" name="s12">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s10</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
</celldesigner:listOfIncludedSpecies>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/included_species_collection4.xml b/converter-CellDesigner/testFiles/invalid/included_species_collection4.xml
index d84317a77e3e25d5448824877a4f6a43cab096be..e737a6a6d6deee3543fa041a83ba30bb5e31210c 100644
--- a/converter-CellDesigner/testFiles/invalid/included_species_collection4.xml
+++ b/converter-CellDesigner/testFiles/invalid/included_species_collection4.xml
@@ -1,15 +1,15 @@
-<celldesigner:listOfIncludedSpecies>
-<celldesigner:species id="s10" name="s10">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
-</celldesigner:annotation>
-</celldesigner:species>
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species id="s10" name="s10">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+</celldesigner:annotation>
+</celldesigner:species>
</celldesigner:listOfIncludedSpecies>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/included_species_collection5.xml b/converter-CellDesigner/testFiles/invalid/included_species_collection5.xml
index 888aed4ed24db7a8f042cfba056ff6715c9a1f0e..8a7a04567a271a01d789876b8f71af051cf68eff 100644
--- a/converter-CellDesigner/testFiles/invalid/included_species_collection5.xml
+++ b/converter-CellDesigner/testFiles/invalid/included_species_collection5.xml
@@ -1,3 +1,3 @@
-<celldesigner:listOfIncludedSpecies>
-<unkTag/>
+<celldesigner:listOfIncludedSpecies>
+<unkTag/>
</celldesigner:listOfIncludedSpecies>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/included_species_collection6.xml b/converter-CellDesigner/testFiles/invalid/included_species_collection6.xml
index f40ba398300ecb7f5c6e3a3b2efa5b1d7add027f..157626af269591b645b88edbf8bf5c01459e75ee 100644
--- a/converter-CellDesigner/testFiles/invalid/included_species_collection6.xml
+++ b/converter-CellDesigner/testFiles/invalid/included_species_collection6.xml
@@ -1,14 +1,14 @@
-<celldesigner:listOfIncludedSpecies>
-<celldesigner:species id="s10" name="s10">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-</celldesigner:annotation>
-</celldesigner:species>
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species id="s10" name="s10">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+</celldesigner:annotation>
+</celldesigner:species>
</celldesigner:listOfIncludedSpecies>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias.xml b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias.xml
index c14c5db90307c7008b766e8e9f9b897c71749e9e..ea5cb8370ed5f070ea2da0271a2a4382e4fd05b6 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias.xml
@@ -1,21 +1,21 @@
-<celldesigner:complexSpeciesAlias id="csa2" species="s3">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="151.0" height="221.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa2" species="s3">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="151.0" height="221.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias2.xml b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias2.xml
index a3464b72e968e09212b3d07885dfbf67acfbebf2..da8f004bb36ebe143ef39204b00d218345726315 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias2.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias2.xml
@@ -1,3 +1,3 @@
-<celldesigner:complexSpeciesAlias id="csa2" species="s3">
-<celldesigner:bla>inactive</celldesigner:bla>
-</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa2" species="s3">
+<celldesigner:bla>inactive</celldesigner:bla>
+</celldesigner:complexSpeciesAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias3.xml b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias3.xml
index 04c8b010b247ccd92fcedad7d1c34cfdb9c97009..6f14d52022278acb426e5bf424de985a6440d7b3 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias3.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias3.xml
@@ -1,21 +1,21 @@
-<celldesigner:complexSpeciesAlias id="csa2" species="s3">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="unusual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="151.0" height="221.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa2" species="s3">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="unusual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="151.0" height="221.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias4.xml b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias4.xml
index 8350cc36256d614caeb5a2699f02cbd8c9366793..721599b232db5b753403d70bf6aedbc3db1400d5 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias4.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias4.xml
@@ -1,21 +1,21 @@
-<celldesigner:complexSpeciesAlias id="csa2" species="s3">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="151.0" height="221.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="unkown state" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa2" species="s3">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="151.0" height="221.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="unkown state" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias5.xml b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias5.xml
index 292bba6e3d6204e7797b23f96424a123f944a349..8606089f4756c9dac20c8593270691b6c088752e 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias5.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias5.xml
@@ -1,21 +1,21 @@
-<celldesigner:complexSpeciesAlias id="csa2" species="s3" compartmentAlias="ca">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="151.0" height="221.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa2" species="s3" compartmentAlias="ca">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="151.0" height="221.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_gene_1.xml b/converter-CellDesigner/testFiles/invalid/invalid_gene_1.xml
index 0bb0451ddeda18eb99351e56912d35f85107dc65..3a68590eaf97077e8e5d965617674b887d278d47 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_gene_1.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_gene_1.xml
@@ -1,3 +1,3 @@
-<celldesigner:gene id="gn3" name="BCL6" type="GENE">
-<celldesigner:bla/>
+<celldesigner:gene id="gn3" name="BCL6" type="GENE">
+<celldesigner:bla/>
</celldesigner:gene>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_gene_2.xml b/converter-CellDesigner/testFiles/invalid/invalid_gene_2.xml
index 00244cc2b899e234930adbaa5e6d6b2b7cec4dd8..61ac67a16d74ff63b65fa1140560151fc6e66dd8 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_gene_2.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_gene_2.xml
@@ -1,6 +1,6 @@
-<celldesigner:gene id="gn3" name="BCL6" type="GENE">
-<celldesigner:listOfRegions>
-<html xmlns="http://www.w3.org/1999/xhtml">
-</html>
-</celldesigner:listOfRegions>
+<celldesigner:gene id="gn3" name="BCL6" type="GENE">
+<celldesigner:listOfRegions>
+<html xmlns="http://www.w3.org/1999/xhtml">
+</html>
+</celldesigner:listOfRegions>
</celldesigner:gene>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_modification_residue.xml b/converter-CellDesigner/testFiles/invalid/invalid_modification_residue.xml
index b32104cee7c032293e510c01b8da64a070519be2..84fb68e6d0ce117c862f8e3b23dac3b305e032bd 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_modification_residue.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_modification_residue.xml
@@ -1,3 +1,3 @@
-<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none">
-<bla/>
-</celldesigner:modificationResidue>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none">
+<bla/>
+</celldesigner:modificationResidue>
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein.xml
index 586e73748dca6d1f9877020cb297629b01492e3d..e39cee0ea733e68b208a0f329f744480523aadc4 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein.xml
@@ -1,2 +1,2 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein10.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein10.xml
index 252648ee0b298d2ecf1eee617427ceef3dbeed46..786bd74c6da18fe8631522ab51f05931d560af5f 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein10.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein10.xml
@@ -1,11 +1,11 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:class>GENE</celldesigner:class>
-<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein11.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein11.xml
index b40e452964ef98d718ee8bdf2d4389de09b557ff..12881f9195ac42765b17fb363434859341da1e79 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein11.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein11.xml
@@ -1,11 +1,11 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:geneReference>pr1116</celldesigner:geneReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:geneReference>pr1116</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein12.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein12.xml
index b4c70762893a7c911c8becaf7a2a424f661898ff..7ee1cdad8abb1c3d0706b46e64a87b81b4a4ccef 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein12.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein12.xml
@@ -1,11 +1,11 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:class>GENE</celldesigner:class>
-<celldesigner:rnaReference>pr1116</celldesigner:rnaReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:rnaReference>pr1116</celldesigner:rnaReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein13.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein13.xml
index 8da810b0fc9a19d7e220a62cd51afc0c55bd6b61..0fecf616ae527862b33da45451bdf583f366305f 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein13.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein13.xml
@@ -1,12 +1,12 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:class>GENE</celldesigner:class>
-<celldesigner:hypothetical>true</celldesigner:hypothetical>
-<celldesigner:antisensernaReference>pr1116</celldesigner:antisensernaReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+<celldesigner:antisensernaReference>pr1116</celldesigner:antisensernaReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein14.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein14.xml
index 21ba7ba1aabe9a353fa7f9d6d5bb4d917af62c4a..3239790cd510fde32aad6c1bde4d9464834cb7bd 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein14.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein14.xml
@@ -1,13 +1,13 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:class>GENE</celldesigner:class>
-<uknNode>GENE</uknNode>
-<celldesigner:hypothetical>true</celldesigner:hypothetical>
-<celldesigner:antisensernaReference>pr1116</celldesigner:antisensernaReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<uknNode>GENE</uknNode>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+<celldesigner:antisensernaReference>pr1116</celldesigner:antisensernaReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein2.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein2.xml
index c2cf173e62b451f7485ed73930f884a6e4423cd3..f8b124466d776b76a5e963fdf96adb314f936325 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein2.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein2.xml
@@ -1,3 +1,3 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<bla/>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<bla/>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein3.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein3.xml
index 59b9da4168d9d6838298d8ea206266b8c8bd332d..effc0711a68a4a28bd9cbf40e2b403db1ed41b8a 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein3.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein3.xml
@@ -1,5 +1,5 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<unk_bla/>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<unk_bla/>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein4.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein4.xml
index 4c00c684f815152edd31116a2637c10f95f83525..a18cf28fd98d16134676d3dcc557e822c15d0d6d 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein4.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein4.xml
@@ -1,4 +1,4 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein5.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein5.xml
index 833df0937922bcf1acd2537d7e955f8d6bea6d74..f991e46f1c3e72a1474e5afb92ef760096c7f283 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein5.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein5.xml
@@ -1,7 +1,7 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<ann_unk/>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<ann_unk/>
+</celldesigner:extension>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein6.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein6.xml
index 9910d3a6105ee568a37b53af4b8d8d7b21a06670..9d731baa24b463f385e61f27706eda884411a68b 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein6.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein6.xml
@@ -1,6 +1,6 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+</celldesigner:extension>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein7.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein7.xml
index 1ff2733782fd416b0c78086885ec07b1623ca3d1..a2acae126ea617ca023ce384989099d7fdf0ab53 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein7.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein7.xml
@@ -1,11 +1,11 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein8.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein8.xml
index 132c8ff43903615b9df5a48634be99f9ac21428e..d42a07902104956104bfb5e1e264362ebc4d613e 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein8.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein8.xml
@@ -1,10 +1,10 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein9.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein9.xml
index fa5e0be4399e60948be1dc2d8f74c08e30171a77..0efef2fb1cfa838f3db05d6ab433e3c712489128 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein9.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein9.xml
@@ -1,11 +1,11 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:class>unknown_protein_class</celldesigner:class>
-<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>unknown_protein_class</celldesigner:class>
+<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/layer.xml b/converter-CellDesigner/testFiles/invalid/layer.xml
index 8c6691cb422b89d445d4cd91f58774863fceccea..d01e773294ac6ceba999ddb064e51d8d633698d2 100644
--- a/converter-CellDesigner/testFiles/invalid/layer.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer.xml
@@ -1,35 +1,35 @@
-<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
-<celldesigner:listOfTexts>
-<celldesigner:unkLayerSpeciesAlias2 />
-<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
-<celldesigner:layerNotes>
-text node
-</celldesigner:layerNotes>
-<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
-<celldesigner:paint color="ff000000"/>
-<celldesigner:font size="11"/>
-</celldesigner:layerSpeciesAlias>
-</celldesigner:listOfTexts>
-<celldesigner:listOfSquares>
-<celldesigner:layerCompartmentAlias type="Oval">
-<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-<celldesigner:layerCompartmentAlias type="Square">
-<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-</celldesigner:listOfSquares>
-<celldesigner:listOfFreeLines>
-<celldesigner:layerFreeLine isArrow="false" isDotted="false">
-<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-<celldesigner:layerFreeLine isArrow="true" isDotted="false">
-<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-</celldesigner:listOfFreeLines>
-</celldesigner:layer>
+<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<celldesigner:listOfTexts>
+<celldesigner:unkLayerSpeciesAlias2 />
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+<celldesigner:listOfSquares>
+<celldesigner:layerCompartmentAlias type="Oval">
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+</celldesigner:listOfSquares>
+<celldesigner:listOfFreeLines>
+<celldesigner:layerFreeLine isArrow="false" isDotted="false">
+<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="false">
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+</celldesigner:listOfFreeLines>
+</celldesigner:layer>
diff --git a/converter-CellDesigner/testFiles/invalid/layer2.xml b/converter-CellDesigner/testFiles/invalid/layer2.xml
index 88661cd0e0750eb3d4ec7452d6ae076da8af7118..34308d7f1746e2d41a94104179058a5c4f126bff 100644
--- a/converter-CellDesigner/testFiles/invalid/layer2.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer2.xml
@@ -1,34 +1,34 @@
-<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
-<celldesigner:listOfTexts>
-<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
-<celldesigner:layerNotes>
-text node
-</celldesigner:layerNotes>
-<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
-<celldesigner:paint color="ff000000"/>
-<celldesigner:font size="11"/>
-</celldesigner:layerSpeciesAlias>
-</celldesigner:listOfTexts>
-<celldesigner:listOfSquares>
-<celldesigner:layerCompartmentAlias type="Custom_Triangle">
-<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-<celldesigner:layerCompartmentAlias type="Square">
-<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-</celldesigner:listOfSquares>
-<celldesigner:listOfFreeLines>
-<celldesigner:layerFreeLine isArrow="false" isDotted="false">
-<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-<celldesigner:layerFreeLine isArrow="true" isDotted="false">
-<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-</celldesigner:listOfFreeLines>
-</celldesigner:layer>
+<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<celldesigner:listOfTexts>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+<celldesigner:listOfSquares>
+<celldesigner:layerCompartmentAlias type="Custom_Triangle">
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+</celldesigner:listOfSquares>
+<celldesigner:listOfFreeLines>
+<celldesigner:layerFreeLine isArrow="false" isDotted="false">
+<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="false">
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+</celldesigner:listOfFreeLines>
+</celldesigner:layer>
diff --git a/converter-CellDesigner/testFiles/invalid/layer3.xml b/converter-CellDesigner/testFiles/invalid/layer3.xml
index d2b37a8acb977ee98b2cf055b853309e3bc9cc61..37dd3a4f5a819eeac973a575356044fbc32db5d3 100644
--- a/converter-CellDesigner/testFiles/invalid/layer3.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer3.xml
@@ -1,35 +1,35 @@
-<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
-<celldesigner:listOfTexts>
-<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
-<celldesigner:layerNotes>
-text node
-</celldesigner:layerNotes>
-<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
-<celldesigner:paint color="ff000000"/>
-<celldesigner:font size="11"/>
-</celldesigner:layerSpeciesAlias>
-</celldesigner:listOfTexts>
-<celldesigner:listOfSquares>
-<celldesigner:customLayerCompartmentAliasTag/>
-<celldesigner:layerCompartmentAlias type="Oval">
-<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-<celldesigner:layerCompartmentAlias type="Square">
-<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-</celldesigner:listOfSquares>
-<celldesigner:listOfFreeLines>
-<celldesigner:layerFreeLine isArrow="false" isDotted="false">
-<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-<celldesigner:layerFreeLine isArrow="true" isDotted="false">
-<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-</celldesigner:listOfFreeLines>
-</celldesigner:layer>
+<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<celldesigner:listOfTexts>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+<celldesigner:listOfSquares>
+<celldesigner:customLayerCompartmentAliasTag/>
+<celldesigner:layerCompartmentAlias type="Oval">
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+</celldesigner:listOfSquares>
+<celldesigner:listOfFreeLines>
+<celldesigner:layerFreeLine isArrow="false" isDotted="false">
+<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="false">
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+</celldesigner:listOfFreeLines>
+</celldesigner:layer>
diff --git a/converter-CellDesigner/testFiles/invalid/layer4.xml b/converter-CellDesigner/testFiles/invalid/layer4.xml
index 596a08d2675d74d85c23934b63bd4bff4ebb43ed..d02105499e3cbbe8264074b4adebc2c8e1f3aa03 100644
--- a/converter-CellDesigner/testFiles/invalid/layer4.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer4.xml
@@ -1,35 +1,35 @@
-<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
-<celldesigner:listOfTexts>
-<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
-<celldesigner:layerNotes>
-text node
-</celldesigner:layerNotes>
-<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
-<celldesigner:paint color="ff000000"/>
-<celldesigner:font size="11"/>
-</celldesigner:layerSpeciesAlias>
-</celldesigner:listOfTexts>
-<celldesigner:listOfSquares>
-<celldesigner:layerCompartmentAlias type="Oval">
-<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-<celldesigner:layerCompartmentAlias type="Square">
-<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-</celldesigner:listOfSquares>
-<celldesigner:listOfFreeLines>
-<celldesigner:customLayerFreeLine isArrow="false" isDotted="false"/>
-<celldesigner:layerFreeLine isArrow="false" isDotted="false">
-<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-<celldesigner:layerFreeLine isArrow="true" isDotted="false">
-<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-</celldesigner:listOfFreeLines>
-</celldesigner:layer>
+<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<celldesigner:listOfTexts>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+<celldesigner:listOfSquares>
+<celldesigner:layerCompartmentAlias type="Oval">
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+</celldesigner:listOfSquares>
+<celldesigner:listOfFreeLines>
+<celldesigner:customLayerFreeLine isArrow="false" isDotted="false"/>
+<celldesigner:layerFreeLine isArrow="false" isDotted="false">
+<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="false">
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+</celldesigner:listOfFreeLines>
+</celldesigner:layer>
diff --git a/converter-CellDesigner/testFiles/invalid/layer5.xml b/converter-CellDesigner/testFiles/invalid/layer5.xml
index 215c1789b6d8f206eaffeb9d0c05f5dce149a8d6..24fac7654783c75365b4022b9beed312999a5304 100644
--- a/converter-CellDesigner/testFiles/invalid/layer5.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer5.xml
@@ -1,35 +1,35 @@
-<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
-<customLayerTag/>
-<celldesigner:listOfTexts>
-<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
-<celldesigner:layerNotes>
-text node
-</celldesigner:layerNotes>
-<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
-<celldesigner:paint color="ff000000"/>
-<celldesigner:font size="11"/>
-</celldesigner:layerSpeciesAlias>
-</celldesigner:listOfTexts>
-<celldesigner:listOfSquares>
-<celldesigner:layerCompartmentAlias type="Oval">
-<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-<celldesigner:layerCompartmentAlias type="Square">
-<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-</celldesigner:listOfSquares>
-<celldesigner:listOfFreeLines>
-<celldesigner:layerFreeLine isArrow="false" isDotted="false">
-<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-<celldesigner:layerFreeLine isArrow="true" isDotted="false">
-<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-</celldesigner:listOfFreeLines>
-</celldesigner:layer>
+<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<customLayerTag/>
+<celldesigner:listOfTexts>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+<celldesigner:listOfSquares>
+<celldesigner:layerCompartmentAlias type="Oval">
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+</celldesigner:listOfSquares>
+<celldesigner:listOfFreeLines>
+<celldesigner:layerFreeLine isArrow="false" isDotted="false">
+<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="false">
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+</celldesigner:listOfFreeLines>
+</celldesigner:layer>
diff --git a/converter-CellDesigner/testFiles/invalid/layer_collection.xml b/converter-CellDesigner/testFiles/invalid/layer_collection.xml
index 654f981181194eeba55c2044a27150e7cbf58a52..d4548963090a8efc5df8c35ebcf519b2181ce199 100644
--- a/converter-CellDesigner/testFiles/invalid/layer_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer_collection.xml
@@ -1,37 +1,37 @@
-<celldesigner:listOfLayers>
-<invalid_node/>
-<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
-<celldesigner:listOfTexts>
-<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
-<celldesigner:layerNotes>
-text node
-</celldesigner:layerNotes>
-<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
-<celldesigner:paint color="ff000000"/>
-<celldesigner:font size="11"/>
-</celldesigner:layerSpeciesAlias>
-</celldesigner:listOfTexts>
-<celldesigner:listOfSquares>
-<celldesigner:layerCompartmentAlias type="Oval">
-<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-<celldesigner:layerCompartmentAlias type="Square">
-<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-</celldesigner:listOfSquares>
-<celldesigner:listOfFreeLines>
-<celldesigner:layerFreeLine isArrow="false" isDotted="false">
-<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-<celldesigner:layerFreeLine isArrow="true" isDotted="false">
-<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-</celldesigner:listOfFreeLines>
-</celldesigner:layer>
+<celldesigner:listOfLayers>
+<invalid_node/>
+<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<celldesigner:listOfTexts>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+<celldesigner:listOfSquares>
+<celldesigner:layerCompartmentAlias type="Oval">
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+</celldesigner:listOfSquares>
+<celldesigner:listOfFreeLines>
+<celldesigner:layerFreeLine isArrow="false" isDotted="false">
+<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="false">
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+</celldesigner:listOfFreeLines>
+</celldesigner:layer>
</celldesigner:listOfLayers>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/layer_line.xml b/converter-CellDesigner/testFiles/invalid/layer_line.xml
index 504007efcffd434be6470af65c0223d7396b3bd7..bdfb7673169d5b67f6788588e5f5ec291c7e0836 100644
--- a/converter-CellDesigner/testFiles/invalid/layer_line.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer_line.xml
@@ -1,5 +1,5 @@
-<celldesigner:layerFreeLine isArrow="true" isDotted="true">
-<inv_content/>
-<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="true">
+<inv_content/>
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
diff --git a/converter-CellDesigner/testFiles/invalid/layer_oval.xml b/converter-CellDesigner/testFiles/invalid/layer_oval.xml
index a1543f53767c6ea651c6040bbed0509782205b56..836be2636259dc3fe83098e5d15879f206b5accd 100644
--- a/converter-CellDesigner/testFiles/invalid/layer_oval.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer_oval.xml
@@ -1,6 +1,6 @@
-<celldesigner:layerCompartmentAlias type="Oval">
-<inv_tag/>
-<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Oval">
+<inv_tag/>
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/layer_square.xml b/converter-CellDesigner/testFiles/invalid/layer_square.xml
index 64bdda46f6ef3d80593e57d6eee686f2bb12a512..ec6a6237861660d0a7d69baeb622f5a96c1e72af 100644
--- a/converter-CellDesigner/testFiles/invalid/layer_square.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer_square.xml
@@ -1,6 +1,6 @@
-<celldesigner:layerCompartmentAlias type="Square">
-<inv_element/>
-<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<inv_element/>
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/layer_text.xml b/converter-CellDesigner/testFiles/invalid/layer_text.xml
index d860055a35be022229cd1ecaae1a6a73f809e397..40d6f92c1ea780a2512b0ec5881243d4ee598396 100644
--- a/converter-CellDesigner/testFiles/invalid/layer_text.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer_text.xml
@@ -1,9 +1,9 @@
-<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
-<inv_tabg/>
-<celldesigner:layerNotes>
-text node
-</celldesigner:layerNotes>
-<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
-<celldesigner:paint color="ff000000"/>
-<celldesigner:font size="11"/>
-</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<inv_tabg/>
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/listOfCompartments.xml b/converter-CellDesigner/testFiles/invalid/listOfCompartments.xml
index 1fb3bacf9c29fd150bb93c417b022fc20be3ecf8..e902591a73b0107d9a73cdc7be34a87173261a48 100644
--- a/converter-CellDesigner/testFiles/invalid/listOfCompartments.xml
+++ b/converter-CellDesigner/testFiles/invalid/listOfCompartments.xml
@@ -1,11 +1,11 @@
-<listOfCompartments>
-<compartment metaid="default" id="default" size="1" units="volume"/>
-<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
-<annotation>
-<celldesigner:extension>
-<celldesigner:name>c1</celldesigner:name>
-</celldesigner:extension>
-</annotation>
-</compartment>
-<compartment2/>
-</listOfCompartments>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c1</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+<compartment2/>
+</listOfCompartments>
diff --git a/converter-CellDesigner/testFiles/invalid/list_of_species_alias.xml b/converter-CellDesigner/testFiles/invalid/list_of_species_alias.xml
index 0d760a7628eb8e9a6bebda4bcfe1d9999ce8b133..e22c3d53af422256190d2c290151c54e112f981e 100644
--- a/converter-CellDesigner/testFiles/invalid/list_of_species_alias.xml
+++ b/converter-CellDesigner/testFiles/invalid/list_of_species_alias.xml
@@ -1,553 +1,553 @@
-<celldesigner:listOfSpeciesAliases>
-<celldesigner:speciesAlias id="sa1" species="s1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="12.0" y="6.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffffff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa2" species="s2">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="165.0" y="43.0" w="80.0" h="50.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="50.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa3" species="s3">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="289.0" y="39.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa4" species="s4">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="419.0" y="45.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffcccc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa5" species="s5">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="0.0" y="118.5" w="90.0" h="25.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="90.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ff66ff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa6" species="s6">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="101.0" y="129.5" w="90.0" h="25.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="90.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffff6666" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa7" species="s7">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="213.0" y="128.0" w="80.0" h="30.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="30.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffcc99ff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa8" species="s8">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="358.5" y="125.5" w="25.0" h="25.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="25.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ff9999ff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa9" species="s9">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="455.0" y="169.5" w="70.0" h="25.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="70.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa10" species="s10">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="0.0" y="186.0" w="80.0" h="30.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="30.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffff00ff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa11" species="s11">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="105.0" y="203.5" w="70.0" h="25.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="70.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="7fcccccc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa12" species="s13">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="401.0" y="235.0" w="30.0" h="30.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="30.0" height="30.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffcccc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa13" species="s14" complexSpeciesAlias="csa1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="279.0" y="233.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="8.0" y="26.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa14" species="s15">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11.0" y="236.0" w="118.0" h="66.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="118.0" height="66.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa15" species="s16">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="160.0" y="332.0" w="119.0" h="63.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="119.0" height="63.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa22" species="s22">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="712.0" y="384.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa23" species="s22">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="918.0" y="427.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa24" species="s20">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="849.0" y="309.0" w="70.0" h="25.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="70.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
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+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="30.0" height="30.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffffcccc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa13" species="s14" complexSpeciesAlias="csa1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="279.0" y="233.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="8.0" y="26.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa14" species="s15">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11.0" y="236.0" w="118.0" h="66.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="118.0" height="66.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa15" species="s16">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="160.0" y="332.0" w="119.0" h="63.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="119.0" height="63.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa22" species="s22">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="712.0" y="384.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa23" species="s22">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="918.0" y="427.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa24" species="s20">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="849.0" y="309.0" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa25" species="s21">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="959.0" y="271.0" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa26" species="s23">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="656.0" y="42.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa27" species="s23">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="695.0" y="239.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa28" species="s24">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="683.0" y="132.0" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa29" species="s25">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="819.0" y="134.0" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa30" species="s2612">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1022.7317629179333" y="209.5" w="140.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2114.4635258358667" y="3282.5"/>
+<celldesigner:boxSize width="140.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa31" species="s841">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1197.2682370820667" y="287.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2281.0" y="3282.5"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa32" species="s2611">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1225.7682370820667" y="66.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2360.5" y="3189.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffffffff" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa33" species="s817">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1243.7682370820667" y="12.50000000000091" w="25.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2364.5" y="3112.500000000001"/>
+<celldesigner:boxSize width="25.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ff9999ff" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa34" species="s815">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1214.2682370820667" y="128.5000000000009" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2267.0" y="3112.500000000001"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa35" species="s4532">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1044.7317629179333" y="27.50000000000091" w="140.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2114.4635258358667" y="3112.500000000001"/>
+<celldesigner:boxSize width="140.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
diff --git a/converter-CellDesigner/testFiles/invalid/list_of_species_alias2.xml b/converter-CellDesigner/testFiles/invalid/list_of_species_alias2.xml
index 1c27ebdd26fa9333c68ae1c56f317ab95bbcff33..ac07e81a9f76ce4c9fb0f968f96587093be8f080 100644
--- a/converter-CellDesigner/testFiles/invalid/list_of_species_alias2.xml
+++ b/converter-CellDesigner/testFiles/invalid/list_of_species_alias2.xml
@@ -1,554 +1,554 @@
-<celldesigner:listOfSpeciesAliases>
-<unk/>
-<celldesigner:speciesAlias id="sa1" species="s1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="12.0" y="6.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffffff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa2" species="s2">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="165.0" y="43.0" w="80.0" h="50.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="50.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa3" species="s3">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="289.0" y="39.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa4" species="s4">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="419.0" y="45.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffcccc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
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+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa28" species="s24">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="683.0" y="132.0" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa29" species="s25">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="819.0" y="134.0" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa30" species="s2612">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1022.7317629179333" y="209.5" w="140.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2114.4635258358667" y="3282.5"/>
+<celldesigner:boxSize width="140.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa31" species="s841">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1197.2682370820667" y="287.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2281.0" y="3282.5"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa32" species="s2611">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1225.7682370820667" y="66.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2360.5" y="3189.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffffffff" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa33" species="s817">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1243.7682370820667" y="12.50000000000091" w="25.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2364.5" y="3112.500000000001"/>
+<celldesigner:boxSize width="25.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ff9999ff" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa34" species="s815">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1214.2682370820667" y="128.5000000000009" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2267.0" y="3112.500000000001"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa35" species="s4532">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1044.7317629179333" y="27.50000000000091" w="140.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2114.4635258358667" y="3112.500000000001"/>
+<celldesigner:boxSize width="140.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
diff --git a/converter-CellDesigner/testFiles/invalid/protein.xml b/converter-CellDesigner/testFiles/invalid/protein.xml
index 8eb55f9abdb78bec4ff784d1833c995884947376..d5e33d960c85c9155e3d3a975e682a2703400fdd 100644
--- a/converter-CellDesigner/testFiles/invalid/protein.xml
+++ b/converter-CellDesigner/testFiles/invalid/protein.xml
@@ -1,16 +1,16 @@
-<celldesigner:protein id="pr23" name="SDHA" type="UNK_TYPE_BLA">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024|UniProtKB:Q0QF01 ISS UniProtKB:Q0QF01 C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20100125 UniProtKB
-UniProtKB P31040 SDHA GO:0005749 PMID:7550341 TAS C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20060419 UniProtKB
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfModificationResidues>
-<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none"/>
-</celldesigner:listOfModificationResidues>
+<celldesigner:protein id="pr23" name="SDHA" type="UNK_TYPE_BLA">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024|UniProtKB:Q0QF01 ISS UniProtKB:Q0QF01 C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20100125 UniProtKB
+UniProtKB P31040 SDHA GO:0005749 PMID:7550341 TAS C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20060419 UniProtKB
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none"/>
+</celldesigner:listOfModificationResidues>
</celldesigner:protein>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/protein2.xml b/converter-CellDesigner/testFiles/invalid/protein2.xml
index 8b19845e6e0135ebe7997a219f36e7cb0b6fedfc..2ecfe74847241232172e85284aad1436d80602ea 100644
--- a/converter-CellDesigner/testFiles/invalid/protein2.xml
+++ b/converter-CellDesigner/testFiles/invalid/protein2.xml
@@ -1,17 +1,17 @@
-<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024|UniProtKB:Q0QF01 ISS UniProtKB:Q0QF01 C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20100125 UniProtKB
-UniProtKB P31040 SDHA GO:0005749 PMID:7550341 TAS C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20060419 UniProtKB
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfModificationResidues>
-<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none"/>
-<unkNode/>
-</celldesigner:listOfModificationResidues>
+<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024|UniProtKB:Q0QF01 ISS UniProtKB:Q0QF01 C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20100125 UniProtKB
+UniProtKB P31040 SDHA GO:0005749 PMID:7550341 TAS C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20060419 UniProtKB
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none"/>
+<unkNode/>
+</celldesigner:listOfModificationResidues>
</celldesigner:protein>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/protein3.xml b/converter-CellDesigner/testFiles/invalid/protein3.xml
index 0ca56fd5bede362b979077a7379c049a7546b46c..674b6a9e859e4e277cd6a60f2f8fb23a12cd2f10 100644
--- a/converter-CellDesigner/testFiles/invalid/protein3.xml
+++ b/converter-CellDesigner/testFiles/invalid/protein3.xml
@@ -1,17 +1,17 @@
-<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024|UniProtKB:Q0QF01 ISS UniProtKB:Q0QF01 C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20100125 UniProtKB
-UniProtKB P31040 SDHA GO:0005749 PMID:7550341 TAS C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20060419 UniProtKB
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfModificationResidues>
-<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none"/>
-</celldesigner:listOfModificationResidues>
-<xxx/>
+<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024|UniProtKB:Q0QF01 ISS UniProtKB:Q0QF01 C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20100125 UniProtKB
+UniProtKB P31040 SDHA GO:0005749 PMID:7550341 TAS C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20060419 UniProtKB
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none"/>
+</celldesigner:listOfModificationResidues>
+<xxx/>
</celldesigner:protein>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/protein4.xml b/converter-CellDesigner/testFiles/invalid/protein4.xml
index cfd7e5b23cabe32291f185776f8fa4bec7f5f896..f84c2a325fc156ad65d7811a402fb33606480fe6 100644
--- a/converter-CellDesigner/testFiles/invalid/protein4.xml
+++ b/converter-CellDesigner/testFiles/invalid/protein4.xml
@@ -1,18 +1,18 @@
-<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024|UniProtKB:Q0QF01 ISS UniProtKB:Q0QF01 C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20100125 UniProtKB
-UniProtKB P31040 SDHA GO:0005749 PMID:7550341 TAS C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20060419 UniProtKB
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfModificationResidues>
-<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none">
-<xxx/>
-</celldesigner:modificationResidue>
-</celldesigner:listOfModificationResidues>
+<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024|UniProtKB:Q0QF01 ISS UniProtKB:Q0QF01 C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20100125 UniProtKB
+UniProtKB P31040 SDHA GO:0005749 PMID:7550341 TAS C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20060419 UniProtKB
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none">
+<xxx/>
+</celldesigner:modificationResidue>
+</celldesigner:listOfModificationResidues>
</celldesigner:protein>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/protein5.xml b/converter-CellDesigner/testFiles/invalid/protein5.xml
index cfd7e5b23cabe32291f185776f8fa4bec7f5f896..f84c2a325fc156ad65d7811a402fb33606480fe6 100644
--- a/converter-CellDesigner/testFiles/invalid/protein5.xml
+++ b/converter-CellDesigner/testFiles/invalid/protein5.xml
@@ -1,18 +1,18 @@
-<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024|UniProtKB:Q0QF01 ISS UniProtKB:Q0QF01 C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20100125 UniProtKB
-UniProtKB P31040 SDHA GO:0005749 PMID:7550341 TAS C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20060419 UniProtKB
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfModificationResidues>
-<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none">
-<xxx/>
-</celldesigner:modificationResidue>
-</celldesigner:listOfModificationResidues>
+<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024|UniProtKB:Q0QF01 ISS UniProtKB:Q0QF01 C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20100125 UniProtKB
+UniProtKB P31040 SDHA GO:0005749 PMID:7550341 TAS C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20060419 UniProtKB
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none">
+<xxx/>
+</celldesigner:modificationResidue>
+</celldesigner:listOfModificationResidues>
</celldesigner:protein>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/protein6.xml b/converter-CellDesigner/testFiles/invalid/protein6.xml
index cfd7e5b23cabe32291f185776f8fa4bec7f5f896..f84c2a325fc156ad65d7811a402fb33606480fe6 100644
--- a/converter-CellDesigner/testFiles/invalid/protein6.xml
+++ b/converter-CellDesigner/testFiles/invalid/protein6.xml
@@ -1,18 +1,18 @@
-<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024|UniProtKB:Q0QF01 ISS UniProtKB:Q0QF01 C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20100125 UniProtKB
-UniProtKB P31040 SDHA GO:0005749 PMID:7550341 TAS C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20060419 UniProtKB
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfModificationResidues>
-<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none">
-<xxx/>
-</celldesigner:modificationResidue>
-</celldesigner:listOfModificationResidues>
+<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024|UniProtKB:Q0QF01 ISS UniProtKB:Q0QF01 C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20100125 UniProtKB
+UniProtKB P31040 SDHA GO:0005749 PMID:7550341 TAS C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20060419 UniProtKB
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none">
+<xxx/>
+</celldesigner:modificationResidue>
+</celldesigner:listOfModificationResidues>
</celldesigner:protein>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/protein_collection.xml b/converter-CellDesigner/testFiles/invalid/protein_collection.xml
index 653c678b4ef205dbbf37d4925545023c37ffc054..b64c6eb84979f99a02ac12793e7b9613cc33d6e0 100644
--- a/converter-CellDesigner/testFiles/invalid/protein_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/protein_collection.xml
@@ -1,3 +1,3 @@
-<celldesigner:listOfProteins>
-<unkproteinnode/>
+<celldesigner:listOfProteins>
+<unkproteinnode/>
</celldesigner:listOfProteins>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/rna.xml b/converter-CellDesigner/testFiles/invalid/rna.xml
index 62e29d7ee272f36fb33b429b67958037ffc7b0b8..15e15b96b189845cfc7386a143e9ccbe3a102889 100644
--- a/converter-CellDesigner/testFiles/invalid/rna.xml
+++ b/converter-CellDesigner/testFiles/invalid/rna.xml
@@ -1,6 +1,6 @@
-<celldesigner:RNA id="rn49" name="TRNAU1" type="RNA">
-<celldesigner:listOfRegions>
-<celldesigner:region id="tr1" size="0.0" pos="0.10569105691056911" type="Modification Site"/>
-<unknode/>
-</celldesigner:listOfRegions>
+<celldesigner:RNA id="rn49" name="TRNAU1" type="RNA">
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" size="0.0" pos="0.10569105691056911" type="Modification Site"/>
+<unknode/>
+</celldesigner:listOfRegions>
</celldesigner:RNA>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/rna2.xml b/converter-CellDesigner/testFiles/invalid/rna2.xml
index 84be995a07a0c51d5bdb3f02fc67cde436da0884..1217e8542429037b3dec24470667f658166bbb12 100644
--- a/converter-CellDesigner/testFiles/invalid/rna2.xml
+++ b/converter-CellDesigner/testFiles/invalid/rna2.xml
@@ -1,6 +1,6 @@
-<celldesigner:RNA id="rn49" name="TRNAU1" type="RNA">
-<celldesigner:listOfRegions>
-<celldesigner:region id="tr1" size="0.0" pos="0.10569105691056911" type="Modification Site"/>
-</celldesigner:listOfRegions>
-<unknode/>
+<celldesigner:RNA id="rn49" name="TRNAU1" type="RNA">
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" size="0.0" pos="0.10569105691056911" type="Modification Site"/>
+</celldesigner:listOfRegions>
+<unknode/>
</celldesigner:RNA>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/rna3.xml b/converter-CellDesigner/testFiles/invalid/rna3.xml
index 4a5d2d45f1f257aafb49da8d9255d4826682b6c2..8ff8c125aa5ea1b4ee793b00154c189c95e8a311 100644
--- a/converter-CellDesigner/testFiles/invalid/rna3.xml
+++ b/converter-CellDesigner/testFiles/invalid/rna3.xml
@@ -1,7 +1,7 @@
-<celldesigner:RNA id="rn49" name="TRNAU1" type="RNA">
-<celldesigner:listOfRegions>
-<celldesigner:region id="tr1" size="0.0" pos="0.10569105691056911" type="Modification Site">
-<unknode/>
-</celldesigner:region >
-</celldesigner:listOfRegions>
+<celldesigner:RNA id="rn49" name="TRNAU1" type="RNA">
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" size="0.0" pos="0.10569105691056911" type="Modification Site">
+<unknode/>
+</celldesigner:region >
+</celldesigner:listOfRegions>
</celldesigner:RNA>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/rna_collection.xml b/converter-CellDesigner/testFiles/invalid/rna_collection.xml
index 04081ecf745d511d55022294258627055605f744..d3ffb5f3e8f4486b8574685026624f6f14eb6768 100644
--- a/converter-CellDesigner/testFiles/invalid/rna_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/rna_collection.xml
@@ -1,5 +1,5 @@
-<celldesigner:listOfRNAs>
-<unknown_node/>
-<celldesigner:RNA id="rn1" name="s5" type="RNA"/>
-<celldesigner:RNA id="rn2" name="s7" type="RNA"/>
+<celldesigner:listOfRNAs>
+<unknown_node/>
+<celldesigner:RNA id="rn1" name="s5" type="RNA"/>
+<celldesigner:RNA id="rn2" name="s7" type="RNA"/>
</celldesigner:listOfRNAs>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/sbml_collection.xml b/converter-CellDesigner/testFiles/invalid/sbml_collection.xml
index 64fb5055e747b142671e6e6e890474012eeabd1d..9dc20a3fd89e7aa81388d7205990ac454be94126 100644
--- a/converter-CellDesigner/testFiles/invalid/sbml_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/sbml_collection.xml
@@ -1,102 +1,102 @@
-<listOfSpecies>
-<unknode/>
-<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>GENE</celldesigner:class>
-<celldesigner:geneReference>gn1</celldesigner:geneReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s4" id="s4" name="s4" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>GENE</celldesigner:class>
-<celldesigner:geneReference>gn2</celldesigner:geneReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s5" id="s5" name="s5" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>RNA</celldesigner:class>
-<celldesigner:rnaReference>rn1</celldesigner:rnaReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s6" id="s6" name="s6" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
-<celldesigner:antisensernaReference>arn1</celldesigner:antisensernaReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s7" id="s7" name="s7" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>RNA</celldesigner:class>
-<celldesigner:rnaReference>rn2</celldesigner:rnaReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s8" id="s8" name="s8" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
-<celldesigner:antisensernaReference>arn2</celldesigner:antisensernaReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s9" id="s9" name="s9" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>COMPLEX</celldesigner:class>
-<celldesigner:name>s9</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
+<listOfSpecies>
+<unknode/>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn1</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s4" id="s4" name="s4" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn2</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s5" id="s5" name="s5" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>rn1</celldesigner:rnaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s6" id="s6" name="s6" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
+<celldesigner:antisensernaReference>arn1</celldesigner:antisensernaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s7" id="s7" name="s7" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>rn2</celldesigner:rnaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s8" id="s8" name="s8" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
+<celldesigner:antisensernaReference>arn2</celldesigner:antisensernaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s9" id="s9" name="s9" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s9</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
</listOfSpecies>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/species_alias.xml b/converter-CellDesigner/testFiles/invalid/species_alias.xml
index 49e4039690f8ee989071be70230c8405383b1922..beec5151a7ee6206c99b453aebc209aea2c097ae 100644
--- a/converter-CellDesigner/testFiles/invalid/species_alias.xml
+++ b/converter-CellDesigner/testFiles/invalid/species_alias.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa36" species="ss78" compartmentAlias="ca1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="ss78" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/species_alias2.xml b/converter-CellDesigner/testFiles/invalid/species_alias2.xml
index 9ae72330ea4720026f59adb4119bfcfa626dca22..45c1c2f61a1a4158babe4d07281be822b90619c2 100644
--- a/converter-CellDesigner/testFiles/invalid/species_alias2.xml
+++ b/converter-CellDesigner/testFiles/invalid/species_alias2.xml
@@ -1,20 +1,20 @@
-<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
-<unk/>
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
+<unk/>
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/species_alias3.xml b/converter-CellDesigner/testFiles/invalid/species_alias3.xml
index c082780aa1baafa388cc27497849ada5804823f2..a9e14fad3e6f1230de997bbe9996237163e5ab01 100644
--- a/converter-CellDesigner/testFiles/invalid/species_alias3.xml
+++ b/converter-CellDesigner/testFiles/invalid/species_alias3.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="unusual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="unusual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/species_alias4.xml b/converter-CellDesigner/testFiles/invalid/species_alias4.xml
index ec93873ff7bc1d82cf7dba17fabc31adc4a307c4..0a65186bf80c82935688034528bbee542cacb10d 100644
--- a/converter-CellDesigner/testFiles/invalid/species_alias4.xml
+++ b/converter-CellDesigner/testFiles/invalid/species_alias4.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ccca1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ccca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/species_alias5.xml b/converter-CellDesigner/testFiles/invalid/species_alias5.xml
index fe54056792bfdca1770f7fd8e6ca4dfedcbb9e01..f8c77a350361d89f44f72f263c79d71e35b98c07 100644
--- a/converter-CellDesigner/testFiles/invalid/species_alias5.xml
+++ b/converter-CellDesigner/testFiles/invalid/species_alias5.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa36" species="s78" complexSpeciesAlias="ccca1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="s78" complexSpeciesAlias="ccca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/species_alias6.xml b/converter-CellDesigner/testFiles/invalid/species_alias6.xml
index 6dfcf60c592655b0e5e3b7c86017e6e1d7e2b6f7..9f5bd07fded55d0227831bc5f5a30ed47a912dc9 100644
--- a/converter-CellDesigner/testFiles/invalid/species_alias6.xml
+++ b/converter-CellDesigner/testFiles/invalid/species_alias6.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa36" species="s78" >
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="unknown" angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="s78" >
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="unknown" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/species_alias_collection.xml b/converter-CellDesigner/testFiles/invalid/species_alias_collection.xml
index fd531560a8165d89ad3b296d57aacc51249ecad3..9d3b3607e2c96a23af1c80125aabdbbb15362670 100644
--- a/converter-CellDesigner/testFiles/invalid/species_alias_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/species_alias_collection.xml
@@ -1,79 +1,79 @@
-<celldesigner:listOfSpeciesAliases>
-<unk/>
-<celldesigner:speciesAlias id="sa8" species="s2594">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="510.83547998986796" y="449.34999999999997" w="261.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="1459.6161980749753" y="5346.0"/>
-<celldesigner:boxSize width="261.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa9" species="s2506">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="506.33547998986796" y="613.8499999999999" w="262.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="1459.1161980749753" y="5539.5"/>
-<celldesigner:boxSize width="262.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa10" species="s2595">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="282.0" y="75.0" w="134.0" h="94.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="134.0" height="94.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="0.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa11" species="s2596">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="483.0" y="76.0" w="82.0" h="96.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="82.0" height="96.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="0.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfSpeciesAliases>
+<unk/>
+<celldesigner:speciesAlias id="sa8" species="s2594">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="510.83547998986796" y="449.34999999999997" w="261.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="1459.6161980749753" y="5346.0"/>
+<celldesigner:boxSize width="261.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa9" species="s2506">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="506.33547998986796" y="613.8499999999999" w="262.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="1459.1161980749753" y="5539.5"/>
+<celldesigner:boxSize width="262.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa10" species="s2595">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="282.0" y="75.0" w="134.0" h="94.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="134.0" height="94.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa11" species="s2596">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="483.0" y="76.0" w="82.0" h="96.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="82.0" height="96.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/block_diagrams.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/block_diagrams.xml
index 9d55f1695028c28f792fe753905a65b68d9af278..15d462cb5d4afada6184abc3ff55fd267bc22d20 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/block_diagrams.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/block_diagrams.xml
@@ -1,15 +1,15 @@
-<celldesigner:listOfBlockDiagrams>
-<celldesigner:blockDiagram protein="pr1">
-<celldesigner:canvas height="312" width="476"/>
-<celldesigner:block height="90" nameOffsetX="-8.0" nameOffsetY="-8.0" width="140" x="100" y="50"/>
-<celldesigner:halo height="150" width="200" x="70" y="20"/>
-<celldesigner:listOfResiduesInBlockDiagram>
-<celldesigner:residueInBlockDiagram id="0" offsetX="-27.0" type="dontcare"/>
-</celldesigner:listOfResiduesInBlockDiagram>
-<celldesigner:listOfExternalNamesForResidue/>
-<celldesigner:listOfBindingSitesInBlockDiagram/>
-<celldesigner:listOfEffectSitesInBlockDiagram/>
-<celldesigner:listOfInternalOperatorsInBlockDiagram/>
-<celldesigner:listOfInternalLinksInBlockDiagram/>
-</celldesigner:blockDiagram>
-</celldesigner:listOfBlockDiagrams>
+<celldesigner:listOfBlockDiagrams>
+<celldesigner:blockDiagram protein="pr1">
+<celldesigner:canvas height="312" width="476"/>
+<celldesigner:block height="90" nameOffsetX="-8.0" nameOffsetY="-8.0" width="140" x="100" y="50"/>
+<celldesigner:halo height="150" width="200" x="70" y="20"/>
+<celldesigner:listOfResiduesInBlockDiagram>
+<celldesigner:residueInBlockDiagram id="0" offsetX="-27.0" type="dontcare"/>
+</celldesigner:listOfResiduesInBlockDiagram>
+<celldesigner:listOfExternalNamesForResidue/>
+<celldesigner:listOfBindingSitesInBlockDiagram/>
+<celldesigner:listOfEffectSitesInBlockDiagram/>
+<celldesigner:listOfInternalOperatorsInBlockDiagram/>
+<celldesigner:listOfInternalLinksInBlockDiagram/>
+</celldesigner:blockDiagram>
+</celldesigner:listOfBlockDiagrams>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml
index d9f1852510debfab242338439cd3b32a0003cf71..bf37613db890d17ecff3ec40fc57b012f9375caf 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml
@@ -1,21 +1,21 @@
-<celldesigner:complexSpeciesAlias id="csa1" species="s2597">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="744.0" y="0.0" w="100.0" h="120.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="100.0" height="120.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa1" species="s2597">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="744.0" y="0.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes.xml
index 11d122e7e9af9c5a2b110b555a7af91b721785c7..07e958faee7d9bb5fd682ca528679300524a2818 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes.xml
@@ -1,10 +1,10 @@
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Description: some notes
-</body>
-</html>
-</celldesigner:notes>
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Description: some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes2.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes2.xml
index c16aea799bf5029d0eb92cf9aa4fc02e69f1e528..fe5db406a203836ada3d7592b72be7b174c84350 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes2.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes2.xml
@@ -1,23 +1,23 @@
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Symbol: SNCA
-Previous Symbols: X1, X2, X3
-Synonyms: Y1, Y2, Y3
-Name: Synuclein alpha (or something)
-Abbreviation: SN
-Formula: form
-MechanicalConfidenceScore: 2
-LowerBound: 2
-UpperBound: 2
-Subsystem: 2
-GeneProteinReaction: 1
-ChargedFormula: 1
-Charge:15
-some notes
-</body>
-</html>
-</celldesigner:notes>
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Symbol: SNCA
+Previous Symbols: X1, X2, X3
+Synonyms: Y1, Y2, Y3
+Name: Synuclein alpha (or something)
+Abbreviation: SN
+Formula: form
+MechanicalConfidenceScore: 2
+LowerBound: 2
+UpperBound: 2
+Subsystem: 2
+GeneProteinReaction: 1
+ChargedFormula: 1
+Charge:15
+some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes3.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes3.xml
index 8a9da0796e112488c13b6f1af8f0c402f90f774f..68f0aadbf7ce91b973d5a570b05d3385e6d72f11 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes3.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes3.xml
@@ -1,11 +1,11 @@
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Description: some notes
-some notes
-</body>
-</html>
-</celldesigner:notes>
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Description: some notes
+some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes4.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes4.xml
index aae1b31a33ac919831923dc43e247d6cc65acf1a..444dade224bdda399f10283c4da4dec8f280c86f 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes4.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes4.xml
@@ -1,11 +1,11 @@
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Description: some notes some notes Symbol: strange2
-some notes some notes Symbol: strange3
-</body>
-</html>
-</celldesigner:notes>
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Description: some notes some notes Symbol: strange2
+some notes some notes Symbol: strange3
+</body>
+</html>
+</celldesigner:notes>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes5.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes5.xml
index f416ace9685d64344ac3634da9c769b41462b916..b4d6531235e9a014514bc722dc172b7c9226f549 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes5.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes5.xml
@@ -1,43 +1,43 @@
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdfa:Description rdf:about="#s6095">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:18429"/></rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family:PTHR11695"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_036344.2"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001139580.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family:ADH_Sf_Zn"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:22949"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001139581.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:22949"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdfa:Description rdf:about="#s6095">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:18429"/></rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family:PTHR11695"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_036344.2"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139580.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family:ADH_Sf_Zn"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139581.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
</rdf:RDF>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes_invalid_charge.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes_invalid_charge.xml
index 1df09c4a025b8441516289a39607b00ad250ced3..8e2a9d5f76a483fecc5a5ff93c8f2859bfae17de 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes_invalid_charge.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes_invalid_charge.xml
@@ -1,11 +1,11 @@
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Charge:a15
-some notes
-</body>
-</html>
-</celldesigner:notes>
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Charge:a15
+some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_gene.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_gene.xml
index 0c05a8d203dfc8718e1340aa48b7177abdab62fb..3d176259f8c172c99f0fff8d06bd5a6d5fc58c1c 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_gene.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_gene.xml
@@ -1,73 +1,73 @@
-<species metaid="s5916" id="s5916" name="Ptgr1" compartment="c20" initialAmount="0" charge="0">
-<notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Symbol: PTGR1
-Name: prostaglandin reductase 1
-Description: RecName: Full=Prostaglandin reductase 1; Short=PRG-1; EC=1.3.1.-; AltName: Full=15-oxoprostaglandin 13-reductase; EC=1.3.1.48; AltName: Full=NADP-dependent leukotriene B4 12-hydroxydehydrogenase; EC=1.3.1.74;
-Previous Symbols: LTB4DH
-Synonyms: LTB4DH
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s6095">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:22949"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</body>
-</html>
-</notes>
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>GENE</celldesigner:class>
-<celldesigner:geneReference>gn95</celldesigner:geneReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s5916">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:18429"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR11695"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_036344.2"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001139580.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3AADH_Sf_Zn"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A22949"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001139581.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
+<species metaid="s5916" id="s5916" name="Ptgr1" compartment="c20" initialAmount="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Symbol: PTGR1
+Name: prostaglandin reductase 1
+Description: RecName: Full=Prostaglandin reductase 1; Short=PRG-1; EC=1.3.1.-; AltName: Full=15-oxoprostaglandin 13-reductase; EC=1.3.1.48; AltName: Full=NADP-dependent leukotriene B4 12-hydroxydehydrogenase; EC=1.3.1.74;
+Previous Symbols: LTB4DH
+Synonyms: LTB4DH
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6095">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn95</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5916">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:18429"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR11695"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_036344.2"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139580.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3AADH_Sf_Zn"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139581.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_ion.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_ion.xml
index 0562f1e8493b6e20df460c1f0c863df38d1a30ab..5c2222a435b30b39aa5a3d4375f4f8b2bf1e9901 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_ion.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_ion.xml
@@ -1,124 +1,124 @@
-<species metaid="s6029" id="s6029" name="Pi" compartment="c1" initialConcentration="0" charge="0">
-<notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Long Name: PiSynonym: Synonym not specifiedAccession: U02720
-Symbol: SERPINA1
-Name: serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1
-Description: RecName: Full=Alpha-1-antitrypsin; AltName: Full=Alpha-1 protease inhibitor; AltName: Full=Alpha-1-antiproteinase; AltName: Full=Serpin A1; Contains: RecName: Full=Short peptide from AAT; Short=SPAAT; Flags: Precursor;
-Previous Symbols: PI
-Synonyms: AAT, PI
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s6095">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:5265"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</body>
-</html>
-</notes>
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>ION</celldesigner:class>
-<celldesigner:name>Pi</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s6029">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121172.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3AProt_inh_serpin"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA35509"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR11461"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121174.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:8941"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001002235.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121175.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121176.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121179.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121173.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121177.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:reactome:REACT_3705"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121178.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001002236.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_000286.3"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A5265"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
+<species metaid="s6029" id="s6029" name="Pi" compartment="c1" initialConcentration="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Long Name: PiSynonym: Synonym not specifiedAccession: U02720
+Symbol: SERPINA1
+Name: serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1
+Description: RecName: Full=Alpha-1-antitrypsin; AltName: Full=Alpha-1 protease inhibitor; AltName: Full=Alpha-1-antiproteinase; AltName: Full=Serpin A1; Contains: RecName: Full=Short peptide from AAT; Short=SPAAT; Flags: Precursor;
+Previous Symbols: PI
+Synonyms: AAT, PI
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6095">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:5265"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ION</celldesigner:class>
+<celldesigner:name>Pi</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6029">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121172.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3AProt_inh_serpin"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA35509"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR11461"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121174.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:8941"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001002235.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121175.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121176.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121179.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121173.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121177.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_3705"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121178.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001002236.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_000286.3"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A5265"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_protein.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_protein.xml
index 586c93a1cb75bdaea3f491f713d64615076951f0..0f8d55a9f69c7fe05edd1eff4180ce09e5b5692c 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_protein.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_protein.xml
@@ -1,63 +1,63 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>protein tyrosine phosphatase, receptor type, C
-also known as CED45
-Symbol: PTPRC
-Name: protein tyrosine phosphatase, receptor type, C
-Description: RecName: Full=Receptor-type tyrosine-protein phosphatase C; EC=3.1.3.48; AltName: Full=Leukocyte common antigen; Short=L-CA; AltName: Full=T200; AltName: CD_antigen=CD45; Flags: Precursor;
-Previous Symbols: CD45
-Synonyms: CD45
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s5456">
-<bqbiol:is>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:entrez.gene:5788"/></rdf:Bag>
-</bqbiol:is>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_002829.2"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:reactome:REACT_13296"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</body>
-</html>
-</notes>
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s5456">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_563578.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA34011"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:9666"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>protein tyrosine phosphatase, receptor type, C
+also known as CED45
+Symbol: PTPRC
+Name: protein tyrosine phosphatase, receptor type, C
+Description: RecName: Full=Receptor-type tyrosine-protein phosphatase C; EC=3.1.3.48; AltName: Full=Leukocyte common antigen; Short=L-CA; AltName: Full=T200; AltName: CD_antigen=CD45; Flags: Precursor;
+Previous Symbols: CD45
+Synonyms: CD45
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5456">
+<bqbiol:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:entrez.gene:5788"/></rdf:Bag>
+</bqbiol:is>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_002829.2"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_13296"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5456">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_563578.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA34011"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:9666"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_rna.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_rna.xml
index 2531787c2590727759a03b265745f69eca7bf70b..a848f327dc38d38126e832a04b89f039b7d817a0 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_rna.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_rna.xml
@@ -1,78 +1,78 @@
-<species metaid="s5914" id="s5914" name="Fmo3" compartment="c20" initialAmount="0" charge="0">
-<notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Symbol: FMO3
-Name: flavin containing monooxygenase 3
-Description: RecName: Full=Dimethylaniline monooxygenase [N-oxide-forming] 3; EC=1.14.13.8; AltName: Full=Dimethylaniline oxidase 3; AltName: Full=FMO II; AltName: Full=FMO form 2; AltName: Full=Hepatic flavin-containing monooxygenase 3; Short=FMO 3;
-Previous Symbols:
-Synonyms:
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s6095">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:2328"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</body>
-</html>
-</notes>
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>RNA</celldesigner:class>
-<celldesigner:rnaReference>rn101</celldesigner:rnaReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s5914">
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:8486388"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001002294.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:reactome:REACT_5740"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA166"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A2328"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_008825.4"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:3771"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:9417913"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
+<species metaid="s5914" id="s5914" name="Fmo3" compartment="c20" initialAmount="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Symbol: FMO3
+Name: flavin containing monooxygenase 3
+Description: RecName: Full=Dimethylaniline monooxygenase [N-oxide-forming] 3; EC=1.14.13.8; AltName: Full=Dimethylaniline oxidase 3; AltName: Full=FMO II; AltName: Full=FMO form 2; AltName: Full=Hepatic flavin-containing monooxygenase 3; Short=FMO 3;
+Previous Symbols:
+Synonyms:
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6095">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:2328"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>rn101</celldesigner:rnaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5914">
+<bqbiol:isVersionOf>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pubmed:8486388"/>
+</rdf:Bag>
+</bqbiol:isVersionOf>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001002294.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_5740"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA166"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A2328"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_008825.4"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:3771"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:isVersionOf>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pubmed:9417913"/>
+</rdf:Bag>
+</bqbiol:isVersionOf>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
</species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias.xml
index fa35a946eb65c193933073ee6ffc4728fc563551..f3e98a79102afd980f9876205615e4f0be22fdc9 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_with_font.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_with_font.xml
index b689e984c9e241514de9833afc45d81ff39752b2..893947c964229bd2c87122606ce6871170ac4f9c 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_with_font.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_with_font.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa1" species="s78">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="78.0" y="207.0" w="307.0" h="110.0"/>
-<celldesigner:font size="30"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="307.0" height="110.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="0.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa1" species="s78">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="78.0" y="207.0" w="307.0" h="110.0"/>
+<celldesigner:font size="30"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="307.0" height="110.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_without_state.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_without_state.xml
index 0c4992aaf3b1104561af3d932e12db86b836d092..267d16430a0c9bc1636be7798c2387a24fdd4e0c 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_without_state.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_without_state.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index 6e3adb813deef75b25ed2e193fd608f3be9dc0e8..c6ec75fd87355738756c169af6a43d3bb3746bf4 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -1,421 +1,421 @@
-package lcsb.mapviewer.converter;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.lang.reflect.Modifier;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipFile;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.zip.DataMiningZipEntryFile;
-import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
-import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
-import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFile;
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.graph.DataMiningSet;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class allows to create complex {@link Model} that contains submaps. It's
- * written in generic way and use {@link IConverter} as a class to parse single
- * submap.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- * class used to create single submap from a file
- */
-public class ComplexZipConverter<T extends IConverter> {
-
- /**
- * Size of the buffer used for accessing single chunk of data from input
- * stream.
- */
- private static final int BUFFER_SIZE = 1024;
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ComplexZipConverter.class);
- /**
- * Class used to create single submap from a file.
- */
- private Class<T> converterClazz;
-
- /**
- * Default constructor. Checks if the class given in the parameter is proper
- * {@link IConverter} implementation.
- *
- * @param clazz
- * {@link IConverter} class used for creation of the single submap
- */
- public ComplexZipConverter(Class<T> clazz) {
- if (Modifier.isAbstract(clazz.getModifiers())) {
- throw new InvalidClassException("Param class cannot be abstract");
- }
-
- if (Modifier.isInterface(clazz.getModifiers())) {
- throw new InvalidClassException("Param class cannot be an interface");
- }
-
- converterClazz = clazz;
- }
-
- /**
- * Creates complex {@link Model} that contains submaps.
- *
- * @param params
- * {@link ComplexZipConverterParams object} with information about
- * data from which result is going to be created
- * @return complex {@link Model} created from input data
- * @throws InvalidInputDataExecption
- * thrown when there is a problem with accessing input data
- */
- public Model createModel(ComplexZipConverterParams params) throws InvalidInputDataExecption {
- try {
- ZipFile zipFile = params.getZipFile();
- Enumeration<? extends ZipEntry> entries;
- String mapping = validateSubmodelInformation(params, zipFile);
-
- IConverter converter = createConverterInstance();
- Map<String, Model> filenameModelMap = new HashMap<String, Model>();
- Map<String, Model> nameModelMap = new HashMap<String, Model>();
-
- entries = zipFile.entries();
- Model result = null;
- List<Layout> layouts = new ArrayList<Layout>();
- List<ImageZipEntryFile> imageEntries = new ArrayList<ImageZipEntryFile>();
- List<DataMiningSet> dataMiningSets = new ArrayList<DataMiningSet>();
- while (entries.hasMoreElements()) {
- ZipEntry entry = entries.nextElement();
- if (!entry.isDirectory()) {
- ZipEntryFile zef = params.getEntry(entry.getName());
- if (zef instanceof ModelZipEntryFile) {
- ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
- InputStream is = zipFile.getInputStream(entry);
- ConverterParams cParams = new ConverterParams();
- cParams.inputStream(is);
- Model model = converter.createModel(cParams);
- model.setName(modelEntryFile.getName());
- filenameModelMap.put(entry.getName(), model);
- nameModelMap.put(FilenameUtils.getBaseName(modelEntryFile.getFilename()), model);
- if (modelEntryFile.isRoot()) {
- result = model;
- }
- } else if (zef instanceof LayoutZipEntryFile) {
- layouts.add(layoutZipEntryFileToLayout(params, zipFile, entry, (LayoutZipEntryFile) zef));
- } else if (zef instanceof ImageZipEntryFile) {
- imageEntries.add((ImageZipEntryFile) zef);
- } else if (zef instanceof DataMiningZipEntryFile) {
- dataMiningSets.add(dataMiningZipEntryToDataMiningSet(zipFile, entry, (DataMiningZipEntryFile) zef));
- } else {
- throw new NotImplementedException("Unknwon entry type: " + zef.getClass());
- }
- }
- }
-
- if (imageEntries.size() > 0) {
- OverviewParser parser = new OverviewParser();
- result.setOverviewImages(parser.parseOverviewLinks(filenameModelMap, imageEntries, params.getVisualizationDir()));
- }
- result.addDataMiningSets(dataMiningSets);
-
- for (Entry<String, Model> entry : filenameModelMap.entrySet()) {
- String filename = entry.getKey();
- Model model = entry.getValue();
- ZipEntryFile zef = params.getEntry(filename);
- if (zef instanceof ModelZipEntryFile) {
- ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
- if (!modelEntryFile.isRoot() && !modelEntryFile.isMappingFile()) {
- ModelSubmodelConnection submodel = new ModelSubmodelConnection(model, modelEntryFile.getType());
- submodel.setName(modelEntryFile.getName());
- result.addSubmodelConnection(submodel);
- }
- }
- }
- for (Layout layout : layouts) {
- Layout topLayout = new Layout(layout);
- result.addLayout(topLayout);
- int modelId = 0;
- topLayout.setDirectory(topLayout.getDirectory() + modelId);
- modelId++;
- for (ModelSubmodelConnection connection : result.getSubmodelConnections()) {
- Layout childLayout = new Layout(layout);
- // we need to set separate directory names for different submodels
- childLayout.setDirectory(childLayout.getDirectory() + modelId);
- modelId++;
- childLayout.setParentLayout(topLayout);
- connection.getSubmodel().addLayout(childLayout);
- }
- }
- Model mappingModel = filenameModelMap.get(mapping);
- if (mappingModel != null) {
- for (Reaction reaction : mappingModel.getReactions()) {
- processReaction(mapping, nameModelMap, result, reaction);
- }
- }
- return result;
- } catch (IOException e) {
- throw new InvalidArgumentException(e);
- }
- }
-
- /**
- * Process a single reaction in mapping file (transfomring reaction into
- * connection between submodels).
- *
- * @param mapping
- * name of the mapping file
- * @param nameModelMap
- * mapping between file names and models
- * @param topModel
- * top model
- * @param reaction
- * reaction to transform into connection
- */
- public void processReaction(String mapping, Map<String, Model> nameModelMap, Model topModel, Reaction reaction) {
- if (reaction.getReactants().size() > 1) {
- topModel.addCreationWarning(
- "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains too many reactants. Skipped");
- } else if (reaction.getProducts().size() > 1) {
- topModel.addCreationWarning(
- "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains too many products. Skipped");
- } else if (reaction.getModifiers().size() > 0) {
- topModel
- .addCreationWarning("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains modifiers. Skipped");
- } else {
- Alias fromAlias = reaction.getReactants().get(0).getAlias();
- Element fromElement = fromAlias.getElement();
- Alias toAlias = reaction.getProducts().get(0).getAlias();
- Element toElement = toAlias.getElement();
- if (!(fromAlias instanceof SpeciesAlias)) {
- topModel.addCreationWarning(
- "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start in species. Skipped");
- } else if (!(toAlias instanceof SpeciesAlias)) {
- topModel.addCreationWarning(
- "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end in species. Skipped");
- } else {
- Species from = (Species) fromElement;
- ComplexAlias complexFrom = ((SpeciesAlias) fromAlias).getComplexAlias();
- Species to = (Species) toElement;
- ComplexAlias complexTo = ((SpeciesAlias) toAlias).getComplexAlias();
- if (complexFrom == null) {
- topModel.addCreationWarning(
- "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start inside complex. Skipped");
- } else if (complexTo == null && (!(toAlias instanceof ComplexAlias))) {
- topModel.addCreationWarning(
- "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end inside complex. Skipped");
- } else {
- if (complexTo == null) {
- complexTo = (ComplexAlias) toAlias;
- }
- String fromName = complexFrom.getElement().getName();
- String toName = complexTo.getElement().getName();
- Model fromModel = nameModelMap.get(fromName);
- Model toModel = nameModelMap.get(toName);
- if (fromModel == null) {
- throw new InvalidArgumentException("Mapping file references to " + fromName + " submodel. But such model doesn't exist");
- } else if (toModel == null) {
- throw new InvalidArgumentException("Mapping file references to " + toName + " submodel. But such model doesn't exist");
- }
- Alias source = fromModel.getAliasByAliasId(from.getName());
- if (source == null) {
- throw new InvalidArgumentException("Mapping file references to element with alias: " + from.getName() + ". But such element doesn't exist");
- }
- Alias dest = null;
- if (!(toAlias instanceof ComplexAlias)) {
- dest = fromModel.getAliasByAliasId(to.getName());
- }
- SubmodelType type = SubmodelType.UNKNOWN;
- if (from instanceof Protein) {
- type = SubmodelType.DOWNSTREAM_TARGETS;
- } else if (from instanceof Phenotype) {
- type = SubmodelType.PATHWAY;
- }
- AliasSubmodelConnection connection = new AliasSubmodelConnection(toModel, type);
- connection.setFromAlias(source);
- connection.setToAlias(dest);
- connection.setName(toModel.getName());
- source.setSubmodel(connection);
- }
- }
- }
- }
-
- /**
- * This method validates if information about model and submodels in the
- * params are sufficient. If not then apropriate exception will be thrown.
- *
- * @param params
- * parameters to validate
- * @param zipFile
- * original {@link ZipFile}
- * @return name of the file containg mapping between submodels
- */
- protected String validateSubmodelInformation(ComplexZipConverterParams params, ZipFile zipFile) {
- Enumeration<? extends ZipEntry> entries = zipFile.entries();
- Set<String> processed = new HashSet<String>();
-
- String root = null;
- String mapping = null;
- while (entries.hasMoreElements()) {
- ZipEntry entry = entries.nextElement();
- if (!entry.isDirectory()) {
- String name = entry.getName();
- ZipEntryFile zef = params.getEntry(name);
- if (zef == null) {
- throw new InvalidArgumentException("No information found in params about file: " + name);
- }
- if (zef instanceof ModelZipEntryFile) {
- ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
- if (modelEntryFile.isRoot()) {
- if (root != null) {
- throw new InvalidArgumentException("Two roots found: " + name + ", " + root + ". There can be only one.");
- }
- root = name;
- }
- if (modelEntryFile.isMappingFile()) {
- if (mapping != null) {
- throw new InvalidArgumentException("Two mapping files found: " + name + ", " + mapping + ". There can be only one.");
- }
- mapping = name;
- }
- }
- processed.add(name);
- }
- }
- if (root == null) {
- throw new InvalidArgumentException("No root map found.");
- }
- for (String entryName : params.getFilenames()) {
- if (!processed.contains(entryName)) {
- throw new InvalidArgumentException("Entry " + entryName + " doesn't exists in the zip file.");
- }
- }
- return mapping;
- }
-
- /**
- * Transforms {@link DataMiningZipEntryFile} into {@link DataMiningSet}.
- *
- * @param zipFile
- * original {@link ZipFile}
- * @param entry
- * entry in a zip file
- * @param dmEntry
- * {@link DataMiningZipEntryFile} to transform
- * @return {@link DataMiningSet} for a given {@link DataMiningZipEntryFile}
- * @throws IOException
- * thrown when there is a problem with accessing {@link ZipFile}
- */
- protected DataMiningSet dataMiningZipEntryToDataMiningSet(ZipFile zipFile, ZipEntry entry, DataMiningZipEntryFile dmEntry) throws IOException {
- DataMiningSet dmSet = new DataMiningSet();
- dmSet.setName(dmEntry.getName());
- dmSet.setInputData(IOUtils.toByteArray(zipFile.getInputStream(entry)));
- dmSet.setDescription(dmEntry.getDescription());
- dmSet.setSource(dmEntry.getSource());
- dmSet.setType(dmEntry.getType());
- return dmSet;
- }
-
- /**
- * Transforms {@link LayoutZipEntryFile} into {@link Layout}.
- *
- * @param zipFile
- * original {@link ZipFile}
- * @param entry
- * entry in a zip file
- * @param params
- * parameters used to make general conversion (we use directory where
- * layout should be stored)
- * @param layoutEntry
- * {@link LayoutZipEntryFile} to transform
- * @return {@link LAyout} for a given {@link LayoutZipEntryFile}
- * @throws IOException
- * thrown when there is a problem with accessing {@link ZipFile}
- */
- protected Layout layoutZipEntryFileToLayout(ComplexZipConverterParams params, ZipFile zipFile, ZipEntry entry, LayoutZipEntryFile layoutEntry)
- throws IOException {
- Layout layout = new Layout();
- layout.setDescription(layoutEntry.getDescription());
- layout.setDirectory(params.getVisualizationDir() + "/" + layoutEntry.getName().replaceAll(" ", "_"));
- UploadedFileEntry fileEntry = new UploadedFileEntry();
- fileEntry.setFileContent(IOUtils.toByteArray(zipFile.getInputStream(entry)));
- fileEntry.setOriginalFileName(entry.getName());
- layout.setInputData(fileEntry);
- layout.setPublicLayout(true);
- layout.setTitle(layoutEntry.getName());
- return layout;
- }
-
- /**
- * Copy file from zip entry into temporary file.
- *
- * @param zipFile
- * input zip file
- * @param entry
- * entry in the zip file
- * @return {@link File} with a copy of data from zip entry
- * @throws IOException
- * thrown when there is a problem with input or output file
- */
- protected File saveFileFromZipFile(ZipFile zipFile, ZipEntry entry) throws IOException {
- InputStream is = zipFile.getInputStream(entry);
- File result = File.createTempFile("temp-file-name", ".png");
- FileOutputStream fos = new FileOutputStream(result);
- byte[] bytes = new byte[BUFFER_SIZE];
- int length;
- while ((length = is.read(bytes)) >= 0) {
- fos.write(bytes, 0, length);
- }
- fos.close();
- return result;
- }
-
- /**
- * Creates inctance of {@link IConverter} used as a template parameter for
- * this class instatiation.
- *
- * @return inctance of {@link IConverter}
- */
- protected IConverter createConverterInstance() {
- IConverter converter;
- try {
- converter = converterClazz.newInstance();
- } catch (InstantiationException e) {
- throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
- } catch (IllegalAccessException e) {
- throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
- }
- return converter;
- }
-}
+package lcsb.mapviewer.converter;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.lang.reflect.Modifier;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidClassException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.zip.DataMiningZipEntryFile;
+import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
+import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
+import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class allows to create complex {@link Model} that contains submaps. It's
+ * written in generic way and use {@link IConverter} as a class to parse single
+ * submap.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ * class used to create single submap from a file
+ */
+public class ComplexZipConverter<T extends IConverter> {
+
+ /**
+ * Size of the buffer used for accessing single chunk of data from input
+ * stream.
+ */
+ private static final int BUFFER_SIZE = 1024;
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ComplexZipConverter.class);
+ /**
+ * Class used to create single submap from a file.
+ */
+ private Class<T> converterClazz;
+
+ /**
+ * Default constructor. Checks if the class given in the parameter is proper
+ * {@link IConverter} implementation.
+ *
+ * @param clazz
+ * {@link IConverter} class used for creation of the single submap
+ */
+ public ComplexZipConverter(Class<T> clazz) {
+ if (Modifier.isAbstract(clazz.getModifiers())) {
+ throw new InvalidClassException("Param class cannot be abstract");
+ }
+
+ if (Modifier.isInterface(clazz.getModifiers())) {
+ throw new InvalidClassException("Param class cannot be an interface");
+ }
+
+ converterClazz = clazz;
+ }
+
+ /**
+ * Creates complex {@link Model} that contains submaps.
+ *
+ * @param params
+ * {@link ComplexZipConverterParams object} with information about
+ * data from which result is going to be created
+ * @return complex {@link Model} created from input data
+ * @throws InvalidInputDataExecption
+ * thrown when there is a problem with accessing input data
+ */
+ public Model createModel(ComplexZipConverterParams params) throws InvalidInputDataExecption {
+ try {
+ ZipFile zipFile = params.getZipFile();
+ Enumeration<? extends ZipEntry> entries;
+ String mapping = validateSubmodelInformation(params, zipFile);
+
+ IConverter converter = createConverterInstance();
+ Map<String, Model> filenameModelMap = new HashMap<String, Model>();
+ Map<String, Model> nameModelMap = new HashMap<String, Model>();
+
+ entries = zipFile.entries();
+ Model result = null;
+ List<Layout> layouts = new ArrayList<Layout>();
+ List<ImageZipEntryFile> imageEntries = new ArrayList<ImageZipEntryFile>();
+ List<DataMiningSet> dataMiningSets = new ArrayList<DataMiningSet>();
+ while (entries.hasMoreElements()) {
+ ZipEntry entry = entries.nextElement();
+ if (!entry.isDirectory()) {
+ ZipEntryFile zef = params.getEntry(entry.getName());
+ if (zef instanceof ModelZipEntryFile) {
+ ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
+ InputStream is = zipFile.getInputStream(entry);
+ ConverterParams cParams = new ConverterParams();
+ cParams.inputStream(is);
+ Model model = converter.createModel(cParams);
+ model.setName(modelEntryFile.getName());
+ filenameModelMap.put(entry.getName(), model);
+ nameModelMap.put(FilenameUtils.getBaseName(modelEntryFile.getFilename()), model);
+ if (modelEntryFile.isRoot()) {
+ result = model;
+ }
+ } else if (zef instanceof LayoutZipEntryFile) {
+ layouts.add(layoutZipEntryFileToLayout(params, zipFile, entry, (LayoutZipEntryFile) zef));
+ } else if (zef instanceof ImageZipEntryFile) {
+ imageEntries.add((ImageZipEntryFile) zef);
+ } else if (zef instanceof DataMiningZipEntryFile) {
+ dataMiningSets.add(dataMiningZipEntryToDataMiningSet(zipFile, entry, (DataMiningZipEntryFile) zef));
+ } else {
+ throw new NotImplementedException("Unknwon entry type: " + zef.getClass());
+ }
+ }
+ }
+
+ if (imageEntries.size() > 0) {
+ OverviewParser parser = new OverviewParser();
+ result.setOverviewImages(parser.parseOverviewLinks(filenameModelMap, imageEntries, params.getVisualizationDir()));
+ }
+ result.addDataMiningSets(dataMiningSets);
+
+ for (Entry<String, Model> entry : filenameModelMap.entrySet()) {
+ String filename = entry.getKey();
+ Model model = entry.getValue();
+ ZipEntryFile zef = params.getEntry(filename);
+ if (zef instanceof ModelZipEntryFile) {
+ ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
+ if (!modelEntryFile.isRoot() && !modelEntryFile.isMappingFile()) {
+ ModelSubmodelConnection submodel = new ModelSubmodelConnection(model, modelEntryFile.getType());
+ submodel.setName(modelEntryFile.getName());
+ result.addSubmodelConnection(submodel);
+ }
+ }
+ }
+ for (Layout layout : layouts) {
+ Layout topLayout = new Layout(layout);
+ result.addLayout(topLayout);
+ int modelId = 0;
+ topLayout.setDirectory(topLayout.getDirectory() + modelId);
+ modelId++;
+ for (ModelSubmodelConnection connection : result.getSubmodelConnections()) {
+ Layout childLayout = new Layout(layout);
+ // we need to set separate directory names for different submodels
+ childLayout.setDirectory(childLayout.getDirectory() + modelId);
+ modelId++;
+ childLayout.setParentLayout(topLayout);
+ connection.getSubmodel().addLayout(childLayout);
+ }
+ }
+ Model mappingModel = filenameModelMap.get(mapping);
+ if (mappingModel != null) {
+ for (Reaction reaction : mappingModel.getReactions()) {
+ processReaction(mapping, nameModelMap, result, reaction);
+ }
+ }
+ return result;
+ } catch (IOException e) {
+ throw new InvalidArgumentException(e);
+ }
+ }
+
+ /**
+ * Process a single reaction in mapping file (transfomring reaction into
+ * connection between submodels).
+ *
+ * @param mapping
+ * name of the mapping file
+ * @param nameModelMap
+ * mapping between file names and models
+ * @param topModel
+ * top model
+ * @param reaction
+ * reaction to transform into connection
+ */
+ public void processReaction(String mapping, Map<String, Model> nameModelMap, Model topModel, Reaction reaction) {
+ if (reaction.getReactants().size() > 1) {
+ topModel.addCreationWarning(
+ "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains too many reactants. Skipped");
+ } else if (reaction.getProducts().size() > 1) {
+ topModel.addCreationWarning(
+ "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains too many products. Skipped");
+ } else if (reaction.getModifiers().size() > 0) {
+ topModel
+ .addCreationWarning("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains modifiers. Skipped");
+ } else {
+ Alias fromAlias = reaction.getReactants().get(0).getAlias();
+ Element fromElement = fromAlias.getElement();
+ Alias toAlias = reaction.getProducts().get(0).getAlias();
+ Element toElement = toAlias.getElement();
+ if (!(fromAlias instanceof SpeciesAlias)) {
+ topModel.addCreationWarning(
+ "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start in species. Skipped");
+ } else if (!(toAlias instanceof SpeciesAlias)) {
+ topModel.addCreationWarning(
+ "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end in species. Skipped");
+ } else {
+ Species from = (Species) fromElement;
+ ComplexAlias complexFrom = ((SpeciesAlias) fromAlias).getComplexAlias();
+ Species to = (Species) toElement;
+ ComplexAlias complexTo = ((SpeciesAlias) toAlias).getComplexAlias();
+ if (complexFrom == null) {
+ topModel.addCreationWarning(
+ "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start inside complex. Skipped");
+ } else if (complexTo == null && (!(toAlias instanceof ComplexAlias))) {
+ topModel.addCreationWarning(
+ "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end inside complex. Skipped");
+ } else {
+ if (complexTo == null) {
+ complexTo = (ComplexAlias) toAlias;
+ }
+ String fromName = complexFrom.getElement().getName();
+ String toName = complexTo.getElement().getName();
+ Model fromModel = nameModelMap.get(fromName);
+ Model toModel = nameModelMap.get(toName);
+ if (fromModel == null) {
+ throw new InvalidArgumentException("Mapping file references to " + fromName + " submodel. But such model doesn't exist");
+ } else if (toModel == null) {
+ throw new InvalidArgumentException("Mapping file references to " + toName + " submodel. But such model doesn't exist");
+ }
+ Alias source = fromModel.getAliasByAliasId(from.getName());
+ if (source == null) {
+ throw new InvalidArgumentException("Mapping file references to element with alias: " + from.getName() + ". But such element doesn't exist");
+ }
+ Alias dest = null;
+ if (!(toAlias instanceof ComplexAlias)) {
+ dest = fromModel.getAliasByAliasId(to.getName());
+ }
+ SubmodelType type = SubmodelType.UNKNOWN;
+ if (from instanceof Protein) {
+ type = SubmodelType.DOWNSTREAM_TARGETS;
+ } else if (from instanceof Phenotype) {
+ type = SubmodelType.PATHWAY;
+ }
+ AliasSubmodelConnection connection = new AliasSubmodelConnection(toModel, type);
+ connection.setFromAlias(source);
+ connection.setToAlias(dest);
+ connection.setName(toModel.getName());
+ source.setSubmodel(connection);
+ }
+ }
+ }
+ }
+
+ /**
+ * This method validates if information about model and submodels in the
+ * params are sufficient. If not then apropriate exception will be thrown.
+ *
+ * @param params
+ * parameters to validate
+ * @param zipFile
+ * original {@link ZipFile}
+ * @return name of the file containg mapping between submodels
+ */
+ protected String validateSubmodelInformation(ComplexZipConverterParams params, ZipFile zipFile) {
+ Enumeration<? extends ZipEntry> entries = zipFile.entries();
+ Set<String> processed = new HashSet<String>();
+
+ String root = null;
+ String mapping = null;
+ while (entries.hasMoreElements()) {
+ ZipEntry entry = entries.nextElement();
+ if (!entry.isDirectory()) {
+ String name = entry.getName();
+ ZipEntryFile zef = params.getEntry(name);
+ if (zef == null) {
+ throw new InvalidArgumentException("No information found in params about file: " + name);
+ }
+ if (zef instanceof ModelZipEntryFile) {
+ ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
+ if (modelEntryFile.isRoot()) {
+ if (root != null) {
+ throw new InvalidArgumentException("Two roots found: " + name + ", " + root + ". There can be only one.");
+ }
+ root = name;
+ }
+ if (modelEntryFile.isMappingFile()) {
+ if (mapping != null) {
+ throw new InvalidArgumentException("Two mapping files found: " + name + ", " + mapping + ". There can be only one.");
+ }
+ mapping = name;
+ }
+ }
+ processed.add(name);
+ }
+ }
+ if (root == null) {
+ throw new InvalidArgumentException("No root map found.");
+ }
+ for (String entryName : params.getFilenames()) {
+ if (!processed.contains(entryName)) {
+ throw new InvalidArgumentException("Entry " + entryName + " doesn't exists in the zip file.");
+ }
+ }
+ return mapping;
+ }
+
+ /**
+ * Transforms {@link DataMiningZipEntryFile} into {@link DataMiningSet}.
+ *
+ * @param zipFile
+ * original {@link ZipFile}
+ * @param entry
+ * entry in a zip file
+ * @param dmEntry
+ * {@link DataMiningZipEntryFile} to transform
+ * @return {@link DataMiningSet} for a given {@link DataMiningZipEntryFile}
+ * @throws IOException
+ * thrown when there is a problem with accessing {@link ZipFile}
+ */
+ protected DataMiningSet dataMiningZipEntryToDataMiningSet(ZipFile zipFile, ZipEntry entry, DataMiningZipEntryFile dmEntry) throws IOException {
+ DataMiningSet dmSet = new DataMiningSet();
+ dmSet.setName(dmEntry.getName());
+ dmSet.setInputData(IOUtils.toByteArray(zipFile.getInputStream(entry)));
+ dmSet.setDescription(dmEntry.getDescription());
+ dmSet.setSource(dmEntry.getSource());
+ dmSet.setType(dmEntry.getType());
+ return dmSet;
+ }
+
+ /**
+ * Transforms {@link LayoutZipEntryFile} into {@link Layout}.
+ *
+ * @param zipFile
+ * original {@link ZipFile}
+ * @param entry
+ * entry in a zip file
+ * @param params
+ * parameters used to make general conversion (we use directory where
+ * layout should be stored)
+ * @param layoutEntry
+ * {@link LayoutZipEntryFile} to transform
+ * @return {@link LAyout} for a given {@link LayoutZipEntryFile}
+ * @throws IOException
+ * thrown when there is a problem with accessing {@link ZipFile}
+ */
+ protected Layout layoutZipEntryFileToLayout(ComplexZipConverterParams params, ZipFile zipFile, ZipEntry entry, LayoutZipEntryFile layoutEntry)
+ throws IOException {
+ Layout layout = new Layout();
+ layout.setDescription(layoutEntry.getDescription());
+ layout.setDirectory(params.getVisualizationDir() + "/" + layoutEntry.getName().replaceAll(" ", "_"));
+ UploadedFileEntry fileEntry = new UploadedFileEntry();
+ fileEntry.setFileContent(IOUtils.toByteArray(zipFile.getInputStream(entry)));
+ fileEntry.setOriginalFileName(entry.getName());
+ layout.setInputData(fileEntry);
+ layout.setPublicLayout(true);
+ layout.setTitle(layoutEntry.getName());
+ return layout;
+ }
+
+ /**
+ * Copy file from zip entry into temporary file.
+ *
+ * @param zipFile
+ * input zip file
+ * @param entry
+ * entry in the zip file
+ * @return {@link File} with a copy of data from zip entry
+ * @throws IOException
+ * thrown when there is a problem with input or output file
+ */
+ protected File saveFileFromZipFile(ZipFile zipFile, ZipEntry entry) throws IOException {
+ InputStream is = zipFile.getInputStream(entry);
+ File result = File.createTempFile("temp-file-name", ".png");
+ FileOutputStream fos = new FileOutputStream(result);
+ byte[] bytes = new byte[BUFFER_SIZE];
+ int length;
+ while ((length = is.read(bytes)) >= 0) {
+ fos.write(bytes, 0, length);
+ }
+ fos.close();
+ return result;
+ }
+
+ /**
+ * Creates inctance of {@link IConverter} used as a template parameter for
+ * this class instatiation.
+ *
+ * @return inctance of {@link IConverter}
+ */
+ protected IConverter createConverterInstance() {
+ IConverter converter;
+ try {
+ converter = converterClazz.newInstance();
+ } catch (InstantiationException e) {
+ throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
+ } catch (IllegalAccessException e) {
+ throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
+ }
+ return converter;
+ }
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java
index f1e0095ad6ce099c86fbc1ca9f1dc774032a9719..bcc0546a33d55ec779b80d99ae846a4be925ce54 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java
@@ -1,82 +1,82 @@
-package lcsb.mapviewer.converter;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Interface used for reading data from file and putting it into {@link Model}
- * object.
- *
- * @author Piotr Gawron
- *
- */
-public interface IConverter {
-
- /**
- * Parse input source and transformes it into a model object.
- *
- * @param params
- * input params used for reading data
- * @return model obtained from inut source
- * @throws InvalidInputDataExecption
- * thrown when input parameters are invalid
- */
-
- Model createModel(ConverterParams params) throws InvalidInputDataExecption;
-
- /**
- * Export model to {@link InputStream}.
- *
- * @param model
- * model to be exported
- * @return {@link InputStream} with exported data
- * @throws InconsistentModelException
- * thrown when given model is inconsistent and unable to be exported
- * @throws ConverterException
- * thrown when there is unknown problem in a converter
- */
- InputStream exportModelToInputStream(Model model) throws ConverterException, InconsistentModelException;
-
- /**
- * Export model to {@link File}.
- *
- * @param model
- * model to be exported
- * @param filePath
- * exported file path
- * @return {@link File} with exported data
- * @throws InconsistentModelException
- * thrown when given model is inconsistent and unable to be exported
- * @throws ConverterException
- * thrown when there is unknown problem in a converter
- * @throws IOException thrown when there is a problem with writing to file
- */
- File exportModelToFile(Model model, String filePath) throws ConverterException, InconsistentModelException, IOException;
-
- /**
- * Returns a common name of data format used in the converter.
- *
- * @return common name of data format used in the converter
- */
- String getCommonName();
-
- /**
- * Returns {@link MimeType} of the exported data.
- *
- * @return {@link MimeType} of the exported data
- */
- MimeType getMimeType();
-
- /**
- * Returns extension of the exported file.
- *
- * @return extension of the exported file
- */
- String getFileExtension();
-
-}
+package lcsb.mapviewer.converter;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * Interface used for reading data from file and putting it into {@link Model}
+ * object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface IConverter {
+
+ /**
+ * Parse input source and transformes it into a model object.
+ *
+ * @param params
+ * input params used for reading data
+ * @return model obtained from inut source
+ * @throws InvalidInputDataExecption
+ * thrown when input parameters are invalid
+ */
+
+ Model createModel(ConverterParams params) throws InvalidInputDataExecption;
+
+ /**
+ * Export model to {@link InputStream}.
+ *
+ * @param model
+ * model to be exported
+ * @return {@link InputStream} with exported data
+ * @throws InconsistentModelException
+ * thrown when given model is inconsistent and unable to be exported
+ * @throws ConverterException
+ * thrown when there is unknown problem in a converter
+ */
+ InputStream exportModelToInputStream(Model model) throws ConverterException, InconsistentModelException;
+
+ /**
+ * Export model to {@link File}.
+ *
+ * @param model
+ * model to be exported
+ * @param filePath
+ * exported file path
+ * @return {@link File} with exported data
+ * @throws InconsistentModelException
+ * thrown when given model is inconsistent and unable to be exported
+ * @throws ConverterException
+ * thrown when there is unknown problem in a converter
+ * @throws IOException thrown when there is a problem with writing to file
+ */
+ File exportModelToFile(Model model, String filePath) throws ConverterException, InconsistentModelException, IOException;
+
+ /**
+ * Returns a common name of data format used in the converter.
+ *
+ * @return common name of data format used in the converter
+ */
+ String getCommonName();
+
+ /**
+ * Returns {@link MimeType} of the exported data.
+ *
+ * @return {@link MimeType} of the exported data
+ */
+ MimeType getMimeType();
+
+ /**
+ * Returns extension of the exported file.
+ *
+ * @return extension of the exported file
+ */
+ String getFileExtension();
+
+}
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java b/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
index ceed4f3913f03297ba9c6cc1cccfdb54dfa99591..19a555096aca975a490583e4de9cbd11bf6b347b 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
@@ -1,13 +1,13 @@
-package lcsb.mapviewer.converter;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ ComplexZipConverterTest.class, //
- OverviewParserTest.class,//
-})
-public class AllTests {
-
-}
+package lcsb.mapviewer.converter;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ ComplexZipConverterTest.class, //
+ OverviewParserTest.class,//
+})
+public class AllTests {
+
+}
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
index f6a8929e558072bcedd933cae8ac7da1057af16c..9d328c20fbd0dc996eafc9735ab68a0e3ea9afa7 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
@@ -1,610 +1,610 @@
-package lcsb.mapviewer.converter;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Point2D;
-import java.io.File;
-import java.io.InputStream;
-import java.util.Enumeration;
-import java.util.List;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipFile;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewLink;
-import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ComplexZipConverterTest {
- private static Logger logger = Logger.getLogger(ComplexZipConverterTest.class);
-
- private abstract class AbstractConverter implements IConverter {
-
- }
-
- private interface InterfaceConverter extends IConverter {
-
- }
-
- public static class MockConverter implements IConverter {
-
- @Override
- public Model createModel(ConverterParams params) {
- Model result = new ModelFullIndexed(null);
-
- Protein s1 = new GenericProtein();
- s1.setElementId("s1");
- SpeciesAlias sa1 = new SpeciesAlias(s1);
- sa1.setAliasId("sa1");
- result.addAlias(sa1);
- result.addElement(s1);
-
- Protein s2 = new GenericProtein();
- s2.setElementId("s2");
- SpeciesAlias sa2 = new SpeciesAlias(s2);
- sa2.setAliasId("sa2");
- result.addAlias(sa2);
- result.addElement(s2);
-
- Protein s3 = new GenericProtein();
- s3.setElementId("s3");
- SpeciesAlias sa3 = new SpeciesAlias(s3);
- sa3.setAliasId("sa3");
- result.addAlias(sa3);
- result.addElement(s3);
-
- Phenotype s4 = new Phenotype();
- s4.setElementId("s4");
- SpeciesAlias sa4 = new SpeciesAlias(s4);
- sa4.setAliasId("sa4");
- result.addAlias(sa4);
- result.addElement(s4);
-
- ComplexSpecies cs1 = new ComplexSpecies();
- ComplexAlias ca1 = new ComplexAlias(cs1);
- ca1.setAliasId("ca1");
- cs1.setElementId("cs1");
- cs1.setName("main");
- result.addAlias(ca1);
- result.addElement(cs1);
- Protein s5 = new GenericProtein();
- s5.setElementId("s5");
- s5.setName("sa1");
- SpeciesAlias sa5 = new SpeciesAlias(s5);
- sa5.setAliasId("sa5");
- result.addAlias(sa5);
- result.addElement(s5);
- ca1.addAlias(sa5);
- cs1.addElement(s5);
- Phenotype s6 = new Phenotype();
- s6.setElementId("s6");
- s6.setName("sa4");
- SpeciesAlias sa6 = new SpeciesAlias(s6);
- sa6.setAliasId("sa6");
- result.addAlias(sa6);
- result.addElement(s6);
- ca1.addAlias(sa6);
- cs1.addElement(s6);
-
- ComplexSpecies cs2 = new ComplexSpecies();
- ComplexAlias ca2 = new ComplexAlias(cs2);
- ca2.setAliasId("ca2");
- cs2.setElementId("cs2");
- cs2.setName("s1");
- result.addAlias(ca2);
- result.addElement(cs2);
- Protein s7 = new GenericProtein();
- s7.setElementId("s7");
- s7.setName("sa1");
- SpeciesAlias sa7 = new SpeciesAlias(s7);
- sa7.setAliasId("sa7");
- result.addAlias(sa7);
- result.addElement(s7);
- ca2.addAlias(sa7);
- cs2.addElement(s7);
-
- ComplexSpecies cs3 = new ComplexSpecies();
- ComplexAlias ca3 = new ComplexAlias(cs3);
- ca3.setAliasId("ca3");
- cs3.setElementId("cs3");
- cs3.setName("s2");
- result.addAlias(ca3);
- result.addElement(cs3);
-
- ComplexSpecies cs4 = new ComplexSpecies();
- ComplexAlias ca4 = new ComplexAlias(cs4);
- ca4.setAliasId("ca4");
- cs4.setElementId("cs4");
- cs4.setName("s3");
- result.addAlias(ca4);
- result.addElement(cs4);
-
- Reaction r1 = new TransportReaction();
- r1.addReactant(new Reactant(sa5, s5));
- r1.addProduct(new Product(sa7, s7));
- result.addReaction(r1);
-
- Reaction r2 = new TransportReaction();
- r2.addReactant(new Reactant(sa6, s6));
- r2.addProduct(new Product(ca3, cs3));
- result.addReaction(r2);
-
- Reaction r3 = new TransportReaction();
- r3.addReactant(new Reactant(sa7, s7));
- r3.addProduct(new Product(ca4, cs4));
- result.addReaction(r3);
- return result;
- }
-
- @Override
- public InputStream exportModelToInputStream(Model model) throws InconsistentModelException {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public File exportModelToFile(Model model, String filePath) throws InconsistentModelException {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public String getCommonName() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public MimeType getMimeType() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public String getFileExtension() {
- // TODO Auto-generated method stub
- return null;
- }
-
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() throws Exception {
- try {
- try {
- new ComplexZipConverter<AbstractConverter>(AbstractConverter.class);
- fail("Exception expected");
- } catch (InvalidClassException e) {
-
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testConstructor2() throws Exception {
- try {
- try {
- new ComplexZipConverter<InterfaceConverter>(InterfaceConverter.class);
- fail("Exception expected");
- } catch (InvalidClassException e) {
-
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testConstructor3() throws Exception {
- try {
- new ComplexZipConverter<MockConverter>(MockConverter.class);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testParamsOk() throws Exception {
- try {
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- Model model = converter.createModel(params);
- assertNotNull(model);
- assertEquals("main", model.getName());
- assertEquals(3, model.getSubmodelConnections().size());
-
- Model s1Model = null;
- Model s2Model = null;
- Model s3Model = null;
-
- for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
- if (submodel.getName().equals("s1")) {
- s1Model = submodel.getSubmodel().getModel();
- }
- if (submodel.getName().equals("s2")) {
- s2Model = submodel.getSubmodel().getModel();
- }
- if (submodel.getName().equals("s3")) {
- s3Model = submodel.getSubmodel().getModel();
- }
- }
- assertNotNull(s1Model);
- assertNotNull(s2Model);
- assertNotNull(s3Model);
-
- Alias al1 = model.getAliasByAliasId("sa1");
- assertNotNull(al1.getSubmodel());
- assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
- assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
-
- Alias al2 = model.getAliasByAliasId("sa2");
- assertNull(al2.getSubmodel());
-
- Alias al4 = model.getAliasByAliasId("sa4");
- assertNotNull(al4.getSubmodel());
- assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
- assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
-
- Alias s1_al1 = s1Model.getAliasByAliasId("sa1");
- assertNotNull(s1_al1.getSubmodel());
- assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
- assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testChangeModelZipEntry() throws Exception {
- try {
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s12", false, false, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- Model model = converter.createModel(params);
- assertNotNull(model);
- assertEquals("main", model.getName());
- assertEquals(3, model.getSubmodelConnections().size());
-
- Model s1Model = null;
- Model s2Model = null;
- Model s3Model = null;
-
- for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
- if (submodel.getName().equals("s12")) {
- s1Model = submodel.getSubmodel().getModel();
- }
- if (submodel.getName().equals("s2")) {
- s2Model = submodel.getSubmodel().getModel();
- }
- if (submodel.getName().equals("s3")) {
- s3Model = submodel.getSubmodel().getModel();
- }
- }
- assertNotNull(s1Model);
- assertNotNull(s2Model);
- assertNotNull(s3Model);
-
- Alias al1 = model.getAliasByAliasId("sa1");
- assertNotNull(al1.getSubmodel());
- assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
- assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
-
- Alias al2 = model.getAliasByAliasId("sa2");
- assertNull(al2.getSubmodel());
-
- Alias al4 = model.getAliasByAliasId("sa4");
- assertNotNull(al4.getSubmodel());
- assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
- assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
-
- Alias s1_al1 = s1Model.getAliasByAliasId("sa1");
- assertNotNull(s1_al1.getSubmodel());
- assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
- assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testParamsMissing() throws Exception {
- try {
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- try {
- converter.createModel(params);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testParamsInvalid1() throws Exception {
- try {
- // two mains
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s1", true, false, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- try {
- converter.createModel(params);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testParamsInvalid2() throws Exception {
- try {
- // zero mains
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", false, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- try {
- converter.createModel(params);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testParamsInvalid3() throws Exception {
- try {
- // two mappings
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s1", false, true, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- try {
- converter.createModel(params);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testParamsMissingMapping() throws Exception {
- try {
- // zero mappings (should be ok)
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
- Model model = converter.createModel(params);
-
- assertNotNull(model);
-
- assertEquals(4, model.getSubmodelConnections().size());
-
- for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
- if (submodel.getName().equals("s1")) {
- assertEquals(SubmodelType.DOWNSTREAM_TARGETS, submodel.getType());
- } else if (submodel.getName().equals("s2")) {
- assertEquals(SubmodelType.PATHWAY, submodel.getType());
- } else if (submodel.getName().equals("s3")) {
- assertEquals(SubmodelType.UNKNOWN, submodel.getType());
- } else if (submodel.getName().equals("mapping")) {
- assertEquals(SubmodelType.UNKNOWN, submodel.getType());
- }
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testTooManyParams() throws Exception {
- try {
- // zero mappings (should be ok)
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
- params.entry(new ModelZipEntryFile("blabla.xml", "s3", false, false, SubmodelType.UNKNOWN));
- try {
- converter.createModel(params);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidMappingFile() throws Exception {
- try {
- // zero mappings (should be ok)
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/invalid_mapping.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- try {
- Model model = converter.createModel(params);
- for (String string : model.getCreationWarnings()) {
- logger.debug(string);
- }
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testOverviewImageLink() throws Exception {
- try {
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
- ZipFile zipFile = new ZipFile("testFiles/complex_model_with_img.zip");
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(zipFile);
-
- ZipEntryFileFactory factory = new ZipEntryFileFactory();
- Enumeration<? extends ZipEntry> entries = zipFile.entries();
- while (entries.hasMoreElements()) {
- ZipEntry entry = entries.nextElement();
- if (!entry.isDirectory()) {
- params.entry(factory.createZipEntryFile(entry, zipFile));
- }
- }
-
- Model model = converter.createModel(params);
- assertNotNull(model);
- assertEquals("main", model.getName());
-
- List<OverviewImage> result = model.getOverviewImages();
-
- assertNotNull(result);
- assertEquals(1, result.size());
-
- OverviewImage img = result.get(0);
-
- assertEquals("test.png", img.getFilename());
- assertEquals((Integer) 639, img.getHeight());
- assertEquals((Integer) 963, img.getWidth());
- assertEquals(2, img.getLinks().size());
-
- OverviewLink link = img.getLinks().get(0);
- List<Point2D> polygon = link.getPolygonCoordinates();
- assertEquals(4, polygon.size());
-
- assertTrue(link instanceof OverviewModelLink);
-
- OverviewModelLink mLink = (OverviewModelLink) link;
- assertEquals((Integer) 10, mLink.getxCoord());
- assertEquals((Integer) 10, mLink.getyCoord());
- assertEquals((Integer) 3, mLink.getZoomLevel());
- assertEquals(model, mLink.getLinkedModel());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
-}
+package lcsb.mapviewer.converter;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+import java.io.File;
+import java.io.InputStream;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidClassException;
+import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.OverviewLink;
+import lcsb.mapviewer.model.map.OverviewModelLink;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.ComplexSpecies;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ComplexZipConverterTest {
+ private static Logger logger = Logger.getLogger(ComplexZipConverterTest.class);
+
+ private abstract class AbstractConverter implements IConverter {
+
+ }
+
+ private interface InterfaceConverter extends IConverter {
+
+ }
+
+ public static class MockConverter implements IConverter {
+
+ @Override
+ public Model createModel(ConverterParams params) {
+ Model result = new ModelFullIndexed(null);
+
+ Protein s1 = new GenericProtein();
+ s1.setElementId("s1");
+ SpeciesAlias sa1 = new SpeciesAlias(s1);
+ sa1.setAliasId("sa1");
+ result.addAlias(sa1);
+ result.addElement(s1);
+
+ Protein s2 = new GenericProtein();
+ s2.setElementId("s2");
+ SpeciesAlias sa2 = new SpeciesAlias(s2);
+ sa2.setAliasId("sa2");
+ result.addAlias(sa2);
+ result.addElement(s2);
+
+ Protein s3 = new GenericProtein();
+ s3.setElementId("s3");
+ SpeciesAlias sa3 = new SpeciesAlias(s3);
+ sa3.setAliasId("sa3");
+ result.addAlias(sa3);
+ result.addElement(s3);
+
+ Phenotype s4 = new Phenotype();
+ s4.setElementId("s4");
+ SpeciesAlias sa4 = new SpeciesAlias(s4);
+ sa4.setAliasId("sa4");
+ result.addAlias(sa4);
+ result.addElement(s4);
+
+ ComplexSpecies cs1 = new ComplexSpecies();
+ ComplexAlias ca1 = new ComplexAlias(cs1);
+ ca1.setAliasId("ca1");
+ cs1.setElementId("cs1");
+ cs1.setName("main");
+ result.addAlias(ca1);
+ result.addElement(cs1);
+ Protein s5 = new GenericProtein();
+ s5.setElementId("s5");
+ s5.setName("sa1");
+ SpeciesAlias sa5 = new SpeciesAlias(s5);
+ sa5.setAliasId("sa5");
+ result.addAlias(sa5);
+ result.addElement(s5);
+ ca1.addAlias(sa5);
+ cs1.addElement(s5);
+ Phenotype s6 = new Phenotype();
+ s6.setElementId("s6");
+ s6.setName("sa4");
+ SpeciesAlias sa6 = new SpeciesAlias(s6);
+ sa6.setAliasId("sa6");
+ result.addAlias(sa6);
+ result.addElement(s6);
+ ca1.addAlias(sa6);
+ cs1.addElement(s6);
+
+ ComplexSpecies cs2 = new ComplexSpecies();
+ ComplexAlias ca2 = new ComplexAlias(cs2);
+ ca2.setAliasId("ca2");
+ cs2.setElementId("cs2");
+ cs2.setName("s1");
+ result.addAlias(ca2);
+ result.addElement(cs2);
+ Protein s7 = new GenericProtein();
+ s7.setElementId("s7");
+ s7.setName("sa1");
+ SpeciesAlias sa7 = new SpeciesAlias(s7);
+ sa7.setAliasId("sa7");
+ result.addAlias(sa7);
+ result.addElement(s7);
+ ca2.addAlias(sa7);
+ cs2.addElement(s7);
+
+ ComplexSpecies cs3 = new ComplexSpecies();
+ ComplexAlias ca3 = new ComplexAlias(cs3);
+ ca3.setAliasId("ca3");
+ cs3.setElementId("cs3");
+ cs3.setName("s2");
+ result.addAlias(ca3);
+ result.addElement(cs3);
+
+ ComplexSpecies cs4 = new ComplexSpecies();
+ ComplexAlias ca4 = new ComplexAlias(cs4);
+ ca4.setAliasId("ca4");
+ cs4.setElementId("cs4");
+ cs4.setName("s3");
+ result.addAlias(ca4);
+ result.addElement(cs4);
+
+ Reaction r1 = new TransportReaction();
+ r1.addReactant(new Reactant(sa5, s5));
+ r1.addProduct(new Product(sa7, s7));
+ result.addReaction(r1);
+
+ Reaction r2 = new TransportReaction();
+ r2.addReactant(new Reactant(sa6, s6));
+ r2.addProduct(new Product(ca3, cs3));
+ result.addReaction(r2);
+
+ Reaction r3 = new TransportReaction();
+ r3.addReactant(new Reactant(sa7, s7));
+ r3.addProduct(new Product(ca4, cs4));
+ result.addReaction(r3);
+ return result;
+ }
+
+ @Override
+ public InputStream exportModelToInputStream(Model model) throws InconsistentModelException {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public File exportModelToFile(Model model, String filePath) throws InconsistentModelException {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getCommonName() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public MimeType getMimeType() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getFileExtension() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() throws Exception {
+ try {
+ try {
+ new ComplexZipConverter<AbstractConverter>(AbstractConverter.class);
+ fail("Exception expected");
+ } catch (InvalidClassException e) {
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testConstructor2() throws Exception {
+ try {
+ try {
+ new ComplexZipConverter<InterfaceConverter>(InterfaceConverter.class);
+ fail("Exception expected");
+ } catch (InvalidClassException e) {
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testConstructor3() throws Exception {
+ try {
+ new ComplexZipConverter<MockConverter>(MockConverter.class);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testParamsOk() throws Exception {
+ try {
+ ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+ Model model = converter.createModel(params);
+ assertNotNull(model);
+ assertEquals("main", model.getName());
+ assertEquals(3, model.getSubmodelConnections().size());
+
+ Model s1Model = null;
+ Model s2Model = null;
+ Model s3Model = null;
+
+ for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
+ if (submodel.getName().equals("s1")) {
+ s1Model = submodel.getSubmodel().getModel();
+ }
+ if (submodel.getName().equals("s2")) {
+ s2Model = submodel.getSubmodel().getModel();
+ }
+ if (submodel.getName().equals("s3")) {
+ s3Model = submodel.getSubmodel().getModel();
+ }
+ }
+ assertNotNull(s1Model);
+ assertNotNull(s2Model);
+ assertNotNull(s3Model);
+
+ Alias al1 = model.getAliasByAliasId("sa1");
+ assertNotNull(al1.getSubmodel());
+ assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
+ assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
+
+ Alias al2 = model.getAliasByAliasId("sa2");
+ assertNull(al2.getSubmodel());
+
+ Alias al4 = model.getAliasByAliasId("sa4");
+ assertNotNull(al4.getSubmodel());
+ assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
+ assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
+
+ Alias s1_al1 = s1Model.getAliasByAliasId("sa1");
+ assertNotNull(s1_al1.getSubmodel());
+ assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
+ assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testChangeModelZipEntry() throws Exception {
+ try {
+ ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s12", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+ Model model = converter.createModel(params);
+ assertNotNull(model);
+ assertEquals("main", model.getName());
+ assertEquals(3, model.getSubmodelConnections().size());
+
+ Model s1Model = null;
+ Model s2Model = null;
+ Model s3Model = null;
+
+ for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
+ if (submodel.getName().equals("s12")) {
+ s1Model = submodel.getSubmodel().getModel();
+ }
+ if (submodel.getName().equals("s2")) {
+ s2Model = submodel.getSubmodel().getModel();
+ }
+ if (submodel.getName().equals("s3")) {
+ s3Model = submodel.getSubmodel().getModel();
+ }
+ }
+ assertNotNull(s1Model);
+ assertNotNull(s2Model);
+ assertNotNull(s3Model);
+
+ Alias al1 = model.getAliasByAliasId("sa1");
+ assertNotNull(al1.getSubmodel());
+ assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
+ assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
+
+ Alias al2 = model.getAliasByAliasId("sa2");
+ assertNull(al2.getSubmodel());
+
+ Alias al4 = model.getAliasByAliasId("sa4");
+ assertNotNull(al4.getSubmodel());
+ assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
+ assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
+
+ Alias s1_al1 = s1Model.getAliasByAliasId("sa1");
+ assertNotNull(s1_al1.getSubmodel());
+ assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
+ assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testParamsMissing() throws Exception {
+ try {
+ ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+ try {
+ converter.createModel(params);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testParamsInvalid1() throws Exception {
+ try {
+ // two mains
+ ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s1", true, false, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+ try {
+ converter.createModel(params);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testParamsInvalid2() throws Exception {
+ try {
+ // zero mains
+ ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", false, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+ try {
+ converter.createModel(params);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testParamsInvalid3() throws Exception {
+ try {
+ // two mappings
+ ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s1", false, true, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+ try {
+ converter.createModel(params);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testParamsMissingMapping() throws Exception {
+ try {
+ // zero mappings (should be ok)
+ ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
+ Model model = converter.createModel(params);
+
+ assertNotNull(model);
+
+ assertEquals(4, model.getSubmodelConnections().size());
+
+ for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
+ if (submodel.getName().equals("s1")) {
+ assertEquals(SubmodelType.DOWNSTREAM_TARGETS, submodel.getType());
+ } else if (submodel.getName().equals("s2")) {
+ assertEquals(SubmodelType.PATHWAY, submodel.getType());
+ } else if (submodel.getName().equals("s3")) {
+ assertEquals(SubmodelType.UNKNOWN, submodel.getType());
+ } else if (submodel.getName().equals("mapping")) {
+ assertEquals(SubmodelType.UNKNOWN, submodel.getType());
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testTooManyParams() throws Exception {
+ try {
+ // zero mappings (should be ok)
+ ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
+ params.entry(new ModelZipEntryFile("blabla.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ try {
+ converter.createModel(params);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidMappingFile() throws Exception {
+ try {
+ // zero mappings (should be ok)
+ ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/invalid_mapping.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+ try {
+ Model model = converter.createModel(params);
+ for (String string : model.getCreationWarnings()) {
+ logger.debug(string);
+ }
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testOverviewImageLink() throws Exception {
+ try {
+ ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ZipFile zipFile = new ZipFile("testFiles/complex_model_with_img.zip");
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(zipFile);
+
+ ZipEntryFileFactory factory = new ZipEntryFileFactory();
+ Enumeration<? extends ZipEntry> entries = zipFile.entries();
+ while (entries.hasMoreElements()) {
+ ZipEntry entry = entries.nextElement();
+ if (!entry.isDirectory()) {
+ params.entry(factory.createZipEntryFile(entry, zipFile));
+ }
+ }
+
+ Model model = converter.createModel(params);
+ assertNotNull(model);
+ assertEquals("main", model.getName());
+
+ List<OverviewImage> result = model.getOverviewImages();
+
+ assertNotNull(result);
+ assertEquals(1, result.size());
+
+ OverviewImage img = result.get(0);
+
+ assertEquals("test.png", img.getFilename());
+ assertEquals((Integer) 639, img.getHeight());
+ assertEquals((Integer) 963, img.getWidth());
+ assertEquals(2, img.getLinks().size());
+
+ OverviewLink link = img.getLinks().get(0);
+ List<Point2D> polygon = link.getPolygonCoordinates();
+ assertEquals(4, polygon.size());
+
+ assertTrue(link instanceof OverviewModelLink);
+
+ OverviewModelLink mLink = (OverviewModelLink) link;
+ assertEquals((Integer) 10, mLink.getxCoord());
+ assertEquals((Integer) 10, mLink.getyCoord());
+ assertEquals((Integer) 3, mLink.getZoomLevel());
+ assertEquals(model, mLink.getLinkedModel());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+}
diff --git a/converter/tmp/test.png b/converter/tmp/test.png
new file mode 100644
index 0000000000000000000000000000000000000000..adbe702689a43364dc6f0a6cebedcc9277388a9c
Binary files /dev/null and b/converter/tmp/test.png differ
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
index adbf07b637721f47fd1f635597c851522f5af768..73e2aa0ff7437d3171b7b1eddeb2cc83f321c88c 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -1,356 +1,356 @@
-package lcsb.mapviewer.commands;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.ArrowTypeData;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This {@link ModelCommand} colors a model (nodes and reactions) according to
- * set of {@link ColorSchema rules}.
- *
- * @author Piotr Gawron
- *
- */
-public class ColorModelCommand extends ModelCommand {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ColorModelCommand.class);
-
- /**
- * Set of color schemas used in this command to color model.
- */
- private Collection<ColorSchema> schemas;
-
- /**
- * Default constructor.
- *
- * @param model
- * original model
- * @param schemas
- * set of color schemas used in this command to color model.
- */
- public ColorModelCommand(Model model, Collection<ColorSchema> schemas) {
- super(model);
- this.schemas = schemas;
- }
-
- /**
- * Applies color schema into the reaction.
- *
- * @param reaction
- * object to be colored
- * @param schema
- * color schema to be used
- * @throws InvalidColorSchemaException
- * thrown when alias was already colored by other schema
- */
- private void applyColor(Reaction reaction, ColorSchema schema) throws InvalidColorSchemaException {
- if (!reaction.getReactants().get(0).getLine().getColor().equals(Color.BLACK)) {
- throw new InvalidColorSchemaException("At least two rows try to set color to reaction: " + reaction.getIdReaction());
- }
-
- Color color = schema.getNormalizedColor();
- for (AbstractNode node : reaction.getNodes()) {
- node.getLine().setColor(color);
- if (schema.getLineWidth() != null) {
- node.getLine().setWidth(schema.getLineWidth());
- }
- }
- if (schema.getReverseReaction() != null && schema.getReverseReaction()) {
- ArrowTypeData atdBegining = reaction.getReactants().get(0).getLine().getBeginAtd();
- ArrowTypeData atdEnd = reaction.getProducts().get(0).getLine().getEndAtd();
- for (Reactant reactant : reaction.getReactants()) {
- reactant.getLine().setBeginAtd(atdEnd);
- }
- for (Product product : reaction.getProducts()) {
- product.getLine().setEndAtd(atdBegining);
- }
- }
- }
-
- /**
- * Checks if the coloring schema should be used for the reaction.
- *
- * @param reaction
- * reaction to which coloring schema is checked
- * @param schema
- * coloring schema
- * @return <code>true</code> if coloring schema should be used for alias,
- * <code>false</code> otherwise
- */
- private boolean match(Reaction reaction, ColorSchema schema) {
- if (schema.getName() != null) {
- return false;
- }
-
- if (schema.getReactionIdentifier() != null && schema.getReactionIdentifier().equalsIgnoreCase(reaction.getIdReaction())) {
- return true;
- }
- if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
- MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
-
- if (reaction.getMiriamData().contains(md)) {
- return true;
- }
- }
- for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
- if (pair.getRight() != null && !pair.getRight().equals("")) {
-
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, pair.getLeft(), pair.getRight());
- if (reaction.getMiriamData().contains(md)) {
- return true;
- }
- }
- }
-
- return false;
- }
-
- /**
- * Applies color schema into the alias.
- *
- * @param alias
- * object to be colored
- * @param schema
- * color schema to be used
- * @throws InvalidColorSchemaException
- * thrown when alias was already colored by other schema
- */
- private void applyColor(Alias alias, ColorSchema schema) throws InvalidColorSchemaException {
- if (alias instanceof SpeciesAlias) {
- Species species = ((SpeciesAlias) alias).getSpecies();
-
- if (!alias.getColor().equals(Color.WHITE)) {
- throw new InvalidColorSchemaException("At least two rows try to set color to element: " + species.getName());
- }
-
- alias.setColor(schema.getNormalizedColor());
- }
-
- }
-
- /**
- * Checks if the coloring schema should be used for the alias.
- *
- * @param alias
- * alias to which coloring schema is checked
- * @param schema
- * coloring schema
- * @return <code>true</code> if coloring schema should be used for alias,
- * <code>false</code> otherwise
- */
- protected boolean match(Alias alias, ColorSchema schema) {
- if (alias instanceof SpeciesAlias) {
- Species species = ((SpeciesAlias) alias).getSpecies();
- if (schema.getName() != null) {
- if (!species.getName().equalsIgnoreCase(schema.getName())) {
- return false;
- }
- }
- if (schema.getTypes().size() > 0) {
- if (!schema.getTypes().contains(species.getClass())) {
- return false;
- }
- }
- if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
- MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
-
- if (!species.getMiriamData().contains(md)) {
- return false;
- }
- }
- for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
- if (pair.getRight() != null && !pair.getRight().equals("")) {
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, pair.getLeft(), pair.getRight());
- if (!species.getMiriamData().contains(md)) {
- return false;
- }
- }
- }
-
- if (schema.getCompartments().size() > 0) {
- boolean found = false;
- for (CompartmentAlias cAlias : alias.getModelData().getModel().getCompartmentsAliases()) {
- for (String compartmentName : schema.getCompartments()) {
- if (cAlias.getCompartment() != null) {
- if (cAlias.getCompartment().getName().equalsIgnoreCase(compartmentName)) {
- if (cAlias.cross(alias)) {
- found = true;
- }
- }
- }
- }
- }
- if (!found) {
- return false;
- }
- }
-
- // if we have reaction id to match then reject
- if (schema.getReactionIdentifier() != null) {
- return false;
- }
- return true;
- } else {
- return false;
- }
- }
-
- /**
- * Checks which coloring schemas weren't used in the model coloring process.
- *
- * @return list of schemas that weren't used during coloring
- */
- public Collection<ColorSchema> getMissingSchema() {
- List<ColorSchema> result = new ArrayList<ColorSchema>();
- for (ColorSchema schema : schemas) {
- boolean found = false;
- for (Alias alias : getModel().getAliases()) {
- if (match(alias, schema)) {
- found = true;
- }
- }
- for (Reaction reaction : getModel().getReactions()) {
- if (match(reaction, schema)) {
- found = true;
- }
- }
- if (!found) {
- result.add(schema);
- }
- }
- return result;
- }
-
- /**
- * Returns list of elements ({@link Reaction reactions} and {@link Alias
- * aliases}) that are modified by the coloring command.
- *
- * @return {@link Map}, where key corresponds to modified {@link Reaction} or
- * {@link Alias} and value is a {@link ColorSchema} that should be
- * used for coloring
- * @throws InvalidColorSchemaException
- * thrown when more than one {@link ColorSchema} match an element
- */
- public Map<Object, ColorSchema> getModifiedElements() throws InvalidColorSchemaException {
- Map<Object, ColorSchema> result = new HashMap<>();
-
- List<Model> models = new ArrayList<>();
- models.add(getModel());
- models.addAll(getModel().getSubmodels());
- for (Model model2 : models) {
- for (ColorSchema schema : schemas) {
- for (Alias alias : model2.getAliases()) {
- if (match(alias, schema)) {
- if (result.get(alias) != null && !result.get(alias).getNormalizedColor().equals(Color.WHITE)) {
- throw new InvalidColorSchemaException("Alias " + alias.getAliasId() + " is colored by more than one rule.");
- }
- result.put(alias, schema);
- }
- }
- for (Reaction reaction : model2.getReactions()) {
- if (match(reaction, schema)) {
- if (result.get(reaction) != null && !result.get(reaction).getNormalizedColor().equals(Color.WHITE)) {
- throw new InvalidColorSchemaException("Reaction " + reaction.getIdReaction() + " is colored by more than one rule.");
- }
- result.put(reaction, schema);
- }
- }
- }
- }
- return result;
- }
-
- @Override
- protected void undoImplementation() throws CommandExecutionException {
- throw new NotImplementedException();
-
- }
-
- @Override
- protected void redoImplementation() throws CommandExecutionException {
- throw new NotImplementedException();
- }
-
- /**
- * Colors parameter model using coloring for this command. This method is used
- * internally to color either top {@link Model} or one of it's sumbodels.
- *
- * @param result
- * model to color
- * @param top
- * is the model a top (parent) model
- * @throws InvalidColorSchemaException
- * thrown when set of {@link ColorSchema} is invalid
- */
- private void colorModel(Model result, boolean top) throws InvalidColorSchemaException {
-
- for (Alias alias : result.getAliases()) {
- alias.setColor(Color.WHITE);
- }
- for (Reaction reaction : result.getReactions()) {
- for (AbstractNode node : reaction.getNodes()) {
- node.getLine().setColor(Color.BLACK);
- }
- }
-
- for (ColorSchema schema : schemas) {
- for (Alias alias : result.getAliases()) {
- if (match(alias, schema)) {
- schema.setMatches(schema.getMatches() + 1);
- applyColor(alias, schema);
- }
- }
- for (Reaction reaction : result.getReactions()) {
- if (match(reaction, schema)) {
- schema.setMatches(schema.getMatches() + 1);
- applyColor(reaction, schema);
- }
- }
- }
-
- if (top) {
- for (ModelSubmodelConnection connection : result.getSubmodelConnections()) {
- colorModel(connection.getSubmodel().getModel(), false);
- }
- }
-
- }
-
- @Override
- protected void executeImplementation() throws CommandExecutionException {
- try {
- colorModel(getModel(), true);
- } catch (InvalidColorSchemaException e) {
- throw new CommandExecutionException(e);
- }
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.ArrowTypeData;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This {@link ModelCommand} colors a model (nodes and reactions) according to
+ * set of {@link ColorSchema rules}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ColorModelCommand extends ModelCommand {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ColorModelCommand.class);
+
+ /**
+ * Set of color schemas used in this command to color model.
+ */
+ private Collection<ColorSchema> schemas;
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * original model
+ * @param schemas
+ * set of color schemas used in this command to color model.
+ */
+ public ColorModelCommand(Model model, Collection<ColorSchema> schemas) {
+ super(model);
+ this.schemas = schemas;
+ }
+
+ /**
+ * Applies color schema into the reaction.
+ *
+ * @param reaction
+ * object to be colored
+ * @param schema
+ * color schema to be used
+ * @throws InvalidColorSchemaException
+ * thrown when alias was already colored by other schema
+ */
+ private void applyColor(Reaction reaction, ColorSchema schema) throws InvalidColorSchemaException {
+ if (!reaction.getReactants().get(0).getLine().getColor().equals(Color.BLACK)) {
+ throw new InvalidColorSchemaException("At least two rows try to set color to reaction: " + reaction.getIdReaction());
+ }
+
+ Color color = schema.getNormalizedColor();
+ for (AbstractNode node : reaction.getNodes()) {
+ node.getLine().setColor(color);
+ if (schema.getLineWidth() != null) {
+ node.getLine().setWidth(schema.getLineWidth());
+ }
+ }
+ if (schema.getReverseReaction() != null && schema.getReverseReaction()) {
+ ArrowTypeData atdBegining = reaction.getReactants().get(0).getLine().getBeginAtd();
+ ArrowTypeData atdEnd = reaction.getProducts().get(0).getLine().getEndAtd();
+ for (Reactant reactant : reaction.getReactants()) {
+ reactant.getLine().setBeginAtd(atdEnd);
+ }
+ for (Product product : reaction.getProducts()) {
+ product.getLine().setEndAtd(atdBegining);
+ }
+ }
+ }
+
+ /**
+ * Checks if the coloring schema should be used for the reaction.
+ *
+ * @param reaction
+ * reaction to which coloring schema is checked
+ * @param schema
+ * coloring schema
+ * @return <code>true</code> if coloring schema should be used for alias,
+ * <code>false</code> otherwise
+ */
+ private boolean match(Reaction reaction, ColorSchema schema) {
+ if (schema.getName() != null) {
+ return false;
+ }
+
+ if (schema.getReactionIdentifier() != null && schema.getReactionIdentifier().equalsIgnoreCase(reaction.getIdReaction())) {
+ return true;
+ }
+ if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
+ MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
+
+ if (reaction.getMiriamData().contains(md)) {
+ return true;
+ }
+ }
+ for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
+ if (pair.getRight() != null && !pair.getRight().equals("")) {
+
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, pair.getLeft(), pair.getRight());
+ if (reaction.getMiriamData().contains(md)) {
+ return true;
+ }
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * Applies color schema into the alias.
+ *
+ * @param alias
+ * object to be colored
+ * @param schema
+ * color schema to be used
+ * @throws InvalidColorSchemaException
+ * thrown when alias was already colored by other schema
+ */
+ private void applyColor(Alias alias, ColorSchema schema) throws InvalidColorSchemaException {
+ if (alias instanceof SpeciesAlias) {
+ Species species = ((SpeciesAlias) alias).getSpecies();
+
+ if (!alias.getColor().equals(Color.WHITE)) {
+ throw new InvalidColorSchemaException("At least two rows try to set color to element: " + species.getName());
+ }
+
+ alias.setColor(schema.getNormalizedColor());
+ }
+
+ }
+
+ /**
+ * Checks if the coloring schema should be used for the alias.
+ *
+ * @param alias
+ * alias to which coloring schema is checked
+ * @param schema
+ * coloring schema
+ * @return <code>true</code> if coloring schema should be used for alias,
+ * <code>false</code> otherwise
+ */
+ protected boolean match(Alias alias, ColorSchema schema) {
+ if (alias instanceof SpeciesAlias) {
+ Species species = ((SpeciesAlias) alias).getSpecies();
+ if (schema.getName() != null) {
+ if (!species.getName().equalsIgnoreCase(schema.getName())) {
+ return false;
+ }
+ }
+ if (schema.getTypes().size() > 0) {
+ if (!schema.getTypes().contains(species.getClass())) {
+ return false;
+ }
+ }
+ if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
+ MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
+
+ if (!species.getMiriamData().contains(md)) {
+ return false;
+ }
+ }
+ for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
+ if (pair.getRight() != null && !pair.getRight().equals("")) {
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, pair.getLeft(), pair.getRight());
+ if (!species.getMiriamData().contains(md)) {
+ return false;
+ }
+ }
+ }
+
+ if (schema.getCompartments().size() > 0) {
+ boolean found = false;
+ for (CompartmentAlias cAlias : alias.getModelData().getModel().getCompartmentsAliases()) {
+ for (String compartmentName : schema.getCompartments()) {
+ if (cAlias.getCompartment() != null) {
+ if (cAlias.getCompartment().getName().equalsIgnoreCase(compartmentName)) {
+ if (cAlias.cross(alias)) {
+ found = true;
+ }
+ }
+ }
+ }
+ }
+ if (!found) {
+ return false;
+ }
+ }
+
+ // if we have reaction id to match then reject
+ if (schema.getReactionIdentifier() != null) {
+ return false;
+ }
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * Checks which coloring schemas weren't used in the model coloring process.
+ *
+ * @return list of schemas that weren't used during coloring
+ */
+ public Collection<ColorSchema> getMissingSchema() {
+ List<ColorSchema> result = new ArrayList<ColorSchema>();
+ for (ColorSchema schema : schemas) {
+ boolean found = false;
+ for (Alias alias : getModel().getAliases()) {
+ if (match(alias, schema)) {
+ found = true;
+ }
+ }
+ for (Reaction reaction : getModel().getReactions()) {
+ if (match(reaction, schema)) {
+ found = true;
+ }
+ }
+ if (!found) {
+ result.add(schema);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns list of elements ({@link Reaction reactions} and {@link Alias
+ * aliases}) that are modified by the coloring command.
+ *
+ * @return {@link Map}, where key corresponds to modified {@link Reaction} or
+ * {@link Alias} and value is a {@link ColorSchema} that should be
+ * used for coloring
+ * @throws InvalidColorSchemaException
+ * thrown when more than one {@link ColorSchema} match an element
+ */
+ public Map<Object, ColorSchema> getModifiedElements() throws InvalidColorSchemaException {
+ Map<Object, ColorSchema> result = new HashMap<>();
+
+ List<Model> models = new ArrayList<>();
+ models.add(getModel());
+ models.addAll(getModel().getSubmodels());
+ for (Model model2 : models) {
+ for (ColorSchema schema : schemas) {
+ for (Alias alias : model2.getAliases()) {
+ if (match(alias, schema)) {
+ if (result.get(alias) != null && !result.get(alias).getNormalizedColor().equals(Color.WHITE)) {
+ throw new InvalidColorSchemaException("Alias " + alias.getAliasId() + " is colored by more than one rule.");
+ }
+ result.put(alias, schema);
+ }
+ }
+ for (Reaction reaction : model2.getReactions()) {
+ if (match(reaction, schema)) {
+ if (result.get(reaction) != null && !result.get(reaction).getNormalizedColor().equals(Color.WHITE)) {
+ throw new InvalidColorSchemaException("Reaction " + reaction.getIdReaction() + " is colored by more than one rule.");
+ }
+ result.put(reaction, schema);
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ @Override
+ protected void undoImplementation() throws CommandExecutionException {
+ throw new NotImplementedException();
+
+ }
+
+ @Override
+ protected void redoImplementation() throws CommandExecutionException {
+ throw new NotImplementedException();
+ }
+
+ /**
+ * Colors parameter model using coloring for this command. This method is used
+ * internally to color either top {@link Model} or one of it's sumbodels.
+ *
+ * @param result
+ * model to color
+ * @param top
+ * is the model a top (parent) model
+ * @throws InvalidColorSchemaException
+ * thrown when set of {@link ColorSchema} is invalid
+ */
+ private void colorModel(Model result, boolean top) throws InvalidColorSchemaException {
+
+ for (Alias alias : result.getAliases()) {
+ alias.setColor(Color.WHITE);
+ }
+ for (Reaction reaction : result.getReactions()) {
+ for (AbstractNode node : reaction.getNodes()) {
+ node.getLine().setColor(Color.BLACK);
+ }
+ }
+
+ for (ColorSchema schema : schemas) {
+ for (Alias alias : result.getAliases()) {
+ if (match(alias, schema)) {
+ schema.setMatches(schema.getMatches() + 1);
+ applyColor(alias, schema);
+ }
+ }
+ for (Reaction reaction : result.getReactions()) {
+ if (match(reaction, schema)) {
+ schema.setMatches(schema.getMatches() + 1);
+ applyColor(reaction, schema);
+ }
+ }
+ }
+
+ if (top) {
+ for (ModelSubmodelConnection connection : result.getSubmodelConnections()) {
+ colorModel(connection.getSubmodel().getModel(), false);
+ }
+ }
+
+ }
+
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
+ try {
+ colorModel(getModel(), true);
+ } catch (InvalidColorSchemaException e) {
+ throw new CommandExecutionException(e);
+ }
+ }
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CommandExecutionException.java b/model-command/src/main/java/lcsb/mapviewer/commands/CommandExecutionException.java
index ae9195d4b26686b0a4192608533b1c2dbb9907da..ac6585bebd028cb5bbaca2b38d16569a3e127f09 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CommandExecutionException.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CommandExecutionException.java
@@ -1,55 +1,55 @@
-package lcsb.mapviewer.commands;
-
-/**
- * Exception that is thrown when the data for {@link ModelCommand} is invalid.
- *
- * @author Piotr Gawron
- *
- */
-public class CommandExecutionException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public CommandExecutionException() {
- super();
- }
-
- /**
- * Default constructor with message passed in the argument.
- *
- * @param string
- * message of this exception
- */
- public CommandExecutionException(String string) {
- super(string);
- }
-
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param e
- * parent exception
- */
- public CommandExecutionException(Exception e) {
- super(e.getMessage(), e);
- }
-
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param string
- * message of this exception
- * @param e
- * parent exception
- */
- public CommandExecutionException(String string, Exception e) {
- super(string, e);
- }
-
-}
+package lcsb.mapviewer.commands;
+
+/**
+ * Exception that is thrown when the data for {@link ModelCommand} is invalid.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CommandExecutionException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public CommandExecutionException() {
+ super();
+ }
+
+ /**
+ * Default constructor with message passed in the argument.
+ *
+ * @param string
+ * message of this exception
+ */
+ public CommandExecutionException(String string) {
+ super(string);
+ }
+
+ /**
+ * Public constructor with parent exception that was catched.
+ *
+ * @param e
+ * parent exception
+ */
+ public CommandExecutionException(Exception e) {
+ super(e.getMessage(), e);
+ }
+
+ /**
+ * Public constructor with parent exception that was catched.
+ *
+ * @param string
+ * message of this exception
+ * @param e
+ * parent exception
+ */
+ public CommandExecutionException(String string, Exception e) {
+ super(string, e);
+ }
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
index 98faf4c786d24674b21c3646b34a8292c0c6f3b5..f2419aed93f5654487d9050da293a6b1bcb9f18a 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
@@ -1,476 +1,476 @@
-package lcsb.mapviewer.commands;
-
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.graph.DataMiningSet;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelConnection;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Species;
-
-import org.apache.log4j.Logger;
-
-/**
- * Command that creates a new instance of the model with the same data.
- *
- */
-
-public class CopyCommand extends NewModelCommand {
- /**
- * Defaul class logger.
- */
- private static Logger logger = Logger.getLogger(CopyCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link #model}
- */
- public CopyCommand(Model model) {
- super(model);
- }
-
- /**
- * Executed the operation.
- *
- * @return copy of the model
- */
- public Model execute() {
- Map<Model, Model> copies = new HashMap<Model, Model>();
-
- Model model = getModel();
-
- if (model.getModelData().getParentModels().size() > 0) {
- ModelSubmodelConnection parent = null;
- for (SubmodelConnection connection : model.getModelData().getParentModels()) {
- if (connection instanceof ModelSubmodelConnection) {
- if (parent != null) {
- throw new InvalidArgumentException("It looks like the model is a submodel, but has more than one parent...");
- } else {
- parent = (ModelSubmodelConnection) connection;
- }
- }
- }
- if (parent != null) {
- logger.warn("Dirty copying of submodel");
- CopyCommand copyParentCommand = new CopyCommand(parent.getParentModel().getModel());
- Model copy = copyParentCommand.execute();
- for (ModelSubmodelConnection submodel : copy.getSubmodelConnections()) {
- if (submodel.getName().equals(parent.getName())) {
- return submodel.getSubmodel().getModel();
- }
- }
- throw new InvalidStateException("Problem with copying submodel of a model");
- }
- }
-
- Model result = createNotNestedCopy(model);
-
- copies.put(model, result);
-
- for (ModelSubmodelConnection submodelConnection : model.getSubmodelConnections()) {
- Model submodel = submodelConnection.getSubmodel().getModel();
- Model submodelCopy = createNotNestedCopy(submodel);
- copies.put(submodel, submodelCopy);
- }
- for (Model modelCopy : copies.values()) {
- try {
- assignModelCopies(modelCopy, copies);
- } catch (InvalidModelException e) {
- throw new InvalidArgumentException(e);
- }
- }
- return result;
-
- }
-
- /**
- * Assign information about submodel to the copied links.
- *
- * @param modelCopy
- * copy of a model where substitution should be made
- * @param copies
- * map with map copies
- * @throws InvalidModelException
- * when there is inconsistency in data
- */
- private void assignModelCopies(Model modelCopy, Map<Model, Model> copies) throws InvalidModelException {
- for (ModelSubmodelConnection connection : modelCopy.getSubmodelConnections()) {
- // copy connection reference
- Model original = connection.getSubmodel().getModel();
- Model copy = copies.get(original);
- if (copy == null) {
- throw new InvalidModelException("Original model contain reference to model that wasn't copied");
- }
- connection.setSubmodel(copy);
-
- // copy connection parent reference
- if (connection.getParentModel() != null) {
- original = connection.getParentModel().getModel();
- if (original != null) {
- copy = copies.get(original);
- if (copy == null) {
- if (!copies.values().contains(original)) {
- throw new InvalidModelException("Original model contain reference to model that wasn't copied");
- }
- } else {
- connection.setParentModel(copy);
- }
- }
- }
- }
- for (Alias alias : modelCopy.getAliases()) {
- // if alias has connection to submodel
- if (alias.getSubmodel() != null) {
- AliasSubmodelConnection connection = alias.getSubmodel();
- // copy information about submodel
- Model original = connection.getSubmodel().getModel();
- Model copy = copies.get(original);
- if (copy == null) {
- throw new InvalidModelException("Original model contain reference to model that wasn't copied");
- }
- connection.setSubmodel(copy);
-
- // copy information about original alias
- if (connection.getFromAlias() != null) {
- connection.setFromAlias(modelCopy.getAliasByAliasId(connection.getFromAlias().getAliasId()));
- }
- // copy information about reference alias
- if (connection.getToAlias() != null) {
- connection.setToAlias(modelCopy.getAliasByAliasId(connection.getToAlias().getAliasId()));
- }
- }
- }
- }
-
- /**
- * Creates copy of the model without modifing information about submodels
- * (information about original submodels will be left in the copy).
- *
- * @param model
- * original model to copy
- * @return copy of the model
- */
- protected Model createNotNestedCopy(Model model) {
- Model result = new ModelFullIndexed(null);
-
- result.setSbgnFormat(model.isSbgnFormat());
-
- for (Element element : model.getElements()) {
- result.addElement(element);
- }
- for (Alias alias : model.getAliases()) {
- if (alias instanceof CompartmentAlias) {
- CompartmentAlias copy = ((CompartmentAlias) alias).copy();
- copy.getAliases().clear();
- result.addAlias(copy);
- }
-
- }
-
- for (Alias alias : model.getAliases()) {
- if (alias instanceof SpeciesAlias) {
- SpeciesAlias copy = ((SpeciesAlias) alias).copy();
- copy.setSpecies(result.getSpeciesBySpeciesId(((SpeciesAlias) alias).getSpecies().getElementId()));
- CompartmentAlias ca = copy.getCompartmentAlias();
- Alias parent = copy.getParent();
- copy.setCompartmentAlias(null);
- copy.setParent(null);
-
- // the trick is that in addAlias also some connections are added, so
- // lets clear info about parents
-
- result.addAlias(copy);
-
- if (ca != null) {
- ca = result.getCompartmentAliasByCompartmentAliasId(ca.getAliasId());
- copy.setCompartmentAlias(ca);
- }
- if (parent instanceof CompartmentAlias) {
- ca = (CompartmentAlias) parent;
- ca = result.getCompartmentAliasByCompartmentAliasId(ca.getAliasId());
- copy.setParent(ca);
- }
- } else if (alias instanceof CompartmentAlias) {
- // we already added compartment alias
- continue;
- } else {
- throw new InvalidClassException("Don't know what to do with: " + alias.getClass());
- }
- }
-
- for (Layer layer : model.getLayers()) {
- result.addLayer(layer.copy());
- }
-
- for (Reaction reaction : model.getReactions()) {
- result.addReaction(createCopy(reaction));
- }
-
- assignSimpleDataToCopy(result, model);
- for (Layout layout : model.getLayouts()) {
- result.addLayout(layout.copy());
- }
- result.setProject(model.getProject());
-
- for (Element element : result.getElements()) {
- updateElementReferences(element, model);
- }
- for (Alias alias : result.getAliases()) {
- updateAliasReferences(alias, result, model);
- }
- for (Reaction reaction : result.getReactions()) {
- updateReactionReferences(reaction, result);
- }
- for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- result.addSubmodelConnection(connection.copy());
- }
- for (OverviewImage oi : model.getOverviewImages()) {
- result.addOverviewImage(oi.copy());
- }
- for (DataMiningSet dataMiningSet : model.getDataMiningSets()) {
- result.addDataMiningSet(new DataMiningSet(dataMiningSet));
- }
- return result;
- }
-
- /**
- * Copies simple information about model to the copy.
- *
- * @param copy
- * to this model data will be copied
- * @param original
- * original model
- */
- private void assignSimpleDataToCopy(Model copy, Model original) {
- copy.setMapVersion(original.getMapVersion());
- copy.setName(original.getName());
-
- copy.setCreationDate(original.getCreationDate());
-
- copy.setWidth(original.getWidth());
- copy.setHeight(original.getHeight());
- copy.setNotes(original.getNotes());
- copy.setIdModel(original.getIdModel());
- copy.setZoomLevels(original.getZoomLevels());
- copy.setTileSize(original.getTileSize());
-
- copy.addCreationWarnings(original.getCreationWarnings());
- }
-
- /**
- * Creates copy of the reaction that doesn't contain any references to the
- * original (so we have to substitute all references with the new ones...).
- *
- * @param reaction
- * original reaction
- * @return copy of the reaction
- */
- private Reaction createCopy(Reaction reaction) {
- Reaction copy = reaction.copy();
- reaction.getNodes().clear();
- for (AbstractNode node : copy.getNodes()) {
- reaction.addNode(node);
- }
- copy.getNodes().clear();
-
- for (AbstractNode node : reaction.getNodes()) {
- AbstractNode nodeCopy = node.copy();
- nodeCopy.setLine(new PolylineData(nodeCopy.getLine()));
- copy.addNode(nodeCopy);
- }
-
- for (int i = 0; i < copy.getOperators().size(); i++) {
- NodeOperator nodeCopy = copy.getOperators().get(i);
- NodeOperator nodeOriginal = reaction.getOperators().get(i);
- for (int j = 0; j < nodeCopy.getInputs().size(); j++) {
- AbstractNode input = nodeCopy.getInputs().get(j);
- int index1 = reaction.getOperators().indexOf(input);
- int index2 = reaction.getNodes().indexOf(input);
- if (index1 >= 0) {
- nodeCopy.getInputs().set(j, copy.getOperators().get(index1));
- copy.getOperators().get(index1).setNodeOperatorForInput(nodeCopy);
-
- reaction.getOperators().get(index1).setNodeOperatorForInput(nodeOriginal);
- } else if (index2 >= 0) {
- nodeCopy.getInputs().set(j, copy.getNodes().get(index2));
- copy.getNodes().get(index2).setNodeOperatorForInput(nodeCopy);
-
- reaction.getNodes().get(index2).setNodeOperatorForInput(nodeOriginal);
- } else {
- throw new InvalidStateException("WTF");
- }
- }
-
- for (int j = 0; j < nodeCopy.getOutputs().size(); j++) {
- AbstractNode output = nodeCopy.getOutputs().get(j);
- int index1 = reaction.getOperators().indexOf(output);
- int index2 = reaction.getNodes().indexOf(output);
- if (index1 >= 0) {
- nodeCopy.getOutputs().set(j, copy.getOperators().get(index1));
- copy.getOperators().get(index1).setNodeOperatorForOutput(nodeCopy);
-
- reaction.getOperators().get(index1).setNodeOperatorForOutput(nodeOriginal);
- } else if (index2 >= 0) {
- nodeCopy.getOutputs().set(j, copy.getNodes().get(index2));
- copy.getNodes().get(index2).setNodeOperatorForOutput(nodeCopy);
-
- reaction.getNodes().get(index2).setNodeOperatorForOutput(nodeOriginal);
- } else {
- throw new InvalidStateException("WTF");
- }
- }
- }
-
- return copy;
- }
-
- /**
- * Updates references to elements and aliases in reaction to the objects taken
- * from model.
- *
- * @param reaction
- * references in this reaction will be updated
- * @param model
- * references from this model will be taken
- */
- private void updateReactionReferences(Reaction reaction, Model model) {
- reaction.setModel(model);
- for (ReactionNode rNode : reaction.getReactionNodes()) {
- rNode.setAlias((SpeciesAlias) model.getAliasByAliasId(rNode.getAlias().getAliasId()));
- rNode.setElement(model.getSpeciesBySpeciesId(((Species) rNode.getElement()).getElementId()));
- }
-
- }
-
- /**
- * Updates information (like elements, parent aliases) in the alias with the
- * data from new model.
- *
- * @param alias
- * object to be updated
- * @param model
- * data from this model will be used for update
- * @param originalModel
- * original model from which alias copy was created
- */
- private void updateAliasReferences(Alias alias, Model model, Model originalModel) {
- if (alias instanceof CompartmentAlias) {
- CompartmentAlias compartmentAlias = (CompartmentAlias) alias;
- CompartmentAlias original = originalModel.getCompartmentAliasByCompartmentAliasId(alias.getAliasId());
- for (Alias a : original.getAliases()) {
- compartmentAlias.addAlias(model.getAliasByAliasId(a.getAliasId()));
- }
- String compartmentId = null;
- if (original.getCompartment() != null) {
- compartmentId = original.getCompartment().getElementId();
- }
- compartmentAlias.setCompartment(model.getCompartmentByCompartmentId(compartmentId));
- }
-
- if (alias instanceof ComplexAlias) {
- ComplexAlias ca = (ComplexAlias) alias;
- for (int i = 0; i < ca.getAliases().size(); i++) {
- ca.getAliases().set(i, (SpeciesAlias) model.getAliasByAliasId(ca.getAliases().get(i).getAliasId()));
- }
- }
- if (alias instanceof SpeciesAlias) {
- SpeciesAlias originalAlias = (SpeciesAlias) originalModel.getAliasByAliasId(alias.getAliasId());
- SpeciesAlias sa = (SpeciesAlias) alias;
-
- if (sa.getComplexAlias() != null) {
- sa.setComplexAlias((ComplexAlias) model.getAliasByAliasId(sa.getComplexAlias().getAliasId()));
- }
- sa.setSpecies(model.getSpeciesBySpeciesId(sa.getSpecies().getElementId()));
-
- if (originalAlias.getParent() != null) {
- Alias parent = null;
- parent = model.getAliasByAliasId(originalAlias.getParent().getAliasId());
- sa.setParent(parent);
- }
- }
-
- if (alias.getParent() != null) {
- alias.setParent(model.getAliasByAliasId(alias.getParent().getAliasId()));
- }
-
- alias.setModel(model);
-
- if (alias.getCompartmentAlias() != null) {
- alias.setCompartmentAlias(model.getCompartmentAliasByCompartmentAliasId(alias.getCompartmentAlias().getAliasId()));
- }
- }
-
- /**
- * Updates information (like parent elements, aliases) in the element with the
- * data from new model.
- *
- * @param element
- * object to be updated
- * @param model
- * data from this model will be used for update
- */
- private void updateElementReferences(Element element, Model model) {
-
- if (element.getParent() != null) {
- element.setParent(model.getCompartmentByCompartmentId(((Compartment) element.getParent()).getElementId()));
- }
-
- element.setModel(model);
-
- if (element.getComplex() != null) {
- element.setComplex((ComplexSpecies) model.getSpeciesBySpeciesId(element.getComplex().getElementId()));
- }
-
- if (element instanceof Compartment) {
- Set<Element> elements = ((Compartment) element).getElements();
- Set<Element> newElements = new HashSet<Element>();
- for (Element element2 : elements) {
- if (element2 instanceof Compartment) {
- newElements.add(model.getCompartmentByCompartmentId(element2.getElementId()));
- } else {
- newElements.add(model.getSpeciesBySpeciesId(((Species) element2).getElementId()));
- }
- }
- ((Compartment) element).getElements().clear();
- ((Compartment) element).getElements().addAll(newElements);
- }
-
- if (element instanceof ComplexSpecies) {
- Set<Element> elements = ((ComplexSpecies) element).getElements();
- Set<Element> newElements = new HashSet<Element>();
- for (Element element2 : elements) {
- newElements.add(model.getSpeciesBySpeciesId(((Species) element2).getElementId()));
- }
-
- ((ComplexSpecies) element).getElements().clear();
- ((ComplexSpecies) element).getElements().addAll(newElements);
- }
-
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidClassException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelConnection;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.ComplexSpecies;
+import lcsb.mapviewer.model.map.species.Species;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Command that creates a new instance of the model with the same data.
+ *
+ */
+
+public class CopyCommand extends NewModelCommand {
+ /**
+ * Defaul class logger.
+ */
+ private static Logger logger = Logger.getLogger(CopyCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link #model}
+ */
+ public CopyCommand(Model model) {
+ super(model);
+ }
+
+ /**
+ * Executed the operation.
+ *
+ * @return copy of the model
+ */
+ public Model execute() {
+ Map<Model, Model> copies = new HashMap<Model, Model>();
+
+ Model model = getModel();
+
+ if (model.getModelData().getParentModels().size() > 0) {
+ ModelSubmodelConnection parent = null;
+ for (SubmodelConnection connection : model.getModelData().getParentModels()) {
+ if (connection instanceof ModelSubmodelConnection) {
+ if (parent != null) {
+ throw new InvalidArgumentException("It looks like the model is a submodel, but has more than one parent...");
+ } else {
+ parent = (ModelSubmodelConnection) connection;
+ }
+ }
+ }
+ if (parent != null) {
+ logger.warn("Dirty copying of submodel");
+ CopyCommand copyParentCommand = new CopyCommand(parent.getParentModel().getModel());
+ Model copy = copyParentCommand.execute();
+ for (ModelSubmodelConnection submodel : copy.getSubmodelConnections()) {
+ if (submodel.getName().equals(parent.getName())) {
+ return submodel.getSubmodel().getModel();
+ }
+ }
+ throw new InvalidStateException("Problem with copying submodel of a model");
+ }
+ }
+
+ Model result = createNotNestedCopy(model);
+
+ copies.put(model, result);
+
+ for (ModelSubmodelConnection submodelConnection : model.getSubmodelConnections()) {
+ Model submodel = submodelConnection.getSubmodel().getModel();
+ Model submodelCopy = createNotNestedCopy(submodel);
+ copies.put(submodel, submodelCopy);
+ }
+ for (Model modelCopy : copies.values()) {
+ try {
+ assignModelCopies(modelCopy, copies);
+ } catch (InvalidModelException e) {
+ throw new InvalidArgumentException(e);
+ }
+ }
+ return result;
+
+ }
+
+ /**
+ * Assign information about submodel to the copied links.
+ *
+ * @param modelCopy
+ * copy of a model where substitution should be made
+ * @param copies
+ * map with map copies
+ * @throws InvalidModelException
+ * when there is inconsistency in data
+ */
+ private void assignModelCopies(Model modelCopy, Map<Model, Model> copies) throws InvalidModelException {
+ for (ModelSubmodelConnection connection : modelCopy.getSubmodelConnections()) {
+ // copy connection reference
+ Model original = connection.getSubmodel().getModel();
+ Model copy = copies.get(original);
+ if (copy == null) {
+ throw new InvalidModelException("Original model contain reference to model that wasn't copied");
+ }
+ connection.setSubmodel(copy);
+
+ // copy connection parent reference
+ if (connection.getParentModel() != null) {
+ original = connection.getParentModel().getModel();
+ if (original != null) {
+ copy = copies.get(original);
+ if (copy == null) {
+ if (!copies.values().contains(original)) {
+ throw new InvalidModelException("Original model contain reference to model that wasn't copied");
+ }
+ } else {
+ connection.setParentModel(copy);
+ }
+ }
+ }
+ }
+ for (Alias alias : modelCopy.getAliases()) {
+ // if alias has connection to submodel
+ if (alias.getSubmodel() != null) {
+ AliasSubmodelConnection connection = alias.getSubmodel();
+ // copy information about submodel
+ Model original = connection.getSubmodel().getModel();
+ Model copy = copies.get(original);
+ if (copy == null) {
+ throw new InvalidModelException("Original model contain reference to model that wasn't copied");
+ }
+ connection.setSubmodel(copy);
+
+ // copy information about original alias
+ if (connection.getFromAlias() != null) {
+ connection.setFromAlias(modelCopy.getAliasByAliasId(connection.getFromAlias().getAliasId()));
+ }
+ // copy information about reference alias
+ if (connection.getToAlias() != null) {
+ connection.setToAlias(modelCopy.getAliasByAliasId(connection.getToAlias().getAliasId()));
+ }
+ }
+ }
+ }
+
+ /**
+ * Creates copy of the model without modifing information about submodels
+ * (information about original submodels will be left in the copy).
+ *
+ * @param model
+ * original model to copy
+ * @return copy of the model
+ */
+ protected Model createNotNestedCopy(Model model) {
+ Model result = new ModelFullIndexed(null);
+
+ result.setSbgnFormat(model.isSbgnFormat());
+
+ for (Element element : model.getElements()) {
+ result.addElement(element);
+ }
+ for (Alias alias : model.getAliases()) {
+ if (alias instanceof CompartmentAlias) {
+ CompartmentAlias copy = ((CompartmentAlias) alias).copy();
+ copy.getAliases().clear();
+ result.addAlias(copy);
+ }
+
+ }
+
+ for (Alias alias : model.getAliases()) {
+ if (alias instanceof SpeciesAlias) {
+ SpeciesAlias copy = ((SpeciesAlias) alias).copy();
+ copy.setSpecies(result.getSpeciesBySpeciesId(((SpeciesAlias) alias).getSpecies().getElementId()));
+ CompartmentAlias ca = copy.getCompartmentAlias();
+ Alias parent = copy.getParent();
+ copy.setCompartmentAlias(null);
+ copy.setParent(null);
+
+ // the trick is that in addAlias also some connections are added, so
+ // lets clear info about parents
+
+ result.addAlias(copy);
+
+ if (ca != null) {
+ ca = result.getCompartmentAliasByCompartmentAliasId(ca.getAliasId());
+ copy.setCompartmentAlias(ca);
+ }
+ if (parent instanceof CompartmentAlias) {
+ ca = (CompartmentAlias) parent;
+ ca = result.getCompartmentAliasByCompartmentAliasId(ca.getAliasId());
+ copy.setParent(ca);
+ }
+ } else if (alias instanceof CompartmentAlias) {
+ // we already added compartment alias
+ continue;
+ } else {
+ throw new InvalidClassException("Don't know what to do with: " + alias.getClass());
+ }
+ }
+
+ for (Layer layer : model.getLayers()) {
+ result.addLayer(layer.copy());
+ }
+
+ for (Reaction reaction : model.getReactions()) {
+ result.addReaction(createCopy(reaction));
+ }
+
+ assignSimpleDataToCopy(result, model);
+ for (Layout layout : model.getLayouts()) {
+ result.addLayout(layout.copy());
+ }
+ result.setProject(model.getProject());
+
+ for (Element element : result.getElements()) {
+ updateElementReferences(element, model);
+ }
+ for (Alias alias : result.getAliases()) {
+ updateAliasReferences(alias, result, model);
+ }
+ for (Reaction reaction : result.getReactions()) {
+ updateReactionReferences(reaction, result);
+ }
+ for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+ result.addSubmodelConnection(connection.copy());
+ }
+ for (OverviewImage oi : model.getOverviewImages()) {
+ result.addOverviewImage(oi.copy());
+ }
+ for (DataMiningSet dataMiningSet : model.getDataMiningSets()) {
+ result.addDataMiningSet(new DataMiningSet(dataMiningSet));
+ }
+ return result;
+ }
+
+ /**
+ * Copies simple information about model to the copy.
+ *
+ * @param copy
+ * to this model data will be copied
+ * @param original
+ * original model
+ */
+ private void assignSimpleDataToCopy(Model copy, Model original) {
+ copy.setMapVersion(original.getMapVersion());
+ copy.setName(original.getName());
+
+ copy.setCreationDate(original.getCreationDate());
+
+ copy.setWidth(original.getWidth());
+ copy.setHeight(original.getHeight());
+ copy.setNotes(original.getNotes());
+ copy.setIdModel(original.getIdModel());
+ copy.setZoomLevels(original.getZoomLevels());
+ copy.setTileSize(original.getTileSize());
+
+ copy.addCreationWarnings(original.getCreationWarnings());
+ }
+
+ /**
+ * Creates copy of the reaction that doesn't contain any references to the
+ * original (so we have to substitute all references with the new ones...).
+ *
+ * @param reaction
+ * original reaction
+ * @return copy of the reaction
+ */
+ private Reaction createCopy(Reaction reaction) {
+ Reaction copy = reaction.copy();
+ reaction.getNodes().clear();
+ for (AbstractNode node : copy.getNodes()) {
+ reaction.addNode(node);
+ }
+ copy.getNodes().clear();
+
+ for (AbstractNode node : reaction.getNodes()) {
+ AbstractNode nodeCopy = node.copy();
+ nodeCopy.setLine(new PolylineData(nodeCopy.getLine()));
+ copy.addNode(nodeCopy);
+ }
+
+ for (int i = 0; i < copy.getOperators().size(); i++) {
+ NodeOperator nodeCopy = copy.getOperators().get(i);
+ NodeOperator nodeOriginal = reaction.getOperators().get(i);
+ for (int j = 0; j < nodeCopy.getInputs().size(); j++) {
+ AbstractNode input = nodeCopy.getInputs().get(j);
+ int index1 = reaction.getOperators().indexOf(input);
+ int index2 = reaction.getNodes().indexOf(input);
+ if (index1 >= 0) {
+ nodeCopy.getInputs().set(j, copy.getOperators().get(index1));
+ copy.getOperators().get(index1).setNodeOperatorForInput(nodeCopy);
+
+ reaction.getOperators().get(index1).setNodeOperatorForInput(nodeOriginal);
+ } else if (index2 >= 0) {
+ nodeCopy.getInputs().set(j, copy.getNodes().get(index2));
+ copy.getNodes().get(index2).setNodeOperatorForInput(nodeCopy);
+
+ reaction.getNodes().get(index2).setNodeOperatorForInput(nodeOriginal);
+ } else {
+ throw new InvalidStateException("WTF");
+ }
+ }
+
+ for (int j = 0; j < nodeCopy.getOutputs().size(); j++) {
+ AbstractNode output = nodeCopy.getOutputs().get(j);
+ int index1 = reaction.getOperators().indexOf(output);
+ int index2 = reaction.getNodes().indexOf(output);
+ if (index1 >= 0) {
+ nodeCopy.getOutputs().set(j, copy.getOperators().get(index1));
+ copy.getOperators().get(index1).setNodeOperatorForOutput(nodeCopy);
+
+ reaction.getOperators().get(index1).setNodeOperatorForOutput(nodeOriginal);
+ } else if (index2 >= 0) {
+ nodeCopy.getOutputs().set(j, copy.getNodes().get(index2));
+ copy.getNodes().get(index2).setNodeOperatorForOutput(nodeCopy);
+
+ reaction.getNodes().get(index2).setNodeOperatorForOutput(nodeOriginal);
+ } else {
+ throw new InvalidStateException("WTF");
+ }
+ }
+ }
+
+ return copy;
+ }
+
+ /**
+ * Updates references to elements and aliases in reaction to the objects taken
+ * from model.
+ *
+ * @param reaction
+ * references in this reaction will be updated
+ * @param model
+ * references from this model will be taken
+ */
+ private void updateReactionReferences(Reaction reaction, Model model) {
+ reaction.setModel(model);
+ for (ReactionNode rNode : reaction.getReactionNodes()) {
+ rNode.setAlias((SpeciesAlias) model.getAliasByAliasId(rNode.getAlias().getAliasId()));
+ rNode.setElement(model.getSpeciesBySpeciesId(((Species) rNode.getElement()).getElementId()));
+ }
+
+ }
+
+ /**
+ * Updates information (like elements, parent aliases) in the alias with the
+ * data from new model.
+ *
+ * @param alias
+ * object to be updated
+ * @param model
+ * data from this model will be used for update
+ * @param originalModel
+ * original model from which alias copy was created
+ */
+ private void updateAliasReferences(Alias alias, Model model, Model originalModel) {
+ if (alias instanceof CompartmentAlias) {
+ CompartmentAlias compartmentAlias = (CompartmentAlias) alias;
+ CompartmentAlias original = originalModel.getCompartmentAliasByCompartmentAliasId(alias.getAliasId());
+ for (Alias a : original.getAliases()) {
+ compartmentAlias.addAlias(model.getAliasByAliasId(a.getAliasId()));
+ }
+ String compartmentId = null;
+ if (original.getCompartment() != null) {
+ compartmentId = original.getCompartment().getElementId();
+ }
+ compartmentAlias.setCompartment(model.getCompartmentByCompartmentId(compartmentId));
+ }
+
+ if (alias instanceof ComplexAlias) {
+ ComplexAlias ca = (ComplexAlias) alias;
+ for (int i = 0; i < ca.getAliases().size(); i++) {
+ ca.getAliases().set(i, (SpeciesAlias) model.getAliasByAliasId(ca.getAliases().get(i).getAliasId()));
+ }
+ }
+ if (alias instanceof SpeciesAlias) {
+ SpeciesAlias originalAlias = (SpeciesAlias) originalModel.getAliasByAliasId(alias.getAliasId());
+ SpeciesAlias sa = (SpeciesAlias) alias;
+
+ if (sa.getComplexAlias() != null) {
+ sa.setComplexAlias((ComplexAlias) model.getAliasByAliasId(sa.getComplexAlias().getAliasId()));
+ }
+ sa.setSpecies(model.getSpeciesBySpeciesId(sa.getSpecies().getElementId()));
+
+ if (originalAlias.getParent() != null) {
+ Alias parent = null;
+ parent = model.getAliasByAliasId(originalAlias.getParent().getAliasId());
+ sa.setParent(parent);
+ }
+ }
+
+ if (alias.getParent() != null) {
+ alias.setParent(model.getAliasByAliasId(alias.getParent().getAliasId()));
+ }
+
+ alias.setModel(model);
+
+ if (alias.getCompartmentAlias() != null) {
+ alias.setCompartmentAlias(model.getCompartmentAliasByCompartmentAliasId(alias.getCompartmentAlias().getAliasId()));
+ }
+ }
+
+ /**
+ * Updates information (like parent elements, aliases) in the element with the
+ * data from new model.
+ *
+ * @param element
+ * object to be updated
+ * @param model
+ * data from this model will be used for update
+ */
+ private void updateElementReferences(Element element, Model model) {
+
+ if (element.getParent() != null) {
+ element.setParent(model.getCompartmentByCompartmentId(((Compartment) element.getParent()).getElementId()));
+ }
+
+ element.setModel(model);
+
+ if (element.getComplex() != null) {
+ element.setComplex((ComplexSpecies) model.getSpeciesBySpeciesId(element.getComplex().getElementId()));
+ }
+
+ if (element instanceof Compartment) {
+ Set<Element> elements = ((Compartment) element).getElements();
+ Set<Element> newElements = new HashSet<Element>();
+ for (Element element2 : elements) {
+ if (element2 instanceof Compartment) {
+ newElements.add(model.getCompartmentByCompartmentId(element2.getElementId()));
+ } else {
+ newElements.add(model.getSpeciesBySpeciesId(((Species) element2).getElementId()));
+ }
+ }
+ ((Compartment) element).getElements().clear();
+ ((Compartment) element).getElements().addAll(newElements);
+ }
+
+ if (element instanceof ComplexSpecies) {
+ Set<Element> elements = ((ComplexSpecies) element).getElements();
+ Set<Element> newElements = new HashSet<Element>();
+ for (Element element2 : elements) {
+ newElements.add(model.getSpeciesBySpeciesId(((Species) element2).getElementId()));
+ }
+
+ ((ComplexSpecies) element).getElements().clear();
+ ((ComplexSpecies) element).getElements().addAll(newElements);
+ }
+
+ }
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
index ea5c114dce0a0a99b008182a5e973af1244c210d..c6b66f76d949c539805fcb435247edd0b6c6c1e8 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -1,547 +1,547 @@
-package lcsb.mapviewer.commands;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Species;
-
-import org.apache.log4j.Logger;
-
-/**
- * This {@link ModelCommand command} class allows to transform model into
- * multilevel (nested) component structure. Some artificial compartments will
- * appear. All compartments have information about children compartments. All
- * objects have information about parents.
- *
- *
- */
-public class CreateHierarchyCommand extends ModelCommand {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CreateHierarchyCommand.class);
- /**
- * Natural logarithm of four.
- */
- private static final double LOG_4 = Math.log(4);
-
- /**
- * Top left corner x coordinate of the text associated with compratment.
- */
- private static final double DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
- /**
- * Top left corner y coordinate of the text associated with compratment.
- */
- private static final double DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
-
- /**
- * How many levels are possible.
- */
- private int zoomLevels;
- /**
- * What is the maximum zoom factor in the view.
- */
- private double maxZoomFactor;
-
- /**
- * Default constructor that intializes data.
- *
- * @param model
- * model on which command will be executed
- * @param maxZoomFactor
- * what is the maximum zoom out factor
- * @param zoomLevels
- * how many levels are possible
- */
- public CreateHierarchyCommand(Model model, int zoomLevels, double maxZoomFactor) {
- super(model);
- this.zoomLevels = zoomLevels;
- this.maxZoomFactor = maxZoomFactor;
- }
-
- @Override
- protected void undoImplementation() {
- throw new NotImplementedException();
- }
-
- @Override
- protected void executeImplementation() {
- if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
- throw new InvalidStateException("To execute command, the command must be in CREATED or UNDONE state. " + getStatus() + " found.");
- }
- Model model = getModel();
- List<SpeciesAlias> compacts = new ArrayList<SpeciesAlias>();
- for (Alias alias : model.getAliases()) {
- if (alias instanceof ComplexAlias) {
- if (((ComplexAlias) alias).getState().contains("brief")) {
- compacts.add((SpeciesAlias) alias);
- compacts.addAll(((ComplexAlias) alias).getAliases());
- }
- }
- }
- model.getAliases().removeAll(compacts);
- clean();
- createArtificials();
- assignAliases();
- orderConcludingComplex();
- orderConcludingCompartments();
-
- List<Alias> sortedAliases = model.getAliasesSortedBySize();
- setParentingAndChildreningOfNonComplexChildrens(sortedAliases);
- model.getAliases().addAll(compacts);
- sortedAliases = model.getAliasesSortedBySize();
- preSettingOfVisibilityLevel(sortedAliases, maxZoomFactor);
- settingOfTransparencyLevel(sortedAliases);
-
- assignSpeciesAccordingToAliasComplexes();
-
- setStatus(ModelCommandStatus.EXECUTED);
- }
-
- /**
- * Fixes complexes assignment for species. The fix is based on
- * {@link SpeciesAlias#complexAlias} or {@link Alias#parent} fields.
- */
- private void assignSpeciesAccordingToAliasComplexes() {
- for (SpeciesAlias alias : getModel().getSpeciesAliases()) {
- ComplexAlias complexAlias = null;
- if (alias.getComplexAlias() != null) {
- complexAlias = alias.getComplexAlias();
- } else if (alias.getParent() instanceof ComplexAlias) {
- complexAlias = (ComplexAlias) alias.getParent();
- }
- if (complexAlias != null) {
-
- complexAlias = (ComplexAlias) getModel().getAliasByAliasId(complexAlias.getAliasId());
- Species species = getModel().getSpeciesBySpeciesId(alias.getSpecies().getElementId());
- ComplexSpecies complexSpecies = (ComplexSpecies) getModel().getSpeciesBySpeciesId(complexAlias.getSpecies().getElementId());
- if (species.getComplex() != complexSpecies) {
- species.setComplex(complexSpecies);
- try {
- complexSpecies.addElement(species);
- } catch (InvalidArgumentException e) {
- //this is thrown when species is already part of the complex
- }
- }
- }
- }
-
- }
-
- @Override
- protected void redoImplementation() {
- throw new NotImplementedException();
- }
-
- /**
- * Cleans hierarchical information from the model.
- */
- protected void clean() {
- for (Alias alias : getModel().getAliases()) {
- alias.setParent(null);
- if (alias instanceof ComplexAlias) {
- ((ComplexAlias) alias).getAliases().clear();
- }
- }
- Set<ArtifitialCompartmentAlias> toRemove = new HashSet<ArtifitialCompartmentAlias>();
- for (CompartmentAlias alias : getModel().getCompartmentsAliases()) {
- alias.setParent(null);
- alias.getAliases().clear();
- if (alias instanceof ArtifitialCompartmentAlias) {
- toRemove.add((ArtifitialCompartmentAlias) alias);
- }
- }
- for (ArtifitialCompartmentAlias alias : toRemove) {
- getModel().removeAlias(alias);
- }
- }
-
- /**
- * Creates artifitial compartment alias for rectangles and texts object on
- * additional graphic layers.
- */
- private void createArtificials() {
- Model model = getModel();
- int id = 0;
- for (Layer layer : model.getLayers()) {
- for (LayerRect rect : layer.getRectangles()) {
- String title = "art" + id;
- ArtifitialCompartmentAlias alias = new ArtifitialCompartmentAlias();
- alias.setX(rect.getX());
- alias.setY(rect.getY());
- alias.setWidth(rect.getWidth());
- alias.setHeight(rect.getHeight());
- alias.setColor(rect.getColor());
- alias.setAliasId("art" + (id++));
- alias.setNamePoint(new Point2D.Double(rect.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, rect.getY()
- + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
-
- model.addAlias(alias);
-
- Compartment compartment = new Compartment();
- compartment.setName(title);
- compartment.setElementId("ca_" + title);
- alias.setCompartment(compartment);
- model.addCompartment(compartment);
- }
- for (LayerText text : layer.getTexts()) {
- ArtifitialCompartmentAlias alias = new ArtifitialCompartmentAlias();
- alias.setX(text.getX());
- alias.setY(text.getY());
- alias.setWidth(text.getWidth());
- alias.setHeight(text.getHeight());
- alias.setColor(text.getColor());
- alias.setAliasId((id++) + "");
- alias.setTitle(text.getNotes().trim());
- alias.setNamePoint(new Point2D.Double(text.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, text.getY()
- + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
-
- model.addAlias(alias);
-
- Compartment compartment = new Compartment();
- compartment.setName(text.getNotes().trim());
- compartment.setElementId((id++) + "");
- alias.setCompartment(compartment);
- model.addCompartment(compartment);
- }
- }
- }
-
- /**
- * Assign aliases in hierarchical structure.
- */
- private void assignAliases() {
- assignToComplexes();
- assignToCompartments();
- }
-
- /**
- * Checks if hierarchical structure of complexes is valid.
- */
- private void orderConcludingComplex() {
- orderingComplexesInCompartments();
- orderingComplexesInComplexes();
- List<Alias> list = new ArrayList<Alias>();
- for (Alias alias : getModel().getAliases()) {
- if (alias instanceof ComplexAlias) {
- for (SpeciesAlias specAlias : ((ComplexAlias) alias).getAliases()) {
- if (list.contains(specAlias)) {
- throw new InvalidStateException("Some aliases are in few Complexes");
- }
- }
- if (alias instanceof CompartmentAlias) {
- for (Alias specAlias : ((CompartmentAlias) alias).getAliases()) {
- if (list.contains(specAlias)) {
- throw new InvalidStateException("Some aliases are in few Structures");
- }
- }
- }
- }
- }
- for (Alias alias : getModel().getAliases()) {
- if (alias.getParent() != null) {
- throw new InvalidStateException("WTF");
- }
- }
- parentingInComplexes();
- }
-
- /**
- * Checks if hierarchical structure of compartments is valid.
- */
- private void orderConcludingCompartments() {
- for (CompartmentAlias compartment1 : getModel().getCompartmentsAliases()) {
- for (CompartmentAlias compartment2 : getModel().getCompartmentsAliases()) {
- if (!compartment1.equals(compartment2)) {
- if (compartment1.contains(compartment2)) {
- Set<Alias> duplicates = compartment2.getAliases();
- compartment1.getAliases().removeAll(duplicates);
- }
- }
- }
- }
- }
-
- /**
- * Computes visibility levels for aliases based on the size.
- *
- * @param sortedAliases
- * list of aliases
- * @param maxZoomFactor
- * max scale used on the map
- */
- private void preSettingOfVisibilityLevel(List<Alias> sortedAliases, double maxZoomFactor) {
- for (Alias alias : sortedAliases) {
- double rate = computeRate(alias, Configuration.MIN_VISIBLE_OBJECT_SIZE);
- int logValue = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
- if (alias.getParent() == null) {
- logValue = 0;
- }
- if (logValue >= zoomLevels) {
- if (alias.getParent() instanceof ComplexAlias) {
- logValue = zoomLevels - 1;
- } else {
- logValue = zoomLevels;
- }
- }
- alias.setVisibilityLevel(logValue);
- }
- }
-
- /**
- * Sets transparency level in hierarchical view for compartment alias.
- *
- * @param compartment
- * comaprtment alias
- */
- private void settingTransparencyLevelForCompartment(CompartmentAlias compartment) {
- int maxVisibilityLevel = Integer.MAX_VALUE;
- double rate = computeRate(compartment, Configuration.MAX_VISIBLE_OBJECT_SIZE);
- maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
- for (Alias child : compartment.getAliases()) {
- maxVisibilityLevel = Math.min(maxVisibilityLevel, child.getVisibilityLevel());
- }
- if (maxVisibilityLevel >= zoomLevels) {
- maxVisibilityLevel = zoomLevels;
- }
- if (maxVisibilityLevel <= 0) {
- maxVisibilityLevel = 1;
- }
- compartment.setTransparencyLevel(maxVisibilityLevel);
- for (Alias child : compartment.getAliases()) {
- child.setVisibilityLevel(compartment.getTransparencyLevel());
- }
- }
-
- /**
- * Sets transparency level in hierarchical view for complex alias.
- *
- * @param complex
- * complex alias
- */
- private void settingTransparencyLevelForComplex(ComplexAlias complex) {
- int maxVisibilityLevel = Integer.MAX_VALUE;
- double rate = computeRate(complex, Configuration.MAX_VISIBLE_OBJECT_SIZE);
- maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
- for (Alias child : complex.getAliases()) {
- maxVisibilityLevel = Math.min(maxVisibilityLevel, child.getVisibilityLevel());
- }
- if (maxVisibilityLevel >= zoomLevels) {
- maxVisibilityLevel = zoomLevels;
- }
- if (maxVisibilityLevel <= 0) {
- maxVisibilityLevel = 1;
- }
- complex.setTransparencyLevel(maxVisibilityLevel);
- for (Alias child : complex.getAliases()) {
- child.setVisibilityLevel(complex.getTransparencyLevel());
- }
- }
-
- /**
- * Sets transparency level in hierarchical view for all elements.
- *
- * @param sortedAliases
- * list of aliases
- */
- private void settingOfTransparencyLevel(List<Alias> sortedAliases) {
- for (Alias alias : sortedAliases) {
- if (alias instanceof CompartmentAlias) {
- settingTransparencyLevelForCompartment((CompartmentAlias) alias);
- } else if (alias instanceof ComplexAlias) {
- settingTransparencyLevelForComplex((ComplexAlias) alias);
- } else {
- alias.setTransparencyLevel(0);
- }
- }
- }
-
- /**
- * Removes invalid compartment children.
- *
- * @param sortedAliases
- * list of aliases
- */
- private void setChildrening(List<Alias> sortedAliases) {
- for (Alias compartment : sortedAliases) {
- if (compartment instanceof CompartmentAlias) {
- Set<Alias> removable = new HashSet<Alias>();
- for (Alias alias : ((CompartmentAlias) compartment).getAliases()) {
- if (alias.getParent() != compartment) {
- removable.add(alias);
- }
- }
- ((CompartmentAlias) compartment).getAliases().removeAll(removable);
- }
- }
- }
-
- /**
- * Sets parent for elements.
- *
- * @param sortedAliases
- * list of aliases
- */
- private void setParentingOfNonComplexChildrens(List<Alias> sortedAliases) {
- for (Alias alias : getModel().getAliases()) {
- if (alias.getParent() == null) {
- for (Alias complex : sortedAliases) {
- if (complex instanceof ComplexAlias) {
- if (((ComplexAlias) complex).getAliases().contains(alias)) {
- alias.setParent(complex);
- }
- }
- }
- if (alias.getParent() == null) {
- for (Alias compartment : sortedAliases) {
- if (compartment instanceof CompartmentAlias) {
- if (((CompartmentAlias) compartment).getAliases().contains(alias)) {
- alias.setParent(compartment);
- }
- }
- }
- }
- }
- }
- }
-
- /**
- * Set parents for the elements in hierarchical view.
- *
- * @param sortedAliases
- * list of aliases
- */
- private void setParentingAndChildreningOfNonComplexChildrens(List<Alias> sortedAliases) {
- setParentingOfNonComplexChildrens(sortedAliases);
- setChildrening(sortedAliases);
- }
-
- /**
- * Assign aliases to compartments.
- */
- private void assignToCompartments() {
- for (CompartmentAlias alias : getModel().getCompartmentsAliases()) {
- for (CompartmentAlias alias2 : getModel().getCompartmentsAliases()) {
- if (alias.contains(alias2)) {
- alias.addAlias(alias2);
- }
- }
- for (Alias alias2 : getModel().getAliases()) {
- if (!(alias2 instanceof CompartmentAlias)) {
- if (alias.contains(alias2)) {
- alias.addAlias(alias2);
- }
- }
- }
- }
- }
-
- /**
- * Assign aliases to complexes.
- */
- private void assignToComplexes() {
- for (Alias alias : getModel().getAliases()) {
- if (alias instanceof ComplexAlias) {
- for (Alias alias2 : getModel().getAliases()) {
- if (alias.contains(alias2) && !alias.equals(alias2)) {
- ((ComplexAlias) alias).getAliases().add((SpeciesAlias) alias2);
- }
- }
- }
- }
- }
-
- /**
- * Remove subchildren from complexes.
- */
- private void orderingComplexesInComplexes() {
- for (Alias complex1 : getModel().getAliases()) {
- if (complex1 instanceof ComplexAlias) {
- for (Alias complex2 : getModel().getAliases()) {
- if (complex2 instanceof ComplexAlias) {
- if (!complex1.equals(complex2)) {
- if (complex1.contains(complex2)) {
- List<SpeciesAlias> duplicates = ((ComplexAlias) complex2).getAliases();
- ((ComplexAlias) complex1).getAliases().removeAll(duplicates);
- }
- }
- }
- }
- }
- }
- }
-
- /**
- * Remove subchildren from compartments by complexes.
- */
- private void orderingComplexesInCompartments() {
- for (CompartmentAlias compartment : getModel().getCompartmentsAliases()) {
- for (Alias complex : getModel().getAliases()) {
- if (complex instanceof ComplexAlias) {
- List<SpeciesAlias> duplicates = ((ComplexAlias) complex).getAliases();
- compartment.getAliases().removeAll(duplicates);
- }
- }
- }
- }
-
- /**
- * Sets proper parents after creating hierarchical structure.
- */
- private void parentingInComplexes() {
- for (Alias complex : getModel().getAliases()) {
- if (complex instanceof ComplexAlias) {
- for (Alias child : ((ComplexAlias) complex).getAliases()) {
- if (child instanceof ComplexAlias) {
- if (((ComplexAlias) child).getAliases().contains(complex)) {
- if (complex.getParent() != null) {
- throw new InvalidStateException(((SpeciesAlias) child).getSpecies().getName() + " has parent "
- + ((SpeciesAlias) child).getSpecies().getParent().getName() + " and now again try to add new parent "
- + ((SpeciesAlias) complex).getSpecies().getName());
- }
- child.setParent(complex);
- }
- }
- }
- }
- }
- }
-
- /**
- * Computes the ratio between the minimal object that should be visible, and
- * alias visible on the top level.
- *
- * @param alias
- * alias for which computation is done
- * @param limit
- * size of the minimal visibe object
- * @return ratio between the minimal object that should be visible, and alias
- * visible on the top level
- */
- private double computeRate(Alias alias, double limit) {
- double length = alias.getWidth() / maxZoomFactor;
- double height = alias.getHeight() / maxZoomFactor;
- double size = length * height;
- return (double) Math.ceil(limit / size);
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
+import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.ComplexSpecies;
+import lcsb.mapviewer.model.map.species.Species;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This {@link ModelCommand command} class allows to transform model into
+ * multilevel (nested) component structure. Some artificial compartments will
+ * appear. All compartments have information about children compartments. All
+ * objects have information about parents.
+ *
+ *
+ */
+public class CreateHierarchyCommand extends ModelCommand {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CreateHierarchyCommand.class);
+ /**
+ * Natural logarithm of four.
+ */
+ private static final double LOG_4 = Math.log(4);
+
+ /**
+ * Top left corner x coordinate of the text associated with compratment.
+ */
+ private static final double DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
+ /**
+ * Top left corner y coordinate of the text associated with compratment.
+ */
+ private static final double DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
+
+ /**
+ * How many levels are possible.
+ */
+ private int zoomLevels;
+ /**
+ * What is the maximum zoom factor in the view.
+ */
+ private double maxZoomFactor;
+
+ /**
+ * Default constructor that intializes data.
+ *
+ * @param model
+ * model on which command will be executed
+ * @param maxZoomFactor
+ * what is the maximum zoom out factor
+ * @param zoomLevels
+ * how many levels are possible
+ */
+ public CreateHierarchyCommand(Model model, int zoomLevels, double maxZoomFactor) {
+ super(model);
+ this.zoomLevels = zoomLevels;
+ this.maxZoomFactor = maxZoomFactor;
+ }
+
+ @Override
+ protected void undoImplementation() {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ protected void executeImplementation() {
+ if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
+ throw new InvalidStateException("To execute command, the command must be in CREATED or UNDONE state. " + getStatus() + " found.");
+ }
+ Model model = getModel();
+ List<SpeciesAlias> compacts = new ArrayList<SpeciesAlias>();
+ for (Alias alias : model.getAliases()) {
+ if (alias instanceof ComplexAlias) {
+ if (((ComplexAlias) alias).getState().contains("brief")) {
+ compacts.add((SpeciesAlias) alias);
+ compacts.addAll(((ComplexAlias) alias).getAliases());
+ }
+ }
+ }
+ model.getAliases().removeAll(compacts);
+ clean();
+ createArtificials();
+ assignAliases();
+ orderConcludingComplex();
+ orderConcludingCompartments();
+
+ List<Alias> sortedAliases = model.getAliasesSortedBySize();
+ setParentingAndChildreningOfNonComplexChildrens(sortedAliases);
+ model.getAliases().addAll(compacts);
+ sortedAliases = model.getAliasesSortedBySize();
+ preSettingOfVisibilityLevel(sortedAliases, maxZoomFactor);
+ settingOfTransparencyLevel(sortedAliases);
+
+ assignSpeciesAccordingToAliasComplexes();
+
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
+
+ /**
+ * Fixes complexes assignment for species. The fix is based on
+ * {@link SpeciesAlias#complexAlias} or {@link Alias#parent} fields.
+ */
+ private void assignSpeciesAccordingToAliasComplexes() {
+ for (SpeciesAlias alias : getModel().getSpeciesAliases()) {
+ ComplexAlias complexAlias = null;
+ if (alias.getComplexAlias() != null) {
+ complexAlias = alias.getComplexAlias();
+ } else if (alias.getParent() instanceof ComplexAlias) {
+ complexAlias = (ComplexAlias) alias.getParent();
+ }
+ if (complexAlias != null) {
+
+ complexAlias = (ComplexAlias) getModel().getAliasByAliasId(complexAlias.getAliasId());
+ Species species = getModel().getSpeciesBySpeciesId(alias.getSpecies().getElementId());
+ ComplexSpecies complexSpecies = (ComplexSpecies) getModel().getSpeciesBySpeciesId(complexAlias.getSpecies().getElementId());
+ if (species.getComplex() != complexSpecies) {
+ species.setComplex(complexSpecies);
+ try {
+ complexSpecies.addElement(species);
+ } catch (InvalidArgumentException e) {
+ //this is thrown when species is already part of the complex
+ }
+ }
+ }
+ }
+
+ }
+
+ @Override
+ protected void redoImplementation() {
+ throw new NotImplementedException();
+ }
+
+ /**
+ * Cleans hierarchical information from the model.
+ */
+ protected void clean() {
+ for (Alias alias : getModel().getAliases()) {
+ alias.setParent(null);
+ if (alias instanceof ComplexAlias) {
+ ((ComplexAlias) alias).getAliases().clear();
+ }
+ }
+ Set<ArtifitialCompartmentAlias> toRemove = new HashSet<ArtifitialCompartmentAlias>();
+ for (CompartmentAlias alias : getModel().getCompartmentsAliases()) {
+ alias.setParent(null);
+ alias.getAliases().clear();
+ if (alias instanceof ArtifitialCompartmentAlias) {
+ toRemove.add((ArtifitialCompartmentAlias) alias);
+ }
+ }
+ for (ArtifitialCompartmentAlias alias : toRemove) {
+ getModel().removeAlias(alias);
+ }
+ }
+
+ /**
+ * Creates artifitial compartment alias for rectangles and texts object on
+ * additional graphic layers.
+ */
+ private void createArtificials() {
+ Model model = getModel();
+ int id = 0;
+ for (Layer layer : model.getLayers()) {
+ for (LayerRect rect : layer.getRectangles()) {
+ String title = "art" + id;
+ ArtifitialCompartmentAlias alias = new ArtifitialCompartmentAlias();
+ alias.setX(rect.getX());
+ alias.setY(rect.getY());
+ alias.setWidth(rect.getWidth());
+ alias.setHeight(rect.getHeight());
+ alias.setColor(rect.getColor());
+ alias.setAliasId("art" + (id++));
+ alias.setNamePoint(new Point2D.Double(rect.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, rect.getY()
+ + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
+
+ model.addAlias(alias);
+
+ Compartment compartment = new Compartment();
+ compartment.setName(title);
+ compartment.setElementId("ca_" + title);
+ alias.setCompartment(compartment);
+ model.addCompartment(compartment);
+ }
+ for (LayerText text : layer.getTexts()) {
+ ArtifitialCompartmentAlias alias = new ArtifitialCompartmentAlias();
+ alias.setX(text.getX());
+ alias.setY(text.getY());
+ alias.setWidth(text.getWidth());
+ alias.setHeight(text.getHeight());
+ alias.setColor(text.getColor());
+ alias.setAliasId((id++) + "");
+ alias.setTitle(text.getNotes().trim());
+ alias.setNamePoint(new Point2D.Double(text.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, text.getY()
+ + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
+
+ model.addAlias(alias);
+
+ Compartment compartment = new Compartment();
+ compartment.setName(text.getNotes().trim());
+ compartment.setElementId((id++) + "");
+ alias.setCompartment(compartment);
+ model.addCompartment(compartment);
+ }
+ }
+ }
+
+ /**
+ * Assign aliases in hierarchical structure.
+ */
+ private void assignAliases() {
+ assignToComplexes();
+ assignToCompartments();
+ }
+
+ /**
+ * Checks if hierarchical structure of complexes is valid.
+ */
+ private void orderConcludingComplex() {
+ orderingComplexesInCompartments();
+ orderingComplexesInComplexes();
+ List<Alias> list = new ArrayList<Alias>();
+ for (Alias alias : getModel().getAliases()) {
+ if (alias instanceof ComplexAlias) {
+ for (SpeciesAlias specAlias : ((ComplexAlias) alias).getAliases()) {
+ if (list.contains(specAlias)) {
+ throw new InvalidStateException("Some aliases are in few Complexes");
+ }
+ }
+ if (alias instanceof CompartmentAlias) {
+ for (Alias specAlias : ((CompartmentAlias) alias).getAliases()) {
+ if (list.contains(specAlias)) {
+ throw new InvalidStateException("Some aliases are in few Structures");
+ }
+ }
+ }
+ }
+ }
+ for (Alias alias : getModel().getAliases()) {
+ if (alias.getParent() != null) {
+ throw new InvalidStateException("WTF");
+ }
+ }
+ parentingInComplexes();
+ }
+
+ /**
+ * Checks if hierarchical structure of compartments is valid.
+ */
+ private void orderConcludingCompartments() {
+ for (CompartmentAlias compartment1 : getModel().getCompartmentsAliases()) {
+ for (CompartmentAlias compartment2 : getModel().getCompartmentsAliases()) {
+ if (!compartment1.equals(compartment2)) {
+ if (compartment1.contains(compartment2)) {
+ Set<Alias> duplicates = compartment2.getAliases();
+ compartment1.getAliases().removeAll(duplicates);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Computes visibility levels for aliases based on the size.
+ *
+ * @param sortedAliases
+ * list of aliases
+ * @param maxZoomFactor
+ * max scale used on the map
+ */
+ private void preSettingOfVisibilityLevel(List<Alias> sortedAliases, double maxZoomFactor) {
+ for (Alias alias : sortedAliases) {
+ double rate = computeRate(alias, Configuration.MIN_VISIBLE_OBJECT_SIZE);
+ int logValue = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
+ if (alias.getParent() == null) {
+ logValue = 0;
+ }
+ if (logValue >= zoomLevels) {
+ if (alias.getParent() instanceof ComplexAlias) {
+ logValue = zoomLevels - 1;
+ } else {
+ logValue = zoomLevels;
+ }
+ }
+ alias.setVisibilityLevel(logValue);
+ }
+ }
+
+ /**
+ * Sets transparency level in hierarchical view for compartment alias.
+ *
+ * @param compartment
+ * comaprtment alias
+ */
+ private void settingTransparencyLevelForCompartment(CompartmentAlias compartment) {
+ int maxVisibilityLevel = Integer.MAX_VALUE;
+ double rate = computeRate(compartment, Configuration.MAX_VISIBLE_OBJECT_SIZE);
+ maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
+ for (Alias child : compartment.getAliases()) {
+ maxVisibilityLevel = Math.min(maxVisibilityLevel, child.getVisibilityLevel());
+ }
+ if (maxVisibilityLevel >= zoomLevels) {
+ maxVisibilityLevel = zoomLevels;
+ }
+ if (maxVisibilityLevel <= 0) {
+ maxVisibilityLevel = 1;
+ }
+ compartment.setTransparencyLevel(maxVisibilityLevel);
+ for (Alias child : compartment.getAliases()) {
+ child.setVisibilityLevel(compartment.getTransparencyLevel());
+ }
+ }
+
+ /**
+ * Sets transparency level in hierarchical view for complex alias.
+ *
+ * @param complex
+ * complex alias
+ */
+ private void settingTransparencyLevelForComplex(ComplexAlias complex) {
+ int maxVisibilityLevel = Integer.MAX_VALUE;
+ double rate = computeRate(complex, Configuration.MAX_VISIBLE_OBJECT_SIZE);
+ maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
+ for (Alias child : complex.getAliases()) {
+ maxVisibilityLevel = Math.min(maxVisibilityLevel, child.getVisibilityLevel());
+ }
+ if (maxVisibilityLevel >= zoomLevels) {
+ maxVisibilityLevel = zoomLevels;
+ }
+ if (maxVisibilityLevel <= 0) {
+ maxVisibilityLevel = 1;
+ }
+ complex.setTransparencyLevel(maxVisibilityLevel);
+ for (Alias child : complex.getAliases()) {
+ child.setVisibilityLevel(complex.getTransparencyLevel());
+ }
+ }
+
+ /**
+ * Sets transparency level in hierarchical view for all elements.
+ *
+ * @param sortedAliases
+ * list of aliases
+ */
+ private void settingOfTransparencyLevel(List<Alias> sortedAliases) {
+ for (Alias alias : sortedAliases) {
+ if (alias instanceof CompartmentAlias) {
+ settingTransparencyLevelForCompartment((CompartmentAlias) alias);
+ } else if (alias instanceof ComplexAlias) {
+ settingTransparencyLevelForComplex((ComplexAlias) alias);
+ } else {
+ alias.setTransparencyLevel(0);
+ }
+ }
+ }
+
+ /**
+ * Removes invalid compartment children.
+ *
+ * @param sortedAliases
+ * list of aliases
+ */
+ private void setChildrening(List<Alias> sortedAliases) {
+ for (Alias compartment : sortedAliases) {
+ if (compartment instanceof CompartmentAlias) {
+ Set<Alias> removable = new HashSet<Alias>();
+ for (Alias alias : ((CompartmentAlias) compartment).getAliases()) {
+ if (alias.getParent() != compartment) {
+ removable.add(alias);
+ }
+ }
+ ((CompartmentAlias) compartment).getAliases().removeAll(removable);
+ }
+ }
+ }
+
+ /**
+ * Sets parent for elements.
+ *
+ * @param sortedAliases
+ * list of aliases
+ */
+ private void setParentingOfNonComplexChildrens(List<Alias> sortedAliases) {
+ for (Alias alias : getModel().getAliases()) {
+ if (alias.getParent() == null) {
+ for (Alias complex : sortedAliases) {
+ if (complex instanceof ComplexAlias) {
+ if (((ComplexAlias) complex).getAliases().contains(alias)) {
+ alias.setParent(complex);
+ }
+ }
+ }
+ if (alias.getParent() == null) {
+ for (Alias compartment : sortedAliases) {
+ if (compartment instanceof CompartmentAlias) {
+ if (((CompartmentAlias) compartment).getAliases().contains(alias)) {
+ alias.setParent(compartment);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Set parents for the elements in hierarchical view.
+ *
+ * @param sortedAliases
+ * list of aliases
+ */
+ private void setParentingAndChildreningOfNonComplexChildrens(List<Alias> sortedAliases) {
+ setParentingOfNonComplexChildrens(sortedAliases);
+ setChildrening(sortedAliases);
+ }
+
+ /**
+ * Assign aliases to compartments.
+ */
+ private void assignToCompartments() {
+ for (CompartmentAlias alias : getModel().getCompartmentsAliases()) {
+ for (CompartmentAlias alias2 : getModel().getCompartmentsAliases()) {
+ if (alias.contains(alias2)) {
+ alias.addAlias(alias2);
+ }
+ }
+ for (Alias alias2 : getModel().getAliases()) {
+ if (!(alias2 instanceof CompartmentAlias)) {
+ if (alias.contains(alias2)) {
+ alias.addAlias(alias2);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Assign aliases to complexes.
+ */
+ private void assignToComplexes() {
+ for (Alias alias : getModel().getAliases()) {
+ if (alias instanceof ComplexAlias) {
+ for (Alias alias2 : getModel().getAliases()) {
+ if (alias.contains(alias2) && !alias.equals(alias2)) {
+ ((ComplexAlias) alias).getAliases().add((SpeciesAlias) alias2);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Remove subchildren from complexes.
+ */
+ private void orderingComplexesInComplexes() {
+ for (Alias complex1 : getModel().getAliases()) {
+ if (complex1 instanceof ComplexAlias) {
+ for (Alias complex2 : getModel().getAliases()) {
+ if (complex2 instanceof ComplexAlias) {
+ if (!complex1.equals(complex2)) {
+ if (complex1.contains(complex2)) {
+ List<SpeciesAlias> duplicates = ((ComplexAlias) complex2).getAliases();
+ ((ComplexAlias) complex1).getAliases().removeAll(duplicates);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Remove subchildren from compartments by complexes.
+ */
+ private void orderingComplexesInCompartments() {
+ for (CompartmentAlias compartment : getModel().getCompartmentsAliases()) {
+ for (Alias complex : getModel().getAliases()) {
+ if (complex instanceof ComplexAlias) {
+ List<SpeciesAlias> duplicates = ((ComplexAlias) complex).getAliases();
+ compartment.getAliases().removeAll(duplicates);
+ }
+ }
+ }
+ }
+
+ /**
+ * Sets proper parents after creating hierarchical structure.
+ */
+ private void parentingInComplexes() {
+ for (Alias complex : getModel().getAliases()) {
+ if (complex instanceof ComplexAlias) {
+ for (Alias child : ((ComplexAlias) complex).getAliases()) {
+ if (child instanceof ComplexAlias) {
+ if (((ComplexAlias) child).getAliases().contains(complex)) {
+ if (complex.getParent() != null) {
+ throw new InvalidStateException(((SpeciesAlias) child).getSpecies().getName() + " has parent "
+ + ((SpeciesAlias) child).getSpecies().getParent().getName() + " and now again try to add new parent "
+ + ((SpeciesAlias) complex).getSpecies().getName());
+ }
+ child.setParent(complex);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Computes the ratio between the minimal object that should be visible, and
+ * alias visible on the top level.
+ *
+ * @param alias
+ * alias for which computation is done
+ * @param limit
+ * size of the minimal visibe object
+ * @return ratio between the minimal object that should be visible, and alias
+ * visible on the top level
+ */
+ private double computeRate(Alias alias, double limit) {
+ double length = alias.getWidth() / maxZoomFactor;
+ double height = alias.getHeight() / maxZoomFactor;
+ double size = length * height;
+ return (double) Math.ceil(limit / size);
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
index e9c57cea48e4ff7367a93be03d7e678afdf40650..dfdd85384d7013de73baa7f6dc49ae977c84eb75 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -1,341 +1,341 @@
-package lcsb.mapviewer.commands;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.GenericColorSchema;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-
-public class ColorModelCommandTest extends CommandTestFunctions {
- Logger logger = Logger.getLogger(ColorModelCommandTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- /**
- * Test if all elements were copied - if not hibernate will complain
- *
- * @throws Exception
- *
- */
- @Test
- public void testColorFullModel() throws Exception {
- ModelComparator comparator = new ModelComparator();
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Model model2 = getModelForFile("testFiles/sample.xml", false);
- Model coloredModel = new CopyCommand(model).execute();
-
- List<ColorSchema> schemas = new ArrayList<>();
- ColorSchema schema = new GenericColorSchema();
- schema.setName("CNC");
- schema.setValue(-1.0);
- schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(coloredModel, schemas);
-
- assertFalse(Color.RED.equals(coloredModel.getAliasByAliasId("sa14").getColor()));
-
- factory.execute();
-
- assertEquals(0, comparator.compare(model, model2));
-
- assertFalse(comparator.compare(model, coloredModel) == 0);
-
- assertEquals(Color.RED, coloredModel.getAliasByAliasId("sa14").getColor());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColoring2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/coloring_model.xml", true);
- Collection<ColorSchema> schemas = new ArrayList<>();
- ColorSchema schema = new GenericColorSchema();
- schema.setGeneralIdentifier("HGNC:11138");
- schema.setValue(1.0);
- schemas.add(schema);
- schema = new GenericColorSchema();
- schema.setGeneralIdentifier("CHEBI:CHEBI:15377");
- schema.setValue(1.0);
- schemas.add(schema);
- schema = new GenericColorSchema();
- schema.setGeneralIdentifier("CHEBI:CHEBI:15376");
- schema.setValue(1.0);
- schemas.add(schema);
-
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
- Collection<ColorSchema> missing = factory.getMissingSchema();
-
- assertEquals(1, missing.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionColoring1() throws Exception {
- try {
- Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
- Reaction re4 = model.getReactionByReactionId("re4");
- Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
-
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
- assertFalse(Color.BLACK.equals(re4.getNodes().get(0).getLine().getColor()));
-
- factory.execute();
- re4 = model.getReactionByReactionId("re4");
-
- assertEquals(Color.BLACK, re4.getNodes().get(0).getLine().getColor());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionColoring2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
- Reaction re1 = model.getReactionByReactionId("re1");
- Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorSchema schema = new GenericColorSchema();
- schema.setReactionIdentifier("re1");
- schema.setColor(Color.RED);
- schemas.add(schema);
-
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
- assertEquals(Color.BLACK, re1.getNodes().get(0).getLine().getColor());
-
- factory.execute();
- re1 = model.getReactionByReactionId("re1");
-
- assertEquals(Color.RED, re1.getNodes().get(0).getLine().getColor());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionColoring3() throws Exception {
- try {
- Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
- Reaction re2 = model.getReactionByReactionId("re2");
- Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorSchema schema = new GenericColorSchema();
- schema.setReactionIdentifier("re2");
- schema.setValue(-1.0);
- schemas.add(schema);
-
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
- assertEquals(Color.BLACK, re2.getNodes().get(0).getLine().getColor());
-
- factory.execute();
- re2 = model.getReactionByReactionId("re2");
-
- assertEquals(Color.RED, re2.getNodes().get(0).getLine().getColor());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionColoring4() throws Exception {
- try {
- Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
- Reaction re3 = model.getReactionByReactionId("re3");
- Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorSchema schema = new GenericColorSchema();
- Pair<MiriamType, String> pair = new Pair<MiriamType, String>(MiriamType.PUBMED, "12345");
- List<Pair<MiriamType, String>> identifiers = new ArrayList<Pair<MiriamType, String>>();
- identifiers.add(pair);
-
- schema.setIdentifierColumns(identifiers);
- schema.setValue(-1.0);
- schemas.add(schema);
-
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
-
- assertEquals(Color.BLACK, re3.getNodes().get(0).getLine().getColor());
-
- factory.execute();
- re3 = model.getReactionByReactionId("re3");
-
- assertEquals(Color.RED, re3.getNodes().get(0).getLine().getColor());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColoringComplexModel() throws Exception {
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Model model2 = getModelForFile("testFiles/sample.xml", false);
-
- model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.UNKNOWN, "BLA"));
-
- Collection<ColorSchema> schemas = new ArrayList<>();
- Model coloredModel = new CopyCommand(model).execute();
- new ColorModelCommand(coloredModel, schemas).execute();
-
- Model coloredModel2 = coloredModel.getSubmodelConnections().iterator().next().getSubmodel().getModel();
- Model coloredModel3 = coloredModel.getSubmodelByConnectionName("BLA");
-
- assertFalse(coloredModel2.getAliasByAliasId("sa2").getColor().equals(model2.getAliasByAliasId("sa2").getColor()));
- assertFalse(coloredModel3.getAliasByAliasId("sa2").getColor().equals(model2.getAliasByAliasId("sa2").getColor()));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColoredAliases() throws Exception {
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Collection<ColorSchema> schemas = new ArrayList<>();
- ColorSchema schema = new GenericColorSchema();
- schema.setName("CNC");
- schema.setColor(Color.BLUE);
- schemas.add(schema);
- schema = new GenericColorSchema();
- schema.setName("BDH1");
- schema.setColor(Color.BLUE);
- schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
-
- Map<Object, ColorSchema> map = factory.getModifiedElements();
- assertEquals(2, map.size());
- for (Map.Entry<Object, ColorSchema> entry : map.entrySet()) {
- assertTrue(entry.getKey() instanceof Alias);
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColoredReactions() throws Exception {
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Collection<ColorSchema> schemas = new ArrayList<>();
- ColorSchema schema = new GenericColorSchema();
- schema.setReactionIdentifier("re1");
- schema.setLineWidth(3.0);
- schema.setColor(Color.BLUE);
- schema.setName("");
- schema.setReverseReaction(true);
- schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
-
- Map<Object, ColorSchema> map = factory.getModifiedElements();
- assertEquals(0, map.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColoredReactions2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Collection<ColorSchema> schemas = new ArrayList<>();
- ColorSchema schema = new GenericColorSchema();
- schema.setReactionIdentifier("re1");
- schema.setLineWidth(3.0);
- schema.setColor(Color.BLUE);
- schema.setName(null);
- schema.setReverseReaction(true);
- schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
-
- Map<Object, ColorSchema> map = factory.getModifiedElements();
- assertEquals(1, map.size());
- for (Map.Entry<Object, ColorSchema> entry : map.entrySet()) {
- assertTrue(entry.getKey() instanceof Reaction);
- assertEquals("re1", ((Reaction) entry.getKey()).getIdReaction());
- assertEquals(entry.getValue(), schema);
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAliasMatchWithReactionId() throws Exception {
- try {
- GenericColorSchema colorSchema = new GenericColorSchema();
- colorSchema.setName(null);
- colorSchema.setReactionIdentifier("1");
-
- Alias alias = new SpeciesAlias();
- Protein protein = new GenericProtein();
- protein.setName("test");
- alias.setElement(protein);
-
- List<ColorSchema> schemas = new ArrayList<>();
- schemas.add(colorSchema);
-
- ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas);
-
- assertFalse(factory.match(alias, colorSchema));
-
- colorSchema.setReactionIdentifier(null);
- assertTrue(factory.match(alias, colorSchema));
-
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.GenericColorSchema;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+
+public class ColorModelCommandTest extends CommandTestFunctions {
+ Logger logger = Logger.getLogger(ColorModelCommandTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * Test if all elements were copied - if not hibernate will complain
+ *
+ * @throws Exception
+ *
+ */
+ @Test
+ public void testColorFullModel() throws Exception {
+ ModelComparator comparator = new ModelComparator();
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ Model model2 = getModelForFile("testFiles/sample.xml", false);
+ Model coloredModel = new CopyCommand(model).execute();
+
+ List<ColorSchema> schemas = new ArrayList<>();
+ ColorSchema schema = new GenericColorSchema();
+ schema.setName("CNC");
+ schema.setValue(-1.0);
+ schemas.add(schema);
+ ColorModelCommand factory = new ColorModelCommand(coloredModel, schemas);
+
+ assertFalse(Color.RED.equals(coloredModel.getAliasByAliasId("sa14").getColor()));
+
+ factory.execute();
+
+ assertEquals(0, comparator.compare(model, model2));
+
+ assertFalse(comparator.compare(model, coloredModel) == 0);
+
+ assertEquals(Color.RED, coloredModel.getAliasByAliasId("sa14").getColor());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColoring2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/coloring_model.xml", true);
+ Collection<ColorSchema> schemas = new ArrayList<>();
+ ColorSchema schema = new GenericColorSchema();
+ schema.setGeneralIdentifier("HGNC:11138");
+ schema.setValue(1.0);
+ schemas.add(schema);
+ schema = new GenericColorSchema();
+ schema.setGeneralIdentifier("CHEBI:CHEBI:15377");
+ schema.setValue(1.0);
+ schemas.add(schema);
+ schema = new GenericColorSchema();
+ schema.setGeneralIdentifier("CHEBI:CHEBI:15376");
+ schema.setValue(1.0);
+ schemas.add(schema);
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas);
+ Collection<ColorSchema> missing = factory.getMissingSchema();
+
+ assertEquals(1, missing.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionColoring1() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+ Reaction re4 = model.getReactionByReactionId("re4");
+ Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas);
+ assertFalse(Color.BLACK.equals(re4.getNodes().get(0).getLine().getColor()));
+
+ factory.execute();
+ re4 = model.getReactionByReactionId("re4");
+
+ assertEquals(Color.BLACK, re4.getNodes().get(0).getLine().getColor());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionColoring2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+ Reaction re1 = model.getReactionByReactionId("re1");
+ Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ ColorSchema schema = new GenericColorSchema();
+ schema.setReactionIdentifier("re1");
+ schema.setColor(Color.RED);
+ schemas.add(schema);
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas);
+ assertEquals(Color.BLACK, re1.getNodes().get(0).getLine().getColor());
+
+ factory.execute();
+ re1 = model.getReactionByReactionId("re1");
+
+ assertEquals(Color.RED, re1.getNodes().get(0).getLine().getColor());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionColoring3() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+ Reaction re2 = model.getReactionByReactionId("re2");
+ Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ ColorSchema schema = new GenericColorSchema();
+ schema.setReactionIdentifier("re2");
+ schema.setValue(-1.0);
+ schemas.add(schema);
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas);
+ assertEquals(Color.BLACK, re2.getNodes().get(0).getLine().getColor());
+
+ factory.execute();
+ re2 = model.getReactionByReactionId("re2");
+
+ assertEquals(Color.RED, re2.getNodes().get(0).getLine().getColor());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionColoring4() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+ Reaction re3 = model.getReactionByReactionId("re3");
+ Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ ColorSchema schema = new GenericColorSchema();
+ Pair<MiriamType, String> pair = new Pair<MiriamType, String>(MiriamType.PUBMED, "12345");
+ List<Pair<MiriamType, String>> identifiers = new ArrayList<Pair<MiriamType, String>>();
+ identifiers.add(pair);
+
+ schema.setIdentifierColumns(identifiers);
+ schema.setValue(-1.0);
+ schemas.add(schema);
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas);
+
+ assertEquals(Color.BLACK, re3.getNodes().get(0).getLine().getColor());
+
+ factory.execute();
+ re3 = model.getReactionByReactionId("re3");
+
+ assertEquals(Color.RED, re3.getNodes().get(0).getLine().getColor());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColoringComplexModel() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ Model model2 = getModelForFile("testFiles/sample.xml", false);
+
+ model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.UNKNOWN, "BLA"));
+
+ Collection<ColorSchema> schemas = new ArrayList<>();
+ Model coloredModel = new CopyCommand(model).execute();
+ new ColorModelCommand(coloredModel, schemas).execute();
+
+ Model coloredModel2 = coloredModel.getSubmodelConnections().iterator().next().getSubmodel().getModel();
+ Model coloredModel3 = coloredModel.getSubmodelByConnectionName("BLA");
+
+ assertFalse(coloredModel2.getAliasByAliasId("sa2").getColor().equals(model2.getAliasByAliasId("sa2").getColor()));
+ assertFalse(coloredModel3.getAliasByAliasId("sa2").getColor().equals(model2.getAliasByAliasId("sa2").getColor()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColoredAliases() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ Collection<ColorSchema> schemas = new ArrayList<>();
+ ColorSchema schema = new GenericColorSchema();
+ schema.setName("CNC");
+ schema.setColor(Color.BLUE);
+ schemas.add(schema);
+ schema = new GenericColorSchema();
+ schema.setName("BDH1");
+ schema.setColor(Color.BLUE);
+ schemas.add(schema);
+ ColorModelCommand factory = new ColorModelCommand(model, schemas);
+
+ Map<Object, ColorSchema> map = factory.getModifiedElements();
+ assertEquals(2, map.size());
+ for (Map.Entry<Object, ColorSchema> entry : map.entrySet()) {
+ assertTrue(entry.getKey() instanceof Alias);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColoredReactions() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ Collection<ColorSchema> schemas = new ArrayList<>();
+ ColorSchema schema = new GenericColorSchema();
+ schema.setReactionIdentifier("re1");
+ schema.setLineWidth(3.0);
+ schema.setColor(Color.BLUE);
+ schema.setName("");
+ schema.setReverseReaction(true);
+ schemas.add(schema);
+ ColorModelCommand factory = new ColorModelCommand(model, schemas);
+
+ Map<Object, ColorSchema> map = factory.getModifiedElements();
+ assertEquals(0, map.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColoredReactions2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ Collection<ColorSchema> schemas = new ArrayList<>();
+ ColorSchema schema = new GenericColorSchema();
+ schema.setReactionIdentifier("re1");
+ schema.setLineWidth(3.0);
+ schema.setColor(Color.BLUE);
+ schema.setName(null);
+ schema.setReverseReaction(true);
+ schemas.add(schema);
+ ColorModelCommand factory = new ColorModelCommand(model, schemas);
+
+ Map<Object, ColorSchema> map = factory.getModifiedElements();
+ assertEquals(1, map.size());
+ for (Map.Entry<Object, ColorSchema> entry : map.entrySet()) {
+ assertTrue(entry.getKey() instanceof Reaction);
+ assertEquals("re1", ((Reaction) entry.getKey()).getIdReaction());
+ assertEquals(entry.getValue(), schema);
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAliasMatchWithReactionId() throws Exception {
+ try {
+ GenericColorSchema colorSchema = new GenericColorSchema();
+ colorSchema.setName(null);
+ colorSchema.setReactionIdentifier("1");
+
+ Alias alias = new SpeciesAlias();
+ Protein protein = new GenericProtein();
+ protein.setName("test");
+ alias.setElement(protein);
+
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas);
+
+ assertFalse(factory.match(alias, colorSchema));
+
+ colorSchema.setReactionIdentifier(null);
+ assertTrue(factory.match(alias, colorSchema));
+
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
index 3ceabb3643a4891efe1c924a3735f52e05f13926..ebbeaf037eeed214baf2e04d08ff158c98d1e052 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.commands;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Protein;
-
-import org.apache.log4j.Logger;
-
-public abstract class CommandTestFunctions {
- public double EPSILON = 1e-6;
-
- Logger logger = Logger.getLogger(CommandTestFunctions.class);
-
- private static Map<String, Model> models = new HashMap<String, Model>();
-
- protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
- if (!fromCache) {
- logger.debug("File without cache: " + fileName);
- Model result = new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
- result.setName(null);
- return result;
- }
- Model result = models.get(fileName);
- if (result == null) {
- logger.debug("File to cache: " + fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
- result.setName(null);
- models.put(fileName, result);
- }
- return result;
- }
-
- protected Model createSimpleModel() {
- Model model = new ModelFullIndexed(null);
- Compartment compartment = new Compartment();
- model.addCompartment(compartment);
-
- ComplexSpecies complex = new ComplexSpecies();
- complex.setElementId("complex_id");
-
- Protein protein = new Protein();
- protein.setNotes(null);
- protein.setParent(compartment);
- protein.setElementId("species_id");
- List<String> list = new ArrayList<>();
- list.add("synonym");
- protein.addSynonyms(list);
- List<String> list2 = new ArrayList<>();
- list2.add("f_symbol");
- protein.setFormerSymbols(list2);
- complex.addElement(protein);
-
- model.addElement(protein);
- model.addElement(complex);
-
- ComplexAlias complexAlias = new ComplexAlias();
- complexAlias.setAliasId("complex_alias_id");
- complexAlias.setSpecies(complex);
- model.addAlias(complexAlias);
-
- SpeciesAlias alias = new SpeciesAlias();
- alias.setAliasId("alias_id");
- alias.setSpecies(protein);
- complexAlias.addAlias(alias);
-
- model.addAlias(alias);
-
- return model;
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.ComplexSpecies;
+import lcsb.mapviewer.model.map.species.Protein;
+
+import org.apache.log4j.Logger;
+
+public abstract class CommandTestFunctions {
+ public double EPSILON = 1e-6;
+
+ Logger logger = Logger.getLogger(CommandTestFunctions.class);
+
+ private static Map<String, Model> models = new HashMap<String, Model>();
+
+ protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
+ if (!fromCache) {
+ logger.debug("File without cache: " + fileName);
+ Model result = new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
+ result.setName(null);
+ return result;
+ }
+ Model result = models.get(fileName);
+ if (result == null) {
+ logger.debug("File to cache: " + fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
+ result.setName(null);
+ models.put(fileName, result);
+ }
+ return result;
+ }
+
+ protected Model createSimpleModel() {
+ Model model = new ModelFullIndexed(null);
+ Compartment compartment = new Compartment();
+ model.addCompartment(compartment);
+
+ ComplexSpecies complex = new ComplexSpecies();
+ complex.setElementId("complex_id");
+
+ Protein protein = new Protein();
+ protein.setNotes(null);
+ protein.setParent(compartment);
+ protein.setElementId("species_id");
+ List<String> list = new ArrayList<>();
+ list.add("synonym");
+ protein.addSynonyms(list);
+ List<String> list2 = new ArrayList<>();
+ list2.add("f_symbol");
+ protein.setFormerSymbols(list2);
+ complex.addElement(protein);
+
+ model.addElement(protein);
+ model.addElement(complex);
+
+ ComplexAlias complexAlias = new ComplexAlias();
+ complexAlias.setAliasId("complex_alias_id");
+ complexAlias.setSpecies(complex);
+ model.addAlias(complexAlias);
+
+ SpeciesAlias alias = new SpeciesAlias();
+ alias.setAliasId("alias_id");
+ alias.setSpecies(protein);
+ complexAlias.addAlias(alias);
+
+ model.addAlias(alias);
+
+ return model;
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
index aef0f6d4919934b623c5897a88b20d1c9f68711d..032b83c900d10009ef9170414e48cffbe38dadc1 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -1,344 +1,344 @@
-package lcsb.mapviewer.commands;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
-
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Protein;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CopyCommandTest extends CommandTestFunctions {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCopyModel() {
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- fail("exception occurred");
- }
- }
-
- @Test
- public void testCopyCustomModel() {
- try {
- Model model = new ModelFullIndexed(null);
- Compartment compartment = new Compartment();
- model.addCompartment(compartment);
-
- Protein protein = new Protein();
- protein.setNotes(null);
- protein.setParent(compartment);
- protein.setElementId("A");
-
- model.addElement(protein);
-
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- fail("exception occurred");
- }
- }
-
- @Test
- public void testCopyCustomModel2() {
- try {
- Model model = new ModelFullIndexed(null);
- Compartment compartment = new Compartment();
- model.addCompartment(compartment);
-
- ComplexSpecies complex = new ComplexSpecies();
- complex.setElementId("id");
-
- Protein protein = new Protein();
- protein.setNotes(null);
- protein.setParent(compartment);
- protein.setElementId("A");
- complex.addElement(protein);
-
- model.addElement(protein);
- model.addElement(complex);
-
- ComplexAlias complexAlias = new ComplexAlias();
- complexAlias.setAliasId("id2");
- complexAlias.setSpecies(complex);
- model.addAlias(complexAlias);
-
- SpeciesAlias alias = new SpeciesAlias();
- alias.setAliasId("B");
- alias.setSpecies(protein);
- complexAlias.addAlias(alias);
-
- model.addAlias(alias);
-
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("exception occurred");
- }
- }
-
- @Test
- public void testCopyModel3() throws Exception {
- try {
- Model model = getModelForFile("testFiles/complex_with_state.xml", true);
-
- Model copy = new CopyCommand(model).execute();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(copy);
-
- InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
-
- // check if after conversion to xml everything works
- assertEquals(0, comparator.compare(copy, copy2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModel4() throws Exception {
- try {
- Model model = getModelForFile("testFiles/problematic_description.xml", true);
-
- Model copy = new CopyCommand(model).execute();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(copy);
-
- InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
-
- // check if after conversion to xml everything works
- assertEquals(0, comparator.compare(copy, copy2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModelWithArtifitialAliases() throws Exception {
- try {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
- logger.debug(model.getName());
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- Model copy = new CopyCommand(model).execute();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(copy);
-
- InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
-
- new CreateHierarchyCommand(copy2, 2, 2).execute();
-
- // check if after conversion to xml everything works
- assertEquals(0, comparator.compare(copy, copy2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModelWithSubmodels() throws Exception {
- try {
- Model model = getModel();
- Model model2 = getModel();
- model2.setNotes("ASDSA");
- model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopySubmodel() throws Exception {
- try {
- Model model = getModel();
- Model model2 = getModel();
- model2.setNotes("ASDSA");
- model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS, "name a"));
-
- Model model3 = getModel();
- model3.setNotes("ASDSA");
- model.addSubmodelConnection(new ModelSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name b"));
- Alias alias = model2.getAliasByAliasId("a_id");
- alias.setSubmodel(new AliasSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name c"));
- Model copy = new CopyCommand(model2).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model2, copy));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModelWithSubmodels2() throws Exception {
- try {
- Model model = getModel();
- Model model2 = getModel();
- model2.setNotes("ASDSA2");
-
- model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
- model.getAliasByAliasId("a_id").setSubmodel(new AliasSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testCopyModelWithName() throws Exception {
- try {
- Model model = getModel();
- model.setName("ASDSA2");
-
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModelWithSubmodelsThrowException() throws Exception {
- try {
- Model model = getModel();
- Model model2 = getModel();
- model2.setNotes("ASDSA2");
-
- model.getAliasByAliasId("a_id").setSubmodel(new AliasSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
- try {
- new CopyCommand(model).execute();
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model getModel() {
- Model model = new ModelFullIndexed(null);
- model.setNotes("Some description");
- Protein protein = new Protein();
- protein.setName("ad");
- protein.setElementId("A");
- model.addElement(protein);
-
- SpeciesAlias alias = new SpeciesAlias(protein);
- alias.setAliasId("a_id");
- model.addAlias(alias);
-
- Compartment compartment = new Compartment("default");
- model.addCompartment(compartment);
-
- Layer layer = new Layer();
- layer.setName("layer name");
- model.addLayer(layer);
-
- model.addReaction(new Reaction());
- return model;
- }
-
- @Test
- public void testCopyModelWithImages() throws Exception {
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- OverviewImage oi = new OverviewImage();
- OverviewModelLink oml = new OverviewModelLink();
- oml.setLinkedModel(model);
- oml.setPolygon("1,2");
- oi.addLink(oml);
- model.addOverviewImage(oi);
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
-}
+package lcsb.mapviewer.commands;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.OverviewModelLink;
+import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.ComplexSpecies;
+import lcsb.mapviewer.model.map.species.Protein;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CopyCommandTest extends CommandTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCopyModel() {
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("exception occurred");
+ }
+ }
+
+ @Test
+ public void testCopyCustomModel() {
+ try {
+ Model model = new ModelFullIndexed(null);
+ Compartment compartment = new Compartment();
+ model.addCompartment(compartment);
+
+ Protein protein = new Protein();
+ protein.setNotes(null);
+ protein.setParent(compartment);
+ protein.setElementId("A");
+
+ model.addElement(protein);
+
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("exception occurred");
+ }
+ }
+
+ @Test
+ public void testCopyCustomModel2() {
+ try {
+ Model model = new ModelFullIndexed(null);
+ Compartment compartment = new Compartment();
+ model.addCompartment(compartment);
+
+ ComplexSpecies complex = new ComplexSpecies();
+ complex.setElementId("id");
+
+ Protein protein = new Protein();
+ protein.setNotes(null);
+ protein.setParent(compartment);
+ protein.setElementId("A");
+ complex.addElement(protein);
+
+ model.addElement(protein);
+ model.addElement(complex);
+
+ ComplexAlias complexAlias = new ComplexAlias();
+ complexAlias.setAliasId("id2");
+ complexAlias.setSpecies(complex);
+ model.addAlias(complexAlias);
+
+ SpeciesAlias alias = new SpeciesAlias();
+ alias.setAliasId("B");
+ alias.setSpecies(protein);
+ complexAlias.addAlias(alias);
+
+ model.addAlias(alias);
+
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("exception occurred");
+ }
+ }
+
+ @Test
+ public void testCopyModel3() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/complex_with_state.xml", true);
+
+ Model copy = new CopyCommand(model).execute();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(copy);
+
+ InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+ ModelComparator comparator = new ModelComparator();
+
+ // check if after conversion to xml everything works
+ assertEquals(0, comparator.compare(copy, copy2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModel4() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/problematic_description.xml", true);
+
+ Model copy = new CopyCommand(model).execute();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(copy);
+
+ InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+ ModelComparator comparator = new ModelComparator();
+
+ // check if after conversion to xml everything works
+ assertEquals(0, comparator.compare(copy, copy2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModelWithArtifitialAliases() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+ logger.debug(model.getName());
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ Model copy = new CopyCommand(model).execute();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(copy);
+
+ InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+ ModelComparator comparator = new ModelComparator();
+
+ new CreateHierarchyCommand(copy2, 2, 2).execute();
+
+ // check if after conversion to xml everything works
+ assertEquals(0, comparator.compare(copy, copy2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModelWithSubmodels() throws Exception {
+ try {
+ Model model = getModel();
+ Model model2 = getModel();
+ model2.setNotes("ASDSA");
+ model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopySubmodel() throws Exception {
+ try {
+ Model model = getModel();
+ Model model2 = getModel();
+ model2.setNotes("ASDSA");
+ model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS, "name a"));
+
+ Model model3 = getModel();
+ model3.setNotes("ASDSA");
+ model.addSubmodelConnection(new ModelSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name b"));
+ Alias alias = model2.getAliasByAliasId("a_id");
+ alias.setSubmodel(new AliasSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name c"));
+ Model copy = new CopyCommand(model2).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model2, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModelWithSubmodels2() throws Exception {
+ try {
+ Model model = getModel();
+ Model model2 = getModel();
+ model2.setNotes("ASDSA2");
+
+ model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+ model.getAliasByAliasId("a_id").setSubmodel(new AliasSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testCopyModelWithName() throws Exception {
+ try {
+ Model model = getModel();
+ model.setName("ASDSA2");
+
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModelWithSubmodelsThrowException() throws Exception {
+ try {
+ Model model = getModel();
+ Model model2 = getModel();
+ model2.setNotes("ASDSA2");
+
+ model.getAliasByAliasId("a_id").setSubmodel(new AliasSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+ try {
+ new CopyCommand(model).execute();
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model getModel() {
+ Model model = new ModelFullIndexed(null);
+ model.setNotes("Some description");
+ Protein protein = new Protein();
+ protein.setName("ad");
+ protein.setElementId("A");
+ model.addElement(protein);
+
+ SpeciesAlias alias = new SpeciesAlias(protein);
+ alias.setAliasId("a_id");
+ model.addAlias(alias);
+
+ Compartment compartment = new Compartment("default");
+ model.addCompartment(compartment);
+
+ Layer layer = new Layer();
+ layer.setName("layer name");
+ model.addLayer(layer);
+
+ model.addReaction(new Reaction());
+ return model;
+ }
+
+ @Test
+ public void testCopyModelWithImages() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ OverviewImage oi = new OverviewImage();
+ OverviewModelLink oml = new OverviewModelLink();
+ oml.setLinkedModel(model);
+ oml.setPolygon("1,2");
+ oi.addLink(oml);
+ model.addOverviewImage(oi);
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
index f4f23f6a5c787b3101ee0fe8e1555cd139ab4a5d..4669b97eff91da8bf5a81fa5750fde7b8c9633f3 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
@@ -1,285 +1,285 @@
-package lcsb.mapviewer.commands;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-import java.util.HashSet;
-import java.util.Set;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.model.Model;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CreateHierarchyCommandTest extends CommandTestFunctions {
- Logger logger = Logger.getLogger(CreateHierarchyCommandTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCyclicComplexes() throws Exception {
- try {
- Model model = getModelForFile("testFiles/cyclic_hierarchy_problem.xml", false);
-
- new CreateHierarchyCommand(model, 8, 80).execute();
-
- Alias alias = model.getAliasByAliasId("sa5033");
-
- Set<Alias> parents = new HashSet<Alias>();
- while (alias.getParent() instanceof ComplexAlias) {
- assertFalse("Cyclic nesting", parents.contains(alias.getParent()));
- alias = alias.getParent();
- parents.add(alias);
- }
-
- Set<Integer> levels = new HashSet<Integer>();
- for (Alias a : model.getAliases()) {
- levels.add(a.getVisibilityLevel());
- }
- assertTrue(levels.size() > 2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateHierachy() throws Exception {
- try {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- new CreateHierarchyCommand(model, 2, 2).execute();
- // check if second call will throw an exception...
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateHierachy2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- boolean artifitial = false;
- for (CompartmentAlias a : model.getCompartmentsAliases()) {
- if (a instanceof ArtifitialCompartmentAlias) {
- artifitial = true;
- assertNotNull(a.getCompartment());
- }
- }
- assertTrue("No hierarchical structure element found", artifitial);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRecreateHierachy() throws Exception {
- try {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- int size0 = model.getCompartments().size();
- int aliasSize0 = model.getCompartmentsAliases().size();
-
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- int size = model.getCompartments().size();
- int aliasSize = model.getCompartmentsAliases().size();
-
- assertTrue(size0 != size);
- assertTrue(aliasSize0 != aliasSize);
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- int size2 = model.getCompartments().size();
- int aliasSize2 = model.getCompartmentsAliases().size();
-
- assertEquals(size, size2);
- assertEquals(aliasSize, aliasSize2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateComponentsMinVisibility() throws Exception {
- try {
- double zoomFactor = 39.0625;
- int levels = 6;
-
- Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml", false);
-
- new CreateHierarchyCommand(model, levels, zoomFactor).execute();
-
- for (Alias alias : model.getAliases()) {
- if (alias.getParent() == null) {
- assertTrue("Alias " + alias.getAliasId() + " is not visible at levels highers than " + alias.getVisibilityLevel(), alias.getVisibilityLevel() <= 1);
- }
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateComponentsMaxVisibility() throws Exception {
- try {
- double zoomFactor = 39.0625;
- int levels = 6;
-
- Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml", false);
-
- new CreateHierarchyCommand(model, levels, zoomFactor).execute();
-
- for (Alias alias : model.getAliases()) {
- assertTrue(
- "Alias " + alias.getAliasId() + " is not visible even at the bottom level (visibility: " + alias.getVisibilityLevel() + ") ",
- alias.getVisibilityLevel() <= levels);
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCompactComplexesInNestedView() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/compact_complex_view_problem.xml", false);
- Alias alias = model.getAliasByAliasId("sa1");
- Object parent1 = alias.getParent();
- new CreateHierarchyCommand(model, 3, 16).execute();
- Object parent2 = alias.getParent();
- assertEquals(parent1, parent2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRecallHierachyCreation() throws Exception {
- try {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
- command.execute();
- try {
- command.execute();
- fail("Exception expected");
- } catch (InvalidStateException e) {
-
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testClear() throws Exception {
- try {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
- command.clean();
- for (Alias alias : model.getAliases()) {
- assertNull(alias.getParent());
- if (alias instanceof ComplexAlias) {
- assertTrue(((ComplexAlias) alias).getAliases().isEmpty());
- }
- }
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
- assertNull(alias.getParent());
- assertTrue(alias.getAliases().isEmpty());
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testNestedProblem() throws Exception {
- try {
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- Model model = parser.createModel(new ConverterParams().filename("testFiles/nested_test.xml").sizeAutoAdjust(true));
-
- double zoomFactor = Math.max(model.getHeight(), model.getWidth()) / (256);
- int zoomLevels = (int) Math.ceil(Math.log(zoomFactor) / Math.log(2));
-
- CreateHierarchyCommand command = new CreateHierarchyCommand(model, zoomLevels, zoomFactor);
- command.execute();
-
- for (Alias alias : model.getAliases()) {
- Alias parentAlias = alias.getParent();
- if (parentAlias != null) {
- assertTrue(alias.getVisibilityLevel() >= parentAlias.getVisibilityLevel());
- }
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDisconnectedChildInComplex() throws Exception {
- try {
- Model model = getModelForFile("testFiles/problematic/disconnected_child_in_complex.xml", false);
-
- new CreateHierarchyCommand(model, 8, 80).execute();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xmlString = parser.toXml(model);
- // logger.debug(xmlString);
-
- InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
-
- parser.createModel(new ConverterParams().inputStream(stream));
-
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
-
-}
+package lcsb.mapviewer.commands;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+import java.util.HashSet;
+import java.util.Set;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
+import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.model.Model;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CreateHierarchyCommandTest extends CommandTestFunctions {
+ Logger logger = Logger.getLogger(CreateHierarchyCommandTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCyclicComplexes() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/cyclic_hierarchy_problem.xml", false);
+
+ new CreateHierarchyCommand(model, 8, 80).execute();
+
+ Alias alias = model.getAliasByAliasId("sa5033");
+
+ Set<Alias> parents = new HashSet<Alias>();
+ while (alias.getParent() instanceof ComplexAlias) {
+ assertFalse("Cyclic nesting", parents.contains(alias.getParent()));
+ alias = alias.getParent();
+ parents.add(alias);
+ }
+
+ Set<Integer> levels = new HashSet<Integer>();
+ for (Alias a : model.getAliases()) {
+ levels.add(a.getVisibilityLevel());
+ }
+ assertTrue(levels.size() > 2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateHierachy() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+ new CreateHierarchyCommand(model, 2, 2).execute();
+ // check if second call will throw an exception...
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateHierachy2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ boolean artifitial = false;
+ for (CompartmentAlias a : model.getCompartmentsAliases()) {
+ if (a instanceof ArtifitialCompartmentAlias) {
+ artifitial = true;
+ assertNotNull(a.getCompartment());
+ }
+ }
+ assertTrue("No hierarchical structure element found", artifitial);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRecreateHierachy() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+ int size0 = model.getCompartments().size();
+ int aliasSize0 = model.getCompartmentsAliases().size();
+
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ int size = model.getCompartments().size();
+ int aliasSize = model.getCompartmentsAliases().size();
+
+ assertTrue(size0 != size);
+ assertTrue(aliasSize0 != aliasSize);
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ int size2 = model.getCompartments().size();
+ int aliasSize2 = model.getCompartmentsAliases().size();
+
+ assertEquals(size, size2);
+ assertEquals(aliasSize, aliasSize2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateComponentsMinVisibility() throws Exception {
+ try {
+ double zoomFactor = 39.0625;
+ int levels = 6;
+
+ Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml", false);
+
+ new CreateHierarchyCommand(model, levels, zoomFactor).execute();
+
+ for (Alias alias : model.getAliases()) {
+ if (alias.getParent() == null) {
+ assertTrue("Alias " + alias.getAliasId() + " is not visible at levels highers than " + alias.getVisibilityLevel(), alias.getVisibilityLevel() <= 1);
+ }
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateComponentsMaxVisibility() throws Exception {
+ try {
+ double zoomFactor = 39.0625;
+ int levels = 6;
+
+ Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml", false);
+
+ new CreateHierarchyCommand(model, levels, zoomFactor).execute();
+
+ for (Alias alias : model.getAliases()) {
+ assertTrue(
+ "Alias " + alias.getAliasId() + " is not visible even at the bottom level (visibility: " + alias.getVisibilityLevel() + ") ",
+ alias.getVisibilityLevel() <= levels);
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCompactComplexesInNestedView() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/compact_complex_view_problem.xml", false);
+ Alias alias = model.getAliasByAliasId("sa1");
+ Object parent1 = alias.getParent();
+ new CreateHierarchyCommand(model, 3, 16).execute();
+ Object parent2 = alias.getParent();
+ assertEquals(parent1, parent2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRecallHierachyCreation() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+ CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
+ command.execute();
+ try {
+ command.execute();
+ fail("Exception expected");
+ } catch (InvalidStateException e) {
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testClear() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+ CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
+ command.clean();
+ for (Alias alias : model.getAliases()) {
+ assertNull(alias.getParent());
+ if (alias instanceof ComplexAlias) {
+ assertTrue(((ComplexAlias) alias).getAliases().isEmpty());
+ }
+ }
+ for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ assertNull(alias.getParent());
+ assertTrue(alias.getAliases().isEmpty());
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testNestedProblem() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/nested_test.xml").sizeAutoAdjust(true));
+
+ double zoomFactor = Math.max(model.getHeight(), model.getWidth()) / (256);
+ int zoomLevels = (int) Math.ceil(Math.log(zoomFactor) / Math.log(2));
+
+ CreateHierarchyCommand command = new CreateHierarchyCommand(model, zoomLevels, zoomFactor);
+ command.execute();
+
+ for (Alias alias : model.getAliases()) {
+ Alias parentAlias = alias.getParent();
+ if (parentAlias != null) {
+ assertTrue(alias.getVisibilityLevel() >= parentAlias.getVisibilityLevel());
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDisconnectedChildInComplex() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/problematic/disconnected_child_in_complex.xml", false);
+
+ new CreateHierarchyCommand(model, 8, 80).execute();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xmlString = parser.toXml(model);
+ // logger.debug(xmlString);
+
+ InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
+
+ parser.createModel(new ConverterParams().inputStream(stream));
+
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/Project.java b/model/src/main/java/lcsb/mapviewer/model/Project.java
index 8058df51cc847772c340cbcfd1d19ea5dd872d00..ba235988a14662705b353facc9b89fd8f99bd224 100644
--- a/model/src/main/java/lcsb/mapviewer/model/Project.java
+++ b/model/src/main/java/lcsb/mapviewer/model/Project.java
@@ -1,368 +1,368 @@
-package lcsb.mapviewer.model;
-
-import java.io.Serializable;
-import java.util.HashSet;
-import java.util.Set;
-
-import javax.persistence.Basic;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-
-/**
- * Top level structure in the system. It describes single project and contains
- * all data in it.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "project_table")
-public class Project implements Serializable {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(Project.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Project identifier defined by the user (some meaningful string).
- */
- @Column(name = "project_id", unique = true, nullable = false)
- private String projectId;
-
- /**
- * Project disease.
- */
- @Cascade({ CascadeType.ALL })
- @OneToOne
- private MiriamData disease;
-
- /**
- * Name of the project.
- */
- private String name;
-
- /**
- * Directory where the images on the server will be stored for this project.
- */
- private String directory;
-
- /**
- * Status of the project used during uploading the project to the system.
- */
- private ProjectStatus status = ProjectStatus.UNKNOWN;
-
- /**
- * Progress of single step of project uploading.
- */
- private double progress = 0;
-
- /**
- * Errors connected with the project.
- */
- private String errors = null;
-
- /**
- * Map models in the project.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "project", orphanRemoval = true)
- private Set<ModelData> models = new HashSet<ModelData>();
-
- /**
- * Here we store input file.
- */
- @Basic(fetch = FetchType.LAZY)
- private byte[] inputData;
-
- /**
- * Here we store input file.
- */
- private String inputFileName;
-
- /**
- * Organism associated with the project.
- */
- @Cascade({ CascadeType.ALL })
- @OneToOne
- private MiriamData organism;
-
- /**
- * Default constructor.
- */
- public Project() {
- }
-
- /**
- * Constructor with the project name in the parameter.
- *
- * @param projectName
- * name of the project
- */
- public Project(String projectName) {
- this.projectId = projectName;
- }
-
- /**
- * Adds map model to the project.
- *
- * @param model
- * map to be added
- */
- public void addModel(ModelData model) {
- models.add(model);
- model.setProject(this);
- }
-
- /**
- * Adds map model to the project.
- *
- * @param model
- * map to be added
- */
- public void addModel(Model model) {
- models.add(model.getModelData());
- model.setProject(this);
- }
-
- /**
- * Removes map model from the project.
- *
- * @param model
- * map model to remove
- */
- public void removeModel(ModelData model) {
- models.remove(model);
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return user defined project identifier
- * @see #projectId
- */
- public String getProjectId() {
- return projectId;
- }
-
- /**
- * @param projectId
- * user defined project identifier
- * @see #projectId
- */
- public void setProjectId(String projectId) {
- this.projectId = projectId;
- }
-
- /**
- * @return the status
- * @see #status
- */
- public ProjectStatus getStatus() {
- return status;
- }
-
- /**
- * @param status
- * the status to set
- * @see #status
- */
- public void setStatus(ProjectStatus status) {
- this.status = status;
- }
-
- /**
- * @return the progress
- * @see #progress
- */
- public double getProgress() {
- return progress;
- }
-
- /**
- * @param progress
- * the progress to set
- * @see #progress
- */
- public void setProgress(double progress) {
- this.progress = progress;
- }
-
- /**
- * @return the models
- * @see #models
- */
- public Set<ModelData> getModels() {
- return models;
- }
-
- /**
- * @param models
- * the models to set
- * @see #models
- */
- public void setModels(Set<ModelData> models) {
- this.models = models;
- }
-
- /**
- * @return the errors
- * @see #errors
- */
- public String getErrors() {
- return errors;
- }
-
- /**
- * @param errors
- * the errors to set
- * @see #errors
- */
- public void setErrors(String errors) {
- this.errors = errors;
- }
-
- /**
- * @return the directory
- * @see #directory
- */
- public String getDirectory() {
- return directory;
- }
-
- /**
- * @param directory
- * the directory to set
- * @see #directory
- */
- public void setDirectory(String directory) {
- this.directory = directory;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return disease
- */
- public MiriamData getDisease() {
- return disease;
- }
-
- /**
- * @param disease
- * the disease
- */
- public void setDisease(MiriamData disease) {
- this.disease = disease;
- }
-
- /**
- * @return the inputData
- * @see #inputData
- */
- public byte[] getInputData() {
- return inputData;
- }
-
- /**
- * @param inputData
- * the inputData to set
- * @see #inputData
- */
- public void setInputData(byte[] inputData) {
- this.inputData = inputData;
- }
-
- /**
- * @return the inputFileName
- * @see #inputFileName
- */
- public String getInputFileName() {
- return inputFileName;
- }
-
- /**
- * @param inputFileName
- * the inputFileName to set
- * @see #inputFileName
- */
- public void setInputFileName(String inputFileName) {
- this.inputFileName = inputFileName;
- }
-
- /**
- * @param organism
- * the organism to set
- * @see #organism
- */
- public void setOrganism(MiriamData organism) {
- this.organism = organism;
- }
-
- /**
- * @return the organism
- * @see #organism
- */
- public MiriamData getOrganism() {
- return organism;
- }
-}
+package lcsb.mapviewer.model;
+
+import java.io.Serializable;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.persistence.Basic;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.OneToMany;
+import javax.persistence.OneToOne;
+import javax.persistence.Table;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+
+/**
+ * Top level structure in the system. It describes single project and contains
+ * all data in it.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "project_table")
+public class Project implements Serializable {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(Project.class);
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Project identifier defined by the user (some meaningful string).
+ */
+ @Column(name = "project_id", unique = true, nullable = false)
+ private String projectId;
+
+ /**
+ * Project disease.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToOne
+ private MiriamData disease;
+
+ /**
+ * Name of the project.
+ */
+ private String name;
+
+ /**
+ * Directory where the images on the server will be stored for this project.
+ */
+ private String directory;
+
+ /**
+ * Status of the project used during uploading the project to the system.
+ */
+ private ProjectStatus status = ProjectStatus.UNKNOWN;
+
+ /**
+ * Progress of single step of project uploading.
+ */
+ private double progress = 0;
+
+ /**
+ * Errors connected with the project.
+ */
+ private String errors = null;
+
+ /**
+ * Map models in the project.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "project", orphanRemoval = true)
+ private Set<ModelData> models = new HashSet<ModelData>();
+
+ /**
+ * Here we store input file.
+ */
+ @Basic(fetch = FetchType.LAZY)
+ private byte[] inputData;
+
+ /**
+ * Here we store input file.
+ */
+ private String inputFileName;
+
+ /**
+ * Organism associated with the project.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToOne
+ private MiriamData organism;
+
+ /**
+ * Default constructor.
+ */
+ public Project() {
+ }
+
+ /**
+ * Constructor with the project name in the parameter.
+ *
+ * @param projectName
+ * name of the project
+ */
+ public Project(String projectName) {
+ this.projectId = projectName;
+ }
+
+ /**
+ * Adds map model to the project.
+ *
+ * @param model
+ * map to be added
+ */
+ public void addModel(ModelData model) {
+ models.add(model);
+ model.setProject(this);
+ }
+
+ /**
+ * Adds map model to the project.
+ *
+ * @param model
+ * map to be added
+ */
+ public void addModel(Model model) {
+ models.add(model.getModelData());
+ model.setProject(this);
+ }
+
+ /**
+ * Removes map model from the project.
+ *
+ * @param model
+ * map model to remove
+ */
+ public void removeModel(ModelData model) {
+ models.remove(model);
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return user defined project identifier
+ * @see #projectId
+ */
+ public String getProjectId() {
+ return projectId;
+ }
+
+ /**
+ * @param projectId
+ * user defined project identifier
+ * @see #projectId
+ */
+ public void setProjectId(String projectId) {
+ this.projectId = projectId;
+ }
+
+ /**
+ * @return the status
+ * @see #status
+ */
+ public ProjectStatus getStatus() {
+ return status;
+ }
+
+ /**
+ * @param status
+ * the status to set
+ * @see #status
+ */
+ public void setStatus(ProjectStatus status) {
+ this.status = status;
+ }
+
+ /**
+ * @return the progress
+ * @see #progress
+ */
+ public double getProgress() {
+ return progress;
+ }
+
+ /**
+ * @param progress
+ * the progress to set
+ * @see #progress
+ */
+ public void setProgress(double progress) {
+ this.progress = progress;
+ }
+
+ /**
+ * @return the models
+ * @see #models
+ */
+ public Set<ModelData> getModels() {
+ return models;
+ }
+
+ /**
+ * @param models
+ * the models to set
+ * @see #models
+ */
+ public void setModels(Set<ModelData> models) {
+ this.models = models;
+ }
+
+ /**
+ * @return the errors
+ * @see #errors
+ */
+ public String getErrors() {
+ return errors;
+ }
+
+ /**
+ * @param errors
+ * the errors to set
+ * @see #errors
+ */
+ public void setErrors(String errors) {
+ this.errors = errors;
+ }
+
+ /**
+ * @return the directory
+ * @see #directory
+ */
+ public String getDirectory() {
+ return directory;
+ }
+
+ /**
+ * @param directory
+ * the directory to set
+ * @see #directory
+ */
+ public void setDirectory(String directory) {
+ this.directory = directory;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return disease
+ */
+ public MiriamData getDisease() {
+ return disease;
+ }
+
+ /**
+ * @param disease
+ * the disease
+ */
+ public void setDisease(MiriamData disease) {
+ this.disease = disease;
+ }
+
+ /**
+ * @return the inputData
+ * @see #inputData
+ */
+ public byte[] getInputData() {
+ return inputData;
+ }
+
+ /**
+ * @param inputData
+ * the inputData to set
+ * @see #inputData
+ */
+ public void setInputData(byte[] inputData) {
+ this.inputData = inputData;
+ }
+
+ /**
+ * @return the inputFileName
+ * @see #inputFileName
+ */
+ public String getInputFileName() {
+ return inputFileName;
+ }
+
+ /**
+ * @param inputFileName
+ * the inputFileName to set
+ * @see #inputFileName
+ */
+ public void setInputFileName(String inputFileName) {
+ this.inputFileName = inputFileName;
+ }
+
+ /**
+ * @param organism
+ * the organism to set
+ * @see #organism
+ */
+ public void setOrganism(MiriamData organism) {
+ this.organism = organism;
+ }
+
+ /**
+ * @return the organism
+ * @see #organism
+ */
+ public MiriamData getOrganism() {
+ return organism;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java b/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java
index b796d5bbc39b1b7da3440789e6cf3397d5f9ec4f..9e3151fa16f8d463571698986cce18b71dcf29d1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java
+++ b/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java
@@ -1,110 +1,110 @@
-package lcsb.mapviewer.model;
-
-/**
- * Defines possible statuses when uploading project into system.
- *
- * @author Piotr Gawron
- *
- */
-public enum ProjectStatus {
-
- /**
- * Unknown status.
- */
- UNKNOWN("uninitialized"),
-
- /**
- * Data are parsed by the CellDesigner parser.
- */
- PARSING_DATA("Parsing data"),
-
- /**
- * Model is annotated by the annotation tool.
- */
- ANNOTATING("Annotating"),
-
- /**
- * Model is being uploaded to the database.
- */
- UPLOADING_TO_DB("Uploading to db"),
-
- /**
- * Model is being extended (
- * {@link lcsb.mapviewer.services.utils.IPostLoadModification
- * IPostLoadModification} is processing).
- */
- EXTENDING_MODEL("Data mining"),
-
- /**
- * Images for the projects are being generated.
- */
- GENERATING_IMAGES("Generating images"),
-
- /**
- * Data that are linked to pubmed articles are being cached.
- */
- CACHING("Caching pubmed data"),
-
- /**
- * Project is ready to use.
- */
- DONE("Ok"),
-
- /**
- * There was problem during project creation.
- */
- FAIL("Failure"),
-
- /**
- * Data that are linked to miriam are being cached.
- */
- CACHING_MIRIAM("Caching miriam data"),
-
- /**
- * Miriam data validation.
- */
- VALIDATING_MIRIAM("Validating miriam data"),
-
- /**
- * Removing of the project.
- */
- REMOVING("Project removing"),
-
- /**
- * All chemicals that can be found by map elements are cached.
- */
- CACHING_CHEMICAL("Caching chemical data"),
-
- /**
- * All drugs that can be found by map elements are cached.
- */
- CACHING_DRUG("Caching drug data"),
-
- /**
- * All mirna that can be found by map elements are cached.
- */
- CACHING_MI_RNA("Caching miRNA data");
-
- /**
- * Message used to present the status on the client side.
- */
- private String readableString;
-
- /**
- * Default constructor of the enum with {@link #readableString} parameter.
- *
- * @param readableForm
- * {@link #readableString}
- */
- ProjectStatus(String readableForm) {
- this.readableString = readableForm;
- }
-
- /**
- * @return {@link #readableString}
- */
- public String toString() {
- return readableString;
- }
-
-}
+package lcsb.mapviewer.model;
+
+/**
+ * Defines possible statuses when uploading project into system.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ProjectStatus {
+
+ /**
+ * Unknown status.
+ */
+ UNKNOWN("uninitialized"),
+
+ /**
+ * Data are parsed by the CellDesigner parser.
+ */
+ PARSING_DATA("Parsing data"),
+
+ /**
+ * Model is annotated by the annotation tool.
+ */
+ ANNOTATING("Annotating"),
+
+ /**
+ * Model is being uploaded to the database.
+ */
+ UPLOADING_TO_DB("Uploading to db"),
+
+ /**
+ * Model is being extended (
+ * {@link lcsb.mapviewer.services.utils.IPostLoadModification
+ * IPostLoadModification} is processing).
+ */
+ EXTENDING_MODEL("Data mining"),
+
+ /**
+ * Images for the projects are being generated.
+ */
+ GENERATING_IMAGES("Generating images"),
+
+ /**
+ * Data that are linked to pubmed articles are being cached.
+ */
+ CACHING("Caching pubmed data"),
+
+ /**
+ * Project is ready to use.
+ */
+ DONE("Ok"),
+
+ /**
+ * There was problem during project creation.
+ */
+ FAIL("Failure"),
+
+ /**
+ * Data that are linked to miriam are being cached.
+ */
+ CACHING_MIRIAM("Caching miriam data"),
+
+ /**
+ * Miriam data validation.
+ */
+ VALIDATING_MIRIAM("Validating miriam data"),
+
+ /**
+ * Removing of the project.
+ */
+ REMOVING("Project removing"),
+
+ /**
+ * All chemicals that can be found by map elements are cached.
+ */
+ CACHING_CHEMICAL("Caching chemical data"),
+
+ /**
+ * All drugs that can be found by map elements are cached.
+ */
+ CACHING_DRUG("Caching drug data"),
+
+ /**
+ * All mirna that can be found by map elements are cached.
+ */
+ CACHING_MI_RNA("Caching miRNA data");
+
+ /**
+ * Message used to present the status on the client side.
+ */
+ private String readableString;
+
+ /**
+ * Default constructor of the enum with {@link #readableString} parameter.
+ *
+ * @param readableForm
+ * {@link #readableString}
+ */
+ ProjectStatus(String readableForm) {
+ this.readableString = readableForm;
+ }
+
+ /**
+ * @return {@link #readableString}
+ */
+ public String toString() {
+ return readableString;
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/AllTests.java b/model/src/test/java/lcsb/mapviewer/AllTests.java
index ab3bed5138647072ac990bc3980ffbdaf5d40e29..95fc5378830086cd2232c50cce02ef7ab459c59b 100644
--- a/model/src/test/java/lcsb/mapviewer/AllTests.java
+++ b/model/src/test/java/lcsb/mapviewer/AllTests.java
@@ -1,16 +1,16 @@
-package lcsb.mapviewer;
-
-import lcsb.mapviewer.model.AllModelTests;
-import lcsb.mapviewer.modelutils.map.AllMapUtilTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllModelTests.class,//
- AllMapUtilTests.class,//
-})
-public class AllTests {
-
-}
+package lcsb.mapviewer;
+
+import lcsb.mapviewer.model.AllModelTests;
+import lcsb.mapviewer.modelutils.map.AllMapUtilTests;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllModelTests.class,//
+ AllMapUtilTests.class,//
+})
+public class AllTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java b/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java
index fc9832424e2ea7ee356528aa56f8ea48010caad8..a99c4fe2df8997e6a1a4f4d30dad4f463d313690 100644
--- a/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java
+++ b/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java
@@ -1,32 +1,32 @@
-package lcsb.mapviewer;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
-import org.junit.After;
-import org.junit.Before;
-
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-
-public class ModelTestFunctions {
-
- private EventStorageLoggerAppender appender;
-
- @Before
- public final void _setUp() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- appender = new EventStorageLoggerAppender();
- Logger.getRootLogger().addAppender(appender);
- }
-
- @After
- public final void _tearDown() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- }
-
- protected List<LoggingEvent> getWarnings() {
- return appender.getWarnings();
- }
-
-}
+package lcsb.mapviewer;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.junit.After;
+import org.junit.Before;
+
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+
+public class ModelTestFunctions {
+
+ private EventStorageLoggerAppender appender;
+
+ @Before
+ public final void _setUp() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ appender = new EventStorageLoggerAppender();
+ Logger.getRootLogger().addAppender(appender);
+ }
+
+ @After
+ public final void _tearDown() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+
+ protected List<LoggingEvent> getWarnings() {
+ return appender.getWarnings();
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java b/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
index 9387ffa40afe8c6e777881429d9c812680127f9f..bd4e35c210d35b965131eef4829ecc0aeb8b26c5 100644
--- a/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
@@ -1,24 +1,24 @@
-package lcsb.mapviewer.model;
-
-import lcsb.mapviewer.model.cache.AllCacheTests;
-import lcsb.mapviewer.model.graphics.AllGraphicsTests;
-import lcsb.mapviewer.model.log.AllLogTests;
-import lcsb.mapviewer.model.map.AllMapTests;
-import lcsb.mapviewer.model.user.AllUserTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllCacheTests.class, //
- AllGraphicsTests.class, //
- AllLogTests.class, //
- AllMapTests.class, //
- AllUserTests.class, //
- ProjectStatusTest.class, //
- ProjectTest.class,//
-})
-public class AllModelTests {
-
-}
+package lcsb.mapviewer.model;
+
+import lcsb.mapviewer.model.cache.AllCacheTests;
+import lcsb.mapviewer.model.graphics.AllGraphicsTests;
+import lcsb.mapviewer.model.log.AllLogTests;
+import lcsb.mapviewer.model.map.AllMapTests;
+import lcsb.mapviewer.model.user.AllUserTests;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllCacheTests.class, //
+ AllGraphicsTests.class, //
+ AllLogTests.class, //
+ AllMapTests.class, //
+ AllUserTests.class, //
+ ProjectStatusTest.class, //
+ ProjectTest.class,//
+})
+public class AllModelTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java b/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java
index 0d4cdcdfebb9d749d7cb9827b24343f90a0734ce..3a966d4e01f74e006176a9983a44a0f47ed6495c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.model;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ProjectStatusTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (ProjectStatus type : ProjectStatus.values()) {
- assertNotNull(type);
-
- // for coverage tests
- ProjectStatus.valueOf(type.name());
- type.toString();
- }
- }
-
-}
+package lcsb.mapviewer.model;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ProjectStatusTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (ProjectStatus type : ProjectStatus.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ ProjectStatus.valueOf(type.name());
+ type.toString();
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java b/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
index 4952f2e5073199e26cfa75d06cb56cba197b37cf..917ebae588b496ca276621eaf5dfa8be8574c690 100644
--- a/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
@@ -1,130 +1,130 @@
-package lcsb.mapviewer.model;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-public class ProjectTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Project());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProject() {
- try {
- Project project = new Project("str");
- assertNotNull(project);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddModel() {
- try {
- Model model = new ModelFullIndexed(null);
- Model model2 = new ModelFullIndexed(null);
- Project project = new Project();
- assertEquals(0, project.getModels().size());
- project.addModel(model);
- assertEquals(1, project.getModels().size());
- project.addModel(model);
- assertEquals(1, project.getModels().size());
- project.addModel(model2.getModelData());
- assertEquals(2, project.getModels().size());
- project.removeModel(model2.getModelData());
- assertEquals(1, project.getModels().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- MiriamData organism = new MiriamData();
- int id = 5;
- String projectId = "str";
- ProjectStatus status = ProjectStatus.ANNOTATING;
- double progress = 4.5;
- Set<ModelData> models = new HashSet<>();
- String errors = "eerStr";
- String directory = "dir";
- String name = "name3";
- MiriamData disease = new MiriamData();
- Project project = new Project("str");
-
- project.setId(id);
- assertEquals(id, project.getId());
-
- project.setProjectId(projectId);
- assertEquals(projectId, project.getProjectId());
-
- project.setStatus(status);
- assertEquals(status, project.getStatus());
-
- project.setProgress(progress);
- assertEquals(progress, project.getProgress(), Configuration.EPSILON);
-
- project.setModels(models);
- assertEquals(models, project.getModels());
-
- project.setErrors(errors);
- assertEquals(errors, project.getErrors());
-
- project.setDirectory(directory);
- assertEquals(directory, project.getDirectory());
-
- project.setName(name);
- assertEquals(name, project.getName());
-
- project.setDisease(disease);
- assertEquals(disease, project.getDisease());
-
- String inputFileName = "x";
- byte[] inputData = new byte[] { 1, 2 };
- project.setInputData(inputData);
- assertEquals(inputData, project.getInputData());
-
- project.setInputFileName(inputFileName);
- assertEquals(inputFileName, project.getInputFileName());
-
- project.setOrganism(organism);
- assertEquals(organism, project.getOrganism());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+public class ProjectTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Project());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProject() {
+ try {
+ Project project = new Project("str");
+ assertNotNull(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddModel() {
+ try {
+ Model model = new ModelFullIndexed(null);
+ Model model2 = new ModelFullIndexed(null);
+ Project project = new Project();
+ assertEquals(0, project.getModels().size());
+ project.addModel(model);
+ assertEquals(1, project.getModels().size());
+ project.addModel(model);
+ assertEquals(1, project.getModels().size());
+ project.addModel(model2.getModelData());
+ assertEquals(2, project.getModels().size());
+ project.removeModel(model2.getModelData());
+ assertEquals(1, project.getModels().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ MiriamData organism = new MiriamData();
+ int id = 5;
+ String projectId = "str";
+ ProjectStatus status = ProjectStatus.ANNOTATING;
+ double progress = 4.5;
+ Set<ModelData> models = new HashSet<>();
+ String errors = "eerStr";
+ String directory = "dir";
+ String name = "name3";
+ MiriamData disease = new MiriamData();
+ Project project = new Project("str");
+
+ project.setId(id);
+ assertEquals(id, project.getId());
+
+ project.setProjectId(projectId);
+ assertEquals(projectId, project.getProjectId());
+
+ project.setStatus(status);
+ assertEquals(status, project.getStatus());
+
+ project.setProgress(progress);
+ assertEquals(progress, project.getProgress(), Configuration.EPSILON);
+
+ project.setModels(models);
+ assertEquals(models, project.getModels());
+
+ project.setErrors(errors);
+ assertEquals(errors, project.getErrors());
+
+ project.setDirectory(directory);
+ assertEquals(directory, project.getDirectory());
+
+ project.setName(name);
+ assertEquals(name, project.getName());
+
+ project.setDisease(disease);
+ assertEquals(disease, project.getDisease());
+
+ String inputFileName = "x";
+ byte[] inputData = new byte[] { 1, 2 };
+ project.setInputData(inputData);
+ assertEquals(inputData, project.getInputData());
+
+ project.setInputFileName(inputFileName);
+ assertEquals(inputFileName, project.getInputFileName());
+
+ project.setOrganism(organism);
+ assertEquals(organism, project.getOrganism());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}