diff --git a/.gitignore b/.gitignore
index a835f014ea46a3f4ba1a4b75fd0d8bae20913ff4..cb15bd31b7ef18ef93f0626ade6555547475ac33 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@ map_images/
*/target/
web/src/main/webapp/svnversion.txt
*.war
+/target/
diff --git a/CHANGELOG b/CHANGELOG
index a2e0df44a3e219b497dca08b621f1b274b3975ba..335e550153f90d24799f4f35be877dec6d5c3dd0 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,15 @@
+minerva (10.0.3) stable; urgency=medium
+
+ * Bug fix: login cannot contain whitespace
+ * Bug fix: search for multiple drugs will not return more drugs than
+ queried for
+ * Bug fix: drug list for some proteins (like RHOA) hung webpage
+ * Bug fix: comments on submaps issue
+ * Bug fix: link to submap from comment panel
+ * Overlay coloring can be defined in Configuration
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Thu, 10 Oct 2016 10:01:16 +0200
+
minerva (10.0.2) stable; urgency=medium
* Bug fix: markers for mirna targets visibility
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
index ef61c8e976e766cdf205b3115ea83022334f01e5..34536aadd6ce6da6c461b4e45804d70f1e0126c8 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
@@ -68,7 +68,12 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
/**
* Url that list of all child nodes for chembl ontology term.
*/
- private static final String PARENT_CHILD_API_URL = "https://www.ebi.ac.uk/chembl/api/data/molecule_form?parent=";
+ private static final String PARENT_CHILD_API_URL = "https://www.ebi.ac.uk/chembl/api/data/molecule_form/";
+
+ /**
+ * Suffix that should be added to {@link #PARENT_CHILD_API_URL}.
+ */
+ private static final String PARENT_CHILD_API_URL_SUFFIX = ".xml";
/**
* Url used for finding targets containing uniprot identifiers. Important -
@@ -420,7 +425,7 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
List<Target> targets = new ArrayList<>();
try {
String id = drugId.getResource();
- String query = PARENT_CHILD_API_URL + id;
+ String query = PARENT_CHILD_API_URL + id + PARENT_CHILD_API_URL_SUFFIX;
String page = getWebPageContent(query);
Document document = super.getXmlDocumentFromString(page);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
index 29bee7c1502da3159913fa9388d92f8b9fb868f3..31ae9e1054c9102af86ba23196d2760ae1cb06e2 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
@@ -54,7 +54,7 @@ public class PubmedParser extends CachableInterface implements IExternalService
/**
* Version of the remote API thnat is supported by this connecting class.
*/
- static final String SUPPORTED_VERSION = "4.5.2";
+ static final String SUPPORTED_VERSION = "4.5.3";
/**
* Connector used for accessing data from miriam registry.
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
index 1728b89ca0562b23bae6bfe4db2d880468e9af65..d843e6c88850a26210ba6fa9b5270fd9ee2dc1fe 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
@@ -18,7 +18,6 @@ import java.util.Set;
import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
-import org.junit.Ignore;
import org.junit.Test;
import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
@@ -64,7 +63,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
@Test
public void test1FindDrug() throws Exception {
try {
- //do it with cache turned on
+ // do it with cache turned on
chemblParser.setCache(cache);
Drug drug = chemblParser.findDrug("CABOZANTINIB");
@@ -213,11 +212,11 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
@Test
public void test9FindDrug() throws Exception {
try {
- String n = "PONATINIB";
- Drug test = chemblParser.findDrug(n);
+ String name = "PONATINIB";
+ Drug test = chemblParser.findDrug(name);
assertEquals("CHEMBL1171837", test.getSources().get(0).getResource());
- assertEquals("PONATINIB", test.getName());
+ assertEquals(name, test.getName());
assertNull(test.getDescription());
assertEquals(3, test.getTargets().size());
} catch (Exception e) {
@@ -228,7 +227,6 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
}
@Test
- @Ignore("Bug 452")
public void test10FindDrug() throws Exception {
try {
String n = "DEXAMETHASONE";
diff --git a/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java b/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
new file mode 100644
index 0000000000000000000000000000000000000000..f76dce4edb7f08ab22821bdf6633a1e4a7bff89a
--- /dev/null
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
@@ -0,0 +1,59 @@
+package lcsb.mapviewer.common.geometry;
+
+import java.awt.Color;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+/**
+ * Parser clas to extract {@link Color} objects from {@link String}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ColorParser {
+
+ /**
+ * Base of the hex representation.
+ */
+ private static final int HEX_BASE = 16;
+
+ /**
+ * Length of the string describing color in rgb: "#RRGGBB".
+ */
+ private static final int COLOR_STRING_LENGTH = 7;
+
+ /**
+ * Where starts description of red color in stirng representing color.
+ */
+ private static final int COLOR_SUBSTRING_START_RED = 1;
+
+ /**
+ * Where starts description of green color in stirng representing color.
+ */
+ private static final int COLOR_SUBSTRING_START_GREEN = 3;
+
+ /**
+ * Where starts description of blue color in stirng representing color.
+ */
+ private static final int COLOR_SUBSTRING_START_BLUE = 5;
+
+ /**
+ * Extracts {@link Color} from input {@link String}.
+ *
+ * @param string
+ * text to process
+ * @return {@link Color} obtained from input text
+ */
+ public Color parse(String string) {
+ if (string.charAt(0) != '#') {
+ string = "#" + string;
+ }
+ if (string.length() != COLOR_STRING_LENGTH) {
+ throw new InvalidArgumentException("Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
+ } else {
+ return new Color(Integer.valueOf(string.substring(COLOR_SUBSTRING_START_RED, COLOR_SUBSTRING_START_GREEN), HEX_BASE), //
+ Integer.valueOf(string.substring(COLOR_SUBSTRING_START_GREEN, COLOR_SUBSTRING_START_BLUE), HEX_BASE), //
+ Integer.valueOf(string.substring(COLOR_SUBSTRING_START_BLUE, COLOR_STRING_LENGTH), HEX_BASE));
+ }
+ }
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/geometry/ColorParserTest.java b/commons/src/test/java/lcsb/mapviewer/common/geometry/ColorParserTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..6fde224cd5b10f04b1de254d4c180a6e04dddb43
--- /dev/null
+++ b/commons/src/test/java/lcsb/mapviewer/common/geometry/ColorParserTest.java
@@ -0,0 +1,68 @@
+package lcsb.mapviewer.common.geometry;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+public class ColorParserTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+
+ @Test
+ public void testSetInvalidColor() throws Exception {
+ try {
+ ColorParser parser = new ColorParser();
+ parser.parse("qwe");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetInvalidColor2() throws Exception {
+ try {
+ ColorParser parser = new ColorParser();
+ parser.parse("fffffff");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetColor() throws Exception {
+ try {
+ ColorParser parser = new ColorParser();
+ Color color = parser.parse("#ffffff");
+ assertEquals(Color.WHITE, color);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-graphics/pom.xml b/converter-graphics/pom.xml
index 97ca0f2fc5f8c303f0ada2e28090099813304264..c48f3778fb7caccd86741b6fc26f0c84a9d51681 100644
--- a/converter-graphics/pom.xml
+++ b/converter-graphics/pom.xml
@@ -1,63 +1,70 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>parent</artifactId>
- <version>1.0</version>
- </parent>
- <artifactId>converter-graphics</artifactId>
- <name>MapViewer graphics converter</name>
- <description>Converter that allows to transform model into graphic representation</description>
-
- <dependencies>
-
- <!-- dependency from the MapViewer model -->
-
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>model</artifactId>
- <version>1.0</version>
- </dependency>
-
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>model-command</artifactId>
- <version>1.0</version>
- </dependency>
-
- <!-- Log4J -->
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- <version>${log4j.version}</version>
- </dependency>
-
- <!-- Library used for generating svg -->
- <dependency>
- <groupId>org.apache.xmlgraphics</groupId>
- <artifactId>batik-rasterizer</artifactId>
- <version>${batik.version}</version>
- </dependency>
-
- <dependency>
- <groupId>org.apache.xmlgraphics</groupId>
- <artifactId>batik-svggen</artifactId>
- <version>${batik.version}</version>
- </dependency>
-
- <!-- iText library for generating pdf -->
- <dependency>
- <groupId>com.itextpdf</groupId>
- <artifactId>itextpdf</artifactId>
- <version>${itext.version}</version>
- </dependency>
-
- <dependency>
- <groupId>com.itextpdf</groupId>
- <artifactId>itextpdf</artifactId>
- <version>${itext.version}</version>
- </dependency>
-
- </dependencies>
-
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>parent</artifactId>
+ <version>1.0</version>
+ </parent>
+ <artifactId>converter-graphics</artifactId>
+ <name>MapViewer graphics converter</name>
+ <description>Converter that allows to transform model into graphic representation</description>
+
+ <dependencies>
+
+ <!-- dependency from the MapViewer model -->
+
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>model</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>model-command</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <!-- Log4J -->
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ <version>${log4j.version}</version>
+ </dependency>
+
+ <!-- Library used for generating svg -->
+ <dependency>
+ <groupId>org.apache.xmlgraphics</groupId>
+ <artifactId>batik-rasterizer</artifactId>
+ <version>${batik.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.xmlgraphics</groupId>
+ <artifactId>batik-svggen</artifactId>
+ <version>${batik.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-all</artifactId>
+ <version>${mockito.version}</version>
+ <scope>test</scope>
+ </dependency>
+
+ <!-- iText library for generating pdf -->
+ <dependency>
+ <groupId>com.itextpdf</groupId>
+ <artifactId>itextpdf</artifactId>
+ <version>${itext.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>com.itextpdf</groupId>
+ <artifactId>itextpdf</artifactId>
+ <version>${itext.version}</version>
+ </dependency>
+
+ </dependencies>
+
</project>
\ No newline at end of file
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index efa912097a3a7a923a240cd04f191b28ce4e729e..ad46b1dcf3705e3940a9111a82cbef4830113ca7 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
@@ -14,6 +14,7 @@ import java.util.Map;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.converter.graphics.layer.LayerConverter;
import lcsb.mapviewer.converter.graphics.reaction.ReactionConverter;
@@ -26,6 +27,7 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
* This class is responsible for creation of the image from the model. It's an
@@ -93,6 +95,16 @@ public abstract class AbstractImageGenerator {
*/
private Rectangle2D.Double border = null;
+ /**
+ * Object that helps to convert {@link ColorSchema} values into colors.
+ */
+ private ColorExtractor colorExtractor = null;
+
+ /**
+ * Util class for simple operations on {@link Element elements}.
+ */
+ private ElementUtils eu = new ElementUtils();
+
/**
* This class contains a list of params that are used for drawing.
*
@@ -170,6 +182,16 @@ public abstract class AbstractImageGenerator {
*/
private List<Map<Object, ColorSchema>> visibleLayouts = new ArrayList<>();
+ /**
+ * Color that should be used for drawing overlays with minimum value.
+ */
+ private Color minColor = Color.BLACK;
+
+ /**
+ * Color that should be used for drawing overlays with maximum value.
+ */
+ private Color maxColor = Color.BLACK;
+
/**
* @param scale
* scale to set
@@ -481,6 +503,50 @@ public abstract class AbstractImageGenerator {
return result;
}
+ /**
+ * Returns {@link Color} that should be used for drawing overlays with
+ * maximum value.
+ *
+ * @return {@link Color} that should be used for drawing overlays with
+ * maximum value
+ */
+ public Color getMaxColor() {
+ return maxColor;
+ }
+
+ /**
+ * Returns {@link Color} that should be used for drawing overlays with
+ * minimum value.
+ *
+ * @return {@link Color} that should be used for drawing overlays with
+ * minimum value
+ */
+ public Color getMinColor() {
+ return minColor;
+ }
+
+ /**
+ * @param minColor
+ * minColor to set
+ * @return object with all parameters
+ * @see #minColor
+ */
+ public Params minColor(Color minColor) {
+ this.minColor = minColor;
+ return this;
+ }
+
+ /**
+ * @param maxColor
+ * maxColor to set
+ * @return object with all parameters
+ * @see #maxColor
+ */
+ public Params maxColor(Color maxColor) {
+ this.maxColor = maxColor;
+ return this;
+ }
+
}
/**
@@ -526,6 +592,8 @@ public abstract class AbstractImageGenerator {
this.level = params.getLevel();
this.scale = params.getScale();
+ colorExtractor = new ColorExtractor(params.getMinColor(), params.getMaxColor());
+
// set border frame extended by a margin
border = new Rectangle2D.Double(
params.getX() - SINGLE_FRAME_MARGIN, params.getY() - SINGLE_FRAME_MARGIN, params.getWidth() * scale + 2 * SINGLE_FRAME_MARGIN,
@@ -557,17 +625,18 @@ public abstract class AbstractImageGenerator {
// Get the SBGN display format option from the model
this.sbgnFormat = params.getModel().isSbgnFormat();
- // Correct order of displaying is: aliases, reactions, compartments, layers.
+ // Correct order of displaying is: elements, reactions, compartments,
+ // layers.
// In this way we can display all reactions and overlay them by compartments
// or layers if they should be solid and hide complexity behind it
- // draw all aliases
- for (Element alias : params.getModel().getSortedSpeciesList()) {
- // draw only aliases that don't have parents (aren't included in any
+ // draw all elements
+ for (Element element : params.getModel().getSortedSpeciesList()) {
+ // draw only elements that don't have parents (aren't included in any
// compartment/complexes)
- if (alias instanceof Species) {
- if (((Species) alias).getComplex() == null) {
- drawAlias((Species) alias, params.getVisibleLayoutsForElement(alias));
+ if (element instanceof Species) {
+ if (((Species) element).getComplex() == null) {
+ drawSpecies((Species) element, params.getVisibleLayoutsForElement(element));
}
}
}
@@ -576,11 +645,11 @@ public abstract class AbstractImageGenerator {
drawReaction(reaction, params.getVisibleLayoutsForElement(reaction));
}
// draw all compartments
- for (Compartment ca : params.getModel().getSortedCompartments()) {
- // draw only aliases that don't have parents (aren't included in any
+ for (Compartment compartment : params.getModel().getSortedCompartments()) {
+ // draw only compartment that don't have parents (aren't included in any
// compartment/complexes)
- if (ca.getCompartment() == null) {
- drawCompartmentAlias(ca, params.isNested(), params.getVisibleLayoutsForElement(ca), params);
+ if (compartment.getCompartment() == null) {
+ drawCompartment(compartment, params.isNested(), params.getVisibleLayoutsForElement(compartment), params);
}
}
@@ -611,25 +680,26 @@ public abstract class AbstractImageGenerator {
}
/**
- * This method draw a compartment alias on a graphics.
+ * This method draw a {@link Compartment} on a graphics.
*
- * @param compAlias
+ * @param compartment
* object that we want to draw
* @param nested
* are the compartments drawn in hierarchical view
* @param visibleLayouts
- * list of {@link ColorSchema} used for coloring alias in layouts
+ * list of {@link ColorSchema} used for coloring element in layouts
* @param params
* list of all params to create apropriate image
* @throws DrawingException
- * thrown when there was a problem with drawing compartment alias
+ * thrown when there was a problem with drawing {@link Compartment}
*/
- protected void drawCompartmentAlias(final Compartment compAlias, final boolean nested, List<ColorSchema> visibleLayouts, Params params)
+ protected void drawCompartment(final Compartment compartment, final boolean nested, List<ColorSchema> visibleLayouts, Params params)
throws DrawingException {
- // If 'compAlias' has not the big enough visibility level then should not be
+ // If 'compartment' has not the big enough visibility level then should not
+ // be
// visible.
- if (compAlias.getVisibilityLevel() > level) {
+ if (compartment.getVisibilityLevel() > level) {
return;
}
@@ -640,25 +710,25 @@ public abstract class AbstractImageGenerator {
*/
boolean fill = true;
- if (compAlias.getTransparencyLevel() <= level) {
+ if (compartment.getTransparencyLevel() <= level) {
fill = false;
}
// get a converter for this compartment
- AliasConverter converter = new AliasConverter(compAlias);
+ ElementConverterImpl converter = new ElementConverterImpl(compartment, colorExtractor);
ConverterParams compartmentParams = new ConverterParams().textCentered(fill).level(level);
if (nested) {
compartmentParams.fill(fill).scale(Math.max(scale, 1));
}
- // we draw compartment alias only when we have hierarchical view or it's
- // standard compartment (not the artifital pathway)
- if (nested || !(compAlias instanceof PathwayCompartment)) {
+ // we draw compartment only when we have hierarchical view or it's
+ // standard compartment (not the pathway)
+ if (nested || !(compartment instanceof PathwayCompartment)) {
try {
- converter.drawAlias(compAlias, graphics, compartmentParams, visibleLayouts);
+ converter.drawElement(compartment, graphics, compartmentParams, visibleLayouts);
} catch (Exception e) {
- throw new DrawingException("Problem with drawing alias \"" + compAlias.getElementId() + "\" (name: \"" + compAlias.getName() + "\").", e);
+ throw new DrawingException(eu.getElementTag(compartment) + "Problem with drawing element.", e);
}
}
@@ -668,48 +738,48 @@ public abstract class AbstractImageGenerator {
if (fill) {
return;
}
- List<Element> result = new ArrayList<Element>();
- result.addAll(compAlias.getElements());
+ List<Element> result = new ArrayList<>();
+ result.addAll(compartment.getElements());
Collections.sort(result, Element.SIZE_COMPARATOR);
// draw all children of this compartment
- for (Element alias : result) {
- // if a child is a standard alias
- if (alias instanceof Species) {
- drawAlias((Species) alias, params.getVisibleLayoutsForElement(alias));
- } else if (alias instanceof Compartment) {
- drawCompartmentAlias((Compartment) alias, nested, params.getVisibleLayoutsForElement(alias), params);
+ for (Element element : result) {
+ // if a child is a standard species
+ if (element instanceof Species) {
+ drawSpecies((Species) element, params.getVisibleLayoutsForElement(element));
+ } else if (element instanceof Compartment) {
+ drawCompartment((Compartment) element, nested, params.getVisibleLayoutsForElement(element), params);
} else {
- // if a child is not a compartment or an alias then we have a
+ // if a child is not a compartment or a species then we have a
// problem
- throw new DrawingException("Unknown AliasType: " + alias.getClass().getName());
+ throw new DrawingException(eu.getElementTag(compartment) + "Unknown Element type");
}
}
- if (!compAlias.containsIdenticalSpecies()) {
- if (!(compAlias instanceof PathwayCompartment)) {
- converter.drawText(compAlias, graphics, compartmentParams);
+ if (!compartment.containsIdenticalSpecies()) {
+ if (!(compartment instanceof PathwayCompartment)) {
+ converter.drawText(compartment, graphics, compartmentParams);
}
}
}
/**
- * This method draw a species alias on a graphics.
+ * This method draw a {@link Species} on a graphics.
*
- * @param alias
+ * @param species
* object to be drawn
* @param visibleLayouts
- * list of {@link ColorSchema} used for coloring alias in layouts
+ * list of {@link ColorSchema} used for coloring species in layouts
* @throws DrawingException
- * thrown when there was a problem with drawing an alias
+ * thrown when there was a problem with drawing a {@link Species}
*/
- protected void drawAlias(final Species alias, List<ColorSchema> visibleLayouts) throws DrawingException {
+ protected void drawSpecies(final Species species, List<ColorSchema> visibleLayouts) throws DrawingException {
- // The displaying of alias is indicated by values of VisibilityLevel. If
+ // The displaying of species is indicated by values of VisibilityLevel. If
// VisibilityLevel is big enough, then it is
// displayed.
- if (alias.getVisibilityLevel() > level) {
+ if (species.getVisibilityLevel() > level) {
return;
}
@@ -718,42 +788,43 @@ public abstract class AbstractImageGenerator {
* most bottom Complexes.
*/
- if (!cross(alias.getBorder())) {
+ if (!cross(species.getBorder())) {
return;
}
boolean rescale = false;
- if (alias instanceof Complex) {
- if (((Complex) alias).getElements().size() == 0) {
+ if (species instanceof Complex) {
+ if (((Complex) species).getElements().size() == 0) {
rescale = true;
- } else if (((Complex) alias).getElements().get(0).getVisibilityLevel() > level) {
+ } else if (((Complex) species).getElements().get(0).getVisibilityLevel() > level) {
rescale = true;
}
}
// at the beginning try to find an appropriate converter
- AliasConverter converter = new AliasConverter(alias, sbgnFormat);
+ ElementConverterImpl converter = new ElementConverterImpl(species, sbgnFormat, colorExtractor);
double customScale = 1;
if (rescale) {
customScale = scale;
}
try {
- converter.drawAlias(alias, graphics, new ConverterParams().scale(customScale).textCentered(rescale).level(level).sbgnFormat(sbgnFormat), visibleLayouts);
+ converter
+ .drawElement(species, graphics, new ConverterParams().scale(customScale).textCentered(rescale).level(level).sbgnFormat(sbgnFormat), visibleLayouts);
} catch (Exception e) {
- throw new DrawingException("Problem with drawing alias \"" + alias.getElementId() + "\".", e);
+ throw new DrawingException(eu.getElementTag(species) + "Problem with drawing element.", e);
}
- // if the alias is a complex alias then we may want to draw children
+ // if the species is a complex then we may want to draw children
// objects
- if (alias instanceof Complex) {
- Complex complex = (Complex) alias;
+ if (species instanceof Complex) {
+ Complex complex = (Complex) species;
// before drawing children check if the view is not set to brief
// mode
if (!complex.getState().equalsIgnoreCase("brief")) {
// depending on current zoom level, children are drawn or not
if (complex.getTransparencyLevel() <= level) {
for (Species a : complex.getElements()) {
- drawAlias(a, visibleLayouts);
+ drawSpecies(a, visibleLayouts);
}
}
}
@@ -772,7 +843,7 @@ public abstract class AbstractImageGenerator {
if (!cross(reaction.getLines())) {
return;
}
- ReactionConverter converter = new ReactionConverter();
+ ReactionConverter converter = new ReactionConverter(colorExtractor);
converter.drawReaction(reaction, graphics, sbgnFormat, visibleLayouts);
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AliasConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AliasConverter.java
deleted file mode 100644
index 1a16acb1e47488a4f637628e0099d9f5167b4996..0000000000000000000000000000000000000000
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AliasConverter.java
+++ /dev/null
@@ -1,207 +0,0 @@
-package lcsb.mapviewer.converter.graphics;
-
-import java.awt.Graphics2D;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.graphics.compartment.ArtifitialCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.BottomSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.LeftSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.OvalCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.RightSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.SquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.TopSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.species.AntisenseRnaConverter;
-import lcsb.mapviewer.converter.graphics.species.ComplexConverter;
-import lcsb.mapviewer.converter.graphics.species.DegradedConverter;
-import lcsb.mapviewer.converter.graphics.species.DrugConverter;
-import lcsb.mapviewer.converter.graphics.species.GeneConverter;
-import lcsb.mapviewer.converter.graphics.species.IonConverter;
-import lcsb.mapviewer.converter.graphics.species.PhenotypeConverter;
-import lcsb.mapviewer.converter.graphics.species.ProteinConverter;
-import lcsb.mapviewer.converter.graphics.species.RnaConverter;
-import lcsb.mapviewer.converter.graphics.species.SBGNNucleicAcidFeatureConverter;
-import lcsb.mapviewer.converter.graphics.species.SimpleMoleculeConverter;
-import lcsb.mapviewer.converter.graphics.species.UnknownConverter;
-import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.OvalCompartment;
-import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.SquareCompartment;
-import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Degraded;
-import lcsb.mapviewer.model.map.species.Drug;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.IonChannelProtein;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.ReceptorProtein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
-import lcsb.mapviewer.model.map.species.Unknown;
-
-/**
- * This class is designed to convert any type of alias into a graphic glyph that
- * will be visualized on the graphgics2d object. It contains static instances of
- * converter for every type and use one that is needed for currently processed
- * alias.
- *
- * @author Piotr Gawron
- *
- */
-public class AliasConverter implements IAliasConverter<Element> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(AliasConverter.class.getName());
-
- // *****************************************************************
- //
- // STATIC PART
- //
- // *****************************************************************
-
- /**
- * Static map of graphic alias converters used for conversion of aliases. Key
- * in this map is a class of alias. Value is the converter that can process
- * this type of alias.
- */
- private static Map<Class<? extends Element>, IAliasConverter<?>> aliasConverters = new HashMap<Class<? extends Element>, IAliasConverter<?>>();
-
- static {
- // at the beginning lets add all implemented aliases
-
- // for element reference
- addAliasConverter(GenericProtein.class, new ProteinConverter());
- addAliasConverter(IonChannelProtein.class, new ProteinConverter());
- addAliasConverter(ReceptorProtein.class, new ProteinConverter());
- addAliasConverter(TruncatedProtein.class, new ProteinConverter());
- addAliasConverter(Degraded.class, new DegradedConverter());
- addAliasConverter(Complex.class, new ComplexConverter());
- addAliasConverter(SimpleMolecule.class, new SimpleMoleculeConverter());
- addAliasConverter(Drug.class, new DrugConverter());
- addAliasConverter(Ion.class, new IonConverter());
- addAliasConverter(Phenotype.class, new PhenotypeConverter());
- addAliasConverter(Rna.class, new RnaConverter());
- addAliasConverter(AntisenseRna.class, new AntisenseRnaConverter());
- addAliasConverter(Gene.class, new GeneConverter());
- addAliasConverter(Unknown.class, new UnknownConverter());
-
- // for compartment aliases
- addAliasConverter(SquareCompartment.class, new SquareCompartmentConverter());
- addAliasConverter(OvalCompartment.class, new OvalCompartmentConverter());
- addAliasConverter(PathwayCompartment.class, new ArtifitialCompartmentConverter());
- addAliasConverter(BottomSquareCompartment.class, new BottomSquareCompartmentConverter());
- addAliasConverter(TopSquareCompartment.class, new TopSquareCompartmentConverter());
- addAliasConverter(LeftSquareCompartment.class, new LeftSquareCompartmentConverter());
- addAliasConverter(RightSquareCompartment.class, new RightSquareCompartmentConverter());
-
- }
-
- /**
- * Method that set a converter for specific alias type.
- *
- * @param clazz
- * class type of alias
- * @param converter
- * converter that should be used for conversion of this alias
- */
- protected static void addAliasConverter(final Class<? extends Element> clazz, final IAliasConverter<?> converter) {
- if (aliasConverters.get(clazz) != null) {
- logger.warn("Converter for " + clazz + " has been already added");
- }
- aliasConverters.put(clazz, converter);
- }
-
- /**
- * Returns a converter for given alias. If converter doesn't exist then null
- * is returned.
- *
- * @param alias
- * alias for which we are loooking for a converter
- * @return converter that can be applied for the given alias; null if such
- * converter doesn't exist
- */
- private static IAliasConverter<? extends Element> getConverterForAlias(final Element alias) {
- if (alias == null) {
- throw new InvalidArgumentException("alias cannot be null");
- }
- IAliasConverter<?> result = aliasConverters.get(alias.getClass());
- return result;
- }
-
- // *******************************************************
- //
- // NON-STATIC CLASS DEFINITION
- //
- // *******************************************************
-
- /**
- * Converter used for conversion of the alias given in constructor.
- */
- @SuppressWarnings("rawtypes")
- private IAliasConverter aliasConverter = null;
-
- /**
- * Support constructor. Used in case of SBGN format display
- *
- * @param alias
- * alias for which this converter will be used
- * @param sbgnFormat
- * boolean value indicating if SBGN display format should be used
- */
- public AliasConverter(final Element alias, final boolean sbgnFormat) {
-
- // If alias is a nucleic acid feature to be displayed in SBGN
- if (sbgnFormat && (alias instanceof AntisenseRna || alias instanceof Rna || alias instanceof Gene)) {
- aliasConverter = new SBGNNucleicAcidFeatureConverter();
- } else {
- // If not, at the beginning try to find an appropriate converter
- aliasConverter = getConverterForAlias(alias);
- }
-
- // if we don't know which converter to use then throw an exception
- if (aliasConverter == null) {
- throw new InvalidArgumentException("Unknown converter for class: " + alias.getClass() + ". Alias id: " + alias.getElementId());
- }
- }
-
- /**
- * Default constructor.
- *
- * @param alias
- * alias for which this converter will be used
- */
- public AliasConverter(final Element alias) {
- this(alias, false);
- }
-
- @SuppressWarnings("unchecked")
- @Override
- public void drawAlias(final Element alias, final Graphics2D graphics, final ConverterParams params) {
- aliasConverter.drawAlias(alias, graphics, params);
- }
-
- @SuppressWarnings("unchecked")
- @Override
- public void drawText(final Element compAlias, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
- aliasConverter.drawText(compAlias, graphics, params);
- }
-
- @SuppressWarnings("unchecked")
- @Override
- public void drawAlias(Element alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
- aliasConverter.drawAlias(alias, graphics, params, visualizedLayoutsColorSchemas);
- }
-}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/IAliasConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ElementConverter.java
similarity index 86%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/IAliasConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ElementConverter.java
index d06ea04b21b468695840450ee1b1ca3689a82188..d1992b796ce8c4c30531713a9f4e9451cfd89a05 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/IAliasConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ElementConverter.java
@@ -15,7 +15,7 @@ import lcsb.mapviewer.model.map.species.Element;
* @param <T>
* class of alias to convert
*/
-public interface IAliasConverter<T extends Element> {
+public interface ElementConverter<T extends Element> {
/**
* Alpha value (0..255) used for visualizing layout data that are normally
* visualized in javascript.
@@ -35,7 +35,7 @@ public interface IAliasConverter<T extends Element> {
* {@link ConverterParams}
*
*/
- void drawAlias(T alias, Graphics2D graphics, ConverterParams params);
+ void drawElement(T alias, Graphics2D graphics, ConverterParams params);
/**
* This function draw representation of the alias on the graphics object.
@@ -53,7 +53,7 @@ public interface IAliasConverter<T extends Element> {
* alias in different layouts that should be overlayed on the alias
*
*/
- void drawAlias(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas);
+ void drawElement(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas);
/**
* This function will find proper font size to display text within it. Then it
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ElementConverterImpl.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ElementConverterImpl.java
new file mode 100644
index 0000000000000000000000000000000000000000..e96615f6ef559df3540a69e0ad871d6760fa35bd
--- /dev/null
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ElementConverterImpl.java
@@ -0,0 +1,192 @@
+package lcsb.mapviewer.converter.graphics;
+
+import java.awt.Graphics2D;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.graphics.compartment.BottomSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.compartment.LeftSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.compartment.OvalCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.compartment.PathwayCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.compartment.RightSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.compartment.SquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.compartment.TopSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.species.AntisenseRnaConverter;
+import lcsb.mapviewer.converter.graphics.species.ComplexConverter;
+import lcsb.mapviewer.converter.graphics.species.DegradedConverter;
+import lcsb.mapviewer.converter.graphics.species.DrugConverter;
+import lcsb.mapviewer.converter.graphics.species.GeneConverter;
+import lcsb.mapviewer.converter.graphics.species.IonConverter;
+import lcsb.mapviewer.converter.graphics.species.PhenotypeConverter;
+import lcsb.mapviewer.converter.graphics.species.ProteinConverter;
+import lcsb.mapviewer.converter.graphics.species.RnaConverter;
+import lcsb.mapviewer.converter.graphics.species.SBGNNucleicAcidFeatureConverter;
+import lcsb.mapviewer.converter.graphics.species.SimpleMoleculeConverter;
+import lcsb.mapviewer.converter.graphics.species.UnknownConverter;
+import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.OvalCompartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
+import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+/**
+ * This class is designed to convert any type of {@link Element} into a graphic
+ * glyph that will be visualized on the {@link Graphics2D} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ElementConverterImpl implements ElementConverter<Element> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ElementConverterImpl.class.getName());
+
+ /**
+ * Returns a converter for given element. If converter doesn't exist then
+ * exception is thrown.
+ *
+ * @param element
+ * {@link Element} for which we are loooking for a converter
+ * @param colorExtractor
+ * object that helps to convert overlay values into colors
+ * @return converter that can be applied for the given element
+ */
+ private ElementConverter<? extends Element> getConverterForElement(Element element, ColorExtractor colorExtractor) {
+ if (element == null) {
+ throw new InvalidArgumentException("element cannot be null");
+ }
+ if (element instanceof GenericProtein) {
+ return new ProteinConverter(colorExtractor);
+ } else if (element instanceof IonChannelProtein) {
+ return new ProteinConverter(colorExtractor);
+ } else if (element instanceof ReceptorProtein) {
+ return new ProteinConverter(colorExtractor);
+ } else if (element instanceof TruncatedProtein) {
+ return new ProteinConverter(colorExtractor);
+ } else if (element instanceof Degraded) {
+ return new DegradedConverter(colorExtractor);
+ } else if (element instanceof Complex) {
+ return new ComplexConverter(colorExtractor);
+ } else if (element instanceof SimpleMolecule) {
+ return new SimpleMoleculeConverter(colorExtractor);
+ } else if (element instanceof Drug) {
+ return new DrugConverter(colorExtractor);
+ } else if (element instanceof Ion) {
+ return new IonConverter(colorExtractor);
+ } else if (element instanceof Phenotype) {
+ return new PhenotypeConverter(colorExtractor);
+ } else if (element instanceof Rna) {
+ return new RnaConverter(colorExtractor);
+ } else if (element instanceof AntisenseRna) {
+ return new AntisenseRnaConverter(colorExtractor);
+ } else if (element instanceof Gene) {
+ return new GeneConverter(colorExtractor);
+ } else if (element instanceof Unknown) {
+ return new UnknownConverter(colorExtractor);
+ } else if (element instanceof SquareCompartment) {
+ return new SquareCompartmentConverter(colorExtractor);
+ } else if (element instanceof OvalCompartment) {
+ return new OvalCompartmentConverter(colorExtractor);
+ } else if (element instanceof PathwayCompartment) {
+ return new PathwayCompartmentConverter(colorExtractor);
+ } else if (element instanceof BottomSquareCompartment) {
+ return new BottomSquareCompartmentConverter(colorExtractor);
+ } else if (element instanceof TopSquareCompartment) {
+ return new TopSquareCompartmentConverter(colorExtractor);
+ } else if (element instanceof LeftSquareCompartment) {
+ return new LeftSquareCompartmentConverter(colorExtractor);
+ } else if (element instanceof RightSquareCompartment) {
+ return new RightSquareCompartmentConverter(colorExtractor);
+ } else {
+ throw new NotImplementedException(new ElementUtils().getElementTag(element) + "Unknown element class");
+ }
+ }
+
+ /**
+ * Converter used for conversion of the {@link Element} given in constructor.
+ */
+ @SuppressWarnings("rawtypes")
+ private ElementConverter elementConverter = null;
+
+ /**
+ * Support constructor. Used in case of SBGN format display
+ *
+ * @param element
+ * {@link Element} for which this converter will be used
+ * @param colorExtractor
+ * object that helps to convert overlay values into colors
+ * @param sbgnFormat
+ * boolean value indicating if SBGN display format should be used
+ */
+ public ElementConverterImpl(final Element element, final boolean sbgnFormat, ColorExtractor colorExtractor) {
+
+ // If element is a nucleic acid feature to be displayed in SBGN
+ if (sbgnFormat && (element instanceof AntisenseRna || element instanceof Rna || element instanceof Gene)) {
+ elementConverter = new SBGNNucleicAcidFeatureConverter(colorExtractor);
+ } else {
+ // If not, at the beginning try to find an appropriate converter
+ elementConverter = getConverterForElement(element, colorExtractor);
+ }
+
+ // if we don't know which converter to use then throw an exception
+ if (elementConverter == null) {
+ throw new InvalidArgumentException("Unknown converter for class: " + element.getClass() + ". Element id: " + element.getElementId());
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * object that helps to convert overlay values into colors
+ * @param element
+ * {@link Element} for which this converter will be used
+ */
+ public ElementConverterImpl(final Element element, ColorExtractor colorExtractor) {
+ this(element, false, colorExtractor);
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public void drawElement(final Element element, final Graphics2D graphics, final ConverterParams params) {
+ elementConverter.drawElement(element, graphics, params);
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public void drawText(final Element element, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ elementConverter.drawText(element, graphics, params);
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public void drawElement(Element element, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
+ elementConverter.drawElement(element, graphics, params, visualizedLayoutsColorSchemas);
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java
index 6c244b13891361d1139e88140ad0a512e502102d..9498239a8b6119e74b3b51136d462066af9f336a 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java
@@ -1,172 +1,173 @@
-package lcsb.mapviewer.converter.graphics;
-
-import java.io.IOException;
-import java.lang.reflect.InvocationTargetException;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-/**
- * This class is a util class containing information about all currently
- * available implementations of {@link AbstractImageGenerator} class.
- *
- * @author Piotr Gawron
- *
- */
-public class ImageGenerators {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ImageGenerators.class);
- /**
- * List of {@link AbstractImageGenerator} classes available in the system.
- */
- private List<Pair<String, Class<? extends AbstractImageGenerator>>> availableGenerators;
-
- /**
- * List of all possible objects extending {@link AbstractImageGenerator}
- * interface that are available in the system.
- */
- private List<AbstractImageGenerator> generatorInstances = null;
-
- /**
- * Default constructor.
- */
- public ImageGenerators() {
- try {
- availableGenerators = new ArrayList<Pair<String, Class<? extends AbstractImageGenerator>>>();
- Model model = new ModelFullIndexed(null);
- AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().//
- model(model).//
- width(1).//
- height(1);
- generatorInstances = new ArrayList<>();
- generatorInstances.add(new PngImageGenerator(params));
- generatorInstances.add(new PdfImageGenerator(params));
-// generatorInstances.add(new SvgImageGenerator(params));
-// generatorInstances.add(new JpgImageGenerator(params));
- for (AbstractImageGenerator abstractImageGenerator : generatorInstances) {
- availableGenerators.add(new Pair<String, Class<? extends AbstractImageGenerator>>(abstractImageGenerator.getFormatName(), abstractImageGenerator
- .getClass()));
- }
-
- } catch (DrawingException e) {
- throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
- }
- }
-
- /**
- * Returns {@link #availableGenerators}.
- *
- * @return {@link #availableGenerators}
- */
- public List<Pair<String, Class<? extends AbstractImageGenerator>>> getAvailableImageGenerators() {
- return availableGenerators;
- }
-
- /**
- * Generates image and saves it to a file.
- *
- * @param generatorClass
- * which {@link AbstractImageGenerator} should be used to generate an
- * image
- * @param params
- * parameters of the image generation process (scaling, size,
- * nesting, etc)
- * @param filename
- * name of the file where result should be saved
- * @return {@link MimeType} of the generated object
- * @throws IOException
- * thrown when there is a problem with output file
- */
- public MimeType generate(Class<? extends AbstractImageGenerator> generatorClass, AbstractImageGenerator.Params params, String filename) throws IOException {
- try {
- AbstractImageGenerator generator = generatorClass.getConstructor(AbstractImageGenerator.Params.class).newInstance(params);
- generator.saveToFile(filename);
- return generator.getMimeType();
- } catch (InstantiationException e) {
- throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
- } catch (IllegalAccessException e) {
- throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
- } catch (IllegalArgumentException e) {
- throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
- } catch (InvocationTargetException e) {
- throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
- } catch (NoSuchMethodException e) {
- throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
- } catch (SecurityException e) {
- throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
- }
- }
-
- /**
- * Generates image and saves it to a file.
- *
- * @param generatorClass
- * name of the {@link AbstractImageGenerator} implementation that
- * should be used to generate an image
- * @param params
- * parameters of the image generation process (scaling, size,
- * nesting, etc)
- * @param filename
- * name of the file where result should be saved
- * @return {@link MimeType} of the generated object
- * @throws IOException
- * thrown when there is a problem with output file
- */
- public MimeType generate(String generatorClass, Params params, String filename) throws IOException {
- for (Pair<String, Class<? extends AbstractImageGenerator>> element : availableGenerators) {
- if (element.getRight().getCanonicalName().equals(generatorClass)) {
- return generate(element.getRight(), params, filename);
- }
- }
- throw new InvalidArgumentException("Unknown class type: " + generatorClass);
-
- }
-
- /**
- * Returns file extension that should be used for files generated by
- * implementation of {@link AbstractImageGenerator} class.
- *
- * @param generatorClass
- * name of the class that extends {@link AbstractImageGenerator}
- * @return file extension that should be used for files generated by
- * implementation of {@link AbstractImageGenerator} class
- */
- public String getExtension(String generatorClass) {
- for (Pair<String, Class<? extends AbstractImageGenerator>> element : availableGenerators) {
- if (element.getRight().getCanonicalName().equals(generatorClass)) {
- return getExtension(element.getRight());
- }
- }
- throw new InvalidArgumentException("Unknown class type: " + generatorClass);
- }
-
- /**
- * Returns file extension that should be used for files generated by
- * implementation of {@link AbstractImageGenerator} class.
- *
- * @param generatorClass
- * class that extends {@link AbstractImageGenerator}
- * @return file extension that should be used for files generated by
- * implementation of {@link AbstractImageGenerator} class
- */
- public String getExtension(Class<? extends AbstractImageGenerator> generatorClass) {
- for (AbstractImageGenerator imageGenerator : generatorInstances) {
- if (generatorClass.isAssignableFrom(imageGenerator.getClass())) {
- return imageGenerator.getFileExtension();
- }
- }
- throw new InvalidArgumentException("Unknown class type: " + generatorClass);
- }
-}
+package lcsb.mapviewer.converter.graphics;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+/**
+ * This class is a util class containing information about all currently
+ * available implementations of {@link AbstractImageGenerator} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ImageGenerators {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ImageGenerators.class);
+ /**
+ * List of {@link AbstractImageGenerator} classes available in the system.
+ */
+ private List<Pair<String, Class<? extends AbstractImageGenerator>>> availableGenerators;
+
+ /**
+ * List of all possible objects extending {@link AbstractImageGenerator}
+ * interface that are available in the system.
+ */
+ private List<AbstractImageGenerator> generatorInstances = null;
+
+ /**
+ * Default constructor.
+ */
+ public ImageGenerators() {
+ try {
+ availableGenerators = new ArrayList<Pair<String, Class<? extends AbstractImageGenerator>>>();
+ Model model = new ModelFullIndexed(null);
+ AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().//
+ model(model).//
+ width(1).//
+ minColor(Color.WHITE).maxColor(Color.WHITE).height(1);
+ generatorInstances = new ArrayList<>();
+ generatorInstances.add(new PngImageGenerator(params));
+ generatorInstances.add(new PdfImageGenerator(params));
+ // generatorInstances.add(new SvgImageGenerator(params));
+ // generatorInstances.add(new JpgImageGenerator(params));
+ for (AbstractImageGenerator abstractImageGenerator : generatorInstances) {
+ availableGenerators
+ .add(new Pair<String, Class<? extends AbstractImageGenerator>>(abstractImageGenerator.getFormatName(), abstractImageGenerator.getClass()));
+ }
+
+ } catch (DrawingException e) {
+ throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
+ }
+ }
+
+ /**
+ * Returns {@link #availableGenerators}.
+ *
+ * @return {@link #availableGenerators}
+ */
+ public List<Pair<String, Class<? extends AbstractImageGenerator>>> getAvailableImageGenerators() {
+ return availableGenerators;
+ }
+
+ /**
+ * Generates image and saves it to a file.
+ *
+ * @param generatorClass
+ * which {@link AbstractImageGenerator} should be used to generate an
+ * image
+ * @param params
+ * parameters of the image generation process (scaling, size,
+ * nesting, etc)
+ * @param filename
+ * name of the file where result should be saved
+ * @return {@link MimeType} of the generated object
+ * @throws IOException
+ * thrown when there is a problem with output file
+ */
+ public MimeType generate(Class<? extends AbstractImageGenerator> generatorClass, AbstractImageGenerator.Params params, String filename) throws IOException {
+ try {
+ AbstractImageGenerator generator = generatorClass.getConstructor(AbstractImageGenerator.Params.class).newInstance(params);
+ generator.saveToFile(filename);
+ return generator.getMimeType();
+ } catch (InstantiationException e) {
+ throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
+ } catch (IllegalAccessException e) {
+ throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
+ } catch (IllegalArgumentException e) {
+ throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
+ } catch (InvocationTargetException e) {
+ throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
+ } catch (NoSuchMethodException e) {
+ throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
+ } catch (SecurityException e) {
+ throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
+ }
+ }
+
+ /**
+ * Generates image and saves it to a file.
+ *
+ * @param generatorClass
+ * name of the {@link AbstractImageGenerator} implementation that
+ * should be used to generate an image
+ * @param params
+ * parameters of the image generation process (scaling, size,
+ * nesting, etc)
+ * @param filename
+ * name of the file where result should be saved
+ * @return {@link MimeType} of the generated object
+ * @throws IOException
+ * thrown when there is a problem with output file
+ */
+ public MimeType generate(String generatorClass, Params params, String filename) throws IOException {
+ for (Pair<String, Class<? extends AbstractImageGenerator>> element : availableGenerators) {
+ if (element.getRight().getCanonicalName().equals(generatorClass)) {
+ return generate(element.getRight(), params, filename);
+ }
+ }
+ throw new InvalidArgumentException("Unknown class type: " + generatorClass);
+
+ }
+
+ /**
+ * Returns file extension that should be used for files generated by
+ * implementation of {@link AbstractImageGenerator} class.
+ *
+ * @param generatorClass
+ * name of the class that extends {@link AbstractImageGenerator}
+ * @return file extension that should be used for files generated by
+ * implementation of {@link AbstractImageGenerator} class
+ */
+ public String getExtension(String generatorClass) {
+ for (Pair<String, Class<? extends AbstractImageGenerator>> element : availableGenerators) {
+ if (element.getRight().getCanonicalName().equals(generatorClass)) {
+ return getExtension(element.getRight());
+ }
+ }
+ throw new InvalidArgumentException("Unknown class type: " + generatorClass);
+ }
+
+ /**
+ * Returns file extension that should be used for files generated by
+ * implementation of {@link AbstractImageGenerator} class.
+ *
+ * @param generatorClass
+ * class that extends {@link AbstractImageGenerator}
+ * @return file extension that should be used for files generated by
+ * implementation of {@link AbstractImageGenerator} class
+ */
+ public String getExtension(Class<? extends AbstractImageGenerator> generatorClass) {
+ for (AbstractImageGenerator imageGenerator : generatorInstances) {
+ if (generatorClass.isAssignableFrom(imageGenerator.getClass())) {
+ return imageGenerator.getFileExtension();
+ }
+ }
+ throw new InvalidArgumentException("Unknown class type: " + generatorClass);
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/BottomSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/BottomSquareCompartmentConverter.java
index 25d9cdd4f3a5f8996c28ad3132986912046a1ede..07087ec3cda0e74b620bdda4b2b59ed1a0e90fe5 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/BottomSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/BottomSquareCompartmentConverter.java
@@ -9,9 +9,12 @@ import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Species;
import org.apache.log4j.Logger;
@@ -29,8 +32,19 @@ public class BottomSquareCompartmentConverter extends CompartmentConverter<Botto
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(BottomSquareCompartmentConverter.class.getName());
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public BottomSquareCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
@Override
- public void drawAlias(final BottomSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(final BottomSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of colors and line
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/CompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/CompartmentConverter.java
index 0c13be576a94d63084d3ce6c71666edb38080af4..ce31fb93bb7d3440fb7c0aeb93c28c7a37cc4e09 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/CompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/CompartmentConverter.java
@@ -8,12 +8,13 @@ import java.util.List;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.geometry.EllipseTransformation;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.IAliasConverter;
+import lcsb.mapviewer.converter.graphics.ElementConverter;
import lcsb.mapviewer.converter.graphics.geometry.FontFinder;
import lcsb.mapviewer.converter.graphics.geometry.RectangleTooSmallException;
import lcsb.mapviewer.converter.graphics.placefinder.PlaceFinder;
@@ -30,7 +31,7 @@ import lcsb.mapviewer.model.map.layout.ColorSchema;
* class for which the comparator is created
*
*/
-public abstract class CompartmentConverter<T extends Compartment> implements IAliasConverter<T> {
+public abstract class CompartmentConverter<T extends Compartment> implements ElementConverter<T> {
/**
* Default class logger.
@@ -79,9 +80,20 @@ public abstract class CompartmentConverter<T extends Compartment> implements IAl
private String placeFinderSynchronization = "";
/**
- * Default constructor.
+ * Object that helps to convert {@link ColorSchema} values into colors.
*/
- protected CompartmentConverter() {
+ private ColorExtractor colorExtractor;
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing elements
+ *
+ */
+ protected CompartmentConverter(ColorExtractor colorExtractor) {
+ this.colorExtractor = colorExtractor;
};
@Override
@@ -163,8 +175,8 @@ public abstract class CompartmentConverter<T extends Compartment> implements IAl
}
@Override
- public void drawAlias(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
- drawAlias(alias, graphics, params);
+ public void drawElement(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
+ drawElement(alias, graphics, params);
Color oldColor = graphics.getColor();
int count = 0;
@@ -177,7 +189,7 @@ public abstract class CompartmentConverter<T extends Compartment> implements IAl
int x = (int) (startX * alias.getWidth() + alias.getX());
graphics.drawRect(x, alias.getY().intValue(), (int) width, alias.getHeight().intValue());
- Color color = schema.getNormalizedColor();
+ Color color = colorExtractor.getNormalizedColor(schema);
Color bgAlphaColor = new Color(color.getRed(), color.getGreen(), color.getBlue(), LAYOUT_ALPHA);
graphics.setColor(bgAlphaColor);
graphics.fillRect(x, alias.getY().intValue(), (int) width, alias.getHeight().intValue());
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/LeftSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/LeftSquareCompartmentConverter.java
index 5d3f1a7fa506f6c6fe4d03091ba87469fb5ee1ce..a3cac76c0bfe0a722fcc95c45f004c942ce9431e 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/LeftSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/LeftSquareCompartmentConverter.java
@@ -9,9 +9,11 @@ import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
import org.apache.log4j.Logger;
@@ -22,14 +24,27 @@ import org.apache.log4j.Logger;
*
*/
public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSquareCompartment> {
+
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(LeftSquareCompartmentConverter.class.getName());
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing elements
+ *
+ */
+ public LeftSquareCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
@Override
- public void drawAlias(final LeftSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(final LeftSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/OvalCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/OvalCompartmentConverter.java
index e13e233558f04ca5a2d5562c2e8e1896a5ddb00a..3c385168fb6c31a65aa5eff8c7e1873afa43b57d 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/OvalCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/OvalCompartmentConverter.java
@@ -8,10 +8,13 @@ import java.awt.geom.Area;
import java.awt.geom.Ellipse2D;
import java.awt.geom.Point2D;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.compartment.OvalCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Class responsible for drawing OvalCompartment on the Graphics2D.
@@ -21,6 +24,17 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartment> {
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public OvalCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
/**
* Returns shape representing alias.
*
@@ -33,7 +47,7 @@ public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartme
}
@Override
- public void drawAlias(final OvalCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(final OvalCompartment alias, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/ArtifitialCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/PathwayCompartmentConverter.java
similarity index 64%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/ArtifitialCompartmentConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/PathwayCompartmentConverter.java
index 17dd4f37e2730f74b23630eb67a559ca80999e8c..a3d6fd00ffdb31571a81b3acd9e92cc60a7c9554 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/ArtifitialCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/PathwayCompartmentConverter.java
@@ -7,24 +7,40 @@ import java.awt.Stroke;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Species;
/**
- * This class allows to draw ArtifitialCompartment on the Graphics2D class.
+ * This class allows to draw {@link PathwayCompartment} on the
+ * {@link Graphics2D} class.
*
* @author Piotr Gawron
*
*/
-public class ArtifitialCompartmentConverter extends CompartmentConverter<PathwayCompartment> {
+public class PathwayCompartmentConverter extends CompartmentConverter<PathwayCompartment> {
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public PathwayCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
/**
* Background color of drawn compartments.
*/
- private Color backgroundColor = Color.LIGHT_GRAY;
+ private Color backgroundColor = Color.LIGHT_GRAY;
@Override
- public void drawAlias(final PathwayCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(final PathwayCompartment alias, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of colors and line
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/RightSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/RightSquareCompartmentConverter.java
index 5fa37bec8fa4d36d78c84b0e93c7394ae680bb4c..72099129b6492cce9758c90f0e32d4e25c0d44cf 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/RightSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/RightSquareCompartmentConverter.java
@@ -9,9 +9,12 @@ import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Species;
import org.apache.log4j.Logger;
@@ -22,14 +25,26 @@ import org.apache.log4j.Logger;
*
*/
public class RightSquareCompartmentConverter extends CompartmentConverter<RightSquareCompartment> {
+
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(RightSquareCompartmentConverter.class.getName());
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public RightSquareCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
@Override
- public void drawAlias(final RightSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(final RightSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/SquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/SquareCompartmentConverter.java
index d07657464f021191aebafcdb57b7ca17e1064997..e67b330c239c03743dc7cb27accd089e80a8efc3 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/SquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/SquareCompartmentConverter.java
@@ -8,12 +8,15 @@ import java.awt.geom.Area;
import java.awt.geom.Point2D;
import java.awt.geom.RoundRectangle2D;
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Element;
-
-import org.apache.log4j.Logger;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Class responsible for drawing SquareCompartment on the Graphics2D.
@@ -26,12 +29,23 @@ public class SquareCompartmentConverter extends CompartmentConverter<SquareCompa
* How big is the arc in the corner of rectangle that represents square
* compartment.
*/
- private static final int RECTANGLE_CORNER_ARC_SIZE = 20;
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 20;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SquareCompartmentConverter.class.getName());
+ private static Logger logger = Logger.getLogger(SquareCompartmentConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public SquareCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
/**
* Returns shape representing alias.
@@ -45,7 +59,7 @@ public class SquareCompartmentConverter extends CompartmentConverter<SquareCompa
}
@Override
- public void drawAlias(final SquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(final SquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/TopSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/TopSquareCompartmentConverter.java
index afc5febcff0fffa9647abe7febc0809f126f12a6..b074e084f5a04ee262d697be3c8896df9cf3f0fc 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/TopSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/TopSquareCompartmentConverter.java
@@ -9,9 +9,12 @@ import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Species;
import org.apache.log4j.Logger;
@@ -29,8 +32,19 @@ public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquar
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(TopSquareCompartmentConverter.class.getName());
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public TopSquareCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
@Override
- public void drawAlias(final TopSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(final TopSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/reaction/ReactionConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/reaction/ReactionConverter.java
index 37120db85f0dd98fed970070fd5e19423ab39586..2697266eb836e792f109627dfb8afde82d028b29 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/reaction/ReactionConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/reaction/ReactionConverter.java
@@ -13,6 +13,7 @@ import java.util.List;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.common.geometry.PointTransformation;
@@ -102,12 +103,22 @@ public class ReactionConverter {
*/
private PointTransformation pointTransformation = new PointTransformation();
+ /**
+ * Object that helps to convert {@link ColorSchema} values into colors.
+ */
+ private ColorExtractor colorExtractor;
+
/**
* Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Reaction}
*/
- public ReactionConverter() {
+ public ReactionConverter(ColorExtractor colorExtractor) {
super();
descFont = new Font(Font.SANS_SERIF, Font.BOLD, DESCRIPTION_FONT_SIZE);
+ this.colorExtractor = colorExtractor;
}
/**
@@ -273,7 +284,7 @@ public class ReactionConverter {
private void applyColorSchema(Reaction reaction, ColorSchema colorSchema) {
for (AbstractNode node : reaction.getNodes()) {
PolylineData pd = new PolylineData(node.getLine());
- pd.setColor(colorSchema.getNormalizedColor());
+ pd.setColor(colorExtractor.getNormalizedColor(colorSchema));
if (colorSchema.getLineWidth() != null) {
pd.setWidth(colorSchema.getLineWidth());
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/AntisenseRnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/AntisenseRnaConverter.java
index 1bbb52b6c37c1fda1d805179078cef5cf06b85af..acc16bc98c697e1728e5f007131d20e9e1fc7698 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/AntisenseRnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/AntisenseRnaConverter.java
@@ -13,8 +13,11 @@ import java.awt.geom.Point2D;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
import lcsb.mapviewer.model.map.species.field.ModificationState;
@@ -34,8 +37,20 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(AntisenseRnaConverter.class.getName());
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public AntisenseRnaConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+
@Override
- public void drawAlias(final AntisenseRna alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(final AntisenseRna alias, final Graphics2D graphics, final ConverterParams params) {
GeneralPath path = getAntisenseRnaPath(alias);
Color c = graphics.getColor();
graphics.setColor(alias.getColor());
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ComplexConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ComplexConverter.java
index ac517c50d6d1055edb7b6acd090f136224062e1a..6a59e89cc68ad9229d7118f5df8ebefaac3a4695 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ComplexConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ComplexConverter.java
@@ -11,11 +11,14 @@ import java.awt.geom.PathIterator;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.converter.graphics.geometry.FontFinder;
import lcsb.mapviewer.converter.graphics.geometry.RectangleTooSmallException;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Complex;
/**
@@ -42,8 +45,20 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
*/
private static Logger logger = Logger.getLogger(ComplexConverter.class.getName());
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public ComplexConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+
@Override
- public void drawAlias(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
if (alias.getState().equalsIgnoreCase("complexnoborder")) {
return;
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DegradedConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DegradedConverter.java
index 44c0b254b2033e89cbdfe47bc0ebb7c53673738c..de6bcebb35da9439fd6481b637120d3c3532410d 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DegradedConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DegradedConverter.java
@@ -9,13 +9,16 @@ import java.awt.geom.GeneralPath;
import java.awt.geom.Path2D;
import java.awt.geom.PathIterator;
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Degraded;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
-import org.apache.log4j.Logger;
-
/**
* This class defines methods used for drawing Degraded SpeciesAlias on the
* graphics2d object.
@@ -23,19 +26,31 @@ import org.apache.log4j.Logger;
* @author Piotr Gawron
*
*/
-public class DegradedConverter extends SpeciesConverter<Species> {
+public class DegradedConverter extends SpeciesConverter<Degraded> {
/**
* Part of height of the line used to cross degraded circle that goes behind
* this circle.
*/
- private static final int CROSS_LINE_EXTENDED_LENGTH = 7;
+ private static final int CROSS_LINE_EXTENDED_LENGTH = 7;
+
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(DegradedConverter.class.getName());
+ private static Logger logger = Logger.getLogger(DegradedConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public DegradedConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
@Override
- public void drawAlias(final Species alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(final Degraded alias, final Graphics2D graphics, final ConverterParams params) {
double diameter = getDiameter(alias);
double x = getXCoord(alias, diameter);
double y = getYCoord(alias);
@@ -109,12 +124,12 @@ public class DegradedConverter extends SpeciesConverter<Species> {
}
@Override
- public String getText(final Species alias) {
+ public String getText(Degraded alias) {
return "";
}
@Override
- public PathIterator getBoundPathIterator(final Species alias) {
+ public PathIterator getBoundPathIterator(Degraded alias) {
throw new InvalidStateException("This class doesn't have bound");
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DrugConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DrugConverter.java
index f737787cac91a953f5a6f8091c0035d73f03f50f..f55cf04258bfecf782c8c28dd94e6fddad6b9fc8 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DrugConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DrugConverter.java
@@ -10,7 +10,10 @@ import java.awt.geom.Point2D;
import java.awt.geom.RoundRectangle2D;
import java.util.ArrayList;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Drug;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
@@ -23,22 +26,36 @@ import org.apache.log4j.Logger;
* @author Piotr Gawron
*
*/
-public class DrugConverter extends SpeciesConverter<Species> {
+public class DrugConverter extends SpeciesConverter<Drug> {
+
/**
* Distance between internal and external border of drug graphical
* representation.
*/
private static final int OFFSET_BETWEEN_BORDERS = 4;
+
/**
* How big should be the arc in rectangle for drug representation.
*/
private static final int RECTANGLE_CORNER_ARC_SIZE = 40;
+
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(DrugConverter.class.getName());
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public DrugConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
/**
* Returns shape of the Drug .
*
@@ -51,7 +68,7 @@ public class DrugConverter extends SpeciesConverter<Species> {
}
@Override
- public void drawAlias(final Species alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(Drug alias, final Graphics2D graphics, final ConverterParams params) {
Shape a1 = getDrugShape(alias);
double offset = OFFSET_BETWEEN_BORDERS;
Shape a2 = new RoundRectangle2D.Double(
@@ -99,7 +116,7 @@ public class DrugConverter extends SpeciesConverter<Species> {
}
@Override
- public PathIterator getBoundPathIterator(final Species alias) {
+ public PathIterator getBoundPathIterator(Drug alias) {
return getDrugShape(alias).getPathIterator(new AffineTransform());
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/GeneConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/GeneConverter.java
index 195dd99d7c0a7ff240785f6e204065c75847f6f4..f5493ee149bf9f9270bc0b25eeb205ca0bcf3b2b 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/GeneConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/GeneConverter.java
@@ -13,9 +13,12 @@ import java.awt.geom.Point2D;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.ModificationState;
@@ -33,8 +36,19 @@ public class GeneConverter extends SpeciesConverter<Gene> {
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(GeneConverter.class.getName());
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public GeneConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
@Override
- public void drawAlias(final Gene alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(final Gene alias, final Graphics2D graphics, final ConverterParams params) {
Shape shape = getGeneShape(alias);
Color c = graphics.getColor();
graphics.setColor(alias.getColor());
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/IonConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/IonConverter.java
index 34f5a147c07650ed66011f25c5da64944307be88..fe8699ac7232e1d7468cc45a52834fb9c2309c89 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/IonConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/IonConverter.java
@@ -8,29 +8,44 @@ import java.awt.geom.Ellipse2D;
import java.awt.geom.PathIterator;
import java.awt.geom.Point2D;
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.model.map.species.Species;
-import org.apache.log4j.Logger;
-
/**
* This class defines methods used for drawing SpeciesAlias of
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.Ion Ion} on the {@link Graphics2D}
- * object.
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.Ion
+ * Ion} on the {@link Graphics2D} object.
*
* @author Piotr Gawron
*
*/
-public class IonConverter extends SpeciesConverter<Species> {
+public class IonConverter extends SpeciesConverter<Ion> {
+
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(IonConverter.class.getName());
+ private static Logger logger = Logger.getLogger(IonConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public IonConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
@Override
- public void drawAlias(final Species alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(Ion alias, final Graphics2D graphics, final ConverterParams params) {
double diameter = getDiameter(alias);
double x = getXCoord(alias, diameter);
double y = getYCoord(alias);
@@ -90,12 +105,12 @@ public class IonConverter extends SpeciesConverter<Species> {
}
@Override
- public PathIterator getBoundPathIterator(final Species alias) {
+ public PathIterator getBoundPathIterator(Ion alias) {
throw new InvalidStateException("This class doesn't have bound");
}
@Override
- public Point2D getPointCoordinatesOnBorder(final Species alias, final double angle) {
+ public Point2D getPointCoordinatesOnBorder(Ion alias, final double angle) {
if (alias.getWidth() == 0 && alias.getHeight() == 0) {
logger.warn("Looking for coordinates for the alias with 0 size");
return alias.getCenter();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/PhenotypeConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/PhenotypeConverter.java
index 6dba03ff813dfab8eedbcf7a481e5a3ab5c191e2..4ca043e2104412058387ac522854ba0350a028f6 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/PhenotypeConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/PhenotypeConverter.java
@@ -8,29 +8,43 @@ import java.awt.geom.GeneralPath;
import java.awt.geom.Path2D;
import java.awt.geom.PathIterator;
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-import org.apache.log4j.Logger;
+import lcsb.mapviewer.model.map.species.Phenotype;
/**
* This class defines methods used for drawing SpeciesAlias of
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.Phenotype Phenotype} on the
- * {@link Graphics2D} object.
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.Phenotype
+ * Phenotype} on the {@link Graphics2D} object.
*
* @author Piotr Gawron
*
*/
-public class PhenotypeConverter extends SpeciesConverter<Species> {
+public class PhenotypeConverter extends SpeciesConverter<Phenotype> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(PhenotypeConverter.class.getName());
+ private static Logger logger = Logger.getLogger(PhenotypeConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing elements
+ *
+ */
+ public PhenotypeConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
@Override
- public void drawAlias(final Species alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(Phenotype alias, final Graphics2D graphics, final ConverterParams params) {
GeneralPath path = getPhenotypePath(alias);
Color c = graphics.getColor();
@@ -66,7 +80,7 @@ public class PhenotypeConverter extends SpeciesConverter<Species> {
}
@Override
- public PathIterator getBoundPathIterator(final Species alias) {
+ public PathIterator getBoundPathIterator(Phenotype alias) {
return getPhenotypePath(alias).getPathIterator(new AffineTransform());
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ProteinConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ProteinConverter.java
index 4940e5d439bfb89945ccdecee6ba3fb5ad8f49df..b3af8c09cb91bea6ed909a61ab5a3a002e12a1c3 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ProteinConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ProteinConverter.java
@@ -17,10 +17,12 @@ import java.util.ArrayList;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.IonChannelProtein;
@@ -40,6 +42,7 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*
*/
public class ProteinConverter extends SpeciesConverter<Protein> {
+
/**
* Width of the ion part in the open channel representation.
*/
@@ -63,6 +66,17 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
*/
private ElementUtils eu = new ElementUtils();
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public ProteinConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
/**
* Returns shape of generic protein.
*
@@ -75,7 +89,7 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
}
@Override
- public void drawAlias(final Protein alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(final Protein alias, final Graphics2D graphics, final ConverterParams params) {
// Local variable setting the SBGN visualization
boolean sbgnFormat = params.isSbgnFormat();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/RnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/RnaConverter.java
index 67e92e517fb18929070a49930720d2b0a90453c4..6b13ac398f659d0b965f6f2d8797e720511443e4 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/RnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/RnaConverter.java
@@ -1,3 +1,10 @@
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
package lcsb.mapviewer.converter.graphics.species;
import java.awt.Color;
@@ -13,9 +20,12 @@ import java.awt.geom.Point2D;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.ModificationState;
import lcsb.mapviewer.model.map.species.field.RnaRegion;
@@ -33,8 +43,19 @@ public class RnaConverter extends SpeciesConverter<Rna> {
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(RnaConverter.class.getName());
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public RnaConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
@Override
- public void drawAlias(final Rna alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(final Rna alias, final Graphics2D graphics, final ConverterParams params) {
GeneralPath path = getRnaPath(alias);
Color c = graphics.getColor();
graphics.setColor(alias.getColor());
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SBGNNucleicAcidFeatureConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SBGNNucleicAcidFeatureConverter.java
index 00048fa5567e150811d9ee8296200b2186fe9f8f..8dc25a7ffdc7ca1c1062f006dcc39fc15f75612b 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SBGNNucleicAcidFeatureConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SBGNNucleicAcidFeatureConverter.java
@@ -8,7 +8,9 @@ import java.awt.geom.AffineTransform;
import java.awt.geom.GeneralPath;
import java.awt.geom.PathIterator;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
@@ -28,6 +30,17 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<Species> {
*/
private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public SBGNNucleicAcidFeatureConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
/**
* Returns shape of SBGN Nucleic acid feature.
*
@@ -51,7 +64,7 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<Species> {
}
@Override
- public void drawAlias(Species alias, Graphics2D graphics, ConverterParams params) {
+ public void drawElement(Species alias, Graphics2D graphics, ConverterParams params) {
// Unit of information text - multimer cardinality
String unitOfInformationText = null;
if (alias.getStatePrefix() != null && alias.getStateLabel() != null) {
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SimpleMoleculeConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SimpleMoleculeConverter.java
index 4825edbcbf2efdd98de61165da1f7664898824e0..ca287bfc971da7cc9ab21e0174bc187887b99543 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SimpleMoleculeConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SimpleMoleculeConverter.java
@@ -10,9 +10,12 @@ import java.awt.geom.Point2D;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class defines methods used for drawing {@link SimpleMolecule} on
@@ -27,8 +30,19 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
*/
private static Logger logger = Logger.getLogger(SimpleMoleculeConverter.class.getName());
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public SimpleMoleculeConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
@Override
- public void drawAlias(final SimpleMolecule alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(final SimpleMolecule alias, final Graphics2D graphics, final ConverterParams params) {
int homodir;
if (params.isSbgnFormat()) {
// If the SBGN display mode is set, multimer is shown as two stacked
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverter.java
index 66bb702701978c54629e16a33e64c375c5cf0422..cf3ca8313cb36184ca0b76ab1da5090fe3f8ac53 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverter.java
@@ -15,12 +15,13 @@ import java.util.List;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.geometry.EllipseTransformation;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.IAliasConverter;
+import lcsb.mapviewer.converter.graphics.ElementConverter;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Complex;
@@ -28,15 +29,15 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
- * This class defines basics used for drawing aliases of {@link Species}
- * (node in the graph representation) on the graphics2d object.
+ * This class defines basics used for drawing aliases of {@link Species} (node
+ * in the graph representation) on the graphics2d object.
*
* @param <T>
* alias class that can be drawn with this converter
* @author Piotr Gawron
*
*/
-public abstract class SpeciesConverter<T extends Species> implements IAliasConverter<T> {
+public abstract class SpeciesConverter<T extends Species> implements ElementConverter<T> {
/**
* PI value.
@@ -144,11 +145,21 @@ public abstract class SpeciesConverter<T extends Species> implements IAliasConve
*/
public static final int HOMODIMER_OFFSET = 6;
+ /**
+ * Object that helps to convert {@link ColorSchema} values into colors.
+ */
+ private ColorExtractor colorExtractor;
+
/**
* Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
*/
- protected SpeciesConverter() {
+ protected SpeciesConverter(ColorExtractor colorExtractor) {
structuralFont = new Font(Font.SANS_SERIF, 0, DEFAULT_SPECIES_MODIFIER_FONT_SIZE);
+ this.colorExtractor = colorExtractor;
};
/**
@@ -565,8 +576,8 @@ public abstract class SpeciesConverter<T extends Species> implements IAliasConve
}
@Override
- public void drawAlias(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
- drawAlias(alias, graphics, params);
+ public void drawElement(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
+ drawElement(alias, graphics, params);
Color oldColor = graphics.getColor();
int count = 0;
@@ -579,7 +590,7 @@ public abstract class SpeciesConverter<T extends Species> implements IAliasConve
int x = (int) (startX * alias.getWidth() + alias.getX());
graphics.drawRect(x, alias.getY().intValue(), (int) width, alias.getHeight().intValue());
- Color color = schema.getNormalizedColor();
+ Color color = colorExtractor.getNormalizedColor(schema);
Color bgAlphaColor = new Color(color.getRed(), color.getGreen(), color.getBlue(), LAYOUT_ALPHA);
graphics.setColor(bgAlphaColor);
graphics.fillRect(x, alias.getY().intValue(), (int) width, alias.getHeight().intValue());
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/UnknownConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/UnknownConverter.java
index 7063ad399c80761b16b912cd1c881ed82a1a2ba3..4d2045ebf9b86289bebdfb842b970ed688d1f31c 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/UnknownConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/UnknownConverter.java
@@ -8,29 +8,44 @@ import java.awt.geom.Ellipse2D;
import java.awt.geom.PathIterator;
import java.awt.geom.Point2D;
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Species;
-
-import org.apache.log4j.Logger;
+import lcsb.mapviewer.model.map.species.Unknown;
/**
* This class defines methods used for drawing SpeciesAlias of
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.Unknown Unknown} on the
- * {@link Graphics2D} object.
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.Unknown
+ * Unknown} on the {@link Graphics2D} object.
*
* @author Piotr Gawron
*
*/
-public class UnknownConverter extends SpeciesConverter<Species> {
+public class UnknownConverter extends SpeciesConverter<Unknown> {
+
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(UnknownConverter.class.getName());
+ private static Logger logger = Logger.getLogger(UnknownConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public UnknownConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
@Override
- public void drawAlias(final Species alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawElement(Unknown alias, final Graphics2D graphics, final ConverterParams params) {
if (alias.getActivity()) {
int border = ACTIVITY_BORDER_DISTANCE;
alias.increaseBorder(border);
@@ -51,12 +66,12 @@ public class UnknownConverter extends SpeciesConverter<Species> {
}
@Override
- public PathIterator getBoundPathIterator(final Species alias) {
+ public PathIterator getBoundPathIterator(Unknown alias) {
throw new InvalidStateException("This class doesn't provide boundPath");
}
@Override
- public Point2D getPointCoordinatesOnBorder(final Species alias, final double angle) {
+ public Point2D getPointCoordinatesOnBorder(Unknown alias, final double angle) {
if (alias.getWidth() == 0 && alias.getHeight() == 0) {
logger.warn("Looking for coordinates for unknown of 0 size");
return alias.getCenter();
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
index cf5bba155b99e404d87ee662aaf335f4534d2508..66e7eaa7edd963b522a6713a7e7c66d0bd7ad385 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
@@ -1,11 +1,12 @@
package lcsb.mapviewer.converter.graphics;
-import static org.junit.Assert.fail;
+import java.awt.Color;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
@@ -24,13 +25,14 @@ public class ConverterTest {
@Test
public void test() {
try {
- new AliasConverter(new BottomSquareCompartment("id1"));
- new AliasConverter(new TopSquareCompartment("id2"));
- new AliasConverter(new LeftSquareCompartment("id3"));
- new AliasConverter(new RightSquareCompartment("id4"));
- }catch (Exception e) {
+ ColorExtractor colorExtractor = new ColorExtractor(Color.BLUE, Color.RED);
+ new ElementConverterImpl(new BottomSquareCompartment("id1"), colorExtractor);
+ new ElementConverterImpl(new TopSquareCompartment("id2"), colorExtractor);
+ new ElementConverterImpl(new LeftSquareCompartment("id3"), colorExtractor);
+ new ElementConverterImpl(new RightSquareCompartment("id4"), colorExtractor);
+ } catch (Exception e) {
e.printStackTrace();
- fail("Unknown exception");
+ throw e;
}
}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
index 3ba9e0c966a8b6f4210875b30d435c1147988538..36d384f0070428c4f17bd8681ab851e7a1fa8a9b 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
@@ -1,7 +1,6 @@
package lcsb.mapviewer.converter.graphics;
import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
import java.awt.Color;
import java.awt.Graphics2D;
@@ -13,19 +12,16 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
-import lcsb.mapviewer.converter.graphics.compartment.ArtifitialCompartmentConverter;
import lcsb.mapviewer.converter.graphics.species.ComplexConverter;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
public class NormalImageGeneratorTest {
static Logger logger = Logger.getLogger(NormalImageGenerator.class);
@@ -51,85 +47,19 @@ public class NormalImageGeneratorTest {
}
class TmpComplexConverter extends ComplexConverter {
- @Override
- public void drawText(Complex compAlias, Graphics2D graphics, ConverterParams params) {
- setScale(params.getScale());
- setCentered(params.isTextCentered());
- super.drawText(compAlias, graphics, params);
- }
-
- }
-
- @Test
- public void testComplexConversion() throws Exception {
- scale = null;
- try {
- AliasConverter.addAliasConverter(Complex.class, new TmpComplexConverter());
-
- Model model = createComplexModel();
- new CreateHierarchyCommand(model, 2, 2).execute();
- new PngImageGenerator(new Params().scale(2).width(600).height(600).model(model).level(0).nested(true));
-
- // test if font was scaled
- assertTrue(scale > 1.0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
+ public TmpComplexConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
}
- }
-
- private Model createComplexModel() {
- Model model = new ModelFullIndexed(null);
- model.setWidth(600);
- model.setHeight(600);
- Complex alias = new Complex("1");
- alias.setName("a");
- alias.setX(10);
- alias.setY(10);
- alias.setWidth(200);
- alias.setHeight(50);
- model.addElement(alias);
-
- Species a2 = new GenericProtein("2");
- a2.setName("b");
- a2.setX(10);
- a2.setY(100);
- a2.setWidth(200);
- a2.setHeight(50);
- a2.setFontSize(30);
- model.addElement(a2);
- return model;
- }
-
- class TmpArtifitialConverter extends ArtifitialCompartmentConverter {
@Override
- public void drawText(PathwayCompartment compAlias, Graphics2D graphics, ConverterParams params) {
+ public void drawText(Complex compAlias, Graphics2D graphics, ConverterParams params) {
setScale(params.getScale());
setCentered(params.isTextCentered());
- setArtifitialCalled(true);
super.drawText(compAlias, graphics, params);
}
}
- @Test
- public void testNestedCompartmentsConversion() throws Exception {
- scale = null;
- try {
- AliasConverter.addAliasConverter(PathwayCompartment.class, new TmpArtifitialConverter());
- Model model = createCompartmentModel();
- new CreateHierarchyCommand(model, 2, 2).execute();
- new PngImageGenerator(new Params().scale(2).width(600).height(600).model(model).level(0).nested(true));
-
- assertTrue(centered);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
private Model createCompartmentModel() {
Model model = new ModelFullIndexed(null);
model.setWidth(526);
@@ -164,7 +94,9 @@ public class NormalImageGeneratorTest {
public void testArtifitialInNonHierarchicalView() throws Exception {
scale = null;
try {
- AliasConverter.addAliasConverter(PathwayCompartment.class, new TmpArtifitialConverter());
+ // TODO fix it
+ // AliasConverter.addAliasConverter(PathwayCompartment.class, new
+ // TmpArtifitialConverter());
setArtifitialCalled(false);
Model model = createCompartmentModel();
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/reaction/ReactionConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/reaction/ReactionConverterTest.java
index 199487232b6226636d96a4a9fa18a37e5c9c2538..fa4a9c6b2b145e8f3f3ea2f6b450c254a06d6f96 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/reaction/ReactionConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/reaction/ReactionConverterTest.java
@@ -17,6 +17,7 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
@@ -28,6 +29,8 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
public class ReactionConverterTest {
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+
@Before
public void setUp() throws Exception {
}
@@ -41,7 +44,7 @@ public class ReactionConverterTest {
try {
BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
Graphics2D graphics = bi.createGraphics();
- ReactionConverter rc = new ReactionConverter();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
Reaction reaction = createReaction(5.0);
rc.drawReaction(reaction, graphics, false);
@@ -85,7 +88,7 @@ public class ReactionConverterTest {
try {
BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
Graphics2D graphics = bi.createGraphics();
- ReactionConverter rc = new ReactionConverter();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
Reaction reaction = createReaction(1.0);
rc.drawReaction(reaction, graphics, false);
@@ -132,7 +135,7 @@ public class ReactionConverterTest {
try {
BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
Graphics2D graphics = bi.createGraphics();
- ReactionConverter rc = new ReactionConverter();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
Reaction reaction = createReaction(3.0);
rc.drawReaction(reaction, graphics, false);
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverterTest.java
index 64c6307dd48471c0bbe6b221f1b83f19d7d7f336..bc8c2b2eaf147564f64e636c39878aee078b08c5 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverterTest.java
@@ -5,7 +5,6 @@ import static org.junit.Assert.assertTrue;
import java.awt.Color;
import java.awt.Graphics2D;
-import java.awt.geom.Point2D;
import java.awt.image.BufferedImage;
import java.util.ArrayList;
import java.util.List;
@@ -14,14 +13,16 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
public class SpeciesConverterTest {
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+
@Before
public void setUp() throws Exception {
}
@@ -33,27 +34,22 @@ public class SpeciesConverterTest {
@Test
public void testGetResidueCoords() throws Exception {
try {
- final class Conv extends ProteinConverter {
- public Point2D getCoordinate(Protein alias, double angle) {
- return super.getResidueCoordinates(alias, angle);
- }
- }
GenericProtein alias = new GenericProtein("id");
alias.setX(135);
alias.setY(194.0);
alias.setWidth(130);
alias.setHeight(67);
- Conv conv = new Conv();
- assertEquals(135.0, conv.getCoordinate(alias, 3.141592653589793).getX(), 2);
- assertEquals(265., conv.getCoordinate(alias, 0.0).getX(), 2);
- assertEquals(135.0, conv.getCoordinate(alias, 2.41).getX(), 2);
- assertEquals(194.0, conv.getCoordinate(alias, 1.98).getY(), 2);
- assertEquals(194.0, conv.getCoordinate(alias, 1.59).getY(), 2);
- assertEquals(265.0, conv.getCoordinate(alias, 6.28).getX(), 2);
- assertEquals(261.0, conv.getCoordinate(alias, 4.13).getY(), 2);
- assertEquals(261.0, conv.getCoordinate(alias, 4.86).getY(), 2);
- assertEquals(265.0, conv.getCoordinate(alias, 5.69).getX(), 2);
- assertEquals(194.0, conv.getCoordinate(alias, 0.99).getY(), 2);
+ ProteinConverter conv = new ProteinConverter(null);
+ assertEquals(135.0, conv.getResidueCoordinates(alias, 3.141592653589793).getX(), 2);
+ assertEquals(265., conv.getResidueCoordinates(alias, 0.0).getX(), 2);
+ assertEquals(135.0, conv.getResidueCoordinates(alias, 2.41).getX(), 2);
+ assertEquals(194.0, conv.getResidueCoordinates(alias, 1.98).getY(), 2);
+ assertEquals(194.0, conv.getResidueCoordinates(alias, 1.59).getY(), 2);
+ assertEquals(265.0, conv.getResidueCoordinates(alias, 6.28).getX(), 2);
+ assertEquals(261.0, conv.getResidueCoordinates(alias, 4.13).getY(), 2);
+ assertEquals(261.0, conv.getResidueCoordinates(alias, 4.86).getY(), 2);
+ assertEquals(265.0, conv.getResidueCoordinates(alias, 5.69).getX(), 2);
+ assertEquals(194.0, conv.getResidueCoordinates(alias, 0.99).getY(), 2);
} catch (Exception e) {
e.printStackTrace();
@@ -66,10 +62,10 @@ public class SpeciesConverterTest {
try {
BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
Graphics2D graphics = bi.createGraphics();
- ProteinConverter rc = new ProteinConverter();
+ ProteinConverter rc = new ProteinConverter(colorExtractor);
GenericProtein alias = createAlias();
- rc.drawAlias(alias, graphics, new ConverterParams());
+ rc.drawElement(alias, graphics, new ConverterParams());
int val = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
@@ -83,7 +79,7 @@ public class SpeciesConverterTest {
List<ColorSchema> schemas = new ArrayList<>();
schemas.add(schema);
- rc.drawAlias(alias2, graphics, new ConverterParams(), schemas);
+ rc.drawElement(alias2, graphics, new ConverterParams(), schemas);
int val2 = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
@@ -99,10 +95,10 @@ public class SpeciesConverterTest {
try {
BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
Graphics2D graphics = bi.createGraphics();
- ProteinConverter rc = new ProteinConverter();
+ ProteinConverter rc = new ProteinConverter(colorExtractor);
GenericProtein alias = createAlias();
- rc.drawAlias(alias, graphics, new ConverterParams());
+ rc.drawElement(alias, graphics, new ConverterParams());
int val = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
@@ -116,14 +112,14 @@ public class SpeciesConverterTest {
List<ColorSchema> schemas = new ArrayList<>();
schemas.add(schema);
- rc.drawAlias(alias2, graphics, new ConverterParams(), schemas);
+ rc.drawElement(alias2, graphics, new ConverterParams(), schemas);
int val2 = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
graphics = bi.createGraphics();
- rc.drawAlias(alias2, graphics, new ConverterParams(), new ArrayList<>());
+ rc.drawElement(alias2, graphics, new ConverterParams(), new ArrayList<>());
int val3 = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
@@ -140,10 +136,10 @@ public class SpeciesConverterTest {
try {
BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
Graphics2D graphics = bi.createGraphics();
- ProteinConverter rc = new ProteinConverter();
+ ProteinConverter rc = new ProteinConverter(colorExtractor);
GenericProtein alias = createAlias();
- rc.drawAlias(alias, graphics, new ConverterParams());
+ rc.drawElement(alias, graphics, new ConverterParams());
int val = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
@@ -161,7 +157,7 @@ public class SpeciesConverterTest {
schema.setColor(Color.BLUE);
schemas.add(schema);
- rc.drawAlias(alias2, graphics, new ConverterParams(), schemas);
+ rc.drawElement(alias2, graphics, new ConverterParams(), schemas);
int val2 = bi.getRGB((int) (alias.getX() + alias.getWidth() / 4), (int) alias.getCenterY());
int val3 = bi.getRGB((int) (alias.getCenterX()), (int) alias.getCenterY());
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java
new file mode 100644
index 0000000000000000000000000000000000000000..891434f015e8b5a93073963b4f34532f7317c20f
--- /dev/null
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java
@@ -0,0 +1,46 @@
+package lcsb.mapviewer.commands;
+
+import java.awt.Color;
+import java.util.ArrayList;
+
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * This {@link ModelCommand} clear info about colors in a model.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ClearColorModelCommand extends ModelCommand {
+
+ /**
+ * Coloring command that will clear colors.
+ */
+ private ColorModelCommand colorModelCommand;
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * original model
+ */
+ public ClearColorModelCommand(Model model) {
+ super(model);
+ colorModelCommand = new ColorModelCommand(model, new ArrayList<>(), new ColorExtractor(Color.WHITE, Color.WHITE));
+ }
+
+ @Override
+ protected void undoImplementation() throws CommandExecutionException {
+ colorModelCommand.undo();
+ }
+
+ @Override
+ protected void redoImplementation() throws CommandExecutionException {
+ colorModelCommand.redo();
+ }
+
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
+ colorModelCommand.execute();
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java
new file mode 100644
index 0000000000000000000000000000000000000000..1a6d5d5d31976885404440319dab3dc8e4304507
--- /dev/null
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java
@@ -0,0 +1,96 @@
+package lcsb.mapviewer.commands;
+
+import java.awt.Color;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+
+/**
+ * Class that extracts color that should be used for drawing from
+ * {@link ColorSchema}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ColorExtractor {
+
+ /**
+ * Color that should be used for min values of {@link ColorSchema#value}.
+ */
+ private Color minColor;
+
+ /**
+ * Color that should be used for maxvalues of {@link ColorSchema#value}.
+ */
+ private Color maxColor;
+
+ /**
+ * Default constructor.
+ *
+ * @param minColor
+ * Color that should be used for min values of
+ * {@link ColorSchema#value}
+ * @param maxColor
+ * Color that should be used for max values of
+ * {@link ColorSchema#value}
+ */
+ public ColorExtractor(Color minColor, Color maxColor) {
+ if (minColor == null || maxColor == null) {
+ throw new InvalidArgumentException("Parameters cannot be null");
+ }
+ this.minColor = minColor;
+ this.maxColor = maxColor;
+ }
+
+ /**
+ * Extracts color from {@link ColorSchema} object.
+ *
+ * @param colorSchema
+ * {@link ColorSchema} from which {@link Color} should be extracted
+ *
+ * @return color from {@link ColorSchema} object
+ */
+ public Color getNormalizedColor(ColorSchema colorSchema) {
+ if (colorSchema.getColor() != null) {
+ return colorSchema.getColor();
+ } else {
+ return getColorForValue(colorSchema.getValue());
+ }
+ }
+
+ /**
+ * Returns color from red - green scale for the given normalized double value
+ * (from range -1,1).
+ *
+ * @param value
+ * double value that should be converted into color
+ * @return color for the double value
+ */
+ protected Color getColorForValue(Double value) {
+ if (value > 0) {
+ double ratio = value;
+ return new Color((int) (maxColor.getRed() * ratio), (int) (maxColor.getGreen() * ratio), (int) (maxColor.getBlue() * ratio));
+ }
+ if (value < 0) {
+ double ratio = -value;
+ return new Color((int) (minColor.getRed() * ratio), (int) (minColor.getGreen() * ratio), (int) (minColor.getBlue() * ratio));
+ }
+ return Color.WHITE;
+ }
+
+ /**
+ * @return the minColor
+ * @see #minColor
+ */
+ public Color getMinColor() {
+ return minColor;
+ }
+
+ /**
+ * @return the maxColor
+ * @see #maxColor
+ */
+ public Color getMaxColor() {
+ return maxColor;
+ }
+}
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 87d848c59c4a5217069f0c173a27d0c58afc8398..427c7f77216e77e1ae31c62cef008510adeec1f4 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -12,6 +12,7 @@ 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.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -26,6 +27,7 @@ import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
* This {@link ModelCommand} colors a model (nodes and reactions) according to
@@ -47,17 +49,32 @@ public class ColorModelCommand extends ModelCommand {
*/
private Collection<ColorSchema> schemas;
+ /**
+ * Object that helps to convert {@link ColorSchema} values into colors.
+ *
+ */
+ private ColorExtractor colorExtractor;
+
+ /**
+ * Util class for all {@link AnnotatedObject} elements.
+ */
+ private ElementUtils eu = new ElementUtils();
+
/**
* Default constructor.
*
+ * @param colorExtractor
+ * object that helps to convert {@link ColorSchema} values into
+ * colors
* @param model
* original model
* @param schemas
* set of color schemas used in this command to color model.
*/
- public ColorModelCommand(Model model, Collection<ColorSchema> schemas) {
+ public ColorModelCommand(Model model, Collection<ColorSchema> schemas, ColorExtractor colorExtractor) {
super(model);
this.schemas = schemas;
+ this.colorExtractor = colorExtractor;
}
/**
@@ -68,14 +85,14 @@ public class ColorModelCommand extends ModelCommand {
* @param schema
* color schema to be used
* @throws InvalidColorSchemaException
- * thrown when alias was already colored by other schema
+ * thrown when {@link Reaction} 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();
+ Color color = colorExtractor.getNormalizedColor(schema);
for (AbstractNode node : reaction.getNodes()) {
node.getLine().setColor(color);
if (schema.getLineWidth() != null) {
@@ -101,8 +118,8 @@ public class ColorModelCommand extends ModelCommand {
* 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
+ * @return <code>true</code> if coloring schema should be used for
+ * {@link Reaction}, <code>false</code> otherwise
*/
private boolean match(Reaction reaction, ColorSchema schema) {
if (schema.getName() != null) {
@@ -133,59 +150,57 @@ public class ColorModelCommand extends ModelCommand {
}
/**
- * Applies color schema into the alias.
+ * Applies color schema into the {@link Element}.
*
- * @param alias
+ * @param element
* 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(Element alias, ColorSchema schema) throws InvalidColorSchemaException {
- if (alias instanceof Species) {
- if (!alias.getColor().equals(Color.WHITE)) {
- throw new InvalidColorSchemaException("At least two rows try to set color to element: " + alias.getName());
+ private void applyColor(Element element, ColorSchema schema) throws InvalidColorSchemaException {
+ if (element instanceof Species) {
+ if (!element.getColor().equals(Color.WHITE)) {
+ throw new InvalidColorSchemaException("At least two rows try to set color to element: " + element.getName());
}
-
- alias.setColor(schema.getNormalizedColor());
+ element.setColor(colorExtractor.getNormalizedColor(schema));
}
-
}
/**
- * Checks if the coloring schema should be used for the alias.
+ * Checks if the coloring schema should be used for the {@link Element}.
*
- * @param alias
- * alias to which coloring schema is checked
+ * @param element
+ * {@link Element} for 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
+ * @return <code>true</code> if coloring schema should be used for
+ * {@link Element}, <code>false</code> otherwise
*/
- protected boolean match(Element alias, ColorSchema schema) {
- if (alias instanceof Species) {
+ protected boolean match(Element element, ColorSchema schema) {
+ if (element instanceof Species) {
if (schema.getName() != null) {
- if (!alias.getName().equalsIgnoreCase(schema.getName())) {
+ if (!element.getName().equalsIgnoreCase(schema.getName())) {
return false;
}
}
if (schema.getTypes().size() > 0) {
- if (!schema.getTypes().contains(alias.getClass())) {
+ if (!schema.getTypes().contains(element.getClass())) {
return false;
}
}
if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
- if (!alias.getMiriamData().contains(md)) {
+ if (!element.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 (!alias.getMiriamData().contains(md)) {
+ if (!element.getMiriamData().contains(md)) {
return false;
}
}
@@ -193,10 +208,10 @@ public class ColorModelCommand extends ModelCommand {
if (schema.getCompartments().size() > 0) {
boolean found = false;
- for (Compartment cAlias : alias.getModelData().getModel().getCompartments()) {
+ for (Compartment compartment : element.getModelData().getModel().getCompartments()) {
for (String compartmentName : schema.getCompartments()) {
- if (cAlias.getName().equalsIgnoreCase(compartmentName)) {
- if (cAlias.cross(alias)) {
+ if (compartment.getName().equalsIgnoreCase(compartmentName)) {
+ if (compartment.cross(element)) {
found = true;
}
}
@@ -226,8 +241,8 @@ public class ColorModelCommand extends ModelCommand {
List<ColorSchema> result = new ArrayList<ColorSchema>();
for (ColorSchema schema : schemas) {
boolean found = false;
- for (Element alias : getModel().getElements()) {
- if (match(alias, schema)) {
+ for (Element element : getModel().getElements()) {
+ if (match(element, schema)) {
found = true;
}
}
@@ -245,7 +260,7 @@ public class ColorModelCommand extends ModelCommand {
/**
* Returns list of elements ({@link Reaction reactions} and {@link Element
- * aliases}) that are modified by the coloring command.
+ * elements}) that are modified by the coloring command.
*
* @return {@link Map}, where key corresponds to modified {@link Reaction} or
* {@link Element} and value is a {@link ColorSchema} that should be
@@ -261,18 +276,18 @@ public class ColorModelCommand extends ModelCommand {
models.addAll(getModel().getSubmodels());
for (Model model2 : models) {
for (ColorSchema schema : schemas) {
- for (Element alias : model2.getElements()) {
- if (match(alias, schema)) {
- if (result.get(alias) != null && !result.get(alias).getNormalizedColor().equals(Color.WHITE)) {
- throw new InvalidColorSchemaException("Alias " + alias.getElementId() + " is colored by more than one rule.");
+ for (Element element : model2.getElements()) {
+ if (match(element, schema)) {
+ if (result.get(element) != null && !colorExtractor.getNormalizedColor(result.get(element)).equals(Color.WHITE)) {
+ throw new InvalidColorSchemaException(eu.getElementTag(element) + "Element is colored by more than one rule.");
}
- result.put(alias, schema);
+ result.put(element, 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.");
+ if (result.get(reaction) != null && !colorExtractor.getNormalizedColor(result.get(reaction)).equals(Color.WHITE)) {
+ throw new InvalidColorSchemaException(eu.getElementTag(reaction) + "Reaction is colored by more than one rule.");
}
result.put(reaction, schema);
}
@@ -306,8 +321,8 @@ public class ColorModelCommand extends ModelCommand {
*/
private void colorModel(Model result, boolean top) throws InvalidColorSchemaException {
- for (Element alias : result.getElements()) {
- alias.setColor(Color.WHITE);
+ for (Element element : result.getElements()) {
+ element.setColor(Color.WHITE);
}
for (Reaction reaction : result.getReactions()) {
for (AbstractNode node : reaction.getNodes()) {
@@ -316,10 +331,10 @@ public class ColorModelCommand extends ModelCommand {
}
for (ColorSchema schema : schemas) {
- for (Element alias : result.getElements()) {
- if (match(alias, schema)) {
+ for (Element element : result.getElements()) {
+ if (match(element, schema)) {
schema.setMatches(schema.getMatches() + 1);
- applyColor(alias, schema);
+ applyColor(element, schema);
}
}
for (Reaction reaction : result.getReactions()) {
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 e4972598fac3f1912be32d96b162f0e87a08d37e..14d934650b6eec46884d8f889e27d8e8472fcbbc 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -29,7 +29,9 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
public class ColorModelCommandTest extends CommandTestFunctions {
- Logger logger = Logger.getLogger(ColorModelCommandTest.class);
+ Logger logger = Logger.getLogger(ColorModelCommandTest.class);
+
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
@Before
public void setUp() throws Exception {
@@ -58,7 +60,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
schema.setName("CNC");
schema.setValue(-1.0);
schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(coloredModel, schemas);
+ ColorModelCommand factory = new ColorModelCommand(coloredModel, schemas, colorExtractor);
assertFalse(Color.RED.equals(coloredModel.getElementByElementId("sa14").getColor()));
@@ -94,7 +96,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
schema.setValue(1.0);
schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
Collection<ColorSchema> missing = factory.getMissingSchema();
assertEquals(1, missing.size());
@@ -112,7 +114,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Reaction re4 = model.getReactionByReactionId("re4");
Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
assertFalse(Color.BLACK.equals(re4.getNodes().get(0).getLine().getColor()));
factory.execute();
@@ -137,7 +139,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
schema.setColor(Color.RED);
schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
assertEquals(Color.BLACK, re1.getNodes().get(0).getLine().getColor());
factory.execute();
@@ -162,7 +164,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
schema.setValue(-1.0);
schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
assertEquals(Color.BLACK, re2.getNodes().get(0).getLine().getColor());
factory.execute();
@@ -191,7 +193,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
schema.setValue(-1.0);
schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
assertEquals(Color.BLACK, re3.getNodes().get(0).getLine().getColor());
@@ -216,7 +218,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Collection<ColorSchema> schemas = new ArrayList<>();
Model coloredModel = new CopyCommand(model).execute();
- new ColorModelCommand(coloredModel, schemas).execute();
+ new ColorModelCommand(coloredModel, schemas, colorExtractor).execute();
Model coloredModel2 = coloredModel.getSubmodelConnections().iterator().next().getSubmodel().getModel();
Model coloredModel3 = coloredModel.getSubmodelByConnectionName("BLA");
@@ -243,7 +245,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
schema.setName("BDH1");
schema.setColor(Color.BLUE);
schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
Map<Object, ColorSchema> map = factory.getModifiedElements();
assertEquals(2, map.size());
@@ -268,7 +270,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
schema.setName("");
schema.setReverseReaction(true);
schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
Map<Object, ColorSchema> map = factory.getModifiedElements();
assertEquals(0, map.size());
@@ -290,7 +292,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
schema.setName(null);
schema.setReverseReaction(true);
schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
Map<Object, ColorSchema> map = factory.getModifiedElements();
assertEquals(1, map.size());
@@ -319,7 +321,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
List<ColorSchema> schemas = new ArrayList<>();
schemas.add(colorSchema);
- ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas);
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
assertFalse(factory.match(alias, colorSchema));
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
index 89840fce6753e72466ead3a93a1239b68894c15a..4b2c13e3e2ee5ed59bbd8ffeff5e72869170bfbb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
@@ -26,37 +26,6 @@ public abstract class ColorSchema implements Serializable {
*/
private static final long serialVersionUID = 1L;
- /**
- * Base of the hex representation.
- */
- private static final int HEX_BASE = 16;
-
- /**
- * Length of the string describing color in rgb: "#RRGGBB".
- */
- private static final int COLOR_STRING_LENGTH = 7;
-
- /**
- * Where starts description of red color in stirng representing color.
- */
- private static final int COLOR_SUBSTRING_START_RED = 1;
-
- /**
- * Where starts description of green color in stirng representing color.
- */
- private static final int COLOR_SUBSTRING_START_GREEN = 3;
-
- /**
- * Where starts description of blue color in stirng representing color.
- */
- private static final int COLOR_SUBSTRING_START_BLUE = 5;
-
- /**
- * Defines the maximum value of primary colors in RGB model (every color is
- * from range 0..255).
- */
- private static final int MAX_SINGLE_COLOR_VALUE_IN_RGB_FORMAT = 255;
-
/**
* Name of the {@link Element Element}. If null
* then this field will be skiped.
@@ -197,29 +166,6 @@ public abstract class ColorSchema implements Serializable {
}
}
- /**
- * Sets {@link #color} from the string.
- *
- * @param string
- * color in text representation
- * @throws InvalidColorSchemaException
- * thrown when string describing color is invalid
- */
- public void setColor(String string) throws InvalidColorSchemaException {
- if (string.length() != COLOR_STRING_LENGTH) {
- throw new InvalidColorSchemaException("Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
- }
- if (string.charAt(0) != '#') {
- throw new InvalidColorSchemaException("Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
-
- } else {
- setColor(new Color(Integer.valueOf(string.substring(COLOR_SUBSTRING_START_RED, COLOR_SUBSTRING_START_GREEN), HEX_BASE), //
- Integer.valueOf(string.substring(COLOR_SUBSTRING_START_GREEN, COLOR_SUBSTRING_START_BLUE), HEX_BASE), //
- Integer.valueOf(string.substring(COLOR_SUBSTRING_START_BLUE, COLOR_STRING_LENGTH), HEX_BASE)));
- }
-
- }
-
@Override
public String toString() {
StringBuilder result = new StringBuilder();
@@ -483,39 +429,6 @@ public abstract class ColorSchema implements Serializable {
this.types.add(clazz);
}
- /**
- * Extracts color from {@link ColorSchema} object.
- *
- * @return color from {@link ColorSchema} object
- */
- public Color getNormalizedColor() {
- if (getColor() != null) {
- return getColor();
- } else {
- return getColorForValue(getValue());
- }
- }
-
- /**
- * Returns color from red - green scale for the given normalized double value
- * (from range -1,1).
- *
- * @param value
- * double value that should be converted into color
- * @return color for the double value
- */
- protected Color getColorForValue(Double value) {
- if (value > 0) {
- int val = (int) ((1 - value) * MAX_SINGLE_COLOR_VALUE_IN_RGB_FORMAT);
- return new Color(val, MAX_SINGLE_COLOR_VALUE_IN_RGB_FORMAT, val);
- }
- if (value < 0) {
- int val = (int) ((1 + value) * MAX_SINGLE_COLOR_VALUE_IN_RGB_FORMAT);
- return new Color(MAX_SINGLE_COLOR_VALUE_IN_RGB_FORMAT, val, val);
- }
- return Color.WHITE;
- }
-
/**
* @return the description
* @see #description
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementEditType.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementEditType.java
new file mode 100644
index 0000000000000000000000000000000000000000..2b6256c70aa80e106c834518710bf14809d4b957
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementEditType.java
@@ -0,0 +1,45 @@
+package lcsb.mapviewer.model.user;
+
+/**
+ * Defines how the {@link ConfigurationElementType} should be edited (what kind
+ * of values we are storing).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ConfigurationElementEditType {
+ /**
+ * Double value.
+ */
+ DOUBLE,
+
+ /**
+ * Integer value.
+ */
+ INTEGER,
+
+ /**
+ * String value.
+ */
+ STRING,
+
+ /**
+ * Color value (for color picker).
+ */
+ COLOR,
+
+ /**
+ * Url value.
+ */
+ URL,
+
+ /**
+ * Email value.
+ */
+ EMAIL,
+
+ /**
+ * Password value.
+ */
+ PASSWORD,
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
index d77ddc26da96f9b903854fec6f14f24633f114e7..28da787bfb92ba337c94225b83fa5601e2f71867 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
@@ -1,162 +1,187 @@
-package lcsb.mapviewer.model.user;
-
-/**
- * This enum defines all possible configuration parameter that are configurable
- * by the user.
- *
- * @author Piotr Gawron
- *
- */
-public enum ConfigurationElementType {
-
- /**
- * Email address used for sending email from the system.
- */
- EMAIL_ADDRESS("E-mail address", "your.account@domain.com"), //
-
- /**
- * Login for the email account.
- */
- EMAIL_LOGIN("E-mail server login", "your@login"), //
-
- /**
- * Password for the email account.
- */
- EMAIL_PASSWORD("E-mail server password", "email.secret.password"), //
-
- /**
- * Addres of the imap server.
- */
- EMAIL_IMAP_SERVER("IMAP server", "your.imap.domain.com"), //
-
- /**
- * Address of the smtp server.
- */
- EMAIL_SMTP_SERVER("SMTP server", "your.smtp.domain.com"), //
-
- /**
- * Port used for smtp connection (sending emails).
- */
- EMAIL_SMTP_PORT("SMTP port", "25"), //
-
- /**
- * Default map that should be presented if no map is selected by user side.
- */
- DEFAULT_MAP("Default Project Id", "empty"), //
-
- /**
- * Logo presented in the system.
- */
- LOGO_IMG("Logo icon", "udl.png"), //
-
- /**
- * Address connected to the logo.
- */
- LOGO_LINK("Logo link (after click)", "http://wwwen.uni.lu/"), //
-
- /**
- * Maximum distance (in pixels) that is allowed during finding closest element
- * on the map.
- */
- SEARCH_DISTANCE("Max distance for clicking on element (px)", "10"),
-
- /**
- * Email used for requesting an account (in client side).
- */
- REQUEST_ACCOUNT_EMAIL("Email used for requesting an account", "your.email@domain.com"),
-
- /**
- * Max number of results in search box.
- */
- SEARCH_RESULT_NUMBER("Max number of results in search box. ", "100"),
-
- /**
- * Google Analytics tracking ID used for statistics. This tracking ID should
- * look like "UA-000000-01". More information about tracking ID can be found
- * <a href="https://support.google.com/analytics/answer/1032385?hl=en"> here
- * </a>.
- */
- GOOGLE_ANALYTICS_IDENTIFIER("Google Analytics tracking ID used for statistics", ""),
-
- /**
- * Description of the logo presented in the system.
- */
- LOGO_TEXT("Logo description", "University of Luxembourg"),
-
- /**
- * Domain allowed to connect via x-frame technology.
- */
- X_FRAME_DOMAIN("Domain allowed to connect via x-frame technology", ""),
-
- /**
- * Relative directory (in webapps folder) where big files will be stored.
- */
- BIG_FILE_STORAGE_DIR("Path to store big files", "minerva-big/"),
-
- /**
- * File where legend 1/4 is stored.
- */
- LENGEND_FILE_1("Legend 1 image file", "resources/images/legend_a.png"),
-
- /**
- * File where legend 2/4 is stored.
- */
- LENGEND_FILE_2("Legend 2 image file", "resources/images/legend_b.png"),
-
- /**
- * File where legend 3/4 is stored.
- */
- LENGEND_FILE_3("Legend 3 image file", "resources/images/legend_c.png"),
-
- /**
- * File where legend 4/4 is stored.
- */
- LENGEND_FILE_4("Legend 4 image file", "resources/images/legend_d.png"),
-
- /**
- * File where legend 4/4 is stored.
- */
- USER_MANUAL_FILE("User manual file", "resources/other/user_guide.pdf");
-
-
- /**
- * Default value of the configuration parameter (it will be used only when
- * value doesn't exist in the DAO).
- */
- private String defaultValue = "";
-
- /**
- * Common name used for visualization (query user).
- */
- private String commonName = "";
-
- /**
- * Default constructor.
- *
- * @param commonName
- * common name used for this parameter
- * @param defaultVal
- * default value assigned to this parameter
- */
- ConfigurationElementType(String commonName, String defaultVal) {
- this.defaultValue = defaultVal;
- this.commonName = commonName;
- }
-
- /**
- * @return the defaultValue
- * @see #defaultValue
- */
- public String getDefaultValue() {
- return defaultValue;
- }
-
- /**
- * @return the commonName
- * @see #commonName
- */
- public String getCommonName() {
- return commonName;
- }
-
-}
+package lcsb.mapviewer.model.user;
+
+/**
+ * This enum defines all possible configuration parameter that are configurable
+ * by the user.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ConfigurationElementType {
+
+ /**
+ * Email address used for sending email from the system.
+ */
+ EMAIL_ADDRESS("E-mail address", "your.account@domain.com", ConfigurationElementEditType.EMAIL), //
+
+ /**
+ * Login for the email account.
+ */
+ EMAIL_LOGIN("E-mail server login", "your@login", ConfigurationElementEditType.STRING), //
+
+ /**
+ * Password for the email account.
+ */
+ EMAIL_PASSWORD("E-mail server password", "email.secret.password", ConfigurationElementEditType.PASSWORD), //
+
+ /**
+ * Addres of the imap server.
+ */
+ EMAIL_IMAP_SERVER("IMAP server", "your.imap.domain.com", ConfigurationElementEditType.STRING), //
+
+ /**
+ * Address of the smtp server.
+ */
+ EMAIL_SMTP_SERVER("SMTP server", "your.smtp.domain.com", ConfigurationElementEditType.STRING), //
+
+ /**
+ * Port used for smtp connection (sending emails).
+ */
+ EMAIL_SMTP_PORT("SMTP port", "25", ConfigurationElementEditType.INTEGER), //
+
+ /**
+ * Default map that should be presented if no map is selected by user side.
+ */
+ DEFAULT_MAP("Default Project Id", "empty", ConfigurationElementEditType.STRING), //
+
+ /**
+ * Logo presented in the system.
+ */
+ LOGO_IMG("Logo icon", "udl.png", ConfigurationElementEditType.URL), //
+
+ /**
+ * Address connected to the logo.
+ */
+ LOGO_LINK("Logo link (after click)", "http://wwwen.uni.lu/", ConfigurationElementEditType.URL), //
+
+ /**
+ * Maximum distance (in pixels) that is allowed during finding closest element
+ * on the map.
+ */
+ SEARCH_DISTANCE("Max distance for clicking on element (px)", "10", ConfigurationElementEditType.DOUBLE),
+
+ /**
+ * Email used for requesting an account (in client side).
+ */
+ REQUEST_ACCOUNT_EMAIL("Email used for requesting an account", "your.email@domain.com", ConfigurationElementEditType.EMAIL),
+
+ /**
+ * Max number of results in search box.
+ */
+ SEARCH_RESULT_NUMBER("Max number of results in search box. ", "100", ConfigurationElementEditType.INTEGER),
+
+ /**
+ * Google Analytics tracking ID used for statistics. This tracking ID should
+ * look like "UA-000000-01". More information about tracking ID can be found
+ * <a href="https://support.google.com/analytics/answer/1032385?hl=en"> here
+ * </a>.
+ */
+ GOOGLE_ANALYTICS_IDENTIFIER("Google Analytics tracking ID used for statistics", "", ConfigurationElementEditType.STRING),
+
+ /**
+ * Description of the logo presented in the system.
+ */
+ LOGO_TEXT("Logo description", "University of Luxembourg", ConfigurationElementEditType.STRING),
+
+ /**
+ * Domain allowed to connect via x-frame technology.
+ */
+ X_FRAME_DOMAIN("Domain allowed to connect via x-frame technology", "", ConfigurationElementEditType.URL),
+
+ /**
+ * Relative directory (in webapps folder) where big files will be stored.
+ */
+ BIG_FILE_STORAGE_DIR("Path to store big files", "minerva-big/", ConfigurationElementEditType.STRING),
+
+ /**
+ * File where legend 1/4 is stored.
+ */
+ LENGEND_FILE_1("Legend 1 image file", "resources/images/legend_a.png", ConfigurationElementEditType.URL),
+
+ /**
+ * File where legend 2/4 is stored.
+ */
+ LENGEND_FILE_2("Legend 2 image file", "resources/images/legend_b.png", ConfigurationElementEditType.URL),
+
+ /**
+ * File where legend 3/4 is stored.
+ */
+ LENGEND_FILE_3("Legend 3 image file", "resources/images/legend_c.png", ConfigurationElementEditType.URL),
+
+ /**
+ * File where legend 4/4 is stored.
+ */
+ LENGEND_FILE_4("Legend 4 image file", "resources/images/legend_d.png", ConfigurationElementEditType.URL),
+
+ /**
+ * File where legend 4/4 is stored.
+ */
+ USER_MANUAL_FILE("User manual file", "resources/other/user_guide.pdf", ConfigurationElementEditType.URL),
+
+ /**
+ * Color used for negative overlay values.
+ */
+ MIN_COLOR_VAL("Overlay color for negative values", "FF0000", ConfigurationElementEditType.COLOR),
+
+ /**
+ * Color used for positive overlay values.
+ */
+ MAX_COLOR_VAL("Overlay color for postive values", "0000FF", ConfigurationElementEditType.COLOR);
+
+ /**
+ * Default value of the configuration parameter (it will be used only when
+ * value doesn't exist in the DAO).
+ */
+ private String defaultValue = "";
+
+ /**
+ * Common name used for visualization (query user).
+ */
+ private String commonName = "";
+
+ /**
+ * How we want to edit specific param.
+ */
+ private ConfigurationElementEditType editType = null;
+
+ /**
+ * Default constructor.
+ *
+ * @param commonName
+ * common name used for this parameter
+ * @param editType
+ * type defining how we want to edit this configuration param
+ * @param defaultVal
+ * default value assigned to this parameter
+ */
+ ConfigurationElementType(String commonName, String defaultVal, ConfigurationElementEditType editType) {
+ this.defaultValue = defaultVal;
+ this.commonName = commonName;
+ this.editType = editType;
+ }
+
+ /**
+ * @return the defaultValue
+ * @see #defaultValue
+ */
+ public String getDefaultValue() {
+ return defaultValue;
+ }
+
+ /**
+ * @return the commonName
+ * @see #commonName
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+
+ /**
+ * @return the editType
+ * @see #editType
+ */
+ public ConfigurationElementEditType getEditType() {
+ return editType;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/User.java b/model/src/main/java/lcsb/mapviewer/model/user/User.java
index c35c58ac5c5b020db4ae66d57df25e40bddc675d..3cc421f8f51a6d229836e00d244be48821b286f4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/User.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/User.java
@@ -1,263 +1,312 @@
-package lcsb.mapviewer.model.user;
-
-import java.io.Serializable;
-import java.util.HashSet;
-import java.util.Set;
-
-import javax.persistence.CascadeType;
-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.JoinColumn;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
-
-/**
- * Class representing user.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "user_table")
-public class User implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private Integer id;
-
- /**
- * User login.
- */
- private String login;
-
- /**
- * Password in encrypted form. For the encryption PasswordEncoder spring bean
- * is used.
- */
- private String cryptedPassword;
-
- /**
- * Name of the user.
- */
- private String name;
-
- /**
- * Family name of the user.
- */
- private String surname;
-
- /**
- * Email address of the user.
- */
- private String email;
-
- /**
- * Is the user removed.
- */
- private boolean removed = false;
-
- /**
- * Set of user privileges.
- */
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "user", orphanRemoval = true, cascade = CascadeType.ALL)
- private Set<BasicPrivilege> privileges = new HashSet<BasicPrivilege>();
-
- /**
- * Default annotations schema used by this user.
- */
- @OneToOne(cascade = CascadeType.ALL)
- @JoinColumn(nullable = true)
- private UserAnnotationSchema annotationSchema;
-
- /**
- * Default constructor.
- */
- public User() {
- }
-
- /**
- * Adds privilege to the user.
- *
- * @param privilege
- * privilege to add
- */
- public void addPrivilege(BasicPrivilege privilege) {
- privileges.add(privilege);
- }
-
- /**
- * @return the id
- * @see #id
- */
- public Integer getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(Integer id) {
- this.id = id;
- }
-
- /**
- * @return the login
- * @see #login
- */
- public String getLogin() {
- return login;
- }
-
- /**
- * @param login
- * the login to set
- * @see #login
- */
- public void setLogin(String login) {
- this.login = login;
- }
-
- /**
- * @return the cryptedPassword
- * @see #cryptedPassword
- */
- public String getCryptedPassword() {
- return cryptedPassword;
- }
-
- /**
- * @param cryptedPassword
- * the cryptedPassword to set
- * @see #cryptedPassword
- */
- public void setCryptedPassword(String cryptedPassword) {
- this.cryptedPassword = cryptedPassword;
- }
-
- /**
- * @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 the surname
- * @see #surname
- */
- public String getSurname() {
- return surname;
- }
-
- /**
- * @param surname
- * the surname to set
- * @see #surname
- */
- public void setSurname(String surname) {
- this.surname = surname;
- }
-
- /**
- * @return the email
- * @see #email
- */
- public String getEmail() {
- return email;
- }
-
- /**
- * @param email
- * the email to set
- * @see #email
- */
- public void setEmail(String email) {
- this.email = email;
- }
-
- /**
- * @return the privileges
- * @see #privileges
- */
- public Set<BasicPrivilege> getPrivileges() {
- return privileges;
- }
-
- /**
- * @param privileges
- * the privileges to set
- * @see #privileges
- */
- public void setPrivileges(Set<BasicPrivilege> privileges) {
- this.privileges = privileges;
- }
-
- /**
- * @return the removed
- * @see #removed
- */
- public boolean isRemoved() {
- return removed;
- }
-
- /**
- * @param removed
- * the removed to set
- * @see #removed
- */
- public void setRemoved(boolean removed) {
- this.removed = removed;
- }
-
- /**
- * @return the annotationSchema
- * @see #annotationSchema
- */
- public UserAnnotationSchema getAnnotationSchema() {
- return annotationSchema;
- }
-
- /**
- * @param annotationSchema
- * the annotationSchema to set
- * @see #annotationSchema
- */
- public void setAnnotationSchema(UserAnnotationSchema annotationSchema) {
- this.annotationSchema = annotationSchema;
- if (!this.equals(annotationSchema.getUser())) {
- annotationSchema.setUser(this);
- }
- }
-
- @Override
- public String toString() {
- return "[" + this.getClass().getSimpleName() + "] " + getName() + " " + getSurname();
- }
-
-}
+package lcsb.mapviewer.model.user;
+
+import java.awt.Color;
+import java.io.Serializable;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.persistence.CascadeType;
+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.JoinColumn;
+import javax.persistence.OneToMany;
+import javax.persistence.OneToOne;
+import javax.persistence.Table;
+
+/**
+ * Class representing user.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "user_table")
+public class User implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private Integer id;
+
+ /**
+ * User login.
+ */
+ private String login;
+
+ /**
+ * Password in encrypted form. For the encryption PasswordEncoder spring bean
+ * is used.
+ */
+ private String cryptedPassword;
+
+ /**
+ * Name of the user.
+ */
+ private String name;
+
+ /**
+ * Family name of the user.
+ */
+ private String surname;
+
+ /**
+ * Email address of the user.
+ */
+ private String email;
+
+ /**
+ * User defined color overriding system
+ * {@link ConfigurationElementType#MIN_COLOR_VAL}. Used for coloring minimum
+ * values in overlays.
+ */
+ private Color minColor;
+
+ /**
+ * User defined color overriding system
+ * {@link ConfigurationElementType#MAX_COLOR_VAL}. Used for coloring maximum
+ * values in overlays.
+ */
+ private Color maxColor;
+
+ /**
+ * Is the user removed.
+ */
+ private boolean removed = false;
+
+ /**
+ * Set of user privileges.
+ */
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "user", orphanRemoval = true, cascade = CascadeType.ALL)
+ private Set<BasicPrivilege> privileges = new HashSet<BasicPrivilege>();
+
+ /**
+ * Default annotations schema used by this user.
+ */
+ @OneToOne(cascade = CascadeType.ALL)
+ @JoinColumn(nullable = true)
+ private UserAnnotationSchema annotationSchema;
+
+ /**
+ * Default constructor.
+ */
+ public User() {
+ }
+
+ /**
+ * Adds privilege to the user.
+ *
+ * @param privilege
+ * privilege to add
+ */
+ public void addPrivilege(BasicPrivilege privilege) {
+ privileges.add(privilege);
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public Integer getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(Integer id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the login
+ * @see #login
+ */
+ public String getLogin() {
+ return login;
+ }
+
+ /**
+ * @param login
+ * the login to set
+ * @see #login
+ */
+ public void setLogin(String login) {
+ this.login = login;
+ }
+
+ /**
+ * @return the cryptedPassword
+ * @see #cryptedPassword
+ */
+ public String getCryptedPassword() {
+ return cryptedPassword;
+ }
+
+ /**
+ * @param cryptedPassword
+ * the cryptedPassword to set
+ * @see #cryptedPassword
+ */
+ public void setCryptedPassword(String cryptedPassword) {
+ this.cryptedPassword = cryptedPassword;
+ }
+
+ /**
+ * @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 the surname
+ * @see #surname
+ */
+ public String getSurname() {
+ return surname;
+ }
+
+ /**
+ * @param surname
+ * the surname to set
+ * @see #surname
+ */
+ public void setSurname(String surname) {
+ this.surname = surname;
+ }
+
+ /**
+ * @return the email
+ * @see #email
+ */
+ public String getEmail() {
+ return email;
+ }
+
+ /**
+ * @param email
+ * the email to set
+ * @see #email
+ */
+ public void setEmail(String email) {
+ this.email = email;
+ }
+
+ /**
+ * @return the privileges
+ * @see #privileges
+ */
+ public Set<BasicPrivilege> getPrivileges() {
+ return privileges;
+ }
+
+ /**
+ * @param privileges
+ * the privileges to set
+ * @see #privileges
+ */
+ public void setPrivileges(Set<BasicPrivilege> privileges) {
+ this.privileges = privileges;
+ }
+
+ /**
+ * @return the removed
+ * @see #removed
+ */
+ public boolean isRemoved() {
+ return removed;
+ }
+
+ /**
+ * @param removed
+ * the removed to set
+ * @see #removed
+ */
+ public void setRemoved(boolean removed) {
+ this.removed = removed;
+ }
+
+ /**
+ * @return the annotationSchema
+ * @see #annotationSchema
+ */
+ public UserAnnotationSchema getAnnotationSchema() {
+ return annotationSchema;
+ }
+
+ /**
+ * @param annotationSchema
+ * the annotationSchema to set
+ * @see #annotationSchema
+ */
+ public void setAnnotationSchema(UserAnnotationSchema annotationSchema) {
+ this.annotationSchema = annotationSchema;
+ if (!this.equals(annotationSchema.getUser())) {
+ annotationSchema.setUser(this);
+ }
+ }
+
+ @Override
+ public String toString() {
+ return "[" + this.getClass().getSimpleName() + "] " + getName() + " " + getSurname();
+ }
+
+ /**
+ * @return the minColor
+ * @see #minColor
+ */
+ public Color getMinColor() {
+ return minColor;
+ }
+
+ /**
+ * @param minColor
+ * the minColor to set
+ * @see #minColor
+ */
+ public void setMinColor(Color minColor) {
+ this.minColor = minColor;
+ }
+
+ /**
+ * @return the maxColor
+ * @see #maxColor
+ */
+ public Color getMaxColor() {
+ return maxColor;
+ }
+
+ /**
+ * @param maxColor
+ * the maxColor to set
+ * @see #maxColor
+ */
+ public void setMaxColor(Color maxColor) {
+ this.maxColor = maxColor;
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
index 181cce38fadefea6779a548ccf367130209b1207..afeb53d81fd42d5d4e12e6d71dfe3e2891d8da3b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
@@ -2,7 +2,6 @@ package lcsb.mapviewer.model.map.layout;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
import java.awt.Color;
import java.util.ArrayList;
@@ -75,73 +74,6 @@ public class ColorSchemaTest {
}
}
- @Test
- public void testSetInvalidColor() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- cs.setColor("qwe");
- fail("Exception expected");
- } catch (InvalidColorSchemaException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetInvalidColor2() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- cs.setColor("fffffff");
- fail("Exception expected");
- } catch (InvalidColorSchemaException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetColor() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- cs.setColor("#ffffff");
- assertEquals(Color.WHITE, cs.getColor());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetColorForValue() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- assertEquals(Color.GREEN, cs.getColorForValue(1.0));
- assertEquals(Color.RED, cs.getColorForValue(-1.0));
- assertEquals(Color.WHITE, cs.getColorForValue(0.0));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetNormalizedColor() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- cs.setColor(Color.BLUE);
- assertEquals(Color.BLUE, cs.getNormalizedColor());
-
- cs = new GenericColorSchema();
- cs.setValue(1.0);
- assertEquals(Color.GREEN, cs.getNormalizedColor());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testToString() throws Exception {
try {
diff --git a/persist/src/db/10.0.3/fix_db_20161012.sql b/persist/src/db/10.0.3/fix_db_20161012.sql
new file mode 100644
index 0000000000000000000000000000000000000000..feb19a62f92713f41e2972391a17379c6f2c2410
--- /dev/null
+++ b/persist/src/db/10.0.3/fix_db_20161012.sql
@@ -0,0 +1,2 @@
+alter table user_table add column maxcolor bytea;
+alter table user_table add column mincolor bytea;
diff --git a/service/pom.xml b/service/pom.xml
index b91fcbc8c5ff6cbe6ff2cd8490c47a7cb47ea531..683846f0af0938281b311caf2ece1656b55c0516 100644
--- a/service/pom.xml
+++ b/service/pom.xml
@@ -1,122 +1,131 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
- http://maven.apache.org/xsd/maven-4.0.0.xsd">
-
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>parent</artifactId>
- <version>1.0</version>
- </parent>
-
- <artifactId>service</artifactId>
- <name>Service layer</name>
-
- <dependencies>
-
- <!-- dependency from the MapViewer model -->
-
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>model</artifactId>
- <version>1.0</version>
- </dependency>
-
- <!-- dependency from the MapViewer dao -->
-
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>persist</artifactId>
- <version>1.0</version>
- </dependency>
-
- <!-- dependency from the MapViewer dao -->
-
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>model-command</artifactId>
- <version>1.0</version>
- </dependency>
-
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>annotation</artifactId>
- <version>1.0</version>
- </dependency>
-
- <!-- dependency from the MapViewer cell designer parser -->
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>converter-CellDesigner</artifactId>
- <version>1.0</version>
- </dependency>
-
- <!-- dependency from the MapViewer SBGN-ML parser -->
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>converter-SBGNML</artifactId>
- <version>1.0</version>
- </dependency>
-
- <!-- dependency from the MapViewer graphics converter -->
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>converter-graphics</artifactId>
- <version>1.0</version>
- </dependency>
-
- <!-- Log4J -->
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- <version>${log4j.version}</version>
- </dependency>
-
- <!-- Spring -->
- <dependency>
- <groupId>org.springframework</groupId>
- <artifactId>spring-context</artifactId>
- <version>${springframework.version}</version>
- </dependency>
-
- <!-- Primefaces, used for overlay objects that are passed to the client
- side -->
- <dependency>
- <groupId>org.primefaces</groupId>
- <artifactId>primefaces</artifactId>
- <version>${primafaces.version}</version>
- </dependency>
-
- <!-- Jsf, used for objects that are passed to the client side -->
- <dependency>
- <groupId>com.sun.faces</groupId>
- <artifactId>jsf-api</artifactId>
- <version>${jsf.version}</version>
- </dependency>
-
- <!-- Gson -->
- <dependency>
- <groupId>com.google.code.gson</groupId>
- <artifactId>gson</artifactId>
- <version>${gson.version}</version>
- <scope>compile</scope>
- </dependency>
-
- <dependency>
- <groupId>org.apache.poi</groupId>
- <artifactId>poi</artifactId>
- <version>3.10-FINAL</version>
- </dependency>
- <dependency>
- <groupId>org.apache.poi</groupId>
- <artifactId>poi</artifactId>
- <version>3.12</version>
- </dependency>
- <dependency>
- <groupId>org.apache.poi</groupId>
- <artifactId>poi-ooxml</artifactId>
- <version>3.12</version>
- </dependency>
- </dependencies>
-
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
+ http://maven.apache.org/xsd/maven-4.0.0.xsd">
+
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>parent</artifactId>
+ <version>1.0</version>
+ </parent>
+
+ <artifactId>service</artifactId>
+ <name>Service layer</name>
+
+ <dependencies>
+
+ <!-- dependency from the MapViewer model -->
+
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>model</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <!-- dependency from the MapViewer dao -->
+
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>persist</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <!-- dependency from the MapViewer dao -->
+
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>model-command</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>annotation</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <!-- dependency from the MapViewer cell designer parser -->
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>converter-CellDesigner</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <!-- dependency from the MapViewer SBGN-ML parser -->
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>converter-SBGNML</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <!-- dependency from the MapViewer graphics converter -->
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>converter-graphics</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <!-- Log4J -->
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ <version>${log4j.version}</version>
+ </dependency>
+
+ <!-- Spring -->
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-context</artifactId>
+ <version>${springframework.version}</version>
+ </dependency>
+
+ <!-- Primefaces, used for overlay objects that are passed to the client
+ side -->
+ <dependency>
+ <groupId>org.primefaces</groupId>
+ <artifactId>primefaces</artifactId>
+ <version>${primafaces.version}</version>
+ </dependency>
+
+ <!-- Jsf, used for objects that are passed to the client side -->
+ <dependency>
+ <groupId>com.sun.faces</groupId>
+ <artifactId>jsf-api</artifactId>
+ <version>${jsf.version}</version>
+ </dependency>
+
+ <!-- Gson -->
+ <dependency>
+ <groupId>com.google.code.gson</groupId>
+ <artifactId>gson</artifactId>
+ <version>${gson.version}</version>
+ <scope>compile</scope>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.poi</groupId>
+ <artifactId>poi</artifactId>
+ <version>3.10-FINAL</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.poi</groupId>
+ <artifactId>poi</artifactId>
+ <version>3.12</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.poi</groupId>
+ <artifactId>poi-ooxml</artifactId>
+ <version>3.12</version>
+ </dependency>
+
+<!-- mockito used for testing -->
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-all</artifactId>
+ <version>${mockito.version}</version>
+ <scope>test</scope>
+ </dependency>
+
+ </dependencies>
+
</project>
\ No newline at end of file
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index 599b71bcf3e310bead3f33ac8917bd173c143aca..b01498f5f532dc6c23274980a15b9b4f43c4071a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.services.impl;
+import java.awt.Color;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
@@ -10,6 +11,7 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
+import javax.annotation.PostConstruct;
import javax.mail.MessagingException;
import org.apache.commons.io.IOUtils;
@@ -18,6 +20,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.services.MiriamConnector;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.commands.ColorModelCommand;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.commands.CopyCommand;
@@ -119,6 +122,19 @@ public class LayoutService implements ILayoutService {
@Autowired
private DbUtils dbUtils;
+ /**
+ * Object that sends emails.
+ */
+ private EmailSender emailSender;
+
+ /**
+ * Method called after spring initialized all interfaces.
+ */
+ @PostConstruct
+ public void springInit() {
+ emailSender = new EmailSender(configurationService);
+ }
+
@Override
public boolean userCanAddLayout(Model model, User user) {
// if we don't have privileges to view the object then we cannot add layouts
@@ -277,8 +293,7 @@ public class LayoutService implements ILayoutService {
final Collection<ColorSchema> schemas = reader
.readColorSchema(params.getColorInputStream(), TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
final Model colorModel = new CopyCommand(params.getModel()).execute();
- new ColorModelCommand(params.getModel(), schemas).execute();
- final EmailSender sender = new EmailSender(configurationService);
+ new ColorModelCommand(params.getModel(), schemas, userService.getColorExtractorForUser(params.getUser())).execute();
String[] tmp = params.getDirectory().split("[\\\\/]");
String simpleDir = tmp[tmp.length - 1];
@@ -291,7 +306,7 @@ public class LayoutService implements ILayoutService {
dbUtils.createSessionForCurrentThread();
}
}
- final Map<Model, Integer> layoutIdByModel = new HashMap<Model, Integer>();
+ final Map<Model, Integer> layoutIdByModel = new HashMap<>();
Layout topLayout = new Layout(params.getName(), simpleDir, false);
if (params.getUser() == null) {
@@ -400,7 +415,7 @@ public class LayoutService implements ILayoutService {
layoutDao.update(layout);
try {
- sender.sendEmail(
+ emailSender.sendEmail(
"MapViewer status", "There was a problem with generating layout " + params.getName() + ". Contact administrator to solve this issue.",
params.getUser());
} catch (MessagingException e1) {
@@ -432,7 +447,7 @@ public class LayoutService implements ILayoutService {
// check if we can color our model using this schema,
// if not then exception will be thrown and passed up
try {
- new ColorModelCommand(params.getModel(), schemas).execute();
+ new ColorModelCommand(params.getModel(), schemas, userService.getColorExtractorForUser(params.getUser())).execute();
} catch (CommandExecutionException e) {
throw new InvalidColorSchemaException(e);
}
@@ -601,7 +616,6 @@ public class LayoutService implements ILayoutService {
* thrown when there is a problem with sending email
*/
protected void sendSuccesfullRemoveEmail(String projectId, String layoutName, String email) throws MessagingException {
- EmailSender emailSender = new EmailSender(configurationService);
StringBuilder content = new StringBuilder("Layout " + layoutName + " in map " + projectId + " was successfully removed.<br/>");
emailSender.sendEmail("MapViewer notification", content.toString(), email);
}
@@ -617,7 +631,6 @@ public class LayoutService implements ILayoutService {
* thrown when there is a problem with sending email
*/
protected void sendSuccessfullGenerationEmail(final CreateLayoutParams params, final Collection<ColorSchema> schemas) throws MessagingException {
- EmailSender emailSender = new EmailSender(configurationService);
StringBuilder content = new StringBuilder("Layout " + params.getName() + " generated successfully.\n");
content.append("Result of coloring:<br/>");
@@ -886,9 +899,9 @@ public class LayoutService implements ILayoutService {
public List<LightLayoutAliasView> getAliasesForLayout(Model model, int layoutId) {
try {
ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas;
- schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
- ColorModelCommand command = new ColorModelCommand(model, schemas);
+ Collection<ColorSchema> schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
+ // colors here are not important
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
LightLayoutAliasViewFactory factory = new LightLayoutAliasViewFactory();
List<LightLayoutAliasView> result = new ArrayList<>();
for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
@@ -908,9 +921,9 @@ public class LayoutService implements ILayoutService {
public List<LightLayoutReactionView> getReactionsForLayout(Model model, int layoutId) {
try {
ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas;
- schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
- ColorModelCommand command = new ColorModelCommand(model, schemas);
+ Collection<ColorSchema> schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
+ // colors here are not important
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
LightLayoutReactionViewFactory factory = new LightLayoutReactionViewFactory();
List<LightLayoutReactionView> result = new ArrayList<>();
for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
@@ -932,7 +945,8 @@ public class LayoutService implements ILayoutService {
ColorSchemaReader reader = new ColorSchemaReader();
Collection<ColorSchema> schemas;
schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
- ColorModelCommand command = new ColorModelCommand(model, schemas);
+ // colors here are not important
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
return command.getModifiedElements();
} catch (InvalidColorSchemaException e) {
throw new InvalidStateException(e);
@@ -952,7 +966,8 @@ public class LayoutService implements ILayoutService {
ColorSchemaReader reader = new ColorSchemaReader();
Collection<ColorSchema> schemas;
schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
- ColorModelCommand command = new ColorModelCommand(model, schemas);
+ // colors here are not important
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
FullLayoutAliasViewFactory factory = new FullLayoutAliasViewFactory();
List<FullLayoutAliasView> result = new ArrayList<>();
@@ -972,4 +987,14 @@ public class LayoutService implements ILayoutService {
throw new InvalidStateException(e);
}
}
+
+ @Override
+ public EmailSender getEmailSender() {
+ return emailSender;
+ }
+
+ @Override
+ public void setEmailSender(EmailSender emailSender) {
+ this.emailSender = emailSender;
+ }
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index d011bcb4568127dbafedbae38010cb727c10897b..8288bfdfce3141b5d603d23824545f7fb2b43517 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -36,7 +36,7 @@ import lcsb.mapviewer.annotation.services.TaxonomyBackend;
import lcsb.mapviewer.annotation.services.TaxonomySearchException;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
-import lcsb.mapviewer.commands.ColorModelCommand;
+import lcsb.mapviewer.commands.ClearColorModelCommand;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.commands.CopyCommand;
import lcsb.mapviewer.commands.CreateHierarchyCommand;
@@ -603,7 +603,7 @@ public class ProjectService implements IProjectService {
}
if (layout.getTitle().equals(BuildInLayout.CLEAN.getTitle())) {
output = new CopyCommand(model).execute();
- new ColorModelCommand(output, new ArrayList<>()).execute();
+ new ClearColorModelCommand(output).execute();
}
final double imgCounter = counter;
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
index 4b7a98cd2e38534eb5cbe89fa1666352e5400f8d..3687c437bd4d143220891a882d28d5115eea1021 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
@@ -1,419 +1,465 @@
-package lcsb.mapviewer.services.impl;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import lcsb.mapviewer.common.ObjectUtils;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.log.LogType;
-import lcsb.mapviewer.model.user.BasicPrivilege;
-import lcsb.mapviewer.model.user.ObjectPrivilege;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-import lcsb.mapviewer.persist.dao.user.PrivilegeDao;
-import lcsb.mapviewer.persist.dao.user.UserDao;
-import lcsb.mapviewer.services.interfaces.ILogService;
-import lcsb.mapviewer.services.interfaces.ILogService.LogParams;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.PrivilegeView;
-import lcsb.mapviewer.services.view.UserView;
-import lcsb.mapviewer.services.view.UserView.UserProjectPrivilegeView;
-import lcsb.mapviewer.services.view.UserViewFactory;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.security.crypto.password.PasswordEncoder;
-import org.springframework.transaction.annotation.Transactional;
-
-/**
- * Implementation of the service that manages users.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class UserService implements IUserService {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(UserService.class);
-
- /**
- * Data access object for users.
- */
- @Autowired
- private UserDao userDao;
-
- /**
- * Data access object for projects.
- */
- @Autowired
- private ProjectDao projectDao;
-
- /**
- * Data access object for privileges.
- */
- @Autowired
- private PrivilegeDao privilegeDao;
-
- /**
- * Factory object for {@link UserView} elements.
- */
- @Autowired
- private UserViewFactory userViewFactory;
-
- /**
- * Service that provides password encoding.
- */
- @Autowired
- private PasswordEncoder passwordEncoder;
-
- /**
- * Service used for logging.
- */
- @Autowired
- private ILogService logService;
-
- @Override
- public boolean login(String login, String password) {
- return userDao.getUserByLoginAndPassword(login, password) != null;
- }
-
- @Override
- public boolean userHasPrivilege(User user, PrivilegeType type) {
- return getUserPrivilegeLevel(user, type) > 0;
- }
-
- @Override
- public boolean userHasPrivilege(User user, PrivilegeType type, Object object) {
- return getUserPrivilegeLevel(user, type, object) > 0;
- }
-
- @Override
- public void setUserPrivilege(User user, BasicPrivilege privilege) {
- privilege.setUser(user);
- BasicPrivilege oldPrivilege = null;
- for (BasicPrivilege privilegeIter : user.getPrivileges()) {
- if (privilegeIter.equalsPrivilege(privilege)) {
- oldPrivilege = privilegeIter;
- }
- }
- if (oldPrivilege != null) {
- user.getPrivileges().remove(oldPrivilege);
- oldPrivilege.setUser(null);
- }
- user.getPrivileges().add(privilege);
- updateUser(user);
- userDao.flush();
- }
-
- @Override
- public void addUser(User user) {
- userDao.add(user);
- LogParams params = new LogParams().description("User " + user.getLogin() + " created.")
- .type(LogType.USER_CREATED).object(user);
- logService.log(params);
- }
-
- @Override
- public void updateUser(User user) {
- userDao.update(user);
- }
-
- @Override
- public void deleteUser(User user) {
- userDao.delete(user);
- LogParams params = new LogParams().description("User " + user.getLogin() + " removed.")
- .type(LogType.USER_CREATED).object(user);
- logService.log(params);
- }
-
- @Override
- public User getUserById(int id) {
- User result = userDao.getById(id);
- if (result != null) {
- userDao.refresh(result);
- }
- return result;
- }
-
- @Override
- public User getUserByLogin(String login) {
- User result = userDao.getUserByLogin(login);
- if (result != null) {
- userDao.refresh(result);
- }
- return result;
- }
-
- @Override
- public List<UserView> getAllUserRows() {
- List<Project> projects = projectDao.getAll();
-
- List<UserView> result = new ArrayList<UserView>();
- List<User> fullList = userDao.getAll();
- for (User user : fullList) {
- result.add(userViewFactory.create(user, projects));
- }
-
- return result;
- }
-
- @Override
- public UserView getUserRow(User user) {
- List<Project> projects = projectDao.getAll();
- return userViewFactory.create(user, projects);
- }
-
- @Override
- public void updateUser(UserView userRow) {
- User user = null;
- if (userRow.getIdObject() == null || userRow.getIdObject() == 0) {
- user = new User();
- user.setLogin(userRow.getLogin());
- } else {
- user = getUserById(userRow.getIdObject());
- }
- if (userRow.getPassword() != null && !userRow.getPassword().trim().equals("")) {
- user.setCryptedPassword(passwordEncoder.encode(userRow.getPassword()));
- }
-
- user.setEmail(userRow.getEmail());
- user.setName(userRow.getName());
- user.setSurname(userRow.getSurname());
- if (user.getId() == null) {
- addUser(user);
- } else {
- updateUser(user);
- }
-
- userRow.setIdObject(user.getId());
-
- for (PrivilegeView pRow : userRow.getBasicPrivileges()) {
- if (pRow.getNumeric()) {
- setUserPrivilege(user, new BasicPrivilege(pRow.getLevel(), pRow.getType(), user));
- } else if (pRow.getSelected()) {
- setUserPrivilege(user, new BasicPrivilege(1, pRow.getType(), user));
- } else {
- setUserPrivilege(user, new BasicPrivilege(0, pRow.getType(), user));
- }
- }
- for (UserProjectPrivilegeView upRow : userRow.getProjectPrivileges()) {
- for (PrivilegeView pRow : upRow.getProjectPrivileges()) {
- Project project = projectDao.getById(upRow.getIdObject());
- if (pRow.getNumeric()) {
- setUserPrivilege(user, new ObjectPrivilege(project, pRow.getLevel(), pRow.getType(), user));
- } else if (pRow.getSelected()) {
- setUserPrivilege(user, new ObjectPrivilege(project, 1, pRow.getType(), user));
- } else {
- setUserPrivilege(user, new ObjectPrivilege(project, 0, pRow.getType(), user));
- }
- }
- }
- }
-
- @Override
- public void deleteUser(UserView selectedUser) {
- if (selectedUser.getIdObject() != null && selectedUser.getIdObject() != 0) {
- deleteUser(getUserById(selectedUser.getIdObject()));
- }
- }
-
- @Override
- public void dropPrivilegesForObjectType(PrivilegeType type, int id) {
- // this will be slow when number of user will increase (we fetch all
- // users and drop privileges one by one)
- List<User> users = userDao.getAll();
- for (User user : users) {
- List<BasicPrivilege> toRemove = new ArrayList<BasicPrivilege>();
- for (BasicPrivilege privilege : user.getPrivileges()) {
- if (privilege.getType().equals(type) && privilege instanceof ObjectPrivilege
- && ((ObjectPrivilege) privilege).getIdObject() == id) {
- toRemove.add(privilege);
- }
- }
- if (toRemove.size() > 0) {
- user.getPrivileges().removeAll(toRemove);
- userDao.update(user);
- }
- }
- }
-
- @Override
- public int getUserPrivilegeLevel(User user, PrivilegeType type) {
- if (type.getPrivilegeClassType() != BasicPrivilege.class) {
- throw new InvalidArgumentException("This privilege requires additional information");
- }
- for (BasicPrivilege privilege : user.getPrivileges()) {
- if (privilege.getType().equals(type)) {
- return privilege.getLevel();
- }
- }
- return 0;
- }
-
- @Override
- public int getUserPrivilegeLevel(User user, PrivilegeType type, Object object) {
- if (type.getPrivilegeClassType() != ObjectPrivilege.class) {
- throw new InvalidArgumentException("This privilege doesn't accept object parameter");
- }
- if (object == null) {
- throw new InvalidArgumentException("Object cannot be null");
- }
- if (!type.getPrivilegeObjectType().isAssignableFrom(object.getClass())) {
- throw new InvalidArgumentException("This privilege accept only " + type.getPrivilegeObjectType()
- + " objects parameter, but " + object.getClass() + " class found.");
- }
- Integer id = null;
- try {
- id = ObjectUtils.getIdOfObject(object);
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw new InvalidArgumentException(
- "Internal server error. Problem with accessing id of the parameter object");
- }
- if (id == null) {
- throw new InvalidArgumentException("Parameter object has null id value");
- }
- if (user == null) {
- throw new InvalidArgumentException("User cannot be null");
- }
-
- // refresh user from db
- if (user.getId() != null) {
- user = userDao.getById(user.getId());
- }
- for (BasicPrivilege privilege : user.getPrivileges()) {
- if (privilege.getClass() == ObjectPrivilege.class) {
- ObjectPrivilege oPrivilege = (ObjectPrivilege) privilege;
- if (oPrivilege.getType().equals(type) && oPrivilege.getIdObject().equals(id)) {
- return privilege.getLevel();
- }
- }
- }
- return -1;
- }
-
- @Override
- public void addUser(UserView userRow) {
- updateUser(userRow);
- }
-
- @Override
- public void setUserPrivilege(User user, PrivilegeType type) {
- BasicPrivilege privilege = new BasicPrivilege(1, type, user);
-
- BasicPrivilege oldPrivilege = null;
- for (BasicPrivilege privilegeIter : user.getPrivileges()) {
- if (privilegeIter.getType().equals(type)) {
- oldPrivilege = privilegeIter;
- }
- }
- if (oldPrivilege != null) {
- user.getPrivileges().remove(oldPrivilege);
- oldPrivilege.setUser(null);
- }
- user.getPrivileges().add(privilege);
- updateUser(user);
- userDao.flush();
-
- }
-
- /**
- * @return the userDao
- * @see #userDao
- */
- public UserDao getUserDao() {
- return userDao;
- }
-
- /**
- * @param userDao
- * the userDao to set
- * @see #userDao
- */
- public void setUserDao(UserDao userDao) {
- this.userDao = userDao;
- }
-
- /**
- * @return the projectDao
- * @see #projectDao
- */
- public ProjectDao getProjectDao() {
- return projectDao;
- }
-
- /**
- * @param projectDao
- * the projectDao to set
- * @see #projectDao
- */
- public void setProjectDao(ProjectDao projectDao) {
- this.projectDao = projectDao;
- }
-
- /**
- * @return the privilegeDao
- * @see #privilegeDao
- */
- public PrivilegeDao getPrivilegeDao() {
- return privilegeDao;
- }
-
- /**
- * @param privilegeDao
- * the privilegeDao to set
- * @see #privilegeDao
- */
- public void setPrivilegeDao(PrivilegeDao privilegeDao) {
- this.privilegeDao = privilegeDao;
- }
-
- /**
- * @return the passwordEncoder
- * @see #passwordEncoder
- */
- public PasswordEncoder getPasswordEncoder() {
- return passwordEncoder;
- }
-
- /**
- * @param passwordEncoder
- * the passwordEncoder to set
- * @see #passwordEncoder
- */
- public void setPasswordEncoder(PasswordEncoder passwordEncoder) {
- this.passwordEncoder = passwordEncoder;
- }
-
- @Override
- public UserView createEmptyUserRow() {
- return userViewFactory.create(null);
- }
-
- @Override
- public void updateUsers(Collection<UserView> users) {
- for (UserView user : users) {
- updateUser(user);
- }
- }
-
- /**
- * @param password
- * input password
- * @return encoded password
- */
- @Override
- public String encodePassword(String password) {
- return passwordEncoder.encode(password);
- }
-
- @Override
- public User getUserByNameSurname(String nameSurnameString) {
- return userDao.getUserByNameSurname(nameSurnameString);
- }
-}
+package lcsb.mapviewer.services.impl;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.security.crypto.password.PasswordEncoder;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.common.ObjectUtils;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.geometry.ColorParser;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.log.LogType;
+import lcsb.mapviewer.model.user.BasicPrivilege;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.ObjectPrivilege;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.ProjectDao;
+import lcsb.mapviewer.persist.dao.user.PrivilegeDao;
+import lcsb.mapviewer.persist.dao.user.UserDao;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+import lcsb.mapviewer.services.interfaces.ILogService;
+import lcsb.mapviewer.services.interfaces.ILogService.LogParams;
+import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.view.PrivilegeView;
+import lcsb.mapviewer.services.view.UserView;
+import lcsb.mapviewer.services.view.UserView.UserProjectPrivilegeView;
+import lcsb.mapviewer.services.view.UserViewFactory;
+
+/**
+ * Implementation of the service that manages users.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class UserService implements IUserService {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(UserService.class);
+
+ /**
+ * Data access object for users.
+ */
+ @Autowired
+ private UserDao userDao;
+
+ /**
+ * Data access object for projects.
+ */
+ @Autowired
+ private ProjectDao projectDao;
+
+ /**
+ * Data access object for privileges.
+ */
+ @Autowired
+ private PrivilegeDao privilegeDao;
+
+ /**
+ * Factory object for {@link UserView} elements.
+ */
+ @Autowired
+ private UserViewFactory userViewFactory;
+
+ /**
+ * Service that provides password encoding.
+ */
+ @Autowired
+ private PasswordEncoder passwordEncoder;
+
+ /**
+ * Service used for logging.
+ */
+ @Autowired
+ private ILogService logService;
+
+ /**
+ * Service used for accessing confguration parameters.
+ */
+ @Autowired
+ private IConfigurationService configurationService;
+
+ @Override
+ public boolean login(String login, String password) {
+ return userDao.getUserByLoginAndPassword(login, password) != null;
+ }
+
+ @Override
+ public boolean userHasPrivilege(User user, PrivilegeType type) {
+ return getUserPrivilegeLevel(user, type) > 0;
+ }
+
+ @Override
+ public boolean userHasPrivilege(User user, PrivilegeType type, Object object) {
+ return getUserPrivilegeLevel(user, type, object) > 0;
+ }
+
+ @Override
+ public void setUserPrivilege(User user, BasicPrivilege privilege) {
+ privilege.setUser(user);
+ BasicPrivilege oldPrivilege = null;
+ for (BasicPrivilege privilegeIter : user.getPrivileges()) {
+ if (privilegeIter.equalsPrivilege(privilege)) {
+ oldPrivilege = privilegeIter;
+ }
+ }
+ if (oldPrivilege != null) {
+ user.getPrivileges().remove(oldPrivilege);
+ oldPrivilege.setUser(null);
+ }
+ user.getPrivileges().add(privilege);
+ updateUser(user);
+ userDao.flush();
+ }
+
+ @Override
+ public void addUser(User user) {
+ userDao.add(user);
+ LogParams params = new LogParams().description("User " + user.getLogin() + " created.").type(LogType.USER_CREATED).object(user);
+ logService.log(params);
+ }
+
+ @Override
+ public void updateUser(User user) {
+ userDao.update(user);
+ }
+
+ @Override
+ public void deleteUser(User user) {
+ userDao.delete(user);
+ LogParams params = new LogParams().description("User " + user.getLogin() + " removed.").type(LogType.USER_CREATED).object(user);
+ logService.log(params);
+ }
+
+ @Override
+ public User getUserById(int id) {
+ User result = userDao.getById(id);
+ if (result != null) {
+ userDao.refresh(result);
+ }
+ return result;
+ }
+
+ @Override
+ public User getUserByLogin(String login) {
+ User result = userDao.getUserByLogin(login);
+ if (result != null) {
+ userDao.refresh(result);
+ }
+ return result;
+ }
+
+ @Override
+ public List<UserView> getAllUserRows() {
+ List<Project> projects = projectDao.getAll();
+
+ List<UserView> result = new ArrayList<UserView>();
+ List<User> fullList = userDao.getAll();
+ for (User user : fullList) {
+ result.add(userViewFactory.create(user, projects));
+ }
+
+ return result;
+ }
+
+ @Override
+ public UserView getUserRow(User user) {
+ List<Project> projects = projectDao.getAll();
+ return userViewFactory.create(user, projects);
+ }
+
+ @Override
+ public void updateUser(UserView userRow) {
+ User user = null;
+ if (userRow.getIdObject() == null || userRow.getIdObject() == 0) {
+ user = new User();
+ user.setLogin(userRow.getLogin());
+ } else {
+ user = getUserById(userRow.getIdObject());
+ }
+ if (userRow.getPassword() != null && !userRow.getPassword().trim().equals("")) {
+ user.setCryptedPassword(passwordEncoder.encode(userRow.getPassword()));
+ }
+
+ user.setEmail(userRow.getEmail());
+ user.setName(userRow.getName());
+ user.setSurname(userRow.getSurname());
+ if (user.getId() == null) {
+ addUser(user);
+ } else {
+ updateUser(user);
+ }
+
+ userRow.setIdObject(user.getId());
+
+ for (PrivilegeView pRow : userRow.getBasicPrivileges()) {
+ if (pRow.getNumeric()) {
+ setUserPrivilege(user, new BasicPrivilege(pRow.getLevel(), pRow.getType(), user));
+ } else if (pRow.getSelected()) {
+ setUserPrivilege(user, new BasicPrivilege(1, pRow.getType(), user));
+ } else {
+ setUserPrivilege(user, new BasicPrivilege(0, pRow.getType(), user));
+ }
+ }
+ for (UserProjectPrivilegeView upRow : userRow.getProjectPrivileges()) {
+ for (PrivilegeView pRow : upRow.getProjectPrivileges()) {
+ Project project = projectDao.getById(upRow.getIdObject());
+ if (pRow.getNumeric()) {
+ setUserPrivilege(user, new ObjectPrivilege(project, pRow.getLevel(), pRow.getType(), user));
+ } else if (pRow.getSelected()) {
+ setUserPrivilege(user, new ObjectPrivilege(project, 1, pRow.getType(), user));
+ } else {
+ setUserPrivilege(user, new ObjectPrivilege(project, 0, pRow.getType(), user));
+ }
+ }
+ }
+ }
+
+ @Override
+ public void deleteUser(UserView selectedUser) {
+ if (selectedUser.getIdObject() != null && selectedUser.getIdObject() != 0) {
+ deleteUser(getUserById(selectedUser.getIdObject()));
+ }
+ }
+
+ @Override
+ public void dropPrivilegesForObjectType(PrivilegeType type, int id) {
+ // this will be slow when number of user will increase (we fetch all
+ // users and drop privileges one by one)
+ List<User> users = userDao.getAll();
+ for (User user : users) {
+ List<BasicPrivilege> toRemove = new ArrayList<BasicPrivilege>();
+ for (BasicPrivilege privilege : user.getPrivileges()) {
+ if (privilege.getType().equals(type) && privilege instanceof ObjectPrivilege && ((ObjectPrivilege) privilege).getIdObject() == id) {
+ toRemove.add(privilege);
+ }
+ }
+ if (toRemove.size() > 0) {
+ user.getPrivileges().removeAll(toRemove);
+ userDao.update(user);
+ }
+ }
+ }
+
+ @Override
+ public int getUserPrivilegeLevel(User user, PrivilegeType type) {
+ if (type.getPrivilegeClassType() != BasicPrivilege.class) {
+ throw new InvalidArgumentException("This privilege requires additional information");
+ }
+ for (BasicPrivilege privilege : user.getPrivileges()) {
+ if (privilege.getType().equals(type)) {
+ return privilege.getLevel();
+ }
+ }
+ return 0;
+ }
+
+ @Override
+ public int getUserPrivilegeLevel(User user, PrivilegeType type, Object object) {
+ if (type.getPrivilegeClassType() != ObjectPrivilege.class) {
+ throw new InvalidArgumentException("This privilege doesn't accept object parameter");
+ }
+ if (object == null) {
+ throw new InvalidArgumentException("Object cannot be null");
+ }
+ if (!type.getPrivilegeObjectType().isAssignableFrom(object.getClass())) {
+ throw new InvalidArgumentException(
+ "This privilege accept only " + type.getPrivilegeObjectType() + " objects parameter, but " + object.getClass() + " class found.");
+ }
+ Integer id = null;
+ try {
+ id = ObjectUtils.getIdOfObject(object);
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw new InvalidArgumentException("Internal server error. Problem with accessing id of the parameter object");
+ }
+ if (id == null) {
+ throw new InvalidArgumentException("Parameter object has null id value");
+ }
+ if (user == null) {
+ throw new InvalidArgumentException("User cannot be null");
+ }
+
+ // refresh user from db
+ if (user.getId() != null) {
+ user = userDao.getById(user.getId());
+ }
+ for (BasicPrivilege privilege : user.getPrivileges()) {
+ if (privilege.getClass() == ObjectPrivilege.class) {
+ ObjectPrivilege oPrivilege = (ObjectPrivilege) privilege;
+ if (oPrivilege.getType().equals(type) && oPrivilege.getIdObject().equals(id)) {
+ return privilege.getLevel();
+ }
+ }
+ }
+ return -1;
+ }
+
+ @Override
+ public void addUser(UserView userRow) {
+ updateUser(userRow);
+ }
+
+ @Override
+ public void setUserPrivilege(User user, PrivilegeType type) {
+ BasicPrivilege privilege = new BasicPrivilege(1, type, user);
+
+ BasicPrivilege oldPrivilege = null;
+ for (BasicPrivilege privilegeIter : user.getPrivileges()) {
+ if (privilegeIter.getType().equals(type)) {
+ oldPrivilege = privilegeIter;
+ }
+ }
+ if (oldPrivilege != null) {
+ user.getPrivileges().remove(oldPrivilege);
+ oldPrivilege.setUser(null);
+ }
+ user.getPrivileges().add(privilege);
+ updateUser(user);
+ userDao.flush();
+
+ }
+
+ /**
+ * @return the userDao
+ * @see #userDao
+ */
+ public UserDao getUserDao() {
+ return userDao;
+ }
+
+ /**
+ * @param userDao
+ * the userDao to set
+ * @see #userDao
+ */
+ public void setUserDao(UserDao userDao) {
+ this.userDao = userDao;
+ }
+
+ /**
+ * @return the projectDao
+ * @see #projectDao
+ */
+ public ProjectDao getProjectDao() {
+ return projectDao;
+ }
+
+ /**
+ * @param projectDao
+ * the projectDao to set
+ * @see #projectDao
+ */
+ public void setProjectDao(ProjectDao projectDao) {
+ this.projectDao = projectDao;
+ }
+
+ /**
+ * @return the privilegeDao
+ * @see #privilegeDao
+ */
+ public PrivilegeDao getPrivilegeDao() {
+ return privilegeDao;
+ }
+
+ /**
+ * @param privilegeDao
+ * the privilegeDao to set
+ * @see #privilegeDao
+ */
+ public void setPrivilegeDao(PrivilegeDao privilegeDao) {
+ this.privilegeDao = privilegeDao;
+ }
+
+ /**
+ * @return the passwordEncoder
+ * @see #passwordEncoder
+ */
+ public PasswordEncoder getPasswordEncoder() {
+ return passwordEncoder;
+ }
+
+ /**
+ * @param passwordEncoder
+ * the passwordEncoder to set
+ * @see #passwordEncoder
+ */
+ public void setPasswordEncoder(PasswordEncoder passwordEncoder) {
+ this.passwordEncoder = passwordEncoder;
+ }
+
+ @Override
+ public UserView createEmptyUserRow() {
+ return userViewFactory.create(null);
+ }
+
+ @Override
+ public void updateUsers(Collection<UserView> users) {
+ for (UserView user : users) {
+ updateUser(user);
+ }
+ }
+
+ /**
+ * @param password
+ * input password
+ * @return encoded password
+ */
+ @Override
+ public String encodePassword(String password) {
+ return passwordEncoder.encode(password);
+ }
+
+ @Override
+ public User getUserByNameSurname(String nameSurnameString) {
+ return userDao.getUserByNameSurname(nameSurnameString);
+ }
+
+ @Override
+ public ColorExtractor getColorExtractorForUser(User loggedUser) {
+ Color colorMin = null;
+ Color colorMax = null;
+ if (loggedUser != null) {
+ User dbUser = getUserById(loggedUser.getId());
+ if (dbUser != null) {
+ colorMin = dbUser.getMinColor();
+ colorMax = dbUser.getMaxColor();
+ }
+ }
+ ColorParser parser = new ColorParser();
+
+ if (colorMin == null) {
+ colorMin = parser.parse(configurationService.getConfigurationValue(ConfigurationElementType.MIN_COLOR_VAL));
+ }
+ if (colorMax == null) {
+ colorMax = parser.parse(configurationService.getConfigurationValue(ConfigurationElementType.MAX_COLOR_VAL));
+ }
+ return new ColorExtractor(colorMin, colorMax);
+ }
+
+ /**
+ * @return the configurationService
+ * @see #configurationService
+ */
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
+
+ /**
+ * @param configurationService
+ * the configurationService to set
+ * @see #configurationService
+ */
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
index 98a3696f4e2b3840ae8f7e62fe5b1a0a7096c57c..853599bdbb9c9376b149be8a73ab9a802c49d40a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
@@ -16,6 +16,7 @@ import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.search.layout.FullLayoutAliasView;
import lcsb.mapviewer.services.search.layout.LightLayoutAliasView;
import lcsb.mapviewer.services.search.layout.LightLayoutReactionView;
+import lcsb.mapviewer.services.utils.EmailSender;
import lcsb.mapviewer.services.utils.data.ColorSchemaType;
import lcsb.mapviewer.services.view.LayoutView;
@@ -491,4 +492,19 @@ public interface ILayoutService {
*/
List<FullLayoutAliasView> getFullAliasesForLayoutByIds(Model model, List<Pair<Integer, Integer>> identifiers, int layoutId);
+ /**
+ * Returns {@link EmailSender} used by the service.
+ *
+ * @return {@link EmailSender} used by the service
+ */
+ EmailSender getEmailSender();
+
+ /**
+ * Sets {@link EmailSender} used by the service.
+ *
+ * @param emailSender
+ * {@link EmailSender} used by the service
+ */
+ void setEmailSender(EmailSender emailSender);
+
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
index 67042365b9f581f49455236b6a33305f1779aa1c..aed818b54d8a58a0aa67476ba7cc40cf6f7e8dfe 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
@@ -1,230 +1,241 @@
-package lcsb.mapviewer.services.interfaces;
-
-import java.util.Collection;
-import java.util.List;
-
-import lcsb.mapviewer.model.user.BasicPrivilege;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.view.UserView;
-
-/**
- * Service that manages users.
- *
- * @author Piotr Gawron
- *
- */
-public interface IUserService {
- /**
- * Check if its possible to login using given login and password.
- *
- * @param login
- * user login
- * @param password
- * plan password
- * @return <code>true</code> if credentials are ok, <code>false</code>
- * otherwise
- */
- boolean login(String login, String password);
-
- /**
- * Returns user by login.
- *
- * @param login
- * user login
- * @return user if the login is valid, <code>null</code> otherwise
- */
- User getUserByLogin(String login);
-
- /**
- * Checks if user has a given privilege.
- *
- * @param user
- * user for which the check is performed
- * @param type
- * type of the privilege
- * @return <code>true</code> if user has privilege, <code>false</code>
- * otherwise
- */
- boolean userHasPrivilege(User user, PrivilegeType type);
-
- /**
- * Returns level of the user privilege.
- *
- * @param user
- * user for which the check is performed
- * @param type
- * type of the privilege
- * @return level of the privilege
- */
- int getUserPrivilegeLevel(User user, PrivilegeType type);
-
- /**
- * Checks if user has a given privilege on the object.
- *
- * @param user
- * user for which the check is performed
- * @param type
- * type of the privilege
- * @param object
- * object of the privilege
- * @return <code>true</code> if user has privilege, <code>false</code>
- * otherwise
- */
- boolean userHasPrivilege(User user, PrivilegeType type, Object object);
-
- /**
- * Returns level of the user privilege.
- *
- * @param object
- * object of the privilege
- * @param user
- * user for which the check is performed
- * @param type
- * type of the privilege
- * @return level of the privilege
- */
- int getUserPrivilegeLevel(User user, PrivilegeType type, Object object);
-
- /**
- * Sets the user privilege.
- *
- * @param user
- * user for whom the privilege should be granted/dropped
- * @param privilege
- * user privilege
- */
- void setUserPrivilege(User user, BasicPrivilege privilege);
-
- /**
- * Adds user to the system.
- *
- * @param user
- * user to be added
- */
- void addUser(User user);
-
- /**
- * Updates user in the system.
- *
- * @param user
- * user to be updated
- */
- void updateUser(User user);
-
- /**
- * Removes user from the system.
- *
- * @param user
- * user to be removed
- */
- void deleteUser(User user);
-
- /**
- * Returns user by the database identifier.
- *
- * @param id
- * database identifier
- * @return user for the given identifier, null if user doesn't exist
- *
- */
- User getUserById(int id);
-
- /**
- * Returns user views for all users.
- *
- * @return list of user {@link lcsb.mapviewer.services.view.AbstractView
- * views} for all users
- */
- List<UserView> getAllUserRows();
-
- /**
- * @param user
- * user that will have view.
- * @return view for one user.
- */
- UserView getUserRow(User user);
-
- /**
- * Updates user from user {@link lcsb.mapviewer.services.view.AbstractView
- * view}.
- *
- * @param selectedUser
- * user {@link lcsb.mapviewer.services.view.AbstractView view} to
- * update
- */
- void updateUser(UserView selectedUser);
-
- /**
- * Removes user based on user
- * {@link lcsb.mapviewer.services.view.AbstractView view}.
- *
- * @param selectedUser
- * user {@link lcsb.mapviewer.services.view.AbstractView view} to
- * be removed
- */
- void deleteUser(UserView selectedUser);
-
- /**
- * Creates empty view.
- *
- * @return empty user {@link lcsb.mapviewer.services.view.AbstractView view}
- * .
- */
- UserView createEmptyUserRow();
-
- /**
- * Drops privileges for every user on the given object and type.
- *
- * @param type
- * type of privilege that should be dropped
- * @param objectId
- * identifier of the object to which privileges should be dropped
- */
- void dropPrivilegesForObjectType(PrivilegeType type, int objectId);
-
- /**
- * Adds user from user view.
- *
- * @param selectedUser
- * user view representation that should be added
- */
- void addUser(UserView selectedUser);
-
- /**
- * Adds privilege to the user.
- *
- * @param user
- * user to which privilege should be added
- * @param type
- * type of the privilege
- */
- void setUserPrivilege(User user, PrivilegeType type);
-
- /**
- * Updates users from list of user
- * {@link lcsb.mapviewer.services.view.AbstractView view}.
- *
- * @param users
- * user {@link lcsb.mapviewer.services.view.AbstractView views}
- * to update
- */
- void updateUsers(Collection<UserView> users);
-
- /**
- * @param password
- * input password
- * @return encoded password
- */
- String encodePassword(String password);
-
- /**
- * Returns {@link User} for given "name surname" string.
- *
- * @param nameSurnameString
- * string identifing user with name and surname separated by single
- * space
- * @return {@link User} for given "name surname" string
- */
- User getUserByNameSurname(String nameSurnameString);
-}
+package lcsb.mapviewer.services.interfaces;
+
+import java.util.Collection;
+import java.util.List;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.model.user.BasicPrivilege;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.view.UserView;
+
+/**
+ * Service that manages users.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface IUserService {
+ /**
+ * Check if its possible to login using given login and password.
+ *
+ * @param login
+ * user login
+ * @param password
+ * plan password
+ * @return <code>true</code> if credentials are ok, <code>false</code>
+ * otherwise
+ */
+ boolean login(String login, String password);
+
+ /**
+ * Returns user by login.
+ *
+ * @param login
+ * user login
+ * @return user if the login is valid, <code>null</code> otherwise
+ */
+ User getUserByLogin(String login);
+
+ /**
+ * Checks if user has a given privilege.
+ *
+ * @param user
+ * user for which the check is performed
+ * @param type
+ * type of the privilege
+ * @return <code>true</code> if user has privilege, <code>false</code>
+ * otherwise
+ */
+ boolean userHasPrivilege(User user, PrivilegeType type);
+
+ /**
+ * Returns level of the user privilege.
+ *
+ * @param user
+ * user for which the check is performed
+ * @param type
+ * type of the privilege
+ * @return level of the privilege
+ */
+ int getUserPrivilegeLevel(User user, PrivilegeType type);
+
+ /**
+ * Checks if user has a given privilege on the object.
+ *
+ * @param user
+ * user for which the check is performed
+ * @param type
+ * type of the privilege
+ * @param object
+ * object of the privilege
+ * @return <code>true</code> if user has privilege, <code>false</code>
+ * otherwise
+ */
+ boolean userHasPrivilege(User user, PrivilegeType type, Object object);
+
+ /**
+ * Returns level of the user privilege.
+ *
+ * @param object
+ * object of the privilege
+ * @param user
+ * user for which the check is performed
+ * @param type
+ * type of the privilege
+ * @return level of the privilege
+ */
+ int getUserPrivilegeLevel(User user, PrivilegeType type, Object object);
+
+ /**
+ * Sets the user privilege.
+ *
+ * @param user
+ * user for whom the privilege should be granted/dropped
+ * @param privilege
+ * user privilege
+ */
+ void setUserPrivilege(User user, BasicPrivilege privilege);
+
+ /**
+ * Adds user to the system.
+ *
+ * @param user
+ * user to be added
+ */
+ void addUser(User user);
+
+ /**
+ * Updates user in the system.
+ *
+ * @param user
+ * user to be updated
+ */
+ void updateUser(User user);
+
+ /**
+ * Removes user from the system.
+ *
+ * @param user
+ * user to be removed
+ */
+ void deleteUser(User user);
+
+ /**
+ * Returns user by the database identifier.
+ *
+ * @param id
+ * database identifier
+ * @return user for the given identifier, null if user doesn't exist
+ *
+ */
+ User getUserById(int id);
+
+ /**
+ * Returns user views for all users.
+ *
+ * @return list of user {@link lcsb.mapviewer.services.view.AbstractView
+ * views} for all users
+ */
+ List<UserView> getAllUserRows();
+
+ /**
+ * @param user
+ * user that will have view.
+ * @return view for one user.
+ */
+ UserView getUserRow(User user);
+
+ /**
+ * Updates user from user {@link lcsb.mapviewer.services.view.AbstractView
+ * view}.
+ *
+ * @param selectedUser
+ * user {@link lcsb.mapviewer.services.view.AbstractView view} to
+ * update
+ */
+ void updateUser(UserView selectedUser);
+
+ /**
+ * Removes user based on user {@link lcsb.mapviewer.services.view.AbstractView
+ * view}.
+ *
+ * @param selectedUser
+ * user {@link lcsb.mapviewer.services.view.AbstractView view} to be
+ * removed
+ */
+ void deleteUser(UserView selectedUser);
+
+ /**
+ * Creates empty view.
+ *
+ * @return empty user {@link lcsb.mapviewer.services.view.AbstractView view} .
+ */
+ UserView createEmptyUserRow();
+
+ /**
+ * Drops privileges for every user on the given object and type.
+ *
+ * @param type
+ * type of privilege that should be dropped
+ * @param objectId
+ * identifier of the object to which privileges should be dropped
+ */
+ void dropPrivilegesForObjectType(PrivilegeType type, int objectId);
+
+ /**
+ * Adds user from user view.
+ *
+ * @param selectedUser
+ * user view representation that should be added
+ */
+ void addUser(UserView selectedUser);
+
+ /**
+ * Adds privilege to the user.
+ *
+ * @param user
+ * user to which privilege should be added
+ * @param type
+ * type of the privilege
+ */
+ void setUserPrivilege(User user, PrivilegeType type);
+
+ /**
+ * Updates users from list of user
+ * {@link lcsb.mapviewer.services.view.AbstractView view}.
+ *
+ * @param users
+ * user {@link lcsb.mapviewer.services.view.AbstractView views} to
+ * update
+ */
+ void updateUsers(Collection<UserView> users);
+
+ /**
+ * @param password
+ * input password
+ * @return encoded password
+ */
+ String encodePassword(String password);
+
+ /**
+ * Returns {@link User} for given "name surname" string.
+ *
+ * @param nameSurnameString
+ * string identifing user with name and surname separated by single
+ * space
+ * @return {@link User} for given "name surname" string
+ */
+ User getUserByNameSurname(String nameSurnameString);
+
+ /**
+ * Returns {@link ColorExtractor} that transform overlay values into colors
+ * for given user.
+ *
+ * @param user
+ * {@link User} for which {@link ColorExtractor} will be obtained
+ * @return {@link ColorExtractor} that transform overlay values into colors
+ * for given user
+ */
+ ColorExtractor getColorExtractorForUser(User user);
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
index 83108406d921a8c7a8078530d39ff235801827ce..e39214a40fcc5f1640ccac5a3c2366d9c4e073d3 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
@@ -30,6 +30,7 @@ import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
+import lcsb.mapviewer.services.view.AnnotationView;
/**
* Implementation of the service that allows access information about drugs.
@@ -85,14 +86,25 @@ public class DrugService implements IDrugService {
@Override
public List<DrugView> getByNames(List<String> names, DbSearchCriteria searchCriteria) {
- List<DrugView> result = new ArrayList<DrugView>();
+ List<DrugView> result = new ArrayList<>();
+
+ Set<String> processedDrugIds = new HashSet<>();
int oldSet = searchCriteria.getColorSet();
for (String string : names) {
searchCriteria.colorSet(searchCriteria.getColorSet() + 1);
DrugView drug = getByName(string, searchCriteria);
if (drug != null) {
- result.add(drug);
+ boolean isNewDrug = false;
+ for (AnnotationView id : drug.getDrugLinks()) {
+ if (!processedDrugIds.contains(id.toString())) {
+ isNewDrug = true;
+ }
+ processedDrugIds.add(id.toString());
+ }
+ if (isNewDrug) {
+ result.add(drug);
+ }
}
}
searchCriteria.colorSet(oldSet);
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugView.java b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugView.java
index 640997c1f86dc9d64276076cf69a2a5870ead1a4..7ca8fa38243d77711cd80e28a78eb6a2436fedb9 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugView.java
@@ -66,27 +66,31 @@ public class DrugView extends AbstractView<Drug> implements Serializable, ISearc
* List of links to extenral databases.
*/
private List<AnnotationView> drugLinks = new ArrayList<>();
+
/**
* List of targets for the drug.
*/
- private List<TargetView> targetRows = new ArrayList<>();
+ private List<TargetView> targetRows = new ArrayList<>();
/**
* Description of the drug.
*/
private String description;
+
/**
* Status of blood brain barries for the drug.
*/
private String bloodBrainBarrier = "N/A";
+
/**
* Known brand names.
*/
- private List<String> brandNames = new ArrayList<String>();
+ private List<String> brandNames = new ArrayList<>();
+
/**
* Known synonyms.
*/
- private List<String> synonyms = new ArrayList<String>();
+ private List<String> synonyms = new ArrayList<>();
/**
* Constructor that initialize the data with information from the parameter
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java
index d58e285eff71e012da61010728b7134e70350deb..e42bc74452ab802039cdd8f87ac09afeb0eff40f 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java
@@ -29,7 +29,7 @@ public class FullLayoutAliasViewFactory extends ElementViewFactory<Pair<Element,
ColorSchema schema = pair.getRight();
FullLayoutAliasView result = new FullLayoutAliasView(pair.getLeft());
- result.setColor(schema.getNormalizedColor());
+ result.setColor(schema.getColor());
result.setValue(schema.getValue());
result.setDescription(schema.getDescription());
if (schema instanceof GeneVariationColorSchema) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java
index 4d0c874fd4ccdb43ba5b1fce35c77faa03fa3dba..0f37f3a0afe17a79edab2d9858bb2aed061e0d71 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java
@@ -25,7 +25,7 @@ public class LightLayoutAliasViewFactory extends ElementViewFactory<Pair<Element
@Override
public LightLayoutAliasView create(Pair<Element, ColorSchema> pair) {
LightLayoutAliasView result = new LightLayoutAliasView(pair.getLeft());
- result.setColor(pair.getRight().getNormalizedColor());
+ result.setColor(pair.getRight().getColor());
result.setValue(pair.getRight().getValue());
return result;
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutReactionView.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutReactionView.java
index 8053477586e6fd760889aa7fafeb7b0a767b9631..cf1bec9e84d510b5504e9267b3d7331d482f58f7 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutReactionView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutReactionView.java
@@ -1,115 +1,137 @@
-package lcsb.mapviewer.services.search.layout;
-
-import java.awt.Color;
-
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.services.search.ElementView;
-
-/**
- * Light {@link ElementView view} for {@link Reaction} representing data that
- * should be send to client about reaction related to
- * {@link lcsb.mapviewer.model.map.layout.Layout}.
- *
- * @author Piotr Gawron
- *
- */
-public class LightLayoutReactionView extends ElementView {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Width of highlighted {@link Reaction} in a a layout.
- */
- private Double width;
-
- /**
- * Color used to highlight {@link Reaction} in a layout.
- */
- private Color color;
-
- /**
- * Should the reaction be reversed when visualizing..
- */
- private Boolean reverse;
-
- /**
- * Default constructor.
- *
- * @param reaction
- * original object from which this on is created
- */
- public LightLayoutReactionView(Reaction reaction) {
- super(reaction.getId(), reaction.getModel().getId());
- }
-
- /**
- * Constructor that should be used only for (de)serialization.
- */
- protected LightLayoutReactionView() {
- super();
- }
-
- /**
- * @return the color
- * @see #color
- */
- public Color getColor() {
- return color;
- }
-
- /**
- * @param color
- * the color to set
- * @see #color
- */
- public void setColor(Color color) {
- this.color = color;
- }
-
- @Override
- public String toString() {
- return "[" + this.getClass().getSimpleName() + "] " + //
- "reaction_id: " + getIdObject() + ", " + //
- "width: " + getWidth() + ", " + //
- "color: " + getColor() + ", ";
-
- }
-
- /**
- * @return the width
- * @see #width
- */
- public Double getWidth() {
- return width;
- }
-
- /**
- * @param width
- * the width to set
- * @see #width
- */
- public void setWidth(Double width) {
- this.width = width;
- }
-
- /**
- * @return the reverse
- * @see #reverse
- */
- public Boolean getReverse() {
- return reverse;
- }
-
- /**
- * @param reverse
- * the reverse to set
- * @see #reverse
- */
- public void setReverse(Boolean reverse) {
- this.reverse = reverse;
- }
-
-}
+package lcsb.mapviewer.services.search.layout;
+
+import java.awt.Color;
+
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.services.search.ElementView;
+
+/**
+ * Light {@link ElementView view} for {@link Reaction} representing data that
+ * should be send to client about reaction related to
+ * {@link lcsb.mapviewer.model.map.layout.Layout}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LightLayoutReactionView extends ElementView {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Width of highlighted {@link Reaction} in a a layout.
+ */
+ private Double width;
+
+ /**
+ * Color used to highlight {@link Reaction} in a layout.
+ */
+ private Color color;
+
+ /**
+ * Should the reaction be reversed when visualizing..
+ */
+ private Boolean reverse;
+
+ /**
+ * Normalized value repesenting expresion (used instead of color).
+ */
+ private Double value;
+
+ /**
+ * Default constructor.
+ *
+ * @param reaction
+ * original object from which this on is created
+ */
+ public LightLayoutReactionView(Reaction reaction) {
+ super(reaction.getId(), reaction.getModel().getId());
+ }
+
+ /**
+ * Constructor that should be used only for (de)serialization.
+ */
+ protected LightLayoutReactionView() {
+ super();
+ }
+
+ /**
+ * @return the color
+ * @see #color
+ */
+ public Color getColor() {
+ return color;
+ }
+
+ /**
+ * @param color
+ * the color to set
+ * @see #color
+ */
+ public void setColor(Color color) {
+ this.color = color;
+ }
+
+ @Override
+ public String toString() {
+ return "[" + this.getClass().getSimpleName() + "] " + //
+ "reaction_id: " + getIdObject() + ", " + //
+ "width: " + getWidth() + ", " + //
+ "color: " + getColor() + ", ";
+
+ }
+
+ /**
+ * @return the width
+ * @see #width
+ */
+ public Double getWidth() {
+ return width;
+ }
+
+ /**
+ * @param width
+ * the width to set
+ * @see #width
+ */
+ public void setWidth(Double width) {
+ this.width = width;
+ }
+
+ /**
+ * @return the reverse
+ * @see #reverse
+ */
+ public Boolean getReverse() {
+ return reverse;
+ }
+
+ /**
+ * @param reverse
+ * the reverse to set
+ * @see #reverse
+ */
+ public void setReverse(Boolean reverse) {
+ this.reverse = reverse;
+ }
+
+ /**
+ * @return the value
+ * @see #value
+ */
+ public Double getValue() {
+ return value;
+ }
+
+ /**
+ * @param value
+ * the value to set
+ * @see #value
+ */
+ public void setValue(Double value) {
+ this.value = value;
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutReactionViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutReactionViewFactory.java
index fc7ff5ccacad18cb7a8ae6f8ee6b7cc24a3060ee..2728acc532abc62f22ab274b08a04d095eb4fa08 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutReactionViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutReactionViewFactory.java
@@ -25,7 +25,8 @@ public class LightLayoutReactionViewFactory extends ElementViewFactory<Pair<Reac
@Override
public LightLayoutReactionView create(Pair<Reaction, ColorSchema> pair) {
LightLayoutReactionView result = new LightLayoutReactionView(pair.getLeft());
- result.setColor(pair.getRight().getNormalizedColor());
+ result.setColor(pair.getRight().getColor());
+ result.setValue(pair.getRight().getValue());
result.setWidth(pair.getRight().getLineWidth());
result.setReverse(pair.getRight().getReverseReaction());
return result;
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
index 292e215ede6f12722e724897b5bf0b69798df127..d06c19183f1019116142d54131801dac457b6f4c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -24,6 +24,7 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.TextFileUtils;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.converter.model.celldesigner.species.SpeciesMapping;
import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.map.MiriamData;
@@ -62,6 +63,11 @@ public class ColorSchemaReader {
*/
private static final int MIN_GV_RED_VALUE = 128;
+ /**
+ * Object that parses colors from string.
+ */
+ private ColorParser colorParser = new ColorParser();
+
/**
* Default class logger.
*/
@@ -200,7 +206,7 @@ public class ColorSchemaReader {
}
}
if (colorColumn != null) {
- schema.setColor(values[colorColumn]);
+ schema.setColor(colorParser.parse(values[colorColumn]));
}
if (identifierColumn != null && !values[identifierColumn].equals("")) {
if (mc.isValidIdentifier(values[identifierColumn])) {
@@ -280,7 +286,7 @@ public class ColorSchemaReader {
* @param schema
* {@link ColorSchema} where name should be set
* @param type
- * {@link MiriamType} type of the identifier
+ * {@link MiriamType} type of the identifier
* @param content
* content of the cell where identifier of given type is stored
*/
@@ -496,7 +502,7 @@ public class ColorSchemaReader {
}
if (colorColumn != null) {
- schema.setColor(values[colorColumn]);
+ schema.setColor(colorParser.parse(values[colorColumn]));
}
if (reactionIdentifierColumn != null) {
processReactionIdentifier(schema, values[reactionIdentifierColumn]);
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
index 8e23dbec6d9e88e63ff106a9565930ff2b39c1c4..f852f697bcb65ecf669503a0bd3a3022d3010e0a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
@@ -25,6 +25,7 @@ import org.apache.poi.xssf.usermodel.XSSFWorkbook;
import lcsb.mapviewer.annotation.services.MiriamConnector;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.converter.model.celldesigner.species.SpeciesMapping;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
@@ -48,18 +49,18 @@ public class ColorSchemaXlsxReader {
/**
* @param fileName
- * file name
+ * file name
* @param sheetName
- * sheet name.
+ * sheet name.
* @return list of ColorSchema.
* @throws IOException
- * exception related to opening the input stream.
+ * exception related to opening the input stream.
* @throws InvalidColorSchemaException
- * invalid color schema exception.
+ * invalid color schema exception.
*/
- public Collection<ColorSchema> readColorSchema(String fileName, String sheetName)
- throws IOException, InvalidColorSchemaException {
- List<ColorSchema> result = new ArrayList<ColorSchema>();
+ public Collection<ColorSchema> readColorSchema(String fileName, String sheetName) throws IOException, InvalidColorSchemaException {
+ ColorParser colorParser = new ColorParser();
+ List<ColorSchema> result = new ArrayList<>();
FileInputStream file = null;
Workbook workbook = null;
@@ -134,8 +135,7 @@ public class ColorSchemaXlsxReader {
}
if (!found) {
if (acceptableIdentifiers.keySet().contains(value.toLowerCase())) {
- foundCustomIdentifiers.add(new Pair<MiriamType, Integer>(
- acceptableIdentifiers.get(value.toLowerCase()), columnIndex - 1));
+ foundCustomIdentifiers.add(new Pair<MiriamType, Integer>(acceptableIdentifiers.get(value.toLowerCase()), columnIndex - 1));
} else {
String columnNames = "";
for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
@@ -144,8 +144,7 @@ public class ColorSchemaXlsxReader {
for (String string : acceptableIdentifiers.keySet()) {
columnNames += ", " + string;
}
- throw new InvalidColorSchemaException(
- "Unknown column type: " + value + ". Acceptable column name: " + columnNames);
+ throw new InvalidColorSchemaException("Unknown column type: " + value + ". Acceptable column name: " + columnNames);
}
}
}
@@ -163,15 +162,12 @@ public class ColorSchemaXlsxReader {
throw new InvalidColorSchemaException("Schema can contain only one of these two columns: ");
}
- if (nameColumn == null && identifierColumn == null && foundCustomIdentifiers.size() == 0
- && reactionIdentifierColumn == null) {
- throw new InvalidColorSchemaException(
- "One of these columns is obligatory: name, identifier, reactionIdentifier");
+ if (nameColumn == null && identifierColumn == null && foundCustomIdentifiers.size() == 0 && reactionIdentifierColumn == null) {
+ throw new InvalidColorSchemaException("One of these columns is obligatory: name, identifier, reactionIdentifier");
}
if (valueColumn == null && colorColumn == null) {
- throw new InvalidColorSchemaException(
- "Schema must contain one of these two columns: value, name");
+ throw new InvalidColorSchemaException("Schema must contain one of these two columns: value, name");
}
} else {
@@ -185,13 +181,11 @@ public class ColorSchemaXlsxReader {
cell.setCellType(Cell.CELL_TYPE_STRING);
schema.setValue(Double.parseDouble(cell.getStringCellValue().replace(",", ".")));
} catch (Exception e) {
- throw new InvalidColorSchemaException("[Line " + lineIndex
- + "] Problem with parsing value for value column. Cell value" + cell);
+ throw new InvalidColorSchemaException("[Line " + lineIndex + "] Problem with parsing value for value column. Cell value" + cell);
}
- if (schema.getValue() > 1 + Configuration.EPSILON
- || schema.getValue() < -1 - Configuration.EPSILON) {
- throw new InvalidColorSchemaException("[Line " + lineIndex + "] Value " + schema.getValue()
- + " out of range. Only values between -1 and 1 are allowed.");
+ if (schema.getValue() > 1 + Configuration.EPSILON || schema.getValue() < -1 - Configuration.EPSILON) {
+ throw new InvalidColorSchemaException(
+ "[Line " + lineIndex + "] Value " + schema.getValue() + " out of range. Only values between -1 and 1 are allowed.");
}
}
if (compartmentColumn != null) {
@@ -216,7 +210,7 @@ public class ColorSchemaXlsxReader {
}
}
if (colorColumn != null) {
- schema.setColor(row.getCell(colorColumn).getStringCellValue());
+ schema.setColor(colorParser.parse(row.getCell(colorColumn).getStringCellValue()));
}
if (reactionIdentifierColumn != null) {
schema.setReactionIdentifier(row.getCell(reactionIdentifierColumn).getStringCellValue());
@@ -229,8 +223,7 @@ public class ColorSchemaXlsxReader {
try {
schema.setLineWidth(Double.parseDouble(value.replace(",", ".")));
} catch (NumberFormatException e) {
- throw new InvalidColorSchemaException(
- "[Line " + lineIndex + "] Problem with parsing value: \"" + value + "\"");
+ throw new InvalidColorSchemaException("[Line " + lineIndex + "] Problem with parsing value: \"" + value + "\"");
}
}
}
@@ -249,28 +242,24 @@ public class ColorSchemaXlsxReader {
if (miriamConnector.isValidIdentifier(value)) {
schema.setGeneralIdentifier(value);
} else {
- throw new InvalidColorSchemaException(
- "[Line " + lineIndex + "]" + " Invalid identifier: " + value);
+ throw new InvalidColorSchemaException("[Line " + lineIndex + "]" + " Invalid identifier: " + value);
}
}
}
for (Pair<MiriamType, Integer> pair : foundCustomIdentifiers) {
cell = row.getCell(pair.getRight());
if (cell != null) {
- schema.addIdentifierColumn(
- new Pair<MiriamType, String>(pair.getLeft(), cell.getStringCellValue()));
+ schema.addIdentifierColumn(new Pair<MiriamType, String>(pair.getLeft(), cell.getStringCellValue()));
}
}
- if ((schema.getValue() != null && schema.getColor() != null)
- || (schema.getValue() == null && schema.getColor() == null)) {
+ if ((schema.getValue() != null && schema.getColor() != null) || (schema.getValue() == null && schema.getColor() == null)) {
throw new InvalidColorSchemaException("Value or Color is needed not both");
}
- if (schema.getName() == null && schema.getGeneralIdentifier() == null
- && foundCustomIdentifiers.size() == 0 && schema.getReactionIdentifier() == null) {
- throw new InvalidColorSchemaException(
- "One of these columns values is obligatory: name, identifier, reactionIdentifier");
+ if (schema.getName() == null && schema.getGeneralIdentifier() == null && foundCustomIdentifiers.size() == 0
+ && schema.getReactionIdentifier() == null) {
+ throw new InvalidColorSchemaException("One of these columns values is obligatory: name, identifier, reactionIdentifier");
}
result.add(schema);
}
@@ -292,11 +281,10 @@ public class ColorSchemaXlsxReader {
}
/**
- * Returns list of columns that should be printed for given coloring
- * schemas.
+ * Returns list of columns that should be printed for given coloring schemas.
*
* @param schemas
- * list of schemas
+ * list of schemas
* @return list of columns that should be printed (were set in the coloring
* schemas)
*/
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/CommentView.java b/service/src/main/java/lcsb/mapviewer/services/view/CommentView.java
index b9b0cc85ebc9676957107f1ce2bc171caf2c6d7b..0cffa23ff649c375f47ef58cec582288f11ac1cd 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/CommentView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/CommentView.java
@@ -1,270 +1,292 @@
-package lcsb.mapviewer.services.view;
-
-import java.io.Serializable;
-
-import lcsb.mapviewer.model.map.Comment;
-
-/**
- * View representation of the Comment.
- *
- * @author Piotr Gawron
- *
- */
-
-public class CommentView extends AbstractView<Comment> implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Author of the comment.
- */
- private String author;
-
- /**
- * Email of the comment.
- */
- private String email;
-
- /**
- * Content of the comment.
- */
- private String content;
-
- /**
- * Title of the comment.
- */
- private String title;
-
- /**
- * Is the comment visible on the map.
- */
- private String pinned;
-
- /**
- * Is the comment removed.
- */
- private String removed;
-
- /**
- * X coordinate on the map.
- */
- private String xCoord;
-
- /**
- * Y coordinate on the map.
- */
- private String yCoord;
-
- /**
- * Zoom level at which comment should be investigated on the map (to see
- * details).
- */
- private String zoom;
-
- /**
- * Constructor that initialize the view with the data from original comment.
- *
- * @param comment
- * data required for initialization
- */
- protected CommentView(final Comment comment) {
- super(comment);
- }
-
- /**
- * Default constructor. Should be used only for deserialization.
- */
- protected CommentView() {
- }
-
- /**
- * @return the author
- * @see #author
- */
- public String getAuthor() {
- return author;
- }
-
- /**
- * @param author
- * the author to set
- * @see #author
- */
- public void setAuthor(String author) {
- this.author = author;
- }
-
- /**
- * @return the email
- * @see #email
- */
- public String getEmail() {
- return email;
- }
-
- /**
- * @param email
- * the email to set
- * @see #email
- */
- public void setEmail(String email) {
- this.email = email;
- }
-
- /**
- * @return the content
- * @see #content
- */
- public String getContent() {
- return content;
- }
-
- /**
- * @param content
- * the content to set
- * @see #content
- */
- public void setContent(String content) {
- this.content = content;
- }
-
- /**
- * @return the title
- * @see #title
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * @param title
- * the title to set
- * @see #title
- */
- public void setTitle(String title) {
- this.title = title;
- }
-
- /**
- * @return the pinned
- * @see #pinned
- */
- public String getPinned() {
- return pinned;
- }
-
- /**
- * @param pinned
- * the pinned to set
- * @see #pinned
- */
- public void setPinned(String pinned) {
- this.pinned = pinned;
- }
-
- /**
- * @return the removed
- * @see #removed
- */
- public String getRemoved() {
- return removed;
- }
-
- /**
- * @param removed
- * the removed to set
- * @see #removed
- */
- public void setRemoved(String removed) {
- this.removed = removed;
- }
-
- /**
- * @return the xCoord
- * @see #xCoord
- */
- public String getxCoord() {
- return xCoord;
- }
-
- /**
- * @param xCoord
- * the xCoord to set
- * @see #xCoord
- */
- public void setxCoord(String xCoord) {
- this.xCoord = xCoord;
- }
-
- /**
- * @return the yCoord
- * @see #yCoord
- */
- public String getyCoord() {
- return yCoord;
- }
-
- /**
- * @param yCoord
- * the yCoord to set
- * @see #yCoord
- */
- public void setyCoord(String yCoord) {
- this.yCoord = yCoord;
- }
-
- /**
- * @return the zoom
- * @see #zoom
- */
- public String getZoom() {
- return zoom;
- }
-
- /**
- * @param zoom
- * the zoom to set
- * @see #zoom
- */
- public void setZoom(String zoom) {
- this.zoom = zoom;
- }
-
- /**
- * @param pinned
- * the pinned to set
- * @see #pinned
- */
- public void setPinned(final boolean pinned) {
- if (pinned) {
- setPinned("YES");
- } else {
- setPinned("NO");
- }
- }
-
- /**
- * Sets x coordinate.
- *
- * @param x
- * x coordinate to set
- * @see #xCoord
- */
- public void setxCoord(double x) {
- this.xCoord = x + "";
- }
-
- /**
- * Sets y coordinate.
- *
- * @param y
- * y coordinate to set
- * @see #yCoord
- */
- public void setyCoord(double y) {
- this.yCoord = y + "";
- }
-};
+package lcsb.mapviewer.services.view;
+
+import java.io.Serializable;
+
+import lcsb.mapviewer.model.map.Comment;
+
+/**
+ * View representation of the Comment.
+ *
+ * @author Piotr Gawron
+ *
+ */
+
+public class CommentView extends AbstractView<Comment> implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Author of the comment.
+ */
+ private String author;
+
+ /**
+ * Email of the comment.
+ */
+ private String email;
+
+ /**
+ * Content of the comment.
+ */
+ private String content;
+
+ /**
+ * Title of the comment.
+ */
+ private String title;
+
+ /**
+ * Is the comment visible on the map.
+ */
+ private String pinned;
+
+ /**
+ * Is the comment removed.
+ */
+ private String removed;
+
+ /**
+ * X coordinate on the map.
+ */
+ private String xCoord;
+
+ /**
+ * Y coordinate on the map.
+ */
+ private String yCoord;
+
+ /**
+ * Zoom level at which comment should be investigated on the map (to see
+ * details).
+ */
+ private String zoom;
+
+ /**
+ * Submap on which comment was placed.
+ */
+ private String submap;
+
+ /**
+ * Constructor that initialize the view with the data from original comment.
+ *
+ * @param comment
+ * data required for initialization
+ */
+ protected CommentView(final Comment comment) {
+ super(comment);
+ }
+
+ /**
+ * Default constructor. Should be used only for deserialization.
+ */
+ protected CommentView() {
+ }
+
+ /**
+ * @return the author
+ * @see #author
+ */
+ public String getAuthor() {
+ return author;
+ }
+
+ /**
+ * @param author
+ * the author to set
+ * @see #author
+ */
+ public void setAuthor(String author) {
+ this.author = author;
+ }
+
+ /**
+ * @return the email
+ * @see #email
+ */
+ public String getEmail() {
+ return email;
+ }
+
+ /**
+ * @param email
+ * the email to set
+ * @see #email
+ */
+ public void setEmail(String email) {
+ this.email = email;
+ }
+
+ /**
+ * @return the content
+ * @see #content
+ */
+ public String getContent() {
+ return content;
+ }
+
+ /**
+ * @param content
+ * the content to set
+ * @see #content
+ */
+ public void setContent(String content) {
+ this.content = content;
+ }
+
+ /**
+ * @return the title
+ * @see #title
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * @param title
+ * the title to set
+ * @see #title
+ */
+ public void setTitle(String title) {
+ this.title = title;
+ }
+
+ /**
+ * @return the pinned
+ * @see #pinned
+ */
+ public String getPinned() {
+ return pinned;
+ }
+
+ /**
+ * @param pinned
+ * the pinned to set
+ * @see #pinned
+ */
+ public void setPinned(String pinned) {
+ this.pinned = pinned;
+ }
+
+ /**
+ * @return the removed
+ * @see #removed
+ */
+ public String getRemoved() {
+ return removed;
+ }
+
+ /**
+ * @param removed
+ * the removed to set
+ * @see #removed
+ */
+ public void setRemoved(String removed) {
+ this.removed = removed;
+ }
+
+ /**
+ * @return the xCoord
+ * @see #xCoord
+ */
+ public String getxCoord() {
+ return xCoord;
+ }
+
+ /**
+ * @param xCoord
+ * the xCoord to set
+ * @see #xCoord
+ */
+ public void setxCoord(String xCoord) {
+ this.xCoord = xCoord;
+ }
+
+ /**
+ * @return the yCoord
+ * @see #yCoord
+ */
+ public String getyCoord() {
+ return yCoord;
+ }
+
+ /**
+ * @param yCoord
+ * the yCoord to set
+ * @see #yCoord
+ */
+ public void setyCoord(String yCoord) {
+ this.yCoord = yCoord;
+ }
+
+ /**
+ * @return the zoom
+ * @see #zoom
+ */
+ public String getZoom() {
+ return zoom;
+ }
+
+ /**
+ * @param zoom
+ * the zoom to set
+ * @see #zoom
+ */
+ public void setZoom(String zoom) {
+ this.zoom = zoom;
+ }
+
+ /**
+ * @param pinned
+ * the pinned to set
+ * @see #pinned
+ */
+ public void setPinned(final boolean pinned) {
+ if (pinned) {
+ setPinned("YES");
+ } else {
+ setPinned("NO");
+ }
+ }
+
+ /**
+ * Sets x coordinate.
+ *
+ * @param x
+ * x coordinate to set
+ * @see #xCoord
+ */
+ public void setxCoord(double x) {
+ this.xCoord = x + "";
+ }
+
+ /**
+ * Sets y coordinate.
+ *
+ * @param y
+ * y coordinate to set
+ * @see #yCoord
+ */
+ public void setyCoord(double y) {
+ this.yCoord = y + "";
+ }
+
+ /**
+ * @return the submap
+ * @see #submap
+ */
+ public String getSubmap() {
+ return submap;
+ }
+
+ /**
+ * @param submap
+ * the submap to set
+ * @see #submap
+ */
+ public void setSubmap(String submap) {
+ this.submap = submap;
+ }
+};
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/CommentViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/CommentViewFactory.java
index f3cf4961cdfa55f0bc7a6f9d345732bee46f6deb..09b831833228255f96aa223f8f49373fc0ad7562 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/CommentViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/CommentViewFactory.java
@@ -7,6 +7,7 @@ import org.apache.log4j.Logger;
import com.google.gson.Gson;
import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.Comment;
import lcsb.mapviewer.model.map.model.Model;
@@ -50,15 +51,22 @@ public class CommentViewFactory extends AbstractViewFactory<Comment, CommentView
return result;
}
- result.setAuthor((comment.getName()));
- result.setContent((comment.getContent()));
- result.setEmail((comment.getEmail()));
+ result.setAuthor(comment.getName());
+ result.setContent(comment.getContent());
+ result.setEmail(comment.getEmail());
result.setPinned(comment.isPinned());
if (comment.isDeleted()) {
result.setRemoved("YES (" + comment.getRemoveReason() + ")");
} else {
result.setRemoved("NO");
}
+ if (comment.getSubmodelData() != null) {
+ result.setSubmap(comment.getSubmodelData().getId() + "");
+ model = model.getSubmodelById(comment.getSubmodelData().getId());
+ if (model == null) {
+ throw new InvalidArgumentException("Cannot find submodel with id: " + comment.getSubmodelData().getId());
+ }
+ }
String title = "";
Point2D coordinates = null;
@@ -87,12 +95,11 @@ public class CommentViewFactory extends AbstractViewFactory<Comment, CommentView
}
}
}
- result.setTitle((title));
+ result.setTitle(title);
if (coordinates != null) {
result.setxCoord(coordinates.getX());
result.setyCoord(coordinates.getY());
result.setZoom("" + (Configuration.MIN_ZOOM_LEVEL + model.getZoomLevels() - 1));
-
}
return result;
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ConfigurationServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ConfigurationServiceTest.java
index 0dc9a7020328b4055010efbee47ca62173bcb020..ff1a5e29d35ab08dbf99a4ca3e48de0e5ba7a706 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ConfigurationServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ConfigurationServiceTest.java
@@ -2,7 +2,6 @@ package lcsb.mapviewer.services.impl;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
import java.util.List;
@@ -103,29 +102,4 @@ public class ConfigurationServiceTest extends ServiceTestFunctions {
}
}
- @Test
- public void testGetMemoryUsage() throws Exception {
- try {
- Long size = configurationService.getMemoryUsage();
- Long maxMem = configurationService.getMaxMemory();
- int len = 10000000;
- int t[];
- Integer x = (int) (Math.random() * 1000);
- t = new int[len + x];
- for (int i = 0; i < len; i++) {
- t[i] = (int) Math.random() * 1000 + x;
- x += t[i];
- }
- Long size2 = configurationService.getMemoryUsage();
- Long maxMem2 = configurationService.getMaxMemory();
-
- assertNotNull(x);
- assertEquals(maxMem, maxMem2);
- assertTrue(size2 >= size);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
index b3ff1818218050e179607fdec263a71ae44efb9b..ad2bd21b548a27e2cf1ea9f15fa5b55b87ac04b4 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
@@ -526,5 +526,4 @@ public class ExporterServiceTest extends ServiceTestFunctions {
throw e;
}
}
-
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
index 4db59b43d61c1ef4a91cb425e110ba97551e7b8d..83d7140ecf90c0e98fe78055789589a3255b673d 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
@@ -17,6 +17,7 @@ import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.common.Configuration;
@@ -34,9 +35,11 @@ import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.map.LayoutDao;
import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.ILayoutService.CreateLayoutParams;
import lcsb.mapviewer.services.search.layout.LightLayoutAliasView;
import lcsb.mapviewer.services.search.layout.LightLayoutReactionView;
+import lcsb.mapviewer.services.utils.EmailSender;
import lcsb.mapviewer.services.view.LayoutView;
public class LayoutServiceTest extends ServiceTestFunctions {
@@ -50,6 +53,11 @@ public class LayoutServiceTest extends ServiceTestFunctions {
@Autowired
LayoutDao layoutDao;
+
+ EmailSender originalSender;
+
+ @Autowired
+ ILayoutService layoutService;
@Before
public void setUp() throws Exception {
@@ -60,6 +68,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
// commit at the end of the test case
dbUtils.createSessionForCurrentThread();
+ dbUtils.setAutoFlush(false);
project = projectDao.getProjectByProjectId(projectId);
if (project != null) {
@@ -85,6 +94,9 @@ public class LayoutServiceTest extends ServiceTestFunctions {
createUser2();
userService.addUser(user2);
+
+ originalSender = layoutService.getEmailSender();
+ layoutService.setEmailSender(Mockito.mock(EmailSender.class));
}
@After
@@ -95,7 +107,9 @@ public class LayoutServiceTest extends ServiceTestFunctions {
// close session
dbUtils.closeSessionForCurrentThread();
- }
+
+ layoutService.setEmailSender(originalSender);
+}
@Test
public void testUserCanAddLayout() throws Exception {
@@ -398,41 +412,29 @@ public class LayoutServiceTest extends ServiceTestFunctions {
@Test
public void testInputDataInLayout() throws Exception {
try {
- logger.debug("A");
List<LayoutView> layouts = layoutService.getCustomLayouts(model, user);
- logger.debug("A");
assertNotNull(layouts);
assertEquals(0, layouts.size());
userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
- logger.debug("A");
CreateLayoutParams params = new CreateLayoutParams().name("Test").//
directory("testDir").//
model(model).//
colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
user(user).//
async(false);
- logger.debug("A");
LayoutView row = layoutService.createLayout(params);
- logger.debug("A");
assertNotNull(row);
assertNotNull(row.getIdObject());
- logger.debug("A");
assertTrue("true".equalsIgnoreCase(row.getInputDataAvailable()));
- logger.debug("A");
byte[] inputData = layoutService.getInputDataForLayout(row);
- logger.debug("A");
assertNotNull(inputData);
- logger.debug("A");
byte[] originalData = IOUtils.toByteArray(new FileInputStream("testFiles/enricoData/ge001.txt"));
- logger.debug("A");
assertEquals(new String(originalData, StandardCharsets.UTF_8), new String(inputData, StandardCharsets.UTF_8));
- logger.debug("A");
layoutService.removeLayout(row, null);
- logger.debug("A");
} catch (Exception e) {
e.printStackTrace();
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
index d26b05ac5129c24daac4c86d7824cb5ef073eef4..3d409a1875ba3518299d2c78f88b95ec5cc1d51c 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
@@ -15,6 +15,7 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.commands.ColorModelCommand;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.TextFileUtils;
@@ -35,7 +36,8 @@ import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
import lcsb.mapviewer.services.utils.data.ColorSchemaType;
public class LayoutServiceTest2 {
- Logger logger = Logger.getLogger(LayoutServiceTest2.class);
+ Logger logger = Logger.getLogger(LayoutServiceTest2.class);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
@Before
public void setUp() throws Exception {
@@ -214,7 +216,7 @@ public class LayoutServiceTest2 {
final Collection<ColorSchema> schemas = reader
.readColorSchema(params.getColorInputStream(), TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
- ColorModelCommand command = new ColorModelCommand(model, schemas);
+ ColorModelCommand command = new ColorModelCommand(model, schemas, colorExtractor);
command.execute();
command.getModifiedElements();
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
index 13ba77479e16faf515a042176fcf771fe7977103..4cb1a9685bf767d2ca8bd5c15997f7577282b9e5 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
@@ -19,6 +19,7 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.commands.ColorModelCommand;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.TextFileUtils;
@@ -69,27 +70,27 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
public void testReadGeneVariantsSchema() throws Exception {
try {
File f = new File("testFiles/coloring/gene_variants.txt");
- InputStream in = new FileInputStream(f);
+ InputStream in = new FileInputStream(f);
- byte[] buff = new byte[8000];
+ byte[] buff = new byte[8000];
- int bytesRead = 0;
+ int bytesRead = 0;
- ByteArrayOutputStream bao = new ByteArrayOutputStream();
+ ByteArrayOutputStream bao = new ByteArrayOutputStream();
- while((bytesRead = in.read(buff)) != -1) {
- bao.write(buff, 0, bytesRead);
- }
- in.close();
- bao.close();
+ while ((bytesRead = in.read(buff)) != -1) {
+ bao.write(buff, 0, bytesRead);
+ }
+ in.close();
+ bao.close();
- byte[] data = bao.toByteArray();
+ byte[] data = bao.toByteArray();
- ByteArrayInputStream bin = new ByteArrayInputStream(data);
+ ByteArrayInputStream bin = new ByteArrayInputStream(data);
ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas = reader.readColorSchema(bin,TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(data)));
+ Collection<ColorSchema> schemas = reader.readColorSchema(bin, TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(data)));
assertNotNull(schemas);
assertEquals(3, schemas.size());
} catch (Exception e) {
@@ -189,12 +190,14 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testColoring3() throws Exception {
try {
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+
Model model = getModelForFile("testFiles/coloring/protein_to_color.xml", false);
ColorSchemaReader reader = new ColorSchemaReader();
Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/problematicSchema.txt");
- ColorModelCommand factory = new ColorModelCommand(model, schemas);
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
factory.execute();
assertFalse(model.getElementByElementId("sa1").getColor().equals(Color.WHITE));
@@ -212,7 +215,7 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/schemaWithIdentifiers.txt");
for (ColorSchema colorSchema : schemas) {
- for (Pair<MiriamType,String> pair: colorSchema.getIdentifierColumns()) {
+ for (Pair<MiriamType, String> pair : colorSchema.getIdentifierColumns()) {
assertNotNull(pair.getRight());
assertFalse(pair.getRight().isEmpty());
}
@@ -231,7 +234,7 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/schemaIdWithoutName.txt");
for (ColorSchema colorSchema : schemas) {
- for (Pair<MiriamType,String> pair: colorSchema.getIdentifierColumns()) {
+ for (Pair<MiriamType, String> pair : colorSchema.getIdentifierColumns()) {
assertFalse(pair.getRight().isEmpty());
assertNull(colorSchema.getName());
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/view/CommentViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/view/CommentViewFactoryTest.java
index e187e52775eb09943a3b8542bbb82344a9db6a59..13aeba6fe5b5d9beb2c177d9398dc57587ddb169 100644
--- a/service/src/test/java/lcsb/mapviewer/services/view/CommentViewFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/view/CommentViewFactoryTest.java
@@ -1,46 +1,84 @@
-package lcsb.mapviewer.services.view;
-
-import static org.junit.Assert.assertNotNull;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-public class CommentViewFactoryTest extends ServiceTestFunctions{
-
- @Autowired
- CommentViewFactory commentViewFactory;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCreateEmpty() throws Exception {
- try {
- Object object = commentViewFactory.create(null);
- assertNotNull(object);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testCreateGson() throws Exception {
- try {
- CommentView object = commentViewFactory.create(null);
- assertNotNull(commentViewFactory.createGson(object));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
-}
+package lcsb.mapviewer.services.view;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.model.map.Comment;
+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.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+
+public class CommentViewFactoryTest extends ServiceTestFunctions {
+
+ Logger logger = Logger.getLogger(CommentViewFactoryTest.class);
+
+ @Autowired
+ CommentViewFactory commentViewFactory;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCreateEmpty() throws Exception {
+ try {
+ Object object = commentViewFactory.create(null);
+ assertNotNull(object);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateGson() throws Exception {
+ try {
+ CommentView object = commentViewFactory.create(null);
+ assertNotNull(commentViewFactory.createGson(object));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateOnSubmap() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ Model submodel = new ModelFullIndexed(null);
+ submodel.setId(1);
+ Species species = new GenericProtein("id");
+ species.setId(23);
+ species.setName("ProteinName");
+ submodel.addElement(species);
+
+ model.addSubmodelConnection(new ModelSubmodelConnection(submodel, SubmodelType.UNKNOWN));
+
+ Comment comment = new Comment();
+ comment.setModel(model);
+ comment.setSubmodel(submodel);
+ comment.setTableName(species.getClass());
+ comment.setTableId(species.getId());
+ CommentView object = commentViewFactory.create(comment,model);
+ assertTrue(object.getTitle().contains(species.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/target/.gitignore b/target/.gitignore
deleted file mode 100644
index 456983799efa61b8ec06e3a34596d7314084b921..0000000000000000000000000000000000000000
--- a/target/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-/classes/
-/test-classes/
diff --git a/web/src/main/java/lcsb/mapviewer/bean/AbstractMarkerManagerBean.java b/web/src/main/java/lcsb/mapviewer/bean/AbstractMarkerManagerBean.java
index 31a07505632336a1e841ecace2ad2f514ac51fa4..2ec5a5d19c3b97f84650149c6cbc4b0756376154 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/AbstractMarkerManagerBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/AbstractMarkerManagerBean.java
@@ -109,12 +109,16 @@ public abstract class AbstractMarkerManagerBean<T extends ISearchResultView> ext
if ("".equals(overlayCollection)) {
logger.warn(this.getClass().getSimpleName() + ": Cannot refresh data in JavaScript, because overlayCollection is not set");
} else {
- String json = "null";
+ Gson gsonParser = new Gson();
+ String dataEncoded = "null";
if (dataToSend != null) {
- json = new Gson().toJson(dataToSend);
+ dataEncoded = gsonParser.toJson(dataToSend);
}
- String javascriptCode = "ServerConnector.updateOverviewElementDetailData('" + overlayCollection + "','" + searchResultIdentifier + "',"
- + new Gson().toJson(ei) + ", " + json + ");\n";
+ String nameEncoded = gsonParser.toJson(overlayCollection);
+ String resultResultIdEncoded = gsonParser.toJson(searchResultIdentifier);
+ String elementIdEncoded = gsonParser.toJson(ei);
+ String javascriptCode = "ServerConnector.updateOverviewElementDetailData(" + nameEncoded + "," + resultResultIdEncoded + "," + elementIdEncoded + ", "
+ + dataEncoded + ");\n";
executeJavascript(javascriptCode.toString());
}
}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java b/web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java
index 188034072a1b3516267093ddd444fe835e5a7cc8..57a20716a7a0a113445bb8f54f6321b25a60d9e3 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java
@@ -83,7 +83,7 @@ public class ConfigurationBean extends AbstractManagedBean implements Serializab
/**
* List of values for all possible configurable parameters.
*/
- private List<ConfigurationView> values = new ArrayList<ConfigurationView>();
+ private List<ConfigurationView> values = new ArrayList<>();
/**
* Release version of the framework.
@@ -472,4 +472,26 @@ public class ConfigurationBean extends AbstractManagedBean implements Serializab
return NumberFormat.getInstance().format(configurationService.getMaxMemory()) + " MB";
}
+ /**
+ * Returns {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
+ * representing overlay element with negative values.
+ *
+ * @return {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
+ * representing overlay element with negative values
+ */
+ public String getMinColor() {
+ return valueMap.get(ConfigurationElementType.MIN_COLOR_VAL);
+ }
+
+ /**
+ * Returns {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
+ * representing overlay element with negative values.
+ *
+ * @return {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
+ * representing overlay element with positive values
+ */
+ public String getMaxColor() {
+ return valueMap.get(ConfigurationElementType.MAX_COLOR_VAL);
+ }
+
}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java b/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java
index 41e848d6b1b3e949f73f34ebf588443bcf6b980d..49d95dfe844de83d4b7f94d3e708e1874dcba5d7 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java
@@ -184,13 +184,9 @@ public class DrugBean extends AbstractMarkerManagerBean<DrugView> implements Ser
// drugs are comma separated
List<String> names = splitQuery(query, true);
- int set = 0;
- for (String string : names) {
- DrugView drug = drugService.getByName(string, new DbSearchCriteria().ipAddress(ipAddress).model(model).organisms(mapBean.getOrganism()).colorSet(set++));
- if (drug != null) {
- addResult(drug);
- }
- }
+ List<DrugView> drugs = drugService
+ .getByNames(names, new DbSearchCriteria().ipAddress(ipAddress).model(model).organisms(mapBean.getOrganism()).colorSet(0));
+ addResults(drugs);
// format results
if (getResults().size() == 0) { // if there are no results, add empty drug
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java b/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
index 9650be2c4d8e7bbfba278a4ebc4fb3a2343798dd..5239964562e98d259b70dda5aa2e92be601910bc 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
@@ -34,6 +34,8 @@ import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
import lcsb.mapviewer.bean.MapBean.ClientMapData;
+import lcsb.mapviewer.commands.ClearColorModelCommand;
+import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.commands.ColorModelCommand;
import lcsb.mapviewer.commands.CopyCommand;
import lcsb.mapviewer.commands.SubModelCommand;
@@ -58,11 +60,11 @@ import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Degraded;
import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.model.map.species.Phenotype;
@@ -74,6 +76,7 @@ import lcsb.mapviewer.model.map.species.Unknown;
import lcsb.mapviewer.services.interfaces.IExporterService;
import lcsb.mapviewer.services.interfaces.IExporterService.ExporterParameters;
import lcsb.mapviewer.services.interfaces.ILayoutService;
+import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.utils.ColorSchemaReader;
import lcsb.mapviewer.services.utils.data.BuildInLayout;
import lcsb.mapviewer.services.utils.data.ExportColumn;
@@ -254,6 +257,12 @@ public class ExportBean extends AbstractManagedBean {
@ManagedProperty(value = "#{ExporterService}")
private transient IExporterService exporterService;
+ /**
+ * Service that allows to access data abaout users.
+ */
+ @ManagedProperty(value = "#{UserService}")
+ private transient IUserService userService;
+
/**
* Service that deal with {@link Layout layouts}.
*/
@@ -266,6 +275,12 @@ public class ExportBean extends AbstractManagedBean {
@ManagedProperty(value = "#{mapMB}")
private transient MapBean mapBean;
+ /**
+ * Bean managing currently logged user.
+ */
+ @ManagedProperty(value = "#{userMB}")
+ private transient UserBean userBean;
+
/**
* Default constructor.
*/
@@ -1142,12 +1157,13 @@ public class ExportBean extends AbstractManagedBean {
if (layout.getInputData() != null) {
ColorSchemaReader reader = new ColorSchemaReader();
Collection<ColorSchema> schemas = reader.readColorSchema(layout.getInputData().getFileContent());
- new ColorModelCommand(colorModel, schemas).execute();
+
+ new ColorModelCommand(colorModel, schemas, userService.getColorExtractorForUser(userBean.getLoggedUser())).execute();
} else if (layout.getTitle().equals(BuildInLayout.CLEAN.getTitle())) {
// this might not return true if we change CLEAN.title in future...
// if it's clean then remove coloring
- new ColorModelCommand(colorModel, new HashSet<>()).execute();
+ new ClearColorModelCommand(colorModel).execute();
}
for (Element alias : colorModel.getElements()) {
alias.setVisibilityLevel(0);
@@ -1185,6 +1201,8 @@ public class ExportBean extends AbstractManagedBean {
scale /= 2;
}
+ ColorExtractor colorExtractor = userService.getColorExtractorForUser(userBean.getLoggedUser());
+
Params params = new Params().//
x(minX).//
y(minY).//
@@ -1193,6 +1211,8 @@ public class ExportBean extends AbstractManagedBean {
level(level).//
nested(false).// automatically set nested view as invalid
scale(scale).//
+ minColor(colorExtractor.getMinColor()).//
+ maxColor(colorExtractor.getMaxColor()).//
model(colorModel);
List<Integer> visibleLayoutIds = deserializeIdList(visibleLayouts);
for (Integer integer : visibleLayoutIds) {
@@ -1334,4 +1354,38 @@ public class ExportBean extends AbstractManagedBean {
public void nop() {
}
+ /**
+ * @return the userBean
+ * @see #userBean
+ */
+ public UserBean getUserBean() {
+ return userBean;
+ }
+
+ /**
+ * @param userBean
+ * the userBean to set
+ * @see #userBean
+ */
+ public void setUserBean(UserBean userBean) {
+ this.userBean = userBean;
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java b/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java
index aefdf5dc47eb4a93caf4fe8ffae5a4aa5d39df6c..3f3b3709b74d69d9e8d846def50d887b95f3a752 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java
@@ -232,9 +232,8 @@ public class FeedbackBean extends AbstractMarkerManagerBean<FullCommentView> imp
double lng = Double.parseDouble(lngCoord);
latLng = new LatLng(lat, lng);
- CoordinationConverter cc = new CoordinationConverter(getCurrentTopModel());
-
commentedSubmodel = getCurrentTopModel().getSubmodelById(modelIdentifier);
+ CoordinationConverter cc = new CoordinationConverter(commentedSubmodel);
lastCommentCoordinates = cc.toPoint(latLng);
diff --git a/web/src/main/java/lcsb/mapviewer/validator/LoginValidator.java b/web/src/main/java/lcsb/mapviewer/validator/LoginValidator.java
new file mode 100644
index 0000000000000000000000000000000000000000..a082908bf44b281d10c26696b4dd32f8613a1016
--- /dev/null
+++ b/web/src/main/java/lcsb/mapviewer/validator/LoginValidator.java
@@ -0,0 +1,38 @@
+package lcsb.mapviewer.validator;
+
+import java.util.regex.Pattern;
+
+import javax.faces.application.FacesMessage;
+import javax.faces.component.UIComponent;
+import javax.faces.context.FacesContext;
+import javax.faces.validator.FacesValidator;
+import javax.faces.validator.Validator;
+import javax.faces.validator.ValidatorException;
+
+/**
+ * Validator of login field.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@FacesValidator("loginValidator")
+public class LoginValidator implements Validator {
+
+ /**
+ * Regex pattern used for login validation.
+ */
+ private static final Pattern LOGIN_PATTERN = Pattern.compile("[a-zA-Z0-9_\\.\\-]+");
+
+ @Override
+ public void validate(FacesContext context, UIComponent component, Object value) throws ValidatorException {
+ if (value == null) {
+ return; // Let required="true" handle.
+ }
+ if (!LOGIN_PATTERN.matcher((String) value).matches()) {
+ String summary = "Incorrect login.";
+ String detail = "Only alphanumeric characters and \"-\", \"_\", \".\" special characters are allowed";
+ throw new ValidatorException(new FacesMessage(FacesMessage.SEVERITY_ERROR, summary, detail));
+ }
+ }
+
+}
\ No newline at end of file
diff --git a/web/src/main/java/lcsb/mapviewer/validator/package-info.java b/web/src/main/java/lcsb/mapviewer/validator/package-info.java
new file mode 100644
index 0000000000000000000000000000000000000000..9a25482ee1e1e843c2966da8084edf5c68e0d7e2
--- /dev/null
+++ b/web/src/main/java/lcsb/mapviewer/validator/package-info.java
@@ -0,0 +1,4 @@
+/**
+ * Provides validator for JSF forms.
+ */
+package lcsb.mapviewer.validator;
diff --git a/web/src/main/webapp/WEB-INF/components/map/map.xhtml b/web/src/main/webapp/WEB-INF/components/map/map.xhtml
index 24b62afcea47b6d6608d959a475f5a394e65e62f..cc80c2722f065760219ac9cf52501a14ec6c8262 100644
--- a/web/src/main/webapp/WEB-INF/components/map/map.xhtml
+++ b/web/src/main/webapp/WEB-INF/components/map/map.xhtml
@@ -59,7 +59,14 @@
</h:form>
<h:form id="configurationForm">
- <h:inputHidden id="configurationGson" value="#{mapMB.gsonConfiguration}"/>
+ <h:inputHidden id="configurationGson" value="#{mapMB.gsonConfiguration}"/>
+ </h:form>
+
+ <h:form id="overlayConfigForm">
+ <h:inputHidden id="userMinColor" value="#{userMB.loggedUser.minColor}"/>
+ <h:inputHidden id="userMaxColor" value="#{userMB.loggedUser.maxColor}"/>
+ <h:inputHidden id="systemMinColor" value="#{configurationMB.minColor}"/>
+ <h:inputHidden id="systemMaxColor" value="#{configurationMB.maxColor}"/>
</h:form>
<h:form id="searchForm">
@@ -80,6 +87,12 @@
<p:remoteCommand name="_sendReferenceGenomeDetailRequest" actionListener="#{referenceGenomeMB.requestJavasciptGenomeDetails}" />
</h:form>
+ <h:form id="createSubmodelDialog">
+ <p:remoteCommand name="_createSubmodelDialog" actionListener="#{mapMB.createSubmodelDialog}" async="false"/>
+ </h:form>
+
+
+
<!-- loading dialog used for informing user that data is being loaded -->
<p:dialog header="Loading" widgetVar="loadingDlg" resizable="false" id="loadingDlg"
showEffect="fade" modal="true" closable="false">
diff --git a/web/src/main/webapp/WEB-INF/components/map/submapPanel.xhtml b/web/src/main/webapp/WEB-INF/components/map/submapPanel.xhtml
index 304a6d2987501e4279c1a2fdb2e6962a4aa489eb..c586e22bb27eb641a756351450bed4f9a76dceec 100644
--- a/web/src/main/webapp/WEB-INF/components/map/submapPanel.xhtml
+++ b/web/src/main/webapp/WEB-INF/components/map/submapPanel.xhtml
@@ -19,21 +19,13 @@
<h:panelGroup layout="block" >
<p:dataTable id="submapDataTable" var="submap" value="#{mapMB.mapDataList}">
-<!-- <p:column sortBy="id" headerText="Id">
- <h:outputText id="id" value="#{submap.mapConfig.idObject}" />
- </p:column> -->
-
<p:column sortBy="name" headerText="Name">
<h:outputText id="name" value="#{submap.mapConfig.name}" />
</p:column>
-<!-- <p:column sortBy="type" headerText="Type">
- <h:outputText id="type" value="#{submap.type}" />
- </p:column> -->
-
<p:column headerText="">
<p:commandLink actionListener="#{mapMB.createSubmodelDialog}"
- oncomplete="GuiConnector.openDialog(#{submap.mapConfig.idObject}); customMap.openLayoutById('#{mapMB.selectedLayoutIdentifier}');" id="opener" ajax="true" icon="ui-icon-document" title="View">
+ oncomplete="GuiConnector.openDialog(#{submap.mapConfig.idObject});" id="opener" ajax="true" icon="ui-icon-document" title="View">
<f:param name="submodelId" value="#{submap.mapConfig.idObject}"/>
<p:graphicImage height="24"
width="24"
diff --git a/web/src/main/webapp/admin/comments.xhtml b/web/src/main/webapp/admin/comments.xhtml
index 40bb86deea0ef0fd692ae82d42e4b9c8194621c4..7da4892f98a88aa8c4e2b3adf77565c2c5ef92f4 100644
--- a/web/src/main/webapp/admin/comments.xhtml
+++ b/web/src/main/webapp/admin/comments.xhtml
@@ -29,7 +29,9 @@
</p:column>
<p:column sortBy="title" headerText="Title">
- <h:link value="#{comment.title}" outcome="/index.xhtml?id=#{mapMB.currentMapId}&x=#{comment.xCoord}&y=#{comment.yCoord}&zoom=#{comment.zoom}&comments=on" target="_map"/>
+ <h:link value="#{comment.title}"
+ outcome="/index.xhtml?id=#{mapMB.currentMapId}&x=#{comment.xCoord}&y=#{comment.yCoord}&zoom=#{comment.zoom}&comments=on&submap=#{comment.submap}"
+ target="_map"/>
</p:column>
<p:column sortBy="author" headerText="Author">
diff --git a/web/src/main/webapp/admin/configuration.xhtml b/web/src/main/webapp/admin/configuration.xhtml
index 9202732b32a8ff4f7c5f3eb1402644802258eb47..7c63080fcaff4eed72e339864048b1951a29717f 100644
--- a/web/src/main/webapp/admin/configuration.xhtml
+++ b/web/src/main/webapp/admin/configuration.xhtml
@@ -56,6 +56,7 @@ global parameters of the MINERVA instance. More information can be found in the
<p:column sortBy="value" headerText="Value">
<p:inputText value="#{configuration.value}" />
+ <p:colorPicker value="#{configuration.value}" rendered="#{configuration.type.editType == 'COLOR'}"/>
</p:column>
</p:dataTable>
diff --git a/web/src/main/webapp/admin/users.xhtml b/web/src/main/webapp/admin/users.xhtml
index ecfa0731adc2064ccbf758092cf1f9c6f7be4bb3..ca235f5ae35553b0488c61e12fd51cef0f611d41 100644
--- a/web/src/main/webapp/admin/users.xhtml
+++ b/web/src/main/webapp/admin/users.xhtml
@@ -78,7 +78,7 @@
<h:outputText value="Login:" />
</td>
<td>
- <p:inputText value="#{usersMB.selectedUser.login}" styleClass="bold" rendered="#{empty usersMB.selectedUser.login}"/>
+ <p:inputText value="#{usersMB.selectedUser.login}" styleClass="bold" rendered="#{empty usersMB.selectedUser.login}" validator="loginValidator"/>
<h:outputText autocomplete="off" value="#{usersMB.selectedUser.login}" class="bold" rendered="#{not empty usersMB.selectedUser.login}"/>
</td>
</tr>
diff --git a/web/src/main/webapp/index.xhtml b/web/src/main/webapp/index.xhtml
index e2790ddf3bbfb79d624ae129568f8a5c00324009..74afff6b04596b2ac9603e28cede3e9b4575b136 100644
--- a/web/src/main/webapp/index.xhtml
+++ b/web/src/main/webapp/index.xhtml
@@ -1,252 +1,265 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"
- xmlns:h="http://java.sun.com/jsf/html"
- xmlns:f="http://java.sun.com/jsf/core"
- xmlns:ui="http://java.sun.com/jsf/facelets"
- xmlns:p="http://primefaces.org/ui"
- xmlns:c="http://java.sun.com/jsp/jstl/core"
- >
-
-<f:view contentType="text/html">
-
-
-<h:head>
- <title>#{mapMB.currentProject.name}</title>
-
- <!-- Google Maps API version 3.20 -->
- <script src="https://maps.google.com/maps/api/js?libraries=drawing&v=3.22" type="text/javascript"/>
-
- <link rel="shortcut icon" href="./resources/images/favicon.png" type="image/png" />
-
-<!-- log4javascript library -->
- <h:outputScript library="js" name="log4javascript.js" />
-<!-- configuration for log4javascript -->
- <h:outputScript library="js" name="LogConfig.js" />
-
- <h:outputScript library="js" name="ObjectWithListeners.js"/>
-
- <h:outputScript library="js" name="AbstractCustomMap.js" />
- <h:outputScript library="js" name="AbstractInfoWindow.js"/>
- <h:outputScript library="js" name="AbstractMarker.js"/>
- <h:outputScript library="js" name="Alias.js" />
- <h:outputScript library="js" name="AliasInfoWindow.js" />
- <h:outputScript library="js" name="AliasMarker.js" />
- <h:outputScript library="js" name="AliasOverlay.js" />
- <h:outputScript library="js" name="Configuration.js" />
- <h:outputScript library="js" name="CustomMap.js" />
- <h:outputScript library="js" name="CustomMapOptions.js" />
- <h:outputScript library="js" name="Functions.js" />
- <h:outputScript library="js" name="GeneVariant.js" />
- <h:outputScript library="js" name="GuiConnector.js" />
- <h:outputScript library="js" name="IdentifiedElement.js" />
- <h:outputScript library="js" name="LayoutAlias.js" />
- <h:outputScript library="js" name="LayoutData.js" />
- <h:outputScript library="js" name="LayoutReaction.js" />
- <h:outputScript library="js" name="MapModel.js"/>
- <h:outputScript library="js" name="OverlayCollection.js" />
- <h:outputScript library="js" name="pileup.js"/>
- <h:outputScript library="js" name="PointData.js"/>
- <h:outputScript library="js" name="PointInfoWindow.js"/>
- <h:outputScript library="js" name="PointMarker.js"/>
- <h:outputScript library="js" name="Reaction.js" />
- <h:outputScript library="js" name="ReactionMarker.js" />
- <h:outputScript library="js" name="ReactionInfoWindow.js" />
- <h:outputScript library="js" name="ReactionOverlay.js" />
- <h:outputScript library="js" name="ReferenceGenome.js" />
- <h:outputScript library="js" name="ReferenceGenomeGeneMapping.js" />
- <h:outputScript library="js" name="SearchPanel.js" />
- <h:outputScript library="js" name="ServerConnector.js" />
- <h:outputScript library="js" name="Submap.js" />
- <h:outputScript library="js" name="TabNavi.js" />
- <h:outputScript library="js" name="TouchMap.js" />
-
- <ui:include src="/WEB-INF/components/map/statistics.xhtml" />
-
- <script type="text/javascript">
-//<![CDATA[
- var DEBUG_ON =false;
-
- if (browser.name=="IE") {
- if (browser.version<=8 || browser.compatibilityMode) {
- alert("This webpage works only with Internet Explorer version 9 or greater.\n" +
- "If you have Internet Explorer version 9 or greater and still see this message, please, turn the 'Compatibility modeoff:\n" +
- "Open Internet Explorer and press the Alt key on your keyboard.\n" +
- "Select 'Tools' menu item. \n" +
- "Select the 'Compatibility View' settings option. \n" +
- "Make sure the 'Display all websites in Compatibility View' check box is unchecked and that the 'Compatibility View; list of websites is cleared.\n" +
- "\n"+
- "Alternatively, please, use other browsers: Chrome, Firefox or Safari.");
- }
- }
- var configuration = new Configuration();
-
-function processUrlGetParams() {
- if (GuiConnector.getParams["x"]!=undefined && GuiConnector.getParams["y"]!=undefined){
- ServerConnector.setCenterCoordinateX(GuiConnector.getParams["x"]);
- ServerConnector.setCenterCoordinateY(GuiConnector.getParams["y"]);
- }
- if (GuiConnector.getParams["zoom"]!=undefined ){
- ServerConnector.setZoomLevel(GuiConnector.getParams["zoom"]);
- }
-}
-
-function updateConfig() {
- var json = document.getElementById('configurationForm:configurationGson').value;
-//there are some strange problems here...
- json = json.replace(/\n/g," ");
- configuration.loadFromModelView(JSON.parse(json));
-}
-
-function initMap(){
- processUrlGetParams();
-
- updateConfig();
-
- searchPanel = new SearchPanel(document.getElementById('tabView:mainForm:searchText_input'),
- document.getElementById('tabView:mainForm:searchButton'),
- function(){
- tabViewVar.select(0);
- }
- );
-
- var mapElement = gmtls.getMap();
- if (configuration.MAPS!=null) {
-
- var windowsTouchInterface = ((navigator.appVersion.indexOf("Win")!=-1) && ('ontouchstart' in document.documentElement));
- var overviewDiv = document.getElementById("overviewDiv");
- customMap = new CustomMap({
- map : mapElement,
- configuration : configuration,
- hideDiv : document.getElementById('leftPanel'),
- markerOptimization : !windowsTouchInterface,
- bigLogo : windowsTouchInterface,
- overviewDiv : overviewDiv,
- customTouchInterface: windowsTouchInterface
- });
-
- ServerConnector.setCustomMap(customMap);
- GuiConnector.showGoogleMap();
-
- ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "search"));
- ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "missingConnection"));
- ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "drug",true, true));
- ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "chemical",#{chemicalMB.linkedToDisease()}, #{chemicalMB.linkedToDisease() == true}));
- ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "mirna",true, true));
- ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "comment",false, true));
-
- customMap.refreshOverlays();
-
-
- if (GuiConnector.getParams["search"]!=undefined) {
- searchPanel.search(GuiConnector.getParams["search"]);
- }
-
- if (GuiConnector.getParams["comments"]=="on") {
- document.getElementById('comment_checkbox').click();
- }
- if (GuiConnector.getParams["layout"]!=undefined) {
- document.getElementById('tabView:layoutForm3:hidden2').value=GuiConnector.getParams["layout"];
- getVisualizedLayoutDetails();
- }
-
- }
- //when I try to hide legend from the beginning or in the same thread it's hidden forever... ;/
- setTimeout(function() {
- GuiConnector.hideLegend();
- }, 0);
-}
-
-
-function removeMissingConnection(id) {
- document.getElementById('missingConnectionForm:connectionId').value=""+id;
- dlg4.show();
-}
-
-function removeComment(id) {
- document.getElementById('missingConnectionForm:commentId').value=""+id;
- dlg5.show();
-}
-
-
-//]]>
- </script>
-</h:head>
-<h:body onload="initMap();" >
-<h:outputStylesheet library="css" name="style.css"/>
-<h:outputStylesheet library="css" name="pileup.css"/>
-
- <h:outputScript library="primefaces" name="jquery/jquery.js" target="head" />
- <div class = "containerClass">
- <div id="leftPanel" class ="leftPanelClass">
-
- <ui:include src="/WEB-INF/components/admin/header.xhtml" />
-
-<!-- <div class="tabNavigation">
- <a href="javascript:;" onclick="GuiConnector.tabNaviShow('prev');" class="naviLeft"><i class="fa fa-chevron-left"></i></a>
- <a href="javascript:;" onclick="GuiConnector.tabNaviShow('next');" class="naviRight"><i class="fa fa-chevron-right"></i></a>
- </div>
--->
-
- <p:tabView id="tabView" widgetVar="tabViewVar" styleClass="leftTabView" activeIndex="0" >
- <p:tab id="searchTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-search maintab'></i><br>SEARCH</div>" styleClass="leftTab">
- <ui:include src="/WEB-INF/components/map/searchPanel.xhtml" />
- </p:tab >
- <p:tab id="drugTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-map-marker maintab'></i><br>DRUG</div>" styleClass="leftTab">
- <ui:include src="/WEB-INF/components/map/drugPanel.xhtml" />
- </p:tab >
- <p:tab id="chemicalTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-map-marker maintab'></i><br>CHEMICAL</div>" styleClass="leftTab">
- <ui:include src="/WEB-INF/components/map/chemicalPanel.xhtml" />
- </p:tab >
- <p:tab id="miRNATab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-map-marker maintab'></i><br>MiRNA</div>" styleClass="leftTab">
- <ui:include src="/WEB-INF/components/map/miRNAPanel.xhtml" />
- </p:tab >
- <p:tab id="layoutTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-th-list maintab'></i><br>OVERLAYS</div>" styleClass="leftTab">
- <ui:include src="/WEB-INF/components/map/layoutPanel.xhtml" />
- </p:tab >
- <p:tab id="loginTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-sign-in maintab'></i><br>LOGIN</div>" styleClass="leftTab" rendered ="#{userMB.loggedUser.login=='anonymous'}">
- <ui:include src="/WEB-INF/components/map/loginPanel.xhtml" />
- </p:tab >
- <p:tab id="profileTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-user maintab'></i><br>PROFILE</div>" styleClass="leftTab" rendered ="#{not (userMB.loggedUser.login=='anonymous')}">
- <ui:include src="/WEB-INF/components/map/profilePanel.xhtml" />
- </p:tab >
- <p:tab id="submapTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-sitemap maintab'></i><br>SUBMAPS</div>" styleClass="leftTab">
- <ui:include src="/WEB-INF/components/map/submapPanel.xhtml" />
- </p:tab >
- <p:tab id="infoTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-info maintab'></i><br>PROJECT</div>" styleClass="leftTab">
- <ui:include src="/WEB-INF/components/map/infoPanel.xhtml" />
- </p:tab >
-<!--
-<p:tab id="sample1" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-envelope maintab'></i><br>SAMPLE 1</div>" styleClass="leftTab hide">
-</p:tab >
-
-<p:tab id="sample2" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-envelope maintab'></i><br>SAMPLE 2</div>" styleClass="leftTab hide">
-</p:tab >
-
-<p:tab id="sample3" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-envelope maintab'></i><br>SAMPLE 3</div>" styleClass="leftTab hide">
-</p:tab >
--->
- </p:tabView >
-
-
- <div id="footerLinks">
- <a href="admin.xhtml?id=#{mapMB.currentMapId}" style="float:left; padding-left:25px;"><i class="fa fa-lock" style="font-size:17px"></i> ADMIN</a>
- <a href="#{configurationMB.userManual}" target="_user_manual_" style="float:left; padding-left:50px;"><i class="fa" style="font-size:17px"></i> MANUAL</a>
- <a href="export.xhtml?id=#{mapMB.currentMapId}" style="float:right; padding-right:25px;">EXPORT <i class="fa fa-mail-forward" style="font-size:17px"></i></a>
- </div>
-
- </div>
- <div>
- <ui:include src="/WEB-INF/components/map/map.xhtml" />
- </div>
- </div>
-
- <!--<ui:include src="/WEB-INF/components/map/footer.xhtml" />-->
-
- <ui:include src="/WEB-INF/components/map/feedbackDialog.xhtml" />
- <ui:include src="/WEB-INF/components/map/missingConnectionDialog.xhtml" />
-
-</h:body>
-</f:view>
-</html>
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml"
+ xmlns:h="http://java.sun.com/jsf/html"
+ xmlns:f="http://java.sun.com/jsf/core"
+ xmlns:ui="http://java.sun.com/jsf/facelets"
+ xmlns:p="http://primefaces.org/ui"
+ xmlns:c="http://java.sun.com/jsp/jstl/core"
+ >
+
+<f:view contentType="text/html">
+
+
+<h:head>
+ <title>#{mapMB.currentProject.name}</title>
+
+ <!-- Google Maps API version 3.20 -->
+ <script src="https://maps.google.com/maps/api/js?libraries=drawing&v=3.22" type="text/javascript"/>
+
+ <link rel="shortcut icon" href="./resources/images/favicon.png" type="image/png" />
+
+<!-- log4javascript library -->
+ <h:outputScript library="js" name="log4javascript.js" />
+<!-- configuration for log4javascript -->
+ <h:outputScript library="js" name="LogConfig.js" />
+
+ <h:outputScript library="js" name="ObjectWithListeners.js"/>
+
+ <h:outputScript library="js" name="AbstractCustomMap.js" />
+ <h:outputScript library="js" name="AbstractInfoWindow.js"/>
+ <h:outputScript library="js" name="AbstractMarker.js"/>
+ <h:outputScript library="js" name="AbstractOverlayElement.js"/>
+ <h:outputScript library="js" name="Alias.js" />
+ <h:outputScript library="js" name="AliasInfoWindow.js" />
+ <h:outputScript library="js" name="AliasMarker.js" />
+ <h:outputScript library="js" name="AliasOverlay.js" />
+ <h:outputScript library="js" name="Configuration.js" />
+ <h:outputScript library="js" name="CustomMap.js" />
+ <h:outputScript library="js" name="CustomMapOptions.js" />
+ <h:outputScript library="js" name="Functions.js" />
+ <h:outputScript library="js" name="GeneVariant.js" />
+ <h:outputScript library="js" name="GuiConnector.js" />
+ <h:outputScript library="js" name="IdentifiedElement.js" />
+ <h:outputScript library="js" name="LayoutAlias.js" />
+ <h:outputScript library="js" name="LayoutData.js" />
+ <h:outputScript library="js" name="LayoutReaction.js" />
+ <h:outputScript library="js" name="MapModel.js"/>
+ <h:outputScript library="js" name="OverlayCollection.js" />
+ <h:outputScript library="js" name="pileup.js"/>
+ <h:outputScript library="js" name="PointData.js"/>
+ <h:outputScript library="js" name="PointInfoWindow.js"/>
+ <h:outputScript library="js" name="PointMarker.js"/>
+ <h:outputScript library="js" name="Reaction.js" />
+ <h:outputScript library="js" name="ReactionMarker.js" />
+ <h:outputScript library="js" name="ReactionInfoWindow.js" />
+ <h:outputScript library="js" name="ReactionOverlay.js" />
+ <h:outputScript library="js" name="ReferenceGenome.js" />
+ <h:outputScript library="js" name="ReferenceGenomeGeneMapping.js" />
+ <h:outputScript library="js" name="SearchPanel.js" />
+ <h:outputScript library="js" name="ServerConnector.js" />
+ <h:outputScript library="js" name="Submap.js" />
+ <h:outputScript library="js" name="TabNavi.js" />
+ <h:outputScript library="js" name="TouchMap.js" />
+
+ <ui:include src="/WEB-INF/components/map/statistics.xhtml" />
+
+ <script type="text/javascript">
+//<![CDATA[
+ var DEBUG_ON =false;
+
+ if (browser.name=="IE") {
+ if (browser.version<=8 || browser.compatibilityMode) {
+ alert("This webpage works only with Internet Explorer version 9 or greater.\n" +
+ "If you have Internet Explorer version 9 or greater and still see this message, please, turn the 'Compatibility modeoff:\n" +
+ "Open Internet Explorer and press the Alt key on your keyboard.\n" +
+ "Select 'Tools' menu item. \n" +
+ "Select the 'Compatibility View' settings option. \n" +
+ "Make sure the 'Display all websites in Compatibility View' check box is unchecked and that the 'Compatibility View; list of websites is cleared.\n" +
+ "\n"+
+ "Alternatively, please, use other browsers: Chrome, Firefox or Safari.");
+ }
+ }
+ var configuration = new Configuration();
+
+function processUrlGetParams() {
+ if (GuiConnector.getParams["submap"]==null || configuration.ID_MODEL==GuiConnector.getParams["submap"]) {
+ if (GuiConnector.getParams["x"]!=undefined && GuiConnector.getParams["y"]!=undefined){
+ ServerConnector.setCenterCoordinateX(GuiConnector.getParams["x"]);
+ ServerConnector.setCenterCoordinateY(GuiConnector.getParams["y"]);
+ }
+ if (GuiConnector.getParams["zoom"]!=undefined){
+ ServerConnector.setZoomLevel(GuiConnector.getParams["zoom"]);
+ }
+ }
+}
+
+function updateConfig() {
+ var json = document.getElementById('configurationForm:configurationGson').value;
+//there are some strange problems here...
+ json = json.replace(/\n/g," ");
+ configuration.loadFromModelView(JSON.parse(json));
+}
+
+function initMap(){
+ updateConfig();
+ processUrlGetParams();
+
+
+ searchPanel = new SearchPanel(document.getElementById('tabView:mainForm:searchText_input'),
+ document.getElementById('tabView:mainForm:searchButton'),
+ function(){
+ tabViewVar.select(0);
+ }
+ );
+
+ var mapElement = gmtls.getMap();
+ if (configuration.MAPS!=null) {
+
+ var windowsTouchInterface = ((navigator.appVersion.indexOf("Win")!=-1) && ('ontouchstart' in document.documentElement));
+ var overviewDiv = document.getElementById("overviewDiv");
+ customMap = new CustomMap({
+ map : mapElement,
+ configuration : configuration,
+ hideDiv : document.getElementById('leftPanel'),
+ markerOptimization : !windowsTouchInterface,
+ bigLogo : windowsTouchInterface,
+ overviewDiv : overviewDiv,
+ customTouchInterface: windowsTouchInterface
+ });
+
+ ServerConnector.setCustomMap(customMap);
+ GuiConnector.showGoogleMap();
+
+ ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "search"));
+ ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "missingConnection"));
+ ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "drug",true, true));
+ ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "chemical",#{chemicalMB.linkedToDisease()}, #{chemicalMB.linkedToDisease() == true}));
+ ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "mirna",true, true));
+ ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "comment",false, true));
+
+ customMap.refreshOverlays();
+
+
+ if (GuiConnector.getParams["search"]!=undefined) {
+ searchPanel.search(GuiConnector.getParams["search"]);
+ }
+
+ if (GuiConnector.getParams["comments"]=="on") {
+ document.getElementById('comment_checkbox').click();
+ }
+ if (GuiConnector.getParams["layout"]!=undefined) {
+ document.getElementById('tabView:layoutForm3:hidden2').value=GuiConnector.getParams["layout"];
+ getVisualizedLayoutDetails();
+ }
+
+ }
+ //when I try to hide legend from the beginning or in the same thread it's hidden forever... ;/
+ setTimeout(function() {
+ GuiConnector.hideLegend();
+ var submodelId = GuiConnector.getParams["submap"];
+ if (submodelId!=undefined) {
+ _createSubmodelDialog([{name:'submodelId', value: submodelId}]);
+ //for some reason the call above is not sync (even though it's required)
+ var waitingForResponse = setInterval(function() {
+ if (GuiConnector.getJsPopupForSubmodelId(submodelId)!=null) {
+ GuiConnector.openDialog(submodelId);
+ clearInterval(waitingForResponse);
+ if (GuiConnector.getParams["zoom"]!=undefined){
+ customMap.setZoom(submodelId,parseInt(GuiConnector.getParams["zoom"]));
+ }
+ if (GuiConnector.getParams["x"]!=undefined && GuiConnector.getParams["y"]!=undefined){
+ var x = GuiConnector.getParams["x"];
+ var y = GuiConnector.getParams["y"];
+ var point = new google.maps.Point(x, y);
+ customMap.setCenter(submodelId,point);
+ }
+ }
+ },100);
+ }
+ }, 0);
+}
+
+
+function removeMissingConnection(id) {
+ document.getElementById('missingConnectionForm:connectionId').value=""+id;
+ dlg4.show();
+}
+
+function removeComment(id) {
+ document.getElementById('missingConnectionForm:commentId').value=""+id;
+ dlg5.show();
+}
+
+
+//]]>
+ </script>
+</h:head>
+<h:body onload="initMap();" >
+<h:outputStylesheet library="css" name="style.css"/>
+<h:outputStylesheet library="css" name="pileup.css"/>
+
+ <h:outputScript library="primefaces" name="jquery/jquery.js" target="head" />
+ <div class = "containerClass">
+ <div id="leftPanel" class ="leftPanelClass">
+
+ <ui:include src="/WEB-INF/components/admin/header.xhtml" />
+
+<!-- <div class="tabNavigation">
+ <a href="javascript:;" onclick="GuiConnector.tabNaviShow('prev');" class="naviLeft"><i class="fa fa-chevron-left"></i></a>
+ <a href="javascript:;" onclick="GuiConnector.tabNaviShow('next');" class="naviRight"><i class="fa fa-chevron-right"></i></a>
+ </div>
+-->
+
+ <p:tabView id="tabView" widgetVar="tabViewVar" styleClass="leftTabView" activeIndex="0" >
+ <p:tab id="searchTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-search maintab'></i><br>SEARCH</div>" styleClass="leftTab">
+ <ui:include src="/WEB-INF/components/map/searchPanel.xhtml" />
+ </p:tab >
+ <p:tab id="drugTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-map-marker maintab'></i><br>DRUG</div>" styleClass="leftTab">
+ <ui:include src="/WEB-INF/components/map/drugPanel.xhtml" />
+ </p:tab >
+ <p:tab id="chemicalTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-map-marker maintab'></i><br>CHEMICAL</div>" styleClass="leftTab">
+ <ui:include src="/WEB-INF/components/map/chemicalPanel.xhtml" />
+ </p:tab >
+ <p:tab id="miRNATab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-map-marker maintab'></i><br>MiRNA</div>" styleClass="leftTab">
+ <ui:include src="/WEB-INF/components/map/miRNAPanel.xhtml" />
+ </p:tab >
+ <p:tab id="layoutTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-th-list maintab'></i><br>OVERLAYS</div>" styleClass="leftTab">
+ <ui:include src="/WEB-INF/components/map/layoutPanel.xhtml" />
+ </p:tab >
+ <p:tab id="loginTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-sign-in maintab'></i><br>LOGIN</div>" styleClass="leftTab" rendered ="#{userMB.loggedUser.login=='anonymous'}">
+ <ui:include src="/WEB-INF/components/map/loginPanel.xhtml" />
+ </p:tab >
+ <p:tab id="profileTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-user maintab'></i><br>PROFILE</div>" styleClass="leftTab" rendered ="#{not (userMB.loggedUser.login=='anonymous')}">
+ <ui:include src="/WEB-INF/components/map/profilePanel.xhtml" />
+ </p:tab >
+ <p:tab id="submapTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-sitemap maintab'></i><br>SUBMAPS</div>" styleClass="leftTab">
+ <ui:include src="/WEB-INF/components/map/submapPanel.xhtml" />
+ </p:tab >
+ <p:tab id="infoTab" title="<div class='tngContainer'><div class='tng'></div></div><div class='maintabdiv'><i class='fa fa-info maintab'></i><br>PROJECT</div>" styleClass="leftTab">
+ <ui:include src="/WEB-INF/components/map/infoPanel.xhtml" />
+ </p:tab >
+ </p:tabView >
+
+
+ <div id="footerLinks">
+ <a href="admin.xhtml?id=#{mapMB.currentMapId}" style="float:left; padding-left:25px;"><i class="fa fa-lock" style="font-size:17px"></i> ADMIN</a>
+ <a href="#{configurationMB.userManual}" target="_user_manual_" style="float:left; padding-left:50px;"><i class="fa" style="font-size:17px"></i> MANUAL</a>
+ <a href="export.xhtml?id=#{mapMB.currentMapId}" style="float:right; padding-right:25px;">EXPORT <i class="fa fa-mail-forward" style="font-size:17px"></i></a>
+ </div>
+
+ </div>
+ <div>
+ <ui:include src="/WEB-INF/components/map/map.xhtml" />
+ </div>
+ </div>
+
+ <!--<ui:include src="/WEB-INF/components/map/footer.xhtml" />-->
+
+ <ui:include src="/WEB-INF/components/map/feedbackDialog.xhtml" />
+ <ui:include src="/WEB-INF/components/map/missingConnectionDialog.xhtml" />
+
+</h:body>
+</f:view>
+</html>
diff --git a/web/src/main/webapp/resources/js/AbstractOverlayElement.js b/web/src/main/webapp/resources/js/AbstractOverlayElement.js
new file mode 100644
index 0000000000000000000000000000000000000000..ed6e378901475376998f2680a96b83cfecd38a7f
--- /dev/null
+++ b/web/src/main/webapp/resources/js/AbstractOverlayElement.js
@@ -0,0 +1,45 @@
+/**
+ * Class representing abstract overlay element on the map relevant for a specific
+ * layout.
+ */
+function AbstractOverlayElement() {
+};
+
+AbstractOverlayElement.prototype.overlayToColor = function(elementOverlay) {
+ if (elementOverlay==null) {
+ logger.error("elementOverlay cannot be null!");
+ }
+ if (elementOverlay.color!=null) {
+ return intToColorString(elementOverlay.color.value);
+ } else if (elementOverlay.value!=null) {
+ var ratio =0;
+ var color;
+ if (elementOverlay.value<0) {
+ ratio = -elementOverlay.value;
+ color = ServerConnector.getMinOverlayColorInt();
+ } else {
+ ratio = elementOverlay.value;
+ color = ServerConnector.getMaxOverlayColorInt();
+ }
+ var red = color & 0xFF0000;
+ red = red*ratio;
+ red = parseInt(red);
+ red = red & 0xFF0000;
+
+ var green = color & 0x00FF00;
+ green = green*ratio;
+ green = parseInt(green);
+ green = green & 0x00FF00;
+
+ var blue = color & 0x0000FF;
+ blue = blue*ratio;
+ blue = parseInt(blue);
+ blue = blue & 0x0000FF;
+
+ var color = red | green | blue;
+ return intToColorString(color);
+ } else {
+ logger.error("elementOverlay doesn't have neither color nor value set!");
+ }
+};
+
diff --git a/web/src/main/webapp/resources/js/AliasOverlay.js b/web/src/main/webapp/resources/js/AliasOverlay.js
index 139cb513874055084519eb954bd5b9c27844b682..8fb7581b19ea9132ae4ceefde64979055406f833 100644
--- a/web/src/main/webapp/resources/js/AliasOverlay.js
+++ b/web/src/main/webapp/resources/js/AliasOverlay.js
@@ -1,104 +1,111 @@
-/**
- * Class representing overlay of the alias on the map relevant for a specific
- * layout.
- */
-function AliasOverlay(paramObj, map, aliasData) {
- // google map object associated with the alias
- this.gmapObj = paramObj;
- // AbstractCustomMap where the alias is located
- this.customMap = map;
- // original data
- this.aliasData = aliasData;
-
- var self = this;
- var onclick = (function() {
- var aliasOverlayData = self;
- return function() {
- customMap.openInfoWindowForAlias(aliasOverlayData.aliasData.id,
- aliasOverlayData.customMap.id);
- };
- })();
- google.maps.event.addListener(paramObj, 'click', onclick);
-};
-
-/**
- * Sets Google map to this {@link AliasOverlay}.
- *
- * @param map
- * map to set
- */
-AliasOverlay.prototype.setMap = function(map) {
- this.gmapObj.setMap(map);
-}
-
-/**
- * Function used to recalculate boundaries of the {@link AliasOverlay}.
- * Boundaries define how big part of original alias is taken by this layout
- * visualization.
- *
- * @param startX
- * value between 0..1 defininf where should be the start on OX axis
- * @param endX
- * value between 0..1 defininf where should be the end on OX axis
- */
-AliasOverlay.prototype.setBoundsForAlias = function(startX, endX) {
- var pointA = new google.maps.Point(this.aliasData.x + startX
- * this.aliasData.width, this.aliasData.y);
- var pointB = new google.maps.Point(this.aliasData.x + endX
- * this.aliasData.width, this.aliasData.y + this.aliasData.height);
- var latLngA = this.customMap.fromPointToLatLng(pointA);
- var latLngB = this.customMap.fromPointToLatLng(pointB);
-
- var bounds = new google.maps.LatLngBounds();
- bounds.extend(latLngA);
- bounds.extend(latLngB);
-
- this.gmapObj.setBounds(bounds);
-}
-
-/**
- * Creates {@link AliasOverlay} from input data.
- *
- * @param layoutAlias
- * {@link LayoutAlias} for which overlay is created
- * @param aliasData
- * {@link Alias data} of the alias
- * @param map
- * {@link AbstractCustomMap} where overlay should be placed
- * @param startX
- * this is the ratio on OX axis that should be use as a starting
- * point of the overlay. For instance when there are three layouts to
- * visualize then
- * <ul>
- * <li>the first layout have startX=0.0; endX=0.33333</li>
- * <li>second layout have startX=0.33333; endX=0.66666</li>
- * <li>the last layout have startX=0.66666; endX=1.0</li>
- * </ul>
- * @param endX
- * this is the ratio on OX axis that should be use as a starting
- * point of the overlay
- * @returns {AliasOverlay}
- */
-AliasOverlay.create = function(layoutAlias, aliasData, map, startX, endX) {
- var pointA = new google.maps.Point(aliasData.x + startX * aliasData.width,
- aliasData.y);
- var pointB = new google.maps.Point(aliasData.x + endX * aliasData.width,
- aliasData.y + aliasData.height);
- var latLngA = map.fromPointToLatLng(pointA);
- var latLngB = map.fromPointToLatLng(pointB);
-
- var bounds = new google.maps.LatLngBounds();
- bounds.extend(latLngA);
- bounds.extend(latLngB);
- var color = intToColorString(layoutAlias.color.value);
- var rectangle = new google.maps.Rectangle({
- fillColor : color,
- fillOpacity : 0.8,
- strokeWeight : 1,
- map : map.map,
- bounds : bounds
- });
- var result = new AliasOverlay(rectangle, map, aliasData);
-
- return result;
-};
+/**
+ * Class representing overlay of the alias on the map relevant for a specific
+ * layout.
+ */
+function AliasOverlay(paramObj, map, aliasData) {
+ // call super constructor
+ AbstractOverlayElement.call();
+
+ // google map object associated with the alias
+ this.gmapObj = paramObj;
+ // AbstractCustomMap where the alias is located
+ this.customMap = map;
+ // original data
+ this.aliasData = aliasData;
+
+ var self = this;
+ var onclick = (function() {
+ var aliasOverlayData = self;
+ return function() {
+ customMap.openInfoWindowForAlias(aliasOverlayData.aliasData.id,
+ aliasOverlayData.customMap.id);
+ };
+ })();
+ google.maps.event.addListener(paramObj, 'click', onclick);
+};
+
+AliasOverlay.prototype = Object.create(AbstractOverlayElement.prototype);
+AliasOverlay.prototype.constructor = AliasOverlay;
+
+
+/**
+ * Sets Google map to this {@link AliasOverlay}.
+ *
+ * @param map
+ * map to set
+ */
+AliasOverlay.prototype.setMap = function(map) {
+ this.gmapObj.setMap(map);
+}
+
+/**
+ * Function used to recalculate boundaries of the {@link AliasOverlay}.
+ * Boundaries define how big part of original alias is taken by this layout
+ * visualization.
+ *
+ * @param startX
+ * value between 0..1 defininf where should be the start on OX axis
+ * @param endX
+ * value between 0..1 defininf where should be the end on OX axis
+ */
+AliasOverlay.prototype.setBoundsForAlias = function(startX, endX) {
+ var pointA = new google.maps.Point(this.aliasData.x + startX
+ * this.aliasData.width, this.aliasData.y);
+ var pointB = new google.maps.Point(this.aliasData.x + endX
+ * this.aliasData.width, this.aliasData.y + this.aliasData.height);
+ var latLngA = this.customMap.fromPointToLatLng(pointA);
+ var latLngB = this.customMap.fromPointToLatLng(pointB);
+
+ var bounds = new google.maps.LatLngBounds();
+ bounds.extend(latLngA);
+ bounds.extend(latLngB);
+
+ this.gmapObj.setBounds(bounds);
+}
+
+/**
+ * Creates {@link AliasOverlay} from input data.
+ *
+ * @param layoutAlias
+ * {@link LayoutAlias} for which overlay is created
+ * @param aliasData
+ * {@link Alias data} of the alias
+ * @param map
+ * {@link AbstractCustomMap} where overlay should be placed
+ * @param startX
+ * this is the ratio on OX axis that should be use as a starting
+ * point of the overlay. For instance when there are three layouts to
+ * visualize then
+ * <ul>
+ * <li>the first layout have startX=0.0; endX=0.33333</li>
+ * <li>second layout have startX=0.33333; endX=0.66666</li>
+ * <li>the last layout have startX=0.66666; endX=1.0</li>
+ * </ul>
+ * @param endX
+ * this is the ratio on OX axis that should be use as a starting
+ * point of the overlay
+ * @returns {AliasOverlay}
+ */
+AliasOverlay.create = function(layoutAlias, aliasData, map, startX, endX) {
+ var pointA = new google.maps.Point(aliasData.x + startX * aliasData.width,
+ aliasData.y);
+ var pointB = new google.maps.Point(aliasData.x + endX * aliasData.width,
+ aliasData.y + aliasData.height);
+ var latLngA = map.fromPointToLatLng(pointA);
+ var latLngB = map.fromPointToLatLng(pointB);
+
+ var bounds = new google.maps.LatLngBounds();
+ bounds.extend(latLngA);
+ bounds.extend(latLngB);
+ var rectangle = new google.maps.Rectangle({
+ fillOpacity : 0.8,
+ strokeWeight : 1,
+ map : map.map,
+ bounds : bounds
+ });
+ var result = new AliasOverlay(rectangle, map, aliasData);
+ var color = result.overlayToColor(layoutAlias);
+rectangle.setOptions({fillColor: color});
+
+ return result;
+};
diff --git a/web/src/main/webapp/resources/js/CustomMap.js b/web/src/main/webapp/resources/js/CustomMap.js
index 443eb5ab987b75f740239fd90ee0b9138e924fcf..5cc4d0487070994fe9715650f51739244c79897b 100644
--- a/web/src/main/webapp/resources/js/CustomMap.js
+++ b/web/src/main/webapp/resources/js/CustomMap.js
@@ -1,1735 +1,1741 @@
-/**
- * Default constructor.
- *
- * @param globalMap
- * google.maps.Map object representing the map
- * @param configuration
- * Configuration object representing our data in the map
- * @param bigButtons
- * boolean value determining if the buttons on the map should be big,
- * and if the map is run on the touch interface
- * @param hideDiv
- *
- */
-function CustomMap(options) {
- if (!(options instanceof CustomMapOptions)) {
- options = new CustomMapOptions(options);
- }
- AbstractCustomMap.call(this, options);
-
- // set config parameters
- this.map = options.getMap();
-
- if (options.isCustomTouchInterface()) {
- this._touchInterface = new TouchMap(this);
- }
-
- // create function that override primefaces fitBounds with default google
- // implementation
- var fitBounds = function(bounds) {
- var tmp = this.fitBounds;
- this.fitBounds = google.maps.Map.prototype.fitBounds;
- this.fitBounds(bounds);
- this.fitBounds = tmp;
- };
- this.map.fitBounds2 = fitBounds;
-
- this.buttons = [];
-
- this.createSubmaps();
-
- this.selectedLayouts = [];
-
- this.setupLayouts();
-
- this.createBelt();
-
- this.customizeGoogleMapView();
-
- this.createMapChangedCallbacks();
-
- this.createClientServerListeners();
-
- this.overlayCollections = [];
-
- // which submap is active (where user made interaction for the last time)
- this._activeSubmapId = null;
-
- this.initialized = true;
-
- // list of reference genomes
- this._referenceGenome = [];
-
- ServerConnector.actualizeSessionData();
-}
-
-CustomMap.prototype = Object.create(AbstractCustomMap.prototype);
-
-CustomMap.prototype.constructor = CustomMap;
-
-CustomMap.prototype.createSubmaps = function() {
- this.submaps = [];
- for (var i = 0; i < this.getConfiguration().SUBMODELS.length; i++) {
- this.submaps.push(new Submap(this,
- this.getConfiguration().SUBMODELS[i].ID_MODEL));
- }
-};
-
-CustomMap.prototype.createLogo = function() {
-
- var logoControlDiv = document.createElement('DIV');
- var logo = document.createElement('IMG');
- var url = ServerConnector.getLogoImg();
- if (!/^(f|ht)tps?:\/\//i.test(url)) {
- url = GuiConnector.getImgPrefix() + url;
- }
- logo.src = url;
- logo.style.cursor = 'pointer';
- logo.style.width = "80px";
- logoControlDiv.appendChild(logo);
- google.maps.event.addDomListener(logo, 'click', function() {
- var win = window.open(ServerConnector.getLogoLink(), '_blank');
- win.focus();
- });
- logoControlDiv.index = 0; // used for ordering
- this.map.controls[google.maps.ControlPosition.LEFT_BOTTOM]
- .push(logoControlDiv);
-
- var logoControlDiv = document.createElement('DIV');
- logoControlDiv.style.padding = '5px';
-
- var logo = document.createElement('IMG');
- logo.src = GuiConnector.getImgPrefix()
- + GuiConnector.getLcsbLogoImg(this.bigButtons);
- logo.style.cursor = 'pointer';
- logoControlDiv.appendChild(logo);
- google.maps.event.addDomListener(logo, 'click', function() {
- var win = window.open('http://wwwen.uni.lu/lcsb/', '_blank');
- win.focus();
- });
-
- logoControlDiv.index = 1; // used for ordering
- this.map.controls[google.maps.ControlPosition.RIGHT_BOTTOM]
- .push(logoControlDiv);
-};
-
-CustomMap.prototype.createBelt = function() {
- var self = this;
-
- this.divBelt = document.createElement('DIV');
- this.divBelt.className = "headerBelt";
-
- var hideDivButton = document.createElement('DIV');
- hideDivButton.className = "headerHideDivButton";
-
- var hideButton = document.createElement('button');
- hideButton.id = "hide_button";
- hideButton.className = "headerHideButton";
- hideButton.innerHTML = "<i class='fa fa-chevron-left'></i>";
- // when there is no div to hide we should allow hiding
- if (self.getHideDiv() !== undefined) {
- hideButton.onclick = (function() {
- var button = hideButton;
- var div = self.getHideDiv();
-
- var left = $(PrimeFaces.escapeClientId(self.map.getDiv().id)).offset().left;
- return function() {
- if (button.innerHTML.indexOf('fa-chevron-left') > 0) {
- button.innerHTML = "<i class='fa fa-chevron-right'></i>";
- div.style.display = 'none';
- self.map.getDiv().style.left = "0px";
- } else {
- div.style.display = 'block';
- button.innerHTML = "<i class='fa fa-chevron-left'></i>";
- self.map.getDiv().style.left = left + "px";
- }
- google.maps.event.trigger(self.map, 'resize');
- return false;
- };
- })();
- } else {
- hideButton.disabled = true;
- logger.warn("Left panel hiding disabled");
- }
- hideDivButton.appendChild(hideButton);
- hideDivButton.index = 1; // used for ordering
- this.divBelt.appendChild(hideDivButton);
-
- var controlText = document.createElement('div');
- controlText.className = "headerTextBold";
- controlText.innerHTML = this.getConfiguration().MAP_NAME;
- this.divBelt.appendChild(controlText);
-
- this.map.controls[google.maps.ControlPosition.TOP_LEFT].push(this.divBelt);
-};
-
-CustomMap.prototype.setLegendVisible = function(vis) {
- if (vis) {
- document.getElementById('legend').style.display = 'block';
- } else {
- document.getElementById('legend').style.display = 'none';
- }
-};
-
-CustomMap.prototype.clearOverlays = function() {
- for ( var overlayName in this.overlayCollections) {
- if (this.overlayCollections.hasOwnProperty(overlayName)) {
- var collection = this.overlayCollections[overlayName];
- this.clearOverlayCollection(collection);
- }
- }
-};
-
-CustomMap.prototype.refreshOverlays = function() {
- for ( var overlayName in this.overlayCollections) {
- if (this.overlayCollections.hasOwnProperty(overlayName)) {
- var collection = this.overlayCollections[overlayName];
- collection.refresh();
- }
- }
-};
-
-/**
- * Removes all markers from {@link OverlayCollection}.
- *
- * @param collection
- * {@link OverlayCollection} from which all markers should be removed
- */
-CustomMap.prototype.clearOverlayCollection = function(collection) {
- logger.debug("Clear collection: " + collection.name);
- for ( var key in collection.aliasMarkers) {
- if (collection.aliasMarkers.hasOwnProperty(key)
- && collection.aliasMarkers[key] != null) {
- collection.aliasMarkers[key].setMap(null);
- }
- }
-
- for ( var key in collection.pointMarkers) {
- if (collection.pointMarkers.hasOwnProperty(key)
- && collection.pointMarkers[key] != null) {
-
- collection.pointMarkers[key].setMap(null);
- }
- }
-
- for ( var key in collection.reactionMarkers) {
- if (collection.reactionMarkers.hasOwnProperty(key)
- && collection.reactionMarkers[key] != null) {
- collection.reactionMarkers[key].setMap(null);
- }
- }
-
- collection.aliasMarkers = [];
- collection.pointMarkers = [];
- collection.reactionMarkers = [];
-};
-
-/**
- * Updates data about visualized markers in {@link OverlayCollection}.
- *
- * @param overlayCollection
- * {@link OverlayCollection} with new data to visualize
- * @param fitBounds
- * <code>true</code> id the map should fit bounds to the new
- * elements after update, <code>false</code> otherwise
- */
-CustomMap.prototype.updateOverlayCollection = function(overlayCollection,
- fitBounds) {
- this.clearOverlayCollection(overlayCollection);
- this.renderOverlayCollection(overlayCollection, fitBounds);
-};
-
-/**
- * This method open layout by a given layout identifier (string starting with
- * 'cv' prefix) in a map and all submaps.
- *
- * @param identifier
- * identifier of the layout to present
- */
-CustomMap.prototype.openLayout = function(identifier) {
- logger.debug("Opening layout: " + identifier);
-
- this.map.setMapTypeId(identifier);
-
- var index = null;
- for (var i = 0; i < this.getConfiguration().MAPS.length; i++) {
- if ('cv' + this.getConfiguration().MAPS[i].idObject == identifier) {
- index = i;
- }
- }
- if (index == null) {
- logger.warn("Invalid layout identifier: " + identifier);
- }
- for (var i = 0; i < this.submaps.length; i++) {
- this.submaps[i].openLayout('cv'
- + this.submaps[i].getConfiguration().MAPS[index].idObject);
- }
-};
-
-/**
- * This method open layout by a given database identifier.
- *
- * @param identifier
- * identifier of the layout to present
- */
-CustomMap.prototype.openLayoutById = function(identifier) {
- logger.debug("Opening layout: " + identifier);
- var index = null;
- for (var i = 0; i < configuration.MAPS.length; i++) {
- if (configuration.MAPS[i].idObject == identifier) {
- index = 'cv' + identifier;
- }
- }
-
- // if layout doesn't exist print error
- if (index == null) {
- alert("You have no privileges for selected layout");
- } else {
- this.openLayout(index);
- }
-};
-
-CustomMap.prototype.createMapMenu = function(layoutButtons) {
- var selfMap = this;
-
- var buttons = [];
-
- // create a button for overview images when the image is available
- if (this.getConfiguration().TOP_OVERVIEW_IMAGE != "undefined"
- && this.getConfiguration().TOP_OVERVIEW_IMAGE != null) {
- var submenuButtonDiv = document.createElement('button');
- buttons.push(submenuButtonDiv);
- submenuButtonDiv.id = "overview_button";
- submenuButtonDiv.innerHTML = "<i class='fa fa-sitemap' style='font-size:18px; font-weight:400; padding-right:10px;'></i> SHOW OVERVIEW";
- submenuButtonDiv.className = "overview_button";
- submenuButtonDiv.onclick = (function() {
- return function() {
- selfMap.showOverview();
- return false;
- };
- })();
- this.divBelt.appendChild(submenuButtonDiv);
- }
-
- var rightHeaderMenu = document.createElement('div');
- rightHeaderMenu.className = "rightHeaderMenu";
- var submenuDiv = document.createElement('div');
- submenuDiv.className = "div4checkboxes";
- var submenuButtonDiv = document.createElement('input');
- submenuButtonDiv.type = "checkbox";
- submenuButtonDiv.name = "Comments";
- submenuButtonDiv.id = "comment_checkbox";
- submenuButtonDiv.onclick = (function() {
- var selfButton = submenuButtonDiv;
- return function() {
- selfMap.showComments = selfButton.checked;
- ServerConnector.setShowComments(selfButton.checked);
- if (selfButton.checked) {
- document.getElementById('refresh_comments_button').style.display = 'inline';
- } else {
- document.getElementById('refresh_comments_button').style.display = 'none';
- }
- selfMap.refreshComments();
-
- };
- })();
- var element = document.createElement('label');
- element.innerHTML = "COMMENTS";
- element.setAttribute("for", "comment_checkbox");
- submenuDiv.appendChild(submenuButtonDiv);
- submenuDiv.appendChild(element);
-
- var submenuButtonDiv = document.createElement('input');
- submenuButtonDiv.type = "checkbox";
- submenuButtonDiv.name = "Legend";
- submenuButtonDiv.id = "lengend_checkbox";
- submenuButtonDiv.onclick = (function() {
- var selfButton = submenuButtonDiv;
- return function() {
- if (selfButton.checked) {
- GuiConnector.showLegend();
- } else {
- GuiConnector.hideLegend();
- }
- };
- })();
- element = document.createElement('label');
- element.innerHTML = "LEGEND";
- element.setAttribute("for", "lengend_checkbox");
- submenuDiv.appendChild(submenuButtonDiv);
- submenuDiv.appendChild(element);
-
- submenuButtonDiv = document.createElement('button');
- submenuButtonDiv.id = "refresh_comments_button";
- submenuButtonDiv.innerHTML = "<i class='fa fa-refresh' style='font-size:21px; font-weight:400;'></i>";
- submenuButtonDiv.className = "overview_button";
- submenuButtonDiv.style.display = 'none';
- submenuButtonDiv.onclick = (function() {
- return function() {
- selfMap.refreshComments();
- return false;
- };
- })();
- submenuDiv.appendChild(submenuButtonDiv);
- rightHeaderMenu.appendChild(submenuDiv);
-
- var submenuButtonDiv = document.createElement('button');
- buttons.push(submenuButtonDiv);
- submenuButtonDiv.id = "clear_button";
- submenuButtonDiv.className = "overview_button";
- submenuButtonDiv.innerHTML = "<i class='fa fa-times' style='font-size:18px; font-weight:300; padding-right:10px;'></i> CLEAR";
- submenuButtonDiv.title = "Clear all queries";
- submenuButtonDiv.style.display = 'inline';
- submenuButtonDiv.onclick = (function() {
- return function() {
- selfMap.clearData();
- return false;
- };
- })();
- rightHeaderMenu.appendChild(submenuButtonDiv);
-
- this.divBelt.appendChild(rightHeaderMenu);
-};
-
-CustomMap.prototype.registerSource = function(overlayCollection) {
- this.overlayCollections[overlayCollection.name] = overlayCollection;
- overlayCollection.aliasMarkers = [];
- overlayCollection.pointMarkers = [];
- overlayCollection.reactionMarkers = [];
-};
-
-CustomMap.prototype.refreshComments = function() {
- for ( var overlayName in this.overlayCollections) {
- if (this.overlayCollections.hasOwnProperty(overlayName)
- && overlayName == "comment") {
- var collection = this.overlayCollections[overlayName];
- collection.refresh();
- return;
- }
- }
- throw "comment OverlayCollection not found";
-};
-
-CustomMap.prototype.turnOnOffDrawing = function() {
- var model = this.getSubmodelById(this.getActiveSubmapId());
- if (model != null) {
- model._turnOnOffDrawing();
- } else {
- throw "Cannot find submodel with id: " + this.getActiveSubmapId();
- }
-};
-
-CustomMap.prototype.clearData = function() {
- this.clearOverlays();
- for ( var overlayName in this.overlayCollections) {
- if (this.overlayCollections.hasOwnProperty(overlayName)) {
- ServerConnector.sendClearRequest(overlayName);
- }
- }
-};
-
-CustomMap.prototype.refreshMarkers = function() {
- logger.debug("Refresh Markers: ");
- for ( var overlayName in this.overlayCollections) {
- if (this.overlayCollections.hasOwnProperty(overlayName)) {
- var collection = this.overlayCollections[overlayName];
- this.refreshOverlayMarkers(collection);
- }
- }
-};
-
-CustomMap.prototype.refreshOverlayMarkers = function(overlay) {
- var self = this;
- logger.debug("Refresh overlay: " + overlay.name);
- var boundsArray = [];
- boundsArray[this.getId()] = new google.maps.LatLngBounds();
- for (var i = 0; i < this.submaps.length; i++) {
- boundsArray[this.submaps[i].getId()] = new google.maps.LatLngBounds();
- }
-
- var updated = false;
- var stillMissing = false;
- for ( var key in overlay.aliasMarkers) {
- if (overlay.aliasMarkers.hasOwnProperty(key)
- && overlay.aliasMarkers[key] != null) {
- var alias = overlay.aliasMarkers[key];
- if (alias.getAliasData() == null) {
- var aliasData = alias.getCustomMap().mapModel.getAliasById(alias
- .getId());
- if (aliasData != null) {
- alias.setAliasData(aliasData);
- alias.init();
- alias.show();
- updated = true;
- var bounds = alias.getBounds();
- boundsArray[alias.getCustomMap().getId()].extend(bounds
- .getNorthEast());
- } else {
- stillMissing = true;
- logger.debug("Cannot show alias marker. Data is still not loaded...");
- }
- } else {
- var bounds = alias.getBounds();
- if (!this.isMarkerOptimization()) {
- alias.hide();
- alias.show();
- }
- boundsArray[alias.getCustomMap().getId()].extend(bounds.getNorthEast());
- boundsArray[alias.getCustomMap().getId()].extend(bounds.getSouthWest());
- }
- }
- }
-
- for ( var key in overlay.pointMarkers) {
- if (overlay.pointMarkers.hasOwnProperty(key)
- && overlay.pointMarkers[key] != null) {
- var alias = overlay.pointMarkers[key];
- // we don't need to update this markers because thet data about
- // visualization is
- // already there
- // alias.update();
- var bounds = alias.getBounds();
- if (!this.isMarkerOptimization()) {
- alias.hide();
- alias.show();
- }
- boundsArray[alias.getCustomMap().getId()].extend(bounds.getNorthEast());
- }
- }
-
- for ( var key in overlay.reactionMarkers) {
- if (overlay.reactionMarkers.hasOwnProperty(key)
- && overlay.reactionMarkers[key] != null) {
- var reactionOverlay = overlay.reactionMarkers[key];
- if (reactionOverlay.getReactionData() == null) {
- var reactionData = reactionOverlay.getCustomMap().mapModel
- .getReactionById(reactionOverlay.getId());
- if (reactionData != null) {
- reactionOverlay.setReactionData(reactionData);
- reactionOverlay.init();
- reactionOverlay.show();
- updated = true;
- var bounds = reactionOverlay.getBounds();
- boundsArray[reactionOverlay.getCustomMap().getId()].extend(bounds
- .getNorthEast());
- boundsArray[reactionOverlay.getCustomMap().getId()].extend(bounds
- .getSouthWest());
- } else {
- stillMissing = true;
- logger
- .debug("Cannot show reaction marker. Data is still not loaded...");
- }
- } else {
- var bounds = alias.getBounds();
- if (!this.isMarkerOptimization()) {
- alias.hide();
- alias.show();
- }
- boundsArray[alias.getCustomMap().getId()].extend(bounds.getNorthEast());
- boundsArray[alias.getCustomMap().getId()].extend(bounds.getSouthWest());
- }
-
- }
- }
-
- if (!stillMissing && updated && overlay.fitBounds) {
- for ( var mapId in boundsArray) {
- if (boundsArray.hasOwnProperty(mapId)) {
- var map = this.getSubmodelById(mapId).map;
- var bounds = boundsArray[mapId];
- if (map != null && !bounds.isEmpty()) {
- if (typeof map.fitBounds2 !== "undefined") {
- map.fitBounds2(bounds);
- } else {
- map.fitBounds(bounds);
- }
- }
- }
- }
- }
-};
-
-CustomMap.prototype.openSubmodel = function(id, htmlTag, jsVar) {
- if (jsVar.submapControler == null) {
- var submap = null;
- for (var i = 0; i < this.submaps.length; i++) {
- if (this.submaps[i].getId() == id) {
- submap = this.submaps[i];
- }
- }
- if (submap == null) {
- logger.error("Unknown submap for id: " + id);
- } else {
- submap.init(htmlTag, jsVar);
- submap.openLayout(this.map.getMapTypeId());
- this.refreshOverlays();
-
- // now we have to visualize layouts
- var layouts = [];
-
- // get list of layouts
- for ( var key in this.selectedLayouts) {
- if (this.selectedLayouts.hasOwnProperty(key)
- && this.selectedLayouts[key] == true) {
- layouts.push(key);
- }
- }
-
- // show layouts that should be visualized (resize or show them)
- for (var i = 0; i < layouts.length; i++) {
- var layoutId = layouts[i];
- submap._showSelectedLayout(layoutId, i, layouts.length);
- }
- }
- }
- jsVar.show();
-};
-
-CustomMap.prototype.customizeGoogleMapView = function() {
- var mapOptions = this.creatMapOptions();
- this.map.setOptions(mapOptions);
-
- this.createMapMenu(false);
-
- this.registerMapClickEvents();
-
- this.createLogo();
- // this.createMapVersion();
- google.maps.event.trigger(this.map, 'resize');
- google.maps.event.trigger(this.map, 'maptypeid_changed');
- google.maps.event.trigger(this.map, 'projection_changed');
-
- // center map and zoom in to fit into browser window
- if (this.getConfiguration().fitMapBounds) {
- var bounds = new google.maps.LatLngBounds();
- var point = new google.maps.LatLng(
- this.getConfiguration().topLeftLatLng.lat,
- this.getConfiguration().topLeftLatLng.lng);
- bounds.extend(point);
-
- point = new google.maps.LatLng(
- this.getConfiguration().bottomRightLatLng.lat,
- this.getConfiguration().bottomRightLatLng.lng);
- bounds.extend(point);
-
- if (typeof this.map.fitBounds2 !== "undefined") {
- this.map.fitBounds2(bounds);
- } else {
- this.map.fitBounds(bounds);
- }
- }
-};
-
-CustomMap.prototype.setCenter = function(mapIdentifier, coordinates) {
- if (this.getConfiguration().ID_MODEL == mapIdentifier) {
- this.map.setCenter(coordinates);
- } else {
- openDialog(mapIdentifier);
- for (var i = 0; i < this.submaps.length; i++) {
- if (this.submaps[i].getId() == mapIdentifier) {
- this.submaps[i].map.setCenter(coordinates);
- }
- }
- }
-};
-
-CustomMap.prototype.setZoom = function(mapIdentifier, zoom) {
- if (this.getConfiguration().ID_MODEL == mapIdentifier) {
- this.map.setZoom(zoom);
- } else {
- openDialog(mapIdentifier);
- for (var i = 0; i < this.submaps.length; i++) {
- if (this.submaps[i].getId() == mapIdentifier) {
- this.submaps[i].map.setZoom(zoom);
- }
- }
- }
-};
-
-/**
- * Creates listeners for google.maps.Map object that will actualize the data in
- * user session.
- */
-CustomMap.prototype.createMapChangedCallbacks = function() {
- var customMapSelf = this;
- // listener for changing zoom level
- google.maps.event.addListener(this.map, 'zoom_changed', function() {
- ServerConnector.setZoomLevel(customMapSelf.map.getZoom());
- ServerConnector.actualizeSessionData();
- });
-
- // if we have zoom level data stored in session then restore it
- var level = ServerConnector.getZoomLevel();
- if (parseInt(level) > 0) {
- level = parseInt(level);
- this.map.setZoom(level);
- } else {
- ServerConnector.setZoomLevel(customMapSelf.map.getZoom());
- }
-
- // listener for changing location of the map (moving left/reght/top/bottom
- google.maps.event.addListener(this.map, 'center_changed', function() {
- var coord = customMapSelf.map.getCenter();
- var point = customMapSelf.fromLatLngToPoint(coord);
- ServerConnector.setCenterCoordinateX(point.x);
- ServerConnector.setCenterCoordinateY(point.y);
- ServerConnector.actualizeSessionData();
- });
-
- // if we have coordinate data stored in session then restore it
- var x = ServerConnector.getCenterCoordinateX();
- var y = ServerConnector.getCenterCoordinateY();
- if (!isNaN(x) && !isNaN(y)) {
- var point = new google.maps.Point(x, y);
- var coord = customMapSelf.fromPointToLatLng(point);
- customMapSelf.map.setCenter(coord);
- }
-
- // listener for changing type of layout
- google.maps.event.addListener(this.map, 'maptypeid_changed', function() {
- ServerConnector.setSelectedLayout(customMapSelf.map.getMapTypeId());
- ServerConnector.actualizeParams();
- });
-
- // if we have type of layout stored in the session then restore it
- var mapType = ServerConnector.getSelectedLayout();
- if (mapType != "" && mapType != null) {
- this.openLayout(mapType);
- }
-};
-
-/**
- * Returns submodel (or this model) by identfier of the model.
- *
- * @param identifier
- * identifier of the submodel
- * @returns submodel (or this model) with given identfier of the model
- */
-CustomMap.prototype.getSubmodelById = function(identifier) {
- if (this.getId() == identifier) {
- return this;
- }
- for (var i = 0; i < this.submaps.length; i++) {
- if (this.submaps[i].getId() == identifier) {
- return this.submaps[i];
- }
- }
- return null;
-};
-
-CustomMap.prototype.removeSelection = function() {
- var model = this.getSubmodelById(this.getActiveSubmapId());
- if (model != null) {
- model._removeSelection();
- } else {
- throw "Cannot find submodel with id: " + this.getActiveSubmapId();
- }
-};
-
-/**
- * This method will hide google map view and will present single image overview
- * of the data.
- */
-CustomMap.prototype.showOverview = function(overviewImageId) {
- overviewDialog.syncWindowResize();
- if (this.getOverviewDiv() == "undefined" || this.getOverviewDiv() == null) {
- logger.warn("Cannot show overview, because overview div is undefined");
- } else {
- logger.debug("Show overview");
- overviewDialog.show();
-
- // resize dialog
- var htmlTag = GuiConnector.getOverviewHtmlTag();
-
- var width = Math.floor(window.innerWidth * 2 / 3);
- var height = Math.floor(window.innerHeight * 2 / 3);
-
- htmlTag.style.height = (height + 50) + "px";
- htmlTag.style.width = (width + 20) + "px";
-
- var self = this;
-
- // remove all child nodes from overview div
- while (this.getOverviewDiv().hasChildNodes()) {
- this.getOverviewDiv().removeChild(this.getOverviewDiv().lastChild);
- }
-
- if (overviewImageId == "undefined" || overviewImageId == null) {
- this.overviewImage = this.getConfiguration().TOP_OVERVIEW_IMAGE;
- } else {
- this.overviewImage = null;
- for (var i = 0; i < this.getConfiguration().OVERVIEW_IMAGES.length; i++) {
- if (this.getConfiguration().OVERVIEW_IMAGES[i].idObject == overviewImageId) {
- this.overviewImage = this.getConfiguration().OVERVIEW_IMAGES[i];
- }
- }
-
- if (this.overviewImage == null) {
- logger.warn("Unknown overview image with id = " + overviewImageId);
- this.overviewImage = this.getConfiguration().TOP_OVERVIEW_IMAGE;
- }
- }
-
- // add image to overview div
- this.overviewImageTag = document.createElement("IMG");
- this.overviewImageTag.src = "../map_images/" + this.overviewImage.filename;
- this.getOverviewDiv().appendChild(this.overviewImageTag);
-
- var ratio = 1.0;
-
- // check how image should be resized to fit dialog and resize it manually!!!
- if (width / this.overviewImage.width > height / this.overviewImage.height) {
- this.overviewImageTag.style.height = height + "px";
- ratio = height / this.overviewImage.height;
- width = this.overviewImage.width * ratio;
-
- htmlTag.style.width = (width + 20) + "px";
- } else {
- this.overviewImageTag.style.width = width + "px";
- ratio = width / this.overviewImage.width;
- height = this.overviewImage.height * ratio;
-
- htmlTag.style.height = (height + 50) + "px";
- }
-
- // center dialog
- overviewDialog.jq.css("top", Math.max(0,
- (($(window).height() - overviewDialog.jq.outerHeight()) / 2)
- + $(window).scrollTop())
- + "px");
- overviewDialog.jq.css("left", Math.max(0,
- (($(window).width() - overviewDialog.jq.outerWidth()) / 2)
- + $(window).scrollLeft())
- + "px");
-
- // on click event (what should happen when we click on the image)
- var onclickevent = function getClickPosition(e) {
- var parentPosition = getPosition(e.currentTarget);
- var xPosition = e.clientX - parentPosition.x;
- var yPosition = e.clientY - parentPosition.y;
-
- var imgWidth = self.overviewImageTag.offsetWidth;
-
- var currentRatio = imgWidth / self.overviewImage.width;
-
- var xNormal = xPosition / currentRatio;
- var yNormal = yPosition / currentRatio;
- var point = {
- x : xNormal,
- y : yNormal
- };
-
- var link = null;
- for (var i = 0; i < self.overviewImage.links.length; i++) {
- if (pointInsidePolygon(point, self.overviewImage.links[i].polygon)) {
- if (link == null) {
- link = self.overviewImage.links[i];
- } else {
- logger.warn("More than one link found. Skipping");
- }
- }
- }
- if (link != null) {
- if (link.type == "OverviewModelLink") {
- logger.debug("Opening model from overview. ModelId: "
- + link.modelLinkId);
- logger.debug("link coordinates [" + link.idObject + "]: "
- + link.latLng);
- // TODO min zoom value can be different for every map, it should be
- // changed in the future
- self.showModel(link.modelLinkId, link.latLng, link.zoomLevel
- + self.getConfiguration().MIN_ZOOM);
- overviewDialog.hide();
- } else if (link.type == "OverviewImageLink") {
- logger.debug("Opening image from overview. ImageId: "
- + link.imageLinkId);
- self.showOverview(link.imageLinkId);
- } else if (link.type == "OverviewSearchLink") {
- logger.debug("Sending search query. Query: " + link.query);
- searchPanel.search(link.query);
- overviewDialog.hide();
- } else {
- logger.warn("Unknown type of link: " + link.type
- + ". Don't know what to do... LinkId: " + link.idObject);
- }
- }
- };
-
- this.overviewImageTag.onclick = onclickevent;
-
- // resize canvas where on mouse over highligh will appear
- var canvas = document.getElementById("canvasDebug");
- canvas.width = width;
- canvas.height = height;
- canvas.onclick = onclickevent;
-
- // in debug mode draw clickable shapes
- if (DEBUG_ON) {
- var ctx = canvas.getContext("2d");
- // clear canvas
- ctx.clearRect(0, 0, canvas.width, canvas.height);
- for (var i = 0; i < this.overviewImage.links.length; i++) {
- ctx.beginPath();
- var polygon = this.overviewImage.links[i].polygon;
- for (var j = 0; j < polygon.length; j++) {
- var x = polygon[j].x * ratio;
- var y = polygon[j].y * ratio;
- ctx.moveTo(x, y);
- x = polygon[(j + 1) % polygon.length].x * ratio;
- y = polygon[(j + 1) % polygon.length].y * ratio;
- ctx.lineTo(x, y);
- }
- ctx.stroke();
- }
- }
-
- this.overviewImage.mousePos = {
- x : 0,
- y : 0
- };
-
- // this listener should be called when mouse moves over image, it purpose is
- // to change coursor to pointer when mouse enters clickable polygon and back
- // to normal when mouse leaves such region
- var onmousemove = function getMouseOverPosition(e) {
- var position = getPosition(e.currentTarget);
- position.x = e.clientX - position.x;
- position.y = e.clientY - position.y;
-
- var imgWidth = self.overviewImageTag.offsetWidth;
-
- var currentRatio = imgWidth / self.overviewImage.width;
-
- var xNormal = position.x / currentRatio;
- var yNormal = position.y / currentRatio;
- var point = {
- x : xNormal,
- y : yNormal
- };
-
- if (self.overviewImage.mousePos.x != position.x
- || self.overviewImage.mousePos.y != position.y) {
- self.overviewImage.mousePos = position;
- var link = null;
- for (var i = 0; i < self.overviewImage.links.length; i++) {
- if (pointInsidePolygon(point, self.overviewImage.links[i].polygon)) {
- link = self.overviewImage.links[i];
- }
- }
- if (link == null) {
- e.currentTarget.style.cursor = "auto";
- } else {
- e.currentTarget.style.cursor = "pointer";
- }
- }
- };
-
- // onmousemove listener should be assigned to canvas (which is on top of the
- // image) and overviewimage (just in case something went wrong with resizing
- // canvas)
- canvas.onmousemove = onmousemove;
- this.overviewImageTag.onmousemove = onmousemove;
- }
-};
-
-CustomMap.prototype.showModel = function(id, point, zoomLevel) {
- if (point != "undefined") {
- this.setCenter(id, point);
- } else {
- logger.warn("Center point undefined...");
- }
- if (zoomLevel != "undefined") {
- this.setZoom(id, zoomLevel);
- } else {
- logger.warn("Zoom level undefined...");
- }
-};
-
-/**
- * Adds information about aliases visible in the specific layout.
- *
- * @param layoutId
- * identifier of the layout
- *
- * @param jsonAliases
- * list of aliases in json format
- *
- */
-CustomMap.prototype.addAliasesForLayout = function(layoutId, jsonAliases) {
- logger.debug("Adding aliases for layout: " + layoutId);
-
- // init layout data
- if (this.mapModel.getLayoutDataById(layoutId) == null) {
- this.mapModel.initLayoutData(layoutId);
- for (var i = 0; i < this.submaps.length; i++) {
- this.submaps[i].mapModel.initLayoutData(layoutId);
- }
- }
-
- var aliases = JSON.parse(jsonAliases);
- for (var i = 0; i < aliases.length; i++) {
- var alias = aliases[i];
- var model = this.getSubmodelById(alias.modelId);
- if (model != 'undefined' && model != null) {
- model.mapModel.addAliasForLayout(layoutId, alias);
- } else {
- logger.warn("Unknown model: " + alias.modelId);
- }
- }
-
- this.retrieveMissingAliases();
-}
-
-/**
- * Adds information about aliases.
- *
- * @param jsonAliases
- * list of aliases in json format
- *
- */
-CustomMap.prototype.addAliases = function(aliases) {
- for (var i = 0; i < aliases.length; i++) {
- var alias = aliases[i];
- var model = this.getSubmodelById(alias.modelId);
- if (model != 'undefined' && model != null) {
- model.addAlias(alias);
- } else {
- logger.warn("Unknown model: " + alias.modelId);
- }
- }
- this.callListeners("onAddAliases");
-}
-
-/**
- * This function will ask server for aliases that should be visualized but the
- * data is still missing on the client side.
- */
-CustomMap.prototype.retrieveMissingAliases = function() {
- var ids = [];
- var missing = this.mapModel.getMissingAliasIds();
- for (var j = 0; j < missing.length; j++) {
- ids.push([ this.getId(), missing[j] ]);
- }
- for (var i = 0; i < this.submaps.length; i++) {
- missing = this.submaps[i].mapModel.getMissingAliasIds();
- for (var j = 0; j < missing.length; j++) {
- ids.push([ this.submaps[i].getId(), missing[j] ]);
- }
- }
- if (ids.length > 0) {
- // load data from server about missing aliases
- ServerConnector.retreiveLightAliases(ids);
- }
- if (!ServerConnector.isWaitingForData()) {
- // if we already have everything then just refresh data to be visualized
- this.refreshSelectedLayouts();
- //and close "loading" dialog
- GuiConnector.closeLoadingDialog();
- }
-}
-
-/**
- * Adds layout to be visualized.
- *
- * @param identifier
- * identifier of the layout that should be included in visualization
- */
-CustomMap.prototype.addSelectedLayout = function(identifier, name) {
- logger.debug("Selecting layout: " + identifier);
-
- if (this.selectedLayouts[identifier] == true) {
- logger.warn("Layout " + identifier + " already selected");
- } else {
- this.selectedLayouts[identifier] = true;
-
- // open dialog with info that we are loading data (it takes some time for
- // bigger layouts on big maps)
- GuiConnector.openLoadingDialog();
-
- // if we don't have information about this layout then download it
- if (this.mapModel.getLayoutDataById(identifier) == null) {
- // initialize what we can on client side
- this.mapModel.initLayoutData(identifier, name);
- for (var i = 0; i < this.submaps.length; i++) {
- this.submaps[i].mapModel.initLayoutData(identifier, name);
- }
-
- // load data from server about this layout
- ServerConnector.retreiveActiveAliasesForLayout(identifier);
-
- // load data from server about this layout
- ServerConnector.retreiveActiveReactionsForLayout(identifier);
- }
- if (!ServerConnector.isWaitingForData()) {
- // if we already loaded the data then just visualize it
- this.refreshSelectedLayouts();
- //and close "loading" dialog (if opened)
- GuiConnector.closeLoadingDialog();
- }
- // if we have to load data from server then open info window should be
- // opened
- ServerConnector
- .setVisibleLayouts(JSON.stringify(this.getSelectedLayouts()));
-
- }
-};
-
-/**
- * Returns list of layouts that are selected and visualized by javascript.
- *
- * @return array with a list of selected layotus
- *
- */
-CustomMap.prototype.getSelectedLayouts = function() {
- var layouts = [];
-
- // get list of layouts
- for ( var key in this.selectedLayouts) {
- if (this.selectedLayouts.hasOwnProperty(key)
- && this.selectedLayouts[key] == true) {
- layouts.push(key);
- }
- }
- return layouts;
-}
-
-/**
- * Removes layout from visualization.
- *
- * @param identifier
- * identifier of layout to remove
- *
- */
-CustomMap.prototype.removeSelectedLayout = function(identifier) {
- logger.debug("Removing layout: " + identifier);
-
- if (this.selectedLayouts[identifier] != true) {
- logger.warn("Layout " + identifier + " is not selected");
- } else {
- this.selectedLayouts[identifier] = false;
- this.refreshSelectedLayouts();
- ServerConnector
- .setVisibleLayouts(JSON.stringify(this.getSelectedLayouts()));
- }
-};
-
-/**
- * Refresh visualization of selected layouts.
- */
-CustomMap.prototype.refreshSelectedLayouts = function() {
- logger.debug("Refreshing layouts");
- var layouts = this.getSelectedLayouts();
-
- // show layouts that should be visualized (resize or show them)
- for (var i = 0; i < layouts.length; i++) {
- var layoutId = layouts[i];
- if (this.layoutContainsOverlays(layoutId)) {
- // resize element on the map
- this.resizeSelectedLayout(layoutId, i, layouts.length);
- } else {
- this.showSelectedLayout(layoutId, i, layouts.length);
- }
- }
-
- // remove layouts that were
- for ( var key in this.selectedLayoutOverlays) {
- if (!this.selectedLayouts.hasOwnProperty(key)
- || this.selectedLayouts[key] == false) {
- if (this.layoutContainsOverlays(key)) {
- this.hideSelectedLayout(key);
- }
- }
- }
- this.refreshInfoWindows();
-};
-
-/**
- * Hides layout from the map and all submaps
- *
- * @param layoutId
- * identifier of a layout to hide
- */
-CustomMap.prototype.hideSelectedLayout = function(layoutId) {
- this._hideSelectedLayout(layoutId);
- for (var i = 0; i < this.submaps.length; i++) {
- this.submaps[i]._hideSelectedLayout(layoutId);
- }
-}
-
-/**
- * Resize(refresh) layout on the map and all submaps. Resizing should be called
- * when number of layouts to visualize change.
- *
- * @param layoutId
- * identifier of layout to refresh
- * @param index
- * position of the layout in list of layouts that we visualize
- * @param length
- * number of layouts that we currently visualize
- */
-CustomMap.prototype.resizeSelectedLayout = function(layoutId, index, length) {
- logger.debug("Resize layout: " + layoutId);
- this._resizeSelectedLayout(layoutId, index, length);
- for (var i = 0; i < this.submaps.length; i++) {
- this.submaps[i]._resizeSelectedLayout(layoutId, index, length);
- }
-}
-
-/**
- * Show layout on the map and all submaps.
- *
- * @param layoutId
- * identifier of layout to show
- * @param index
- * position of the layout in list of layouts that we visualize
- * @param length
- * number of layouts that we currently visualize
- */
-CustomMap.prototype.showSelectedLayout = function(layoutId, index, length) {
- logger.debug("Resize layout: " + layoutId);
- this._showSelectedLayout(layoutId, index, length);
- for (var i = 0; i < this.submaps.length; i++) {
- this.submaps[i]._showSelectedLayout(layoutId, index, length);
- }
-}
-
-/**
- * Adds information about reactions visible in the specific layout.
- *
- * @param layoutId
- * identifier of the layout
- *
- * @param jsonAliases
- * list of reactions in json format
- *
- */
-CustomMap.prototype.addReactionsForLayout = function(layoutId, jsonReactions) {
- logger.debug("Adding reactions for layout: " + layoutId);
- var reactions = JSON.parse(jsonReactions);
- for (var i = 0; i < reactions.length; i++) {
- var reaction = reactions[i];
- var model = this.getSubmodelById(reaction.modelId);
- if (model != 'undefined' && model != null) {
- model.mapModel.addReactionForLayout(layoutId, reaction);
- } else {
- logger.warn("Unknown model: " + reaction.modelId);
- }
- }
- this.retrieveMissingReactions();
-}
-
-/**
- * Adds information about reactions.
- *
- * @param jsonAliases
- * list of reactions in json format
- *
- */
-CustomMap.prototype.addReactions = function(jsonReactions) {
- var reactions = JSON.parse(jsonReactions);
- for (var i = 0; i < reactions.length; i++) {
- var reaction = reactions[i];
- var model = this.getSubmodelById(reaction.modelId);
- if (model != 'undefined' && model != null) {
- model.addReaction(reaction);
- } else {
- logger.warn("Unknown model: " + reaction.modelId);
- }
- }
- this.callListeners("onAddReactions");
-}
-
-/**
- * This function will ask server for reactions that should be visualized but the
- * data is still missing on the client side.
- */
-CustomMap.prototype.retrieveMissingReactions = function() {
- var ids = [];
- var missing = this.mapModel.getMissingReactionIds();
- for (var j = 0; j < missing.length; j++) {
- ids.push([ this.getId(), missing[j] ]);
- }
- for (var i = 0; i < this.submaps.length; i++) {
- missing = this.submaps[i].mapModel.getMissingReactionIds();
- for (var j = 0; j < missing.length; j++) {
- ids.push([ this.submaps[i].getId(), missing[j] ]);
- }
- }
- if (ids.length > 0) {
- // load data from server about missing reactions
- ServerConnector.retreiveLightReactions(ids);
- }
- if (!ServerConnector.isWaitingForData()) {
- // if we already have everything then just refresh data to be visualized
- this.refreshSelectedLayouts();
- //and close "loading" dialog (if opened)
- GuiConnector.closeLoadingDialog();
- }
-}
-
-/**
- * This method checks if the layout contains any overlays (like AliasOverlay or
- * ReactionOverlay) that is currently visible on the map.
- *
- * @param layoutId
- * identifier of the layout
- * @returns {Boolean}: <code>true</code> if the layout contains overlays to
- * visualize, <code>false</code> otherwise
- */
-CustomMap.prototype.layoutContainsOverlays = function(layoutId) {
-
- // first, check top map
- if (this.selectedLayoutOverlays.hasOwnProperty(layoutId)
- && this.selectedLayoutOverlays[layoutId].length > 0) {
- return true;
- }
-
- // now check all submaps
- for (var i = 0; i < this.submaps.length; i++) {
- if (this.submaps[i].initialized) {
- if (this.submaps[i].selectedLayoutOverlays.hasOwnProperty(layoutId)
- && this.submaps[i].selectedLayoutOverlays[layoutId].length > 0) {
- return true;
- }
- }
- }
- return false;
-}
-
-/**
- * Refresh content of all {@link AliasInfoWindow} in this map and all submaps.
- */
-CustomMap.prototype.refreshInfoWindows = function() {
- this._refreshInfoWindows();
- // now check all submaps
- for (var i = 0; i < this.submaps.length; i++) {
- this.submaps[i]._refreshInfoWindows();
- }
-}
-
-/**
- * Opens {@link AliasInfoWindow} for an {@link Alias} in a given model/submodel.
- *
- * @param aliasId
- * identifier of {@link Alias}
- * @param modelId
- * identifier of {@link AbstractCustomMap}
- */
-CustomMap.prototype.openInfoWindowForAlias = function(aliasId, modelId) {
- logger.debug("Opening info window for alias: " + aliasId + ", model: "
- + modelId);
- var model = this.getSubmodelById(modelId);
- var alias = model.mapModel.getAliasById(aliasId);
-
- // if we have only simple version of the data then ask server for more details
- if (alias == null || alias.completness == 'SIMPLE') {
- logger.debug("Accessing full alias: " + aliasId);
- var ids = [ [ modelId, aliasId ] ];
- ServerConnector.retreiveFullAliases(ids);
- }
- // open AliasInfoWindow in a right model
- model._openInfoWindowForAlias(aliasId);
-};
-
-/**
- * Renders markers, lines, etc. for elements highlighted in OverlayCollection.
- *
- * @param overlayCollection
- * {@link OverlayCollection} to be processed
- * @param fitBounds
- * <code>true</code> if the borders should fit bounds after
- * creating all elements
- */
-CustomMap.prototype.renderOverlayCollection = function(overlayCollection,
- fitBounds) {
- var elements = overlayCollection.elements;
- var missingElements = false;
-
- var boundsArray = [];
- boundsArray[this.getId()] = new google.maps.LatLngBounds();
- for (var i = 0; i < this.submaps.length; i++) {
- boundsArray[this.submaps[i].getId()] = new google.maps.LatLngBounds();
- }
-
- for (var i = 0; i < elements.length; i++) {
- var element = elements[i];
- var model = this.getSubmodelById(element.modelId);
- if (element.type == "ALIAS") {
- if (overlayCollection.aliasMarkers[element.getId()] != null) {
- logger.warn("More than one marker in " + overlayCollection.name
- + " for alias " + element.getId() + ". Skipping duplicates.");
- } else {
- var aliasData = model.mapModel.getAliasById(element.getId());
- if (aliasData == null) {
- model.mapModel.addMissingAliasId(element.getId());
- missingElements = true;
- }
- var marker = new AliasMarker(element.getId(), element.icon, aliasData,
- model);
- overlayCollection.aliasMarkers[element.getId()] = marker;
- if (!missingElements) {
- var bounds = marker.getBounds();
- boundsArray[element.modelId].extend(bounds.getNorthEast());
- boundsArray[element.modelId].extend(bounds.getSouthWest());
- }
- }
- } else if (element.type == "REACTION") {
- var reactionData = model.mapModel.getReactionById(element.getId());
- if (reactionData == null) {
- model.mapModel.addMissingReactionId(element.getId());
- missingElements = true;
- }
- var marker = null;
- var icon = element.getIcon();
-
- if (icon === null || icon === undefined) {
- // this should happen when we visualize search data (there is
- // no marker, but only flat overlay of the reaction lines)
- //
- marker = new ReactionOverlay(null, reactionData, model, false, element
- .getId());
- } else {
- // when we have icon defined (for instance when it comes from
- // comment) then we don't want to have overlayed reaction lines
- // but icon marker
- marker = new ReactionMarker(element.getId(), icon, reactionData, model);
- }
- overlayCollection.reactionMarkers[element.getId()] = marker;
- if (!missingElements) {
- var bounds = marker.getBounds();
- boundsArray[element.modelId].extend(bounds.getNorthEast());
- boundsArray[element.modelId].extend(bounds.getSouthWest());
-
- }
- } else if (element.type == "POINT") {
- var pointData = model.mapModel.getPointDataByPoint(element.getPoint());
- var marker = new PointMarker(pointData, element.icon, model);
- overlayCollection.pointMarkers[pointData.getId()] = marker;
- if (!missingElements) {
- var bounds = marker.getBounds();
- boundsArray[element.modelId].extend(bounds.getNorthEast());
- boundsArray[element.modelId].extend(bounds.getSouthWest());
- }
- } else {
- logger.warn("Unknown type of the element in overlay: " + element.type);
- }
- var infoWindow = this.getInfoWindowForIdentifiedElement(element);
- if (infoWindow != null) {
- this.retrieveOverlayDetailDataForElement(element, infoWindow
- .getOverlayFullViewArray());
- this.updateInfoWindowForIdentifiedElement(element);
- }
- }
-
- if (missingElements) {
- this.retrieveMissingReactions();
- this.retrieveMissingAliases();
- } else {
- if (elements.length > 0 && fitBounds) {
- for ( var mapId in boundsArray) {
- if (boundsArray.hasOwnProperty(mapId)) {
- var map = this.getSubmodelById(mapId).map;
- var bounds = boundsArray[mapId];
- if (map != null && !bounds.isEmpty()) {
- if (typeof map.fitBounds2 !== "undefined") {
- map.fitBounds2(bounds);
- } else {
- map.fitBounds(bounds);
- }
- }
- }
- }
- }
- }
-};
-
-/**
- * Creates and register listeners to be called on events:
- * <ul>
- * <li>onAddAliases</li>
- * <li>onAddReactions</li>
- * </ul>
- */
-CustomMap.prototype.createClientServerListeners = function() {
- this.registerListenerType("onAddAliases");
- this.registerListenerType("onAddReactions");
-
- var refreshLayoutsFun = function(e) {
- var self = e.object;
- if (!ServerConnector.isWaitingForData()) {
- self.refreshSelectedLayouts();
- //and close "loading" dialog (if opened)
- GuiConnector.closeLoadingDialog();
- }
- };
-
- var refreshOverlaysFun = function(e) {
- e.object.refreshMarkers();
- };
-
- this.addListener("onAddAliases", refreshLayoutsFun);
- this.addListener("onAddAliases", refreshOverlaysFun);
-
- this.addListener("onAddReactions", refreshLayoutsFun);
- this.addListener("onAddReactions", refreshOverlaysFun);
-
-};
-
-/**
- * Opens {@link AbstractInfoWindow} for a marker.
- *
- * @param marker
- * {@link AbstractMarker} for which info window should be opened
- */
-CustomMap.prototype.openInfoWindowForMarker = function(marker) {
- var modelId = marker.getCustomMap().getId();
- var markerId = marker.getId();
- var model = this.getSubmodelById(modelId);
- logger.debug("Opening info window for " + marker.constructor.name + ": "
- + markerId + ", model: " + modelId);
- var elementType = marker.getType();
- if (marker instanceof AliasMarker) {
- var alias = model.mapModel.getAliasById(markerId);
-
- // if we have only simple version of the data then ask server for more
- // details
- if (alias == null || alias.completness == 'SIMPLE') {
- logger.debug("Accessing full alias: " + markerId);
- var ids = [ [ modelId, markerId ] ];
- ServerConnector.retreiveFullAliases(ids);
- }
- } else if (marker instanceof PointMarker) {
- // no special treatment for points
- } else if (marker instanceof ReactionMarker) {
- // no special treatment for reactions
- } else {
- logger.error("Unknown marker type: " + marker.constructor.name);
- }
-
- // open AliasInfoWindow in a right model
- model._openInfoWindowForMarker(marker);
-
- var infoWindow = model.returnInfoWindowForMarker(marker);
-
- var element = new IdentifiedElement({
- objectId : markerId,
- modelId : modelId,
- type : elementType
- });
-
- this.retrieveOverlayDetailDataForElement(element, infoWindow
- .getOverlayFullViewArray());
-
-};
-
-/**
- * Sends requestes to download detailed data about element in all
- * {@link OverlayCollection}.
- *
- * @param element
- * element for which we want to have detailed information
- */
-CustomMap.prototype.retrieveOverlayDetailDataForElement = function(element,
- general) {
- if (general === undefined) {
- logger.warn("general param is undefined!");
- general = [];
- }
- for ( var overlayName in this.overlayCollections) {
- if (this.overlayCollections.hasOwnProperty(overlayName)) {
- var overlay = this.overlayCollections[overlayName];
-
- var generalRequest = general[overlayName];
- if (generalRequest === undefined) {
- logger.warn(
- "No information about general overlay request for overlay: ",
- overlayName);
- generalRequest = false;
- }
- generalRequest = generalRequest || !overlay.allowSearchById();
-
- if (overlay.allowGeneralSearch() || overlay.allowSearchById()) {
- if (overlay.isMissingDetailData(element, generalRequest)) {
- ServerConnector.sendOverlayDetailDataRequest(overlayName, element,
- generalRequest);
- }
- }
- }
- }
-};
-
-/**
- * Updates info window identified by element given as a parameter.
- *
- * @param identifiedElement
- * element for which info window should be updated
- */
-CustomMap.prototype.updateInfoWindowForIdentifiedElement = function(
- identifiedElement) {
- var infoWindow = this.getInfoWindowForIdentifiedElement(identifiedElement);
- if (infoWindow == null) {
- return;
- } else {
- infoWindow.update();
- }
-};
-
-/**
- * Returns data from all {@link OverlayCollection} for a given alias.
- *
- * @param alias
- * {@link Alias} for which overlay data will be returned
- * @param general
- * if true then all elements will be returned, if false then only
- * ones availble right now in the overlay
- * @returns data from all {@link OverlayCollection} for a given alias
- */
-CustomMap.prototype.getOverlayDataForAlias = function(alias, general) {
- var identifiedElement = new IdentifiedElement(alias);
- return this.getOverlayDataForIdentifiedElement(identifiedElement, general);
-};
-
-/**
- * Returns data from all {@link OverlayCollection} for a given reaction.
- *
- * @param reaction
- * {@link Reaction} for which overlay data will be returned
- * @param general
- * if true then all elements will be returned, if false then only
- * ones availble right now in the overlay
- * @returns data from all {@link OverlayCollection} for a given alias
- */
-CustomMap.prototype.getOverlayDataForReaction = function(reaction, general) {
- var identifiedElement = new IdentifiedElement(reaction);
- return this.getOverlayDataForIdentifiedElement(identifiedElement, general);
-};
-
-/**
- * Returns data from all {@link OverlayCollection} for a given {@link PointData}
- *
- * @param point
- * {@link PointData} for which overlay data will be returned
- * @returns data from all {@link OverlayCollection} for a given
- * {@link PointData}
- */
-CustomMap.prototype.getOverlayDataForPoint = function(point, general) {
- var identifiedElement = new IdentifiedElement(point);
- return this.getOverlayDataForIdentifiedElement(identifiedElement, general);
-};
-
-/**
- * Returns data from all {@link OverlayCollection} for element identified by the
- * parameter
- *
- * @param identifiedElement
- * {@link IdentifiedElement} for which overlay data will be returned
- * @returns data from all {@link OverlayCollection} for a given
- * {@link IdentifiedElement}
- */
-CustomMap.prototype.getOverlayDataForIdentifiedElement = function(
- identifiedElement, general) {
- if (general === undefined) {
- logger.warn("general parameter must be defined");
- general = [];
- }
- var result = [];
- for ( var overlayName in this.overlayCollections) {
- if (this.overlayCollections.hasOwnProperty(overlayName)) {
- var overlay = this.overlayCollections[overlayName];
- if (overlay.allowGeneralSearch() || overlay.allowSearchById()) {
- var generalFlag = general[overlay.getName()];
- if (generalFlag === undefined) {
- logger.warn("General flag for overlay: " + overlay.getName()
- + " is not defined, assuming false");
- generalFlag = false;
- }
- result.push({
- overlay : overlay,
- data : overlay.getDetailDataByIdentifiedElement(identifiedElement,
- !overlay.allowSearchById() || generalFlag)
- });
- }
- }
- }
- return result;
-};
-
-/**
- * Returns {@link AbstractInfoWindow} for element identified by the parameter.
- *
- * @param identifiedElement
- * {@link IdentifiedElement} that determines for which element we
- * want {@link AbstractInfoWindow}
- * @returns {@link AbstractInfoWindow} for element identified by the parameter
- */
-CustomMap.prototype.getInfoWindowForIdentifiedElement = function(
- identifiedElement) {
- var model = this.getSubmodelById(identifiedElement.modelId);
- var infoWindow = null;
- if (identifiedElement.type == "ALIAS") {
- infoWindow = model.getAliasInfoWindowById(identifiedElement.getId());
- } else if (identifiedElement.type == "POINT") {
- infoWindow = model.getPointInfoWindowById(identifiedElement.getId());
- } else if (identifiedElement.type == "REACTION") {
- infoWindow = model.getReactionInfoWindowById(identifiedElement.getId());
- } else {
- logger.error("Unknown type of IdentifiedElement: ", identifiedElement);
- }
- return infoWindow;
-};
-
-CustomMap.prototype.getActiveSubmapId = function() {
- return this._activeSubmapId;
-};
-
-CustomMap.prototype.setActiveSubmapId = function(submapId) {
- this._activeSubmapId = submapId;
-};
-
-CustomMap.prototype.updateAliasesForLayout = function(layoutId, jsonAliases) {
- logger.debug("Updating aliases for layout: " + layoutId);
-
- // init layout data
- if (this.mapModel.getLayoutDataById(layoutId) == null) {
- this.mapModel.initLayoutData(layoutId);
- for (var i = 0; i < this.submaps.length; i++) {
- this.submaps[i].mapModel.initLayoutData(layoutId);
- }
- }
-
- var aliases = JSON.parse(jsonAliases);
- for (var i = 0; i < aliases.length; i++) {
- var alias = aliases[i];
- var model = this.getSubmodelById(alias.modelId);
- if (model != 'undefined' && model != null) {
- model.mapModel.updateAliasForLayout(layoutId, alias);
- model.getAliasInfoWindowById(alias.idObject).update();
- } else {
- logger.warn("Unknown model: " + alias.modelId);
- }
- }
-
- this.retrieveMissingAliases();
-};
-
-CustomMap.prototype.getReferenceGenome = function(type, version) {
- var result = null;
- if (this._referenceGenome[type] == null) {
- this._referenceGenome[type] = [];
- }
- if (this._referenceGenome[type][version] == null) {
- ServerConnector.sendReferenceGenomeDetailRequest(type, version);
- this._referenceGenome[type][version] = new ReferenceGenome(null);
- return null;
- } else {
- return this._referenceGenome[type][version];
- }
-};
-
-CustomMap.prototype.updateReferenceGenome = function(type, version, jsonObj) {
- if (this._referenceGenome[type] == null) {
- this._referenceGenome[type] = [];
- }
- this._referenceGenome[type][version] = new ReferenceGenome(jsonObj);
- this.refreshInfoWindows();
-}
+/**
+ * Default constructor.
+ *
+ * @param globalMap
+ * google.maps.Map object representing the map
+ * @param configuration
+ * Configuration object representing our data in the map
+ * @param bigButtons
+ * boolean value determining if the buttons on the map should be big,
+ * and if the map is run on the touch interface
+ * @param hideDiv
+ *
+ */
+function CustomMap(options) {
+ if (!(options instanceof CustomMapOptions)) {
+ options = new CustomMapOptions(options);
+ }
+ AbstractCustomMap.call(this, options);
+
+ // set config parameters
+ this.map = options.getMap();
+
+ if (options.isCustomTouchInterface()) {
+ this._touchInterface = new TouchMap(this);
+ }
+
+ // create function that override primefaces fitBounds with default google
+ // implementation
+ var fitBounds = function(bounds) {
+ var tmp = this.fitBounds;
+ this.fitBounds = google.maps.Map.prototype.fitBounds;
+ this.fitBounds(bounds);
+ this.fitBounds = tmp;
+ };
+ this.map.fitBounds2 = fitBounds;
+
+ this.buttons = [];
+
+ this.createSubmaps();
+
+ this.selectedLayouts = [];
+
+ this.setupLayouts();
+
+ this.createBelt();
+
+ this.customizeGoogleMapView();
+
+ this.createMapChangedCallbacks();
+
+ this.createClientServerListeners();
+
+ this.overlayCollections = [];
+
+ // which submap is active (where user made interaction for the last time)
+ this._activeSubmapId = null;
+
+ this.initialized = true;
+
+ // list of reference genomes
+ this._referenceGenome = [];
+
+ ServerConnector.actualizeSessionData();
+}
+
+CustomMap.prototype = Object.create(AbstractCustomMap.prototype);
+
+CustomMap.prototype.constructor = CustomMap;
+
+CustomMap.prototype.createSubmaps = function() {
+ this.submaps = [];
+ for (var i = 0; i < this.getConfiguration().SUBMODELS.length; i++) {
+ this.submaps.push(new Submap(this,
+ this.getConfiguration().SUBMODELS[i].ID_MODEL));
+ }
+};
+
+CustomMap.prototype.createLogo = function() {
+
+ var logoControlDiv = document.createElement('DIV');
+ var logo = document.createElement('IMG');
+ var url = ServerConnector.getLogoImg();
+ if (!/^(f|ht)tps?:\/\//i.test(url)) {
+ url = GuiConnector.getImgPrefix() + url;
+ }
+ logo.src = url;
+ logo.style.cursor = 'pointer';
+ logo.style.width = "80px";
+ logoControlDiv.appendChild(logo);
+ google.maps.event.addDomListener(logo, 'click', function() {
+ var win = window.open(ServerConnector.getLogoLink(), '_blank');
+ win.focus();
+ });
+ logoControlDiv.index = 0; // used for ordering
+ this.map.controls[google.maps.ControlPosition.LEFT_BOTTOM]
+ .push(logoControlDiv);
+
+ var logoControlDiv = document.createElement('DIV');
+ logoControlDiv.style.padding = '5px';
+
+ var logo = document.createElement('IMG');
+ logo.src = GuiConnector.getImgPrefix()
+ + GuiConnector.getLcsbLogoImg(this.bigButtons);
+ logo.style.cursor = 'pointer';
+ logoControlDiv.appendChild(logo);
+ google.maps.event.addDomListener(logo, 'click', function() {
+ var win = window.open('http://wwwen.uni.lu/lcsb/', '_blank');
+ win.focus();
+ });
+
+ logoControlDiv.index = 1; // used for ordering
+ this.map.controls[google.maps.ControlPosition.RIGHT_BOTTOM]
+ .push(logoControlDiv);
+};
+
+CustomMap.prototype.createBelt = function() {
+ var self = this;
+
+ this.divBelt = document.createElement('DIV');
+ this.divBelt.className = "headerBelt";
+
+ var hideDivButton = document.createElement('DIV');
+ hideDivButton.className = "headerHideDivButton";
+
+ var hideButton = document.createElement('button');
+ hideButton.id = "hide_button";
+ hideButton.className = "headerHideButton";
+ hideButton.innerHTML = "<i class='fa fa-chevron-left'></i>";
+ // when there is no div to hide we should allow hiding
+ if (self.getHideDiv() !== undefined) {
+ hideButton.onclick = (function() {
+ var button = hideButton;
+ var div = self.getHideDiv();
+
+ var left = $(PrimeFaces.escapeClientId(self.map.getDiv().id)).offset().left;
+ return function() {
+ if (button.innerHTML.indexOf('fa-chevron-left') > 0) {
+ button.innerHTML = "<i class='fa fa-chevron-right'></i>";
+ div.style.display = 'none';
+ self.map.getDiv().style.left = "0px";
+ } else {
+ div.style.display = 'block';
+ button.innerHTML = "<i class='fa fa-chevron-left'></i>";
+ self.map.getDiv().style.left = left + "px";
+ }
+ google.maps.event.trigger(self.map, 'resize');
+ return false;
+ };
+ })();
+ } else {
+ hideButton.disabled = true;
+ logger.warn("Left panel hiding disabled");
+ }
+ hideDivButton.appendChild(hideButton);
+ hideDivButton.index = 1; // used for ordering
+ this.divBelt.appendChild(hideDivButton);
+
+ var controlText = document.createElement('div');
+ controlText.className = "headerTextBold";
+ controlText.innerHTML = this.getConfiguration().MAP_NAME;
+ this.divBelt.appendChild(controlText);
+
+ this.map.controls[google.maps.ControlPosition.TOP_LEFT].push(this.divBelt);
+};
+
+CustomMap.prototype.setLegendVisible = function(vis) {
+ if (vis) {
+ document.getElementById('legend').style.display = 'block';
+ } else {
+ document.getElementById('legend').style.display = 'none';
+ }
+};
+
+CustomMap.prototype.clearOverlays = function() {
+ for ( var overlayName in this.overlayCollections) {
+ if (this.overlayCollections.hasOwnProperty(overlayName)) {
+ var collection = this.overlayCollections[overlayName];
+ this.clearOverlayCollection(collection);
+ }
+ }
+};
+
+CustomMap.prototype.refreshOverlays = function() {
+ for ( var overlayName in this.overlayCollections) {
+ if (this.overlayCollections.hasOwnProperty(overlayName)) {
+ var collection = this.overlayCollections[overlayName];
+ collection.refresh();
+ }
+ }
+};
+
+/**
+ * Removes all markers from {@link OverlayCollection}.
+ *
+ * @param collection
+ * {@link OverlayCollection} from which all markers should be removed
+ */
+CustomMap.prototype.clearOverlayCollection = function(collection) {
+ logger.debug("Clear collection: " + collection.name);
+ for ( var key in collection.aliasMarkers) {
+ if (collection.aliasMarkers.hasOwnProperty(key)
+ && collection.aliasMarkers[key] != null) {
+ collection.aliasMarkers[key].setMap(null);
+ }
+ }
+
+ for ( var key in collection.pointMarkers) {
+ if (collection.pointMarkers.hasOwnProperty(key)
+ && collection.pointMarkers[key] != null) {
+
+ collection.pointMarkers[key].setMap(null);
+ }
+ }
+
+ for ( var key in collection.reactionMarkers) {
+ if (collection.reactionMarkers.hasOwnProperty(key)
+ && collection.reactionMarkers[key] != null) {
+ collection.reactionMarkers[key].setMap(null);
+ }
+ }
+
+ collection.aliasMarkers = [];
+ collection.pointMarkers = [];
+ collection.reactionMarkers = [];
+};
+
+/**
+ * Updates data about visualized markers in {@link OverlayCollection}.
+ *
+ * @param overlayCollection
+ * {@link OverlayCollection} with new data to visualize
+ * @param fitBounds
+ * <code>true</code> id the map should fit bounds to the new
+ * elements after update, <code>false</code> otherwise
+ */
+CustomMap.prototype.updateOverlayCollection = function(overlayCollection,
+ fitBounds) {
+ this.clearOverlayCollection(overlayCollection);
+ this.renderOverlayCollection(overlayCollection, fitBounds);
+};
+
+/**
+ * This method open layout by a given layout identifier (string starting with
+ * 'cv' prefix) in a map and all submaps.
+ *
+ * @param identifier
+ * identifier of the layout to present
+ */
+CustomMap.prototype.openLayout = function(identifier) {
+ logger.debug("Opening layout: " + identifier);
+
+ this.map.setMapTypeId(identifier);
+
+ var index = null;
+ for (var i = 0; i < this.getConfiguration().MAPS.length; i++) {
+ if ('cv' + this.getConfiguration().MAPS[i].idObject == identifier) {
+ index = i;
+ }
+ }
+ if (index == null) {
+ logger.warn("Invalid layout identifier: " + identifier);
+ }
+ for (var i = 0; i < this.submaps.length; i++) {
+ this.submaps[i].openLayout('cv'
+ + this.submaps[i].getConfiguration().MAPS[index].idObject);
+ }
+};
+
+/**
+ * This method open layout by a given database identifier.
+ *
+ * @param identifier
+ * identifier of the layout to present
+ */
+CustomMap.prototype.openLayoutById = function(identifier) {
+ logger.debug("Opening layout: " + identifier);
+ var index = null;
+ for (var i = 0; i < configuration.MAPS.length; i++) {
+ if (configuration.MAPS[i].idObject == identifier) {
+ index = 'cv' + identifier;
+ }
+ }
+
+ // if layout doesn't exist print error
+ if (index == null) {
+ alert("You have no privileges for selected layout");
+ } else {
+ this.openLayout(index);
+ }
+};
+
+CustomMap.prototype.createMapMenu = function(layoutButtons) {
+ var selfMap = this;
+
+ var buttons = [];
+
+ // create a button for overview images when the image is available
+ if (this.getConfiguration().TOP_OVERVIEW_IMAGE != "undefined"
+ && this.getConfiguration().TOP_OVERVIEW_IMAGE != null) {
+ var submenuButtonDiv = document.createElement('button');
+ buttons.push(submenuButtonDiv);
+ submenuButtonDiv.id = "overview_button";
+ submenuButtonDiv.innerHTML = "<i class='fa fa-sitemap' style='font-size:18px; font-weight:400; padding-right:10px;'></i> SHOW OVERVIEW";
+ submenuButtonDiv.className = "overview_button";
+ submenuButtonDiv.onclick = (function() {
+ return function() {
+ selfMap.showOverview();
+ return false;
+ };
+ })();
+ this.divBelt.appendChild(submenuButtonDiv);
+ }
+
+ var rightHeaderMenu = document.createElement('div');
+ rightHeaderMenu.className = "rightHeaderMenu";
+ var submenuDiv = document.createElement('div');
+ submenuDiv.className = "div4checkboxes";
+ var submenuButtonDiv = document.createElement('input');
+ submenuButtonDiv.type = "checkbox";
+ submenuButtonDiv.name = "Comments";
+ submenuButtonDiv.id = "comment_checkbox";
+ submenuButtonDiv.onclick = (function() {
+ var selfButton = submenuButtonDiv;
+ return function() {
+ selfMap.showComments = selfButton.checked;
+ ServerConnector.setShowComments(selfButton.checked);
+ if (selfButton.checked) {
+ document.getElementById('refresh_comments_button').style.display = 'inline';
+ } else {
+ document.getElementById('refresh_comments_button').style.display = 'none';
+ }
+ selfMap.refreshComments();
+
+ };
+ })();
+ var element = document.createElement('label');
+ element.innerHTML = "COMMENTS";
+ element.setAttribute("for", "comment_checkbox");
+ submenuDiv.appendChild(submenuButtonDiv);
+ submenuDiv.appendChild(element);
+
+ var submenuButtonDiv = document.createElement('input');
+ submenuButtonDiv.type = "checkbox";
+ submenuButtonDiv.name = "Legend";
+ submenuButtonDiv.id = "lengend_checkbox";
+ submenuButtonDiv.onclick = (function() {
+ var selfButton = submenuButtonDiv;
+ return function() {
+ if (selfButton.checked) {
+ GuiConnector.showLegend();
+ } else {
+ GuiConnector.hideLegend();
+ }
+ };
+ })();
+ element = document.createElement('label');
+ element.innerHTML = "LEGEND";
+ element.setAttribute("for", "lengend_checkbox");
+ submenuDiv.appendChild(submenuButtonDiv);
+ submenuDiv.appendChild(element);
+
+ submenuButtonDiv = document.createElement('button');
+ submenuButtonDiv.id = "refresh_comments_button";
+ submenuButtonDiv.innerHTML = "<i class='fa fa-refresh' style='font-size:21px; font-weight:400;'></i>";
+ submenuButtonDiv.className = "overview_button";
+ submenuButtonDiv.style.display = 'none';
+ submenuButtonDiv.onclick = (function() {
+ return function() {
+ selfMap.refreshComments();
+ return false;
+ };
+ })();
+ submenuDiv.appendChild(submenuButtonDiv);
+ rightHeaderMenu.appendChild(submenuDiv);
+
+ var submenuButtonDiv = document.createElement('button');
+ buttons.push(submenuButtonDiv);
+ submenuButtonDiv.id = "clear_button";
+ submenuButtonDiv.className = "overview_button";
+ submenuButtonDiv.innerHTML = "<i class='fa fa-times' style='font-size:18px; font-weight:300; padding-right:10px;'></i> CLEAR";
+ submenuButtonDiv.title = "Clear all queries";
+ submenuButtonDiv.style.display = 'inline';
+ submenuButtonDiv.onclick = (function() {
+ return function() {
+ selfMap.clearData();
+ return false;
+ };
+ })();
+ rightHeaderMenu.appendChild(submenuButtonDiv);
+
+ this.divBelt.appendChild(rightHeaderMenu);
+};
+
+CustomMap.prototype.registerSource = function(overlayCollection) {
+ this.overlayCollections[overlayCollection.name] = overlayCollection;
+ overlayCollection.aliasMarkers = [];
+ overlayCollection.pointMarkers = [];
+ overlayCollection.reactionMarkers = [];
+};
+
+CustomMap.prototype.refreshComments = function() {
+ for ( var overlayName in this.overlayCollections) {
+ if (this.overlayCollections.hasOwnProperty(overlayName)
+ && overlayName == "comment") {
+ var collection = this.overlayCollections[overlayName];
+ collection.refresh();
+ return;
+ }
+ }
+ throw "comment OverlayCollection not found";
+};
+
+CustomMap.prototype.turnOnOffDrawing = function() {
+ var model = this.getSubmodelById(this.getActiveSubmapId());
+ if (model != null) {
+ model._turnOnOffDrawing();
+ } else {
+ throw "Cannot find submodel with id: " + this.getActiveSubmapId();
+ }
+};
+
+CustomMap.prototype.clearData = function() {
+ this.clearOverlays();
+ for ( var overlayName in this.overlayCollections) {
+ if (this.overlayCollections.hasOwnProperty(overlayName)) {
+ ServerConnector.sendClearRequest(overlayName);
+ }
+ }
+};
+
+CustomMap.prototype.refreshMarkers = function() {
+ logger.debug("Refresh Markers: ");
+ for ( var overlayName in this.overlayCollections) {
+ if (this.overlayCollections.hasOwnProperty(overlayName)) {
+ var collection = this.overlayCollections[overlayName];
+ this.refreshOverlayMarkers(collection);
+ }
+ }
+};
+
+CustomMap.prototype.refreshOverlayMarkers = function(overlay) {
+ var self = this;
+ logger.debug("Refresh overlay: " + overlay.name);
+ var boundsArray = [];
+ boundsArray[this.getId()] = new google.maps.LatLngBounds();
+ for (var i = 0; i < this.submaps.length; i++) {
+ boundsArray[this.submaps[i].getId()] = new google.maps.LatLngBounds();
+ }
+
+ var updated = false;
+ var stillMissing = false;
+ for ( var key in overlay.aliasMarkers) {
+ if (overlay.aliasMarkers.hasOwnProperty(key)
+ && overlay.aliasMarkers[key] != null) {
+ var alias = overlay.aliasMarkers[key];
+ if (alias.getAliasData() == null) {
+ var aliasData = alias.getCustomMap().mapModel.getAliasById(alias
+ .getId());
+ if (aliasData != null) {
+ alias.setAliasData(aliasData);
+ alias.init();
+ alias.show();
+ updated = true;
+ var bounds = alias.getBounds();
+ boundsArray[alias.getCustomMap().getId()].extend(bounds
+ .getNorthEast());
+ } else {
+ stillMissing = true;
+ logger.debug("Cannot show alias marker. Data is still not loaded...");
+ }
+ } else {
+ var bounds = alias.getBounds();
+ if (!this.isMarkerOptimization()) {
+ alias.hide();
+ alias.show();
+ }
+ boundsArray[alias.getCustomMap().getId()].extend(bounds.getNorthEast());
+ boundsArray[alias.getCustomMap().getId()].extend(bounds.getSouthWest());
+ }
+ }
+ }
+
+ for ( var key in overlay.pointMarkers) {
+ if (overlay.pointMarkers.hasOwnProperty(key)
+ && overlay.pointMarkers[key] != null) {
+ var alias = overlay.pointMarkers[key];
+ // we don't need to update this markers because thet data about
+ // visualization is
+ // already there
+ // alias.update();
+ var bounds = alias.getBounds();
+ if (!this.isMarkerOptimization()) {
+ alias.hide();
+ alias.show();
+ }
+ boundsArray[alias.getCustomMap().getId()].extend(bounds.getNorthEast());
+ }
+ }
+
+ for ( var key in overlay.reactionMarkers) {
+ if (overlay.reactionMarkers.hasOwnProperty(key)
+ && overlay.reactionMarkers[key] != null) {
+ var reactionOverlay = overlay.reactionMarkers[key];
+ if (reactionOverlay.getReactionData() == null) {
+ var reactionData = reactionOverlay.getCustomMap().mapModel
+ .getReactionById(reactionOverlay.getId());
+ if (reactionData != null) {
+ reactionOverlay.setReactionData(reactionData);
+ reactionOverlay.init();
+ reactionOverlay.show();
+ updated = true;
+ var bounds = reactionOverlay.getBounds();
+ boundsArray[reactionOverlay.getCustomMap().getId()].extend(bounds
+ .getNorthEast());
+ boundsArray[reactionOverlay.getCustomMap().getId()].extend(bounds
+ .getSouthWest());
+ } else {
+ stillMissing = true;
+ logger
+ .debug("Cannot show reaction marker. Data is still not loaded...");
+ }
+ } else {
+ var bounds = alias.getBounds();
+ if (!this.isMarkerOptimization()) {
+ alias.hide();
+ alias.show();
+ }
+ boundsArray[alias.getCustomMap().getId()].extend(bounds.getNorthEast());
+ boundsArray[alias.getCustomMap().getId()].extend(bounds.getSouthWest());
+ }
+
+ }
+ }
+
+ if (!stillMissing && updated && overlay.fitBounds) {
+ for ( var mapId in boundsArray) {
+ if (boundsArray.hasOwnProperty(mapId)) {
+ var map = this.getSubmodelById(mapId).map;
+ var bounds = boundsArray[mapId];
+ if (map != null && !bounds.isEmpty()) {
+ if (typeof map.fitBounds2 !== "undefined") {
+ map.fitBounds2(bounds);
+ } else {
+ map.fitBounds(bounds);
+ }
+ }
+ }
+ }
+ }
+};
+
+CustomMap.prototype.openSubmodel = function(id, htmlTag, jsVar) {
+ if (jsVar.submapControler == null) {
+ var submap = null;
+ for (var i = 0; i < this.submaps.length; i++) {
+ if (this.submaps[i].getId() == id) {
+ submap = this.submaps[i];
+ }
+ }
+ if (submap == null) {
+ logger.error("Unknown submap for id: " + id);
+ } else {
+ submap.init(htmlTag, jsVar);
+ //we have to perform it on top map, because on submaps id is different
+ this.openLayout(this.map.getMapTypeId());
+
+ this.refreshOverlays();
+
+ // now we have to visualize layouts
+ var layouts = [];
+
+ // get list of layouts
+ for ( var key in this.selectedLayouts) {
+ if (this.selectedLayouts.hasOwnProperty(key)
+ && this.selectedLayouts[key] == true) {
+ layouts.push(key);
+ }
+ }
+
+ // show layouts that should be visualized (resize or show them)
+ for (var i = 0; i < layouts.length; i++) {
+ var layoutId = layouts[i];
+ submap._showSelectedLayout(layoutId, i, layouts.length);
+ }
+ }
+ }
+ jsVar.show();
+
+};
+
+CustomMap.prototype.customizeGoogleMapView = function() {
+ var mapOptions = this.creatMapOptions();
+ this.map.setOptions(mapOptions);
+
+ this.createMapMenu(false);
+
+ this.registerMapClickEvents();
+
+ this.createLogo();
+ // this.createMapVersion();
+ google.maps.event.trigger(this.map, 'resize');
+ google.maps.event.trigger(this.map, 'maptypeid_changed');
+ google.maps.event.trigger(this.map, 'projection_changed');
+
+ // center map and zoom in to fit into browser window
+ if (this.getConfiguration().fitMapBounds) {
+ var bounds = new google.maps.LatLngBounds();
+ var point = new google.maps.LatLng(
+ this.getConfiguration().topLeftLatLng.lat,
+ this.getConfiguration().topLeftLatLng.lng);
+ bounds.extend(point);
+
+ point = new google.maps.LatLng(
+ this.getConfiguration().bottomRightLatLng.lat,
+ this.getConfiguration().bottomRightLatLng.lng);
+ bounds.extend(point);
+
+ if (typeof this.map.fitBounds2 !== "undefined") {
+ this.map.fitBounds2(bounds);
+ } else {
+ this.map.fitBounds(bounds);
+ }
+ }
+};
+
+CustomMap.prototype.setCenter = function(mapIdentifier, coordinates) {
+ if (this.getConfiguration().ID_MODEL == mapIdentifier) {
+ this.map.setCenter(coordinates);
+ } else {
+ GuiConnector.openDialog(mapIdentifier);
+ for (var i = 0; i < this.submaps.length; i++) {
+ if (this.submaps[i].getId() == mapIdentifier) {
+ if (coordinates instanceof google.maps.Point) {
+ coordinates = this.submaps[i].fromPointToLatLng(coordinates);
+ }
+ this.submaps[i].map.setCenter(coordinates);
+ }
+ }
+ }
+};
+
+CustomMap.prototype.setZoom = function(mapIdentifier, zoom) {
+ if (this.getConfiguration().ID_MODEL == mapIdentifier) {
+ this.map.setZoom(zoom);
+ } else {
+ GuiConnector.openDialog(mapIdentifier);
+ for (var i = 0; i < this.submaps.length; i++) {
+ if (this.submaps[i].getId() == mapIdentifier) {
+ this.submaps[i].map.setZoom(zoom);
+ }
+ }
+ }
+};
+
+/**
+ * Creates listeners for google.maps.Map object that will actualize the data in
+ * user session.
+ */
+CustomMap.prototype.createMapChangedCallbacks = function() {
+ var customMapSelf = this;
+ // listener for changing zoom level
+ google.maps.event.addListener(this.map, 'zoom_changed', function() {
+ ServerConnector.setZoomLevel(customMapSelf.map.getZoom());
+ ServerConnector.actualizeSessionData();
+ });
+
+ // if we have zoom level data stored in session then restore it
+ var level = ServerConnector.getZoomLevel();
+ if (parseInt(level) > 0) {
+ level = parseInt(level);
+ this.map.setZoom(level);
+ } else {
+ ServerConnector.setZoomLevel(customMapSelf.map.getZoom());
+ }
+
+ // listener for changing location of the map (moving left/reght/top/bottom
+ google.maps.event.addListener(this.map, 'center_changed', function() {
+ var coord = customMapSelf.map.getCenter();
+ var point = customMapSelf.fromLatLngToPoint(coord);
+ ServerConnector.setCenterCoordinateX(point.x);
+ ServerConnector.setCenterCoordinateY(point.y);
+ ServerConnector.actualizeSessionData();
+ });
+
+ // if we have coordinate data stored in session then restore it
+ var x = ServerConnector.getCenterCoordinateX();
+ var y = ServerConnector.getCenterCoordinateY();
+ if (!isNaN(x) && !isNaN(y)) {
+ var point = new google.maps.Point(x, y);
+ var coord = customMapSelf.fromPointToLatLng(point);
+ customMapSelf.map.setCenter(coord);
+ }
+
+ // listener for changing type of layout
+ google.maps.event.addListener(this.map, 'maptypeid_changed', function() {
+ ServerConnector.setSelectedLayout(customMapSelf.map.getMapTypeId());
+ ServerConnector.actualizeParams();
+ });
+
+ // if we have type of layout stored in the session then restore it
+ var mapType = ServerConnector.getSelectedLayout();
+ if (mapType != "" && mapType != null) {
+ this.openLayout(mapType);
+ }
+};
+
+/**
+ * Returns submodel (or this model) by identfier of the model.
+ *
+ * @param identifier
+ * identifier of the submodel
+ * @returns submodel (or this model) with given identfier of the model
+ */
+CustomMap.prototype.getSubmodelById = function(identifier) {
+ if (this.getId() == identifier) {
+ return this;
+ }
+ for (var i = 0; i < this.submaps.length; i++) {
+ if (this.submaps[i].getId() == identifier) {
+ return this.submaps[i];
+ }
+ }
+ return null;
+};
+
+CustomMap.prototype.removeSelection = function() {
+ var model = this.getSubmodelById(this.getActiveSubmapId());
+ if (model != null) {
+ model._removeSelection();
+ } else {
+ throw "Cannot find submodel with id: " + this.getActiveSubmapId();
+ }
+};
+
+/**
+ * This method will hide google map view and will present single image overview
+ * of the data.
+ */
+CustomMap.prototype.showOverview = function(overviewImageId) {
+ overviewDialog.syncWindowResize();
+ if (this.getOverviewDiv() == "undefined" || this.getOverviewDiv() == null) {
+ logger.warn("Cannot show overview, because overview div is undefined");
+ } else {
+ logger.debug("Show overview");
+ overviewDialog.show();
+
+ // resize dialog
+ var htmlTag = GuiConnector.getOverviewHtmlTag();
+
+ var width = Math.floor(window.innerWidth * 2 / 3);
+ var height = Math.floor(window.innerHeight * 2 / 3);
+
+ htmlTag.style.height = (height + 50) + "px";
+ htmlTag.style.width = (width + 20) + "px";
+
+ var self = this;
+
+ // remove all child nodes from overview div
+ while (this.getOverviewDiv().hasChildNodes()) {
+ this.getOverviewDiv().removeChild(this.getOverviewDiv().lastChild);
+ }
+
+ if (overviewImageId == "undefined" || overviewImageId == null) {
+ this.overviewImage = this.getConfiguration().TOP_OVERVIEW_IMAGE;
+ } else {
+ this.overviewImage = null;
+ for (var i = 0; i < this.getConfiguration().OVERVIEW_IMAGES.length; i++) {
+ if (this.getConfiguration().OVERVIEW_IMAGES[i].idObject == overviewImageId) {
+ this.overviewImage = this.getConfiguration().OVERVIEW_IMAGES[i];
+ }
+ }
+
+ if (this.overviewImage == null) {
+ logger.warn("Unknown overview image with id = " + overviewImageId);
+ this.overviewImage = this.getConfiguration().TOP_OVERVIEW_IMAGE;
+ }
+ }
+
+ // add image to overview div
+ this.overviewImageTag = document.createElement("IMG");
+ this.overviewImageTag.src = "../map_images/" + this.overviewImage.filename;
+ this.getOverviewDiv().appendChild(this.overviewImageTag);
+
+ var ratio = 1.0;
+
+ // check how image should be resized to fit dialog and resize it manually!!!
+ if (width / this.overviewImage.width > height / this.overviewImage.height) {
+ this.overviewImageTag.style.height = height + "px";
+ ratio = height / this.overviewImage.height;
+ width = this.overviewImage.width * ratio;
+
+ htmlTag.style.width = (width + 20) + "px";
+ } else {
+ this.overviewImageTag.style.width = width + "px";
+ ratio = width / this.overviewImage.width;
+ height = this.overviewImage.height * ratio;
+
+ htmlTag.style.height = (height + 50) + "px";
+ }
+
+ // center dialog
+ overviewDialog.jq.css("top", Math.max(0,
+ (($(window).height() - overviewDialog.jq.outerHeight()) / 2)
+ + $(window).scrollTop())
+ + "px");
+ overviewDialog.jq.css("left", Math.max(0,
+ (($(window).width() - overviewDialog.jq.outerWidth()) / 2)
+ + $(window).scrollLeft())
+ + "px");
+
+ // on click event (what should happen when we click on the image)
+ var onclickevent = function getClickPosition(e) {
+ var parentPosition = getPosition(e.currentTarget);
+ var xPosition = e.clientX - parentPosition.x;
+ var yPosition = e.clientY - parentPosition.y;
+
+ var imgWidth = self.overviewImageTag.offsetWidth;
+
+ var currentRatio = imgWidth / self.overviewImage.width;
+
+ var xNormal = xPosition / currentRatio;
+ var yNormal = yPosition / currentRatio;
+ var point = {
+ x : xNormal,
+ y : yNormal
+ };
+
+ var link = null;
+ for (var i = 0; i < self.overviewImage.links.length; i++) {
+ if (pointInsidePolygon(point, self.overviewImage.links[i].polygon)) {
+ if (link == null) {
+ link = self.overviewImage.links[i];
+ } else {
+ logger.warn("More than one link found. Skipping");
+ }
+ }
+ }
+ if (link != null) {
+ if (link.type == "OverviewModelLink") {
+ logger.debug("Opening model from overview. ModelId: "
+ + link.modelLinkId);
+ logger.debug("link coordinates [" + link.idObject + "]: "
+ + link.latLng);
+ // TODO min zoom value can be different for every map, it should be
+ // changed in the future
+ self.showModel(link.modelLinkId, link.latLng, link.zoomLevel
+ + self.getConfiguration().MIN_ZOOM);
+ overviewDialog.hide();
+ } else if (link.type == "OverviewImageLink") {
+ logger.debug("Opening image from overview. ImageId: "
+ + link.imageLinkId);
+ self.showOverview(link.imageLinkId);
+ } else if (link.type == "OverviewSearchLink") {
+ logger.debug("Sending search query. Query: " + link.query);
+ searchPanel.search(link.query);
+ overviewDialog.hide();
+ } else {
+ logger.warn("Unknown type of link: " + link.type
+ + ". Don't know what to do... LinkId: " + link.idObject);
+ }
+ }
+ };
+
+ this.overviewImageTag.onclick = onclickevent;
+
+ // resize canvas where on mouse over highligh will appear
+ var canvas = document.getElementById("canvasDebug");
+ canvas.width = width;
+ canvas.height = height;
+ canvas.onclick = onclickevent;
+
+ // in debug mode draw clickable shapes
+ if (DEBUG_ON) {
+ var ctx = canvas.getContext("2d");
+ // clear canvas
+ ctx.clearRect(0, 0, canvas.width, canvas.height);
+ for (var i = 0; i < this.overviewImage.links.length; i++) {
+ ctx.beginPath();
+ var polygon = this.overviewImage.links[i].polygon;
+ for (var j = 0; j < polygon.length; j++) {
+ var x = polygon[j].x * ratio;
+ var y = polygon[j].y * ratio;
+ ctx.moveTo(x, y);
+ x = polygon[(j + 1) % polygon.length].x * ratio;
+ y = polygon[(j + 1) % polygon.length].y * ratio;
+ ctx.lineTo(x, y);
+ }
+ ctx.stroke();
+ }
+ }
+
+ this.overviewImage.mousePos = {
+ x : 0,
+ y : 0
+ };
+
+ // this listener should be called when mouse moves over image, it purpose is
+ // to change coursor to pointer when mouse enters clickable polygon and back
+ // to normal when mouse leaves such region
+ var onmousemove = function getMouseOverPosition(e) {
+ var position = getPosition(e.currentTarget);
+ position.x = e.clientX - position.x;
+ position.y = e.clientY - position.y;
+
+ var imgWidth = self.overviewImageTag.offsetWidth;
+
+ var currentRatio = imgWidth / self.overviewImage.width;
+
+ var xNormal = position.x / currentRatio;
+ var yNormal = position.y / currentRatio;
+ var point = {
+ x : xNormal,
+ y : yNormal
+ };
+
+ if (self.overviewImage.mousePos.x != position.x
+ || self.overviewImage.mousePos.y != position.y) {
+ self.overviewImage.mousePos = position;
+ var link = null;
+ for (var i = 0; i < self.overviewImage.links.length; i++) {
+ if (pointInsidePolygon(point, self.overviewImage.links[i].polygon)) {
+ link = self.overviewImage.links[i];
+ }
+ }
+ if (link == null) {
+ e.currentTarget.style.cursor = "auto";
+ } else {
+ e.currentTarget.style.cursor = "pointer";
+ }
+ }
+ };
+
+ // onmousemove listener should be assigned to canvas (which is on top of the
+ // image) and overviewimage (just in case something went wrong with resizing
+ // canvas)
+ canvas.onmousemove = onmousemove;
+ this.overviewImageTag.onmousemove = onmousemove;
+ }
+};
+
+CustomMap.prototype.showModel = function(id, point, zoomLevel) {
+ if (point != "undefined") {
+ this.setCenter(id, point);
+ } else {
+ logger.warn("Center point undefined...");
+ }
+ if (zoomLevel != "undefined") {
+ this.setZoom(id, zoomLevel);
+ } else {
+ logger.warn("Zoom level undefined...");
+ }
+};
+
+/**
+ * Adds information about aliases visible in the specific layout.
+ *
+ * @param layoutId
+ * identifier of the layout
+ *
+ * @param jsonAliases
+ * list of aliases in json format
+ *
+ */
+CustomMap.prototype.addAliasesForLayout = function(layoutId, jsonAliases) {
+ logger.debug("Adding aliases for layout: " + layoutId);
+
+ // init layout data
+ if (this.mapModel.getLayoutDataById(layoutId) == null) {
+ this.mapModel.initLayoutData(layoutId);
+ for (var i = 0; i < this.submaps.length; i++) {
+ this.submaps[i].mapModel.initLayoutData(layoutId);
+ }
+ }
+
+ var aliases = JSON.parse(jsonAliases);
+ for (var i = 0; i < aliases.length; i++) {
+ var alias = aliases[i];
+ var model = this.getSubmodelById(alias.modelId);
+ if (model != 'undefined' && model != null) {
+ model.mapModel.addAliasForLayout(layoutId, alias);
+ } else {
+ logger.warn("Unknown model: " + alias.modelId);
+ }
+ }
+
+ this.retrieveMissingAliases();
+}
+
+/**
+ * Adds information about aliases.
+ *
+ * @param jsonAliases
+ * list of aliases in json format
+ *
+ */
+CustomMap.prototype.addAliases = function(aliases) {
+ for (var i = 0; i < aliases.length; i++) {
+ var alias = aliases[i];
+ var model = this.getSubmodelById(alias.modelId);
+ if (model != 'undefined' && model != null) {
+ model.addAlias(alias);
+ } else {
+ logger.warn("Unknown model: " + alias.modelId);
+ }
+ }
+ this.callListeners("onAddAliases");
+}
+
+/**
+ * This function will ask server for aliases that should be visualized but the
+ * data is still missing on the client side.
+ */
+CustomMap.prototype.retrieveMissingAliases = function() {
+ var ids = [];
+ var missing = this.mapModel.getMissingAliasIds();
+ for (var j = 0; j < missing.length; j++) {
+ ids.push([ this.getId(), missing[j] ]);
+ }
+ for (var i = 0; i < this.submaps.length; i++) {
+ missing = this.submaps[i].mapModel.getMissingAliasIds();
+ for (var j = 0; j < missing.length; j++) {
+ ids.push([ this.submaps[i].getId(), missing[j] ]);
+ }
+ }
+ if (ids.length > 0) {
+ // load data from server about missing aliases
+ ServerConnector.retreiveLightAliases(ids);
+ }
+ if (!ServerConnector.isWaitingForData()) {
+ // if we already have everything then just refresh data to be visualized
+ this.refreshSelectedLayouts();
+ //and close "loading" dialog
+ GuiConnector.closeLoadingDialog();
+ }
+}
+
+/**
+ * Adds layout to be visualized.
+ *
+ * @param identifier
+ * identifier of the layout that should be included in visualization
+ */
+CustomMap.prototype.addSelectedLayout = function(identifier, name) {
+ logger.debug("Selecting layout: " + identifier);
+
+ if (this.selectedLayouts[identifier] == true) {
+ logger.warn("Layout " + identifier + " already selected");
+ } else {
+ this.selectedLayouts[identifier] = true;
+
+ // open dialog with info that we are loading data (it takes some time for
+ // bigger layouts on big maps)
+ GuiConnector.openLoadingDialog();
+
+ // if we don't have information about this layout then download it
+ if (this.mapModel.getLayoutDataById(identifier) == null) {
+ // initialize what we can on client side
+ this.mapModel.initLayoutData(identifier, name);
+ for (var i = 0; i < this.submaps.length; i++) {
+ this.submaps[i].mapModel.initLayoutData(identifier, name);
+ }
+
+ // load data from server about this layout
+ ServerConnector.retreiveActiveAliasesForLayout(identifier);
+
+ // load data from server about this layout
+ ServerConnector.retreiveActiveReactionsForLayout(identifier);
+ }
+ if (!ServerConnector.isWaitingForData()) {
+ // if we already loaded the data then just visualize it
+ this.refreshSelectedLayouts();
+ //and close "loading" dialog (if opened)
+ GuiConnector.closeLoadingDialog();
+ }
+ // if we have to load data from server then open info window should be
+ // opened
+ ServerConnector
+ .setVisibleLayouts(JSON.stringify(this.getSelectedLayouts()));
+
+ }
+};
+
+/**
+ * Returns list of layouts that are selected and visualized by javascript.
+ *
+ * @return array with a list of selected layotus
+ *
+ */
+CustomMap.prototype.getSelectedLayouts = function() {
+ var layouts = [];
+
+ // get list of layouts
+ for ( var key in this.selectedLayouts) {
+ if (this.selectedLayouts.hasOwnProperty(key)
+ && this.selectedLayouts[key] == true) {
+ layouts.push(key);
+ }
+ }
+ return layouts;
+}
+
+/**
+ * Removes layout from visualization.
+ *
+ * @param identifier
+ * identifier of layout to remove
+ *
+ */
+CustomMap.prototype.removeSelectedLayout = function(identifier) {
+ logger.debug("Removing layout: " + identifier);
+
+ if (this.selectedLayouts[identifier] != true) {
+ logger.warn("Layout " + identifier + " is not selected");
+ } else {
+ this.selectedLayouts[identifier] = false;
+ this.refreshSelectedLayouts();
+ ServerConnector
+ .setVisibleLayouts(JSON.stringify(this.getSelectedLayouts()));
+ }
+};
+
+/**
+ * Refresh visualization of selected layouts.
+ */
+CustomMap.prototype.refreshSelectedLayouts = function() {
+ logger.debug("Refreshing layouts");
+ var layouts = this.getSelectedLayouts();
+
+ // show layouts that should be visualized (resize or show them)
+ for (var i = 0; i < layouts.length; i++) {
+ var layoutId = layouts[i];
+ if (this.layoutContainsOverlays(layoutId)) {
+ // resize element on the map
+ this.resizeSelectedLayout(layoutId, i, layouts.length);
+ } else {
+ this.showSelectedLayout(layoutId, i, layouts.length);
+ }
+ }
+
+ // remove layouts that were
+ for ( var key in this.selectedLayoutOverlays) {
+ if (!this.selectedLayouts.hasOwnProperty(key)
+ || this.selectedLayouts[key] == false) {
+ if (this.layoutContainsOverlays(key)) {
+ this.hideSelectedLayout(key);
+ }
+ }
+ }
+ this.refreshInfoWindows();
+};
+
+/**
+ * Hides layout from the map and all submaps
+ *
+ * @param layoutId
+ * identifier of a layout to hide
+ */
+CustomMap.prototype.hideSelectedLayout = function(layoutId) {
+ this._hideSelectedLayout(layoutId);
+ for (var i = 0; i < this.submaps.length; i++) {
+ this.submaps[i]._hideSelectedLayout(layoutId);
+ }
+}
+
+/**
+ * Resize(refresh) layout on the map and all submaps. Resizing should be called
+ * when number of layouts to visualize change.
+ *
+ * @param layoutId
+ * identifier of layout to refresh
+ * @param index
+ * position of the layout in list of layouts that we visualize
+ * @param length
+ * number of layouts that we currently visualize
+ */
+CustomMap.prototype.resizeSelectedLayout = function(layoutId, index, length) {
+ logger.debug("Resize layout: " + layoutId);
+ this._resizeSelectedLayout(layoutId, index, length);
+ for (var i = 0; i < this.submaps.length; i++) {
+ this.submaps[i]._resizeSelectedLayout(layoutId, index, length);
+ }
+}
+
+/**
+ * Show layout on the map and all submaps.
+ *
+ * @param layoutId
+ * identifier of layout to show
+ * @param index
+ * position of the layout in list of layouts that we visualize
+ * @param length
+ * number of layouts that we currently visualize
+ */
+CustomMap.prototype.showSelectedLayout = function(layoutId, index, length) {
+ logger.debug("Resize layout: " + layoutId);
+ this._showSelectedLayout(layoutId, index, length);
+ for (var i = 0; i < this.submaps.length; i++) {
+ this.submaps[i]._showSelectedLayout(layoutId, index, length);
+ }
+}
+
+/**
+ * Adds information about reactions visible in the specific layout.
+ *
+ * @param layoutId
+ * identifier of the layout
+ *
+ * @param jsonAliases
+ * list of reactions in json format
+ *
+ */
+CustomMap.prototype.addReactionsForLayout = function(layoutId, jsonReactions) {
+ logger.debug("Adding reactions for layout: " + layoutId);
+ var reactions = JSON.parse(jsonReactions);
+ for (var i = 0; i < reactions.length; i++) {
+ var reaction = reactions[i];
+ var model = this.getSubmodelById(reaction.modelId);
+ if (model != 'undefined' && model != null) {
+ model.mapModel.addReactionForLayout(layoutId, reaction);
+ } else {
+ logger.warn("Unknown model: " + reaction.modelId);
+ }
+ }
+ this.retrieveMissingReactions();
+}
+
+/**
+ * Adds information about reactions.
+ *
+ * @param jsonAliases
+ * list of reactions in json format
+ *
+ */
+CustomMap.prototype.addReactions = function(jsonReactions) {
+ var reactions = JSON.parse(jsonReactions);
+ for (var i = 0; i < reactions.length; i++) {
+ var reaction = reactions[i];
+ var model = this.getSubmodelById(reaction.modelId);
+ if (model != 'undefined' && model != null) {
+ model.addReaction(reaction);
+ } else {
+ logger.warn("Unknown model: " + reaction.modelId);
+ }
+ }
+ this.callListeners("onAddReactions");
+}
+
+/**
+ * This function will ask server for reactions that should be visualized but the
+ * data is still missing on the client side.
+ */
+CustomMap.prototype.retrieveMissingReactions = function() {
+ var ids = [];
+ var missing = this.mapModel.getMissingReactionIds();
+ for (var j = 0; j < missing.length; j++) {
+ ids.push([ this.getId(), missing[j] ]);
+ }
+ for (var i = 0; i < this.submaps.length; i++) {
+ missing = this.submaps[i].mapModel.getMissingReactionIds();
+ for (var j = 0; j < missing.length; j++) {
+ ids.push([ this.submaps[i].getId(), missing[j] ]);
+ }
+ }
+ if (ids.length > 0) {
+ // load data from server about missing reactions
+ ServerConnector.retreiveLightReactions(ids);
+ }
+ if (!ServerConnector.isWaitingForData()) {
+ // if we already have everything then just refresh data to be visualized
+ this.refreshSelectedLayouts();
+ //and close "loading" dialog (if opened)
+ GuiConnector.closeLoadingDialog();
+ }
+}
+
+/**
+ * This method checks if the layout contains any overlays (like AliasOverlay or
+ * ReactionOverlay) that is currently visible on the map.
+ *
+ * @param layoutId
+ * identifier of the layout
+ * @returns {Boolean}: <code>true</code> if the layout contains overlays to
+ * visualize, <code>false</code> otherwise
+ */
+CustomMap.prototype.layoutContainsOverlays = function(layoutId) {
+
+ // first, check top map
+ if (this.selectedLayoutOverlays.hasOwnProperty(layoutId)
+ && this.selectedLayoutOverlays[layoutId].length > 0) {
+ return true;
+ }
+
+ // now check all submaps
+ for (var i = 0; i < this.submaps.length; i++) {
+ if (this.submaps[i].initialized) {
+ if (this.submaps[i].selectedLayoutOverlays.hasOwnProperty(layoutId)
+ && this.submaps[i].selectedLayoutOverlays[layoutId].length > 0) {
+ return true;
+ }
+ }
+ }
+ return false;
+}
+
+/**
+ * Refresh content of all {@link AliasInfoWindow} in this map and all submaps.
+ */
+CustomMap.prototype.refreshInfoWindows = function() {
+ this._refreshInfoWindows();
+ // now check all submaps
+ for (var i = 0; i < this.submaps.length; i++) {
+ this.submaps[i]._refreshInfoWindows();
+ }
+}
+
+/**
+ * Opens {@link AliasInfoWindow} for an {@link Alias} in a given model/submodel.
+ *
+ * @param aliasId
+ * identifier of {@link Alias}
+ * @param modelId
+ * identifier of {@link AbstractCustomMap}
+ */
+CustomMap.prototype.openInfoWindowForAlias = function(aliasId, modelId) {
+ logger.debug("Opening info window for alias: " + aliasId + ", model: "
+ + modelId);
+ var model = this.getSubmodelById(modelId);
+ var alias = model.mapModel.getAliasById(aliasId);
+
+ // if we have only simple version of the data then ask server for more details
+ if (alias == null || alias.completness == 'SIMPLE') {
+ logger.debug("Accessing full alias: " + aliasId);
+ var ids = [ [ modelId, aliasId ] ];
+ ServerConnector.retreiveFullAliases(ids);
+ }
+ // open AliasInfoWindow in a right model
+ model._openInfoWindowForAlias(aliasId);
+};
+
+/**
+ * Renders markers, lines, etc. for elements highlighted in OverlayCollection.
+ *
+ * @param overlayCollection
+ * {@link OverlayCollection} to be processed
+ * @param fitBounds
+ * <code>true</code> if the borders should fit bounds after
+ * creating all elements
+ */
+CustomMap.prototype.renderOverlayCollection = function(overlayCollection,
+ fitBounds) {
+ var elements = overlayCollection.elements;
+ var missingElements = false;
+
+ var boundsArray = [];
+ boundsArray[this.getId()] = new google.maps.LatLngBounds();
+ for (var i = 0; i < this.submaps.length; i++) {
+ boundsArray[this.submaps[i].getId()] = new google.maps.LatLngBounds();
+ }
+
+ for (var i = 0; i < elements.length; i++) {
+ var element = elements[i];
+ var model = this.getSubmodelById(element.modelId);
+ if (element.type == "ALIAS") {
+ if (overlayCollection.aliasMarkers[element.getId()] != null) {
+ logger.warn("More than one marker in " + overlayCollection.name
+ + " for alias " + element.getId() + ". Skipping duplicates.");
+ } else {
+ var aliasData = model.mapModel.getAliasById(element.getId());
+ if (aliasData == null) {
+ model.mapModel.addMissingAliasId(element.getId());
+ missingElements = true;
+ }
+ var marker = new AliasMarker(element.getId(), element.icon, aliasData,
+ model);
+ overlayCollection.aliasMarkers[element.getId()] = marker;
+ if (!missingElements) {
+ var bounds = marker.getBounds();
+ boundsArray[element.modelId].extend(bounds.getNorthEast());
+ boundsArray[element.modelId].extend(bounds.getSouthWest());
+ }
+ }
+ } else if (element.type == "REACTION") {
+ var reactionData = model.mapModel.getReactionById(element.getId());
+ if (reactionData == null) {
+ model.mapModel.addMissingReactionId(element.getId());
+ missingElements = true;
+ }
+ var marker = null;
+ var icon = element.getIcon();
+
+ if (icon === null || icon === undefined) {
+ // this should happen when we visualize search data (there is
+ // no marker, but only flat overlay of the reaction lines)
+ //
+ marker = new ReactionOverlay(null, reactionData, model, false, element
+ .getId());
+ } else {
+ // when we have icon defined (for instance when it comes from
+ // comment) then we don't want to have overlayed reaction lines
+ // but icon marker
+ marker = new ReactionMarker(element.getId(), icon, reactionData, model);
+ }
+ overlayCollection.reactionMarkers[element.getId()] = marker;
+ if (!missingElements) {
+ var bounds = marker.getBounds();
+ boundsArray[element.modelId].extend(bounds.getNorthEast());
+ boundsArray[element.modelId].extend(bounds.getSouthWest());
+
+ }
+ } else if (element.type == "POINT") {
+ var pointData = model.mapModel.getPointDataByPoint(element.getPoint());
+ var marker = new PointMarker(pointData, element.icon, model);
+ overlayCollection.pointMarkers[pointData.getId()] = marker;
+ if (!missingElements) {
+ var bounds = marker.getBounds();
+ boundsArray[element.modelId].extend(bounds.getNorthEast());
+ boundsArray[element.modelId].extend(bounds.getSouthWest());
+ }
+ } else {
+ logger.warn("Unknown type of the element in overlay: " + element.type);
+ }
+ var infoWindow = this.getInfoWindowForIdentifiedElement(element);
+ if (infoWindow != null) {
+ this.retrieveOverlayDetailDataForElement(element, infoWindow
+ .getOverlayFullViewArray());
+ this.updateInfoWindowForIdentifiedElement(element);
+ }
+ }
+
+ if (missingElements) {
+ this.retrieveMissingReactions();
+ this.retrieveMissingAliases();
+ } else {
+ if (elements.length > 0 && fitBounds) {
+ for ( var mapId in boundsArray) {
+ if (boundsArray.hasOwnProperty(mapId)) {
+ var map = this.getSubmodelById(mapId).map;
+ var bounds = boundsArray[mapId];
+ if (map != null && !bounds.isEmpty()) {
+ if (typeof map.fitBounds2 !== "undefined") {
+ map.fitBounds2(bounds);
+ } else {
+ map.fitBounds(bounds);
+ }
+ }
+ }
+ }
+ }
+ }
+};
+
+/**
+ * Creates and register listeners to be called on events:
+ * <ul>
+ * <li>onAddAliases</li>
+ * <li>onAddReactions</li>
+ * </ul>
+ */
+CustomMap.prototype.createClientServerListeners = function() {
+ this.registerListenerType("onAddAliases");
+ this.registerListenerType("onAddReactions");
+
+ var refreshLayoutsFun = function(e) {
+ var self = e.object;
+ if (!ServerConnector.isWaitingForData()) {
+ self.refreshSelectedLayouts();
+ //and close "loading" dialog (if opened)
+ GuiConnector.closeLoadingDialog();
+ }
+ };
+
+ var refreshOverlaysFun = function(e) {
+ e.object.refreshMarkers();
+ };
+
+ this.addListener("onAddAliases", refreshLayoutsFun);
+ this.addListener("onAddAliases", refreshOverlaysFun);
+
+ this.addListener("onAddReactions", refreshLayoutsFun);
+ this.addListener("onAddReactions", refreshOverlaysFun);
+
+};
+
+/**
+ * Opens {@link AbstractInfoWindow} for a marker.
+ *
+ * @param marker
+ * {@link AbstractMarker} for which info window should be opened
+ */
+CustomMap.prototype.openInfoWindowForMarker = function(marker) {
+ var modelId = marker.getCustomMap().getId();
+ var markerId = marker.getId();
+ var model = this.getSubmodelById(modelId);
+ logger.debug("Opening info window for " + marker.constructor.name + ": "
+ + markerId + ", model: " + modelId);
+ var elementType = marker.getType();
+ if (marker instanceof AliasMarker) {
+ var alias = model.mapModel.getAliasById(markerId);
+
+ // if we have only simple version of the data then ask server for more
+ // details
+ if (alias == null || alias.completness == 'SIMPLE') {
+ logger.debug("Accessing full alias: " + markerId);
+ var ids = [ [ modelId, markerId ] ];
+ ServerConnector.retreiveFullAliases(ids);
+ }
+ } else if (marker instanceof PointMarker) {
+ // no special treatment for points
+ } else if (marker instanceof ReactionMarker) {
+ // no special treatment for reactions
+ } else {
+ logger.error("Unknown marker type: " + marker.constructor.name);
+ }
+
+ // open AliasInfoWindow in a right model
+ model._openInfoWindowForMarker(marker);
+
+ var infoWindow = model.returnInfoWindowForMarker(marker);
+
+ var element = new IdentifiedElement({
+ objectId : markerId,
+ modelId : modelId,
+ type : elementType
+ });
+
+ this.retrieveOverlayDetailDataForElement(element, infoWindow
+ .getOverlayFullViewArray());
+
+};
+
+/**
+ * Sends requestes to download detailed data about element in all
+ * {@link OverlayCollection}.
+ *
+ * @param element
+ * element for which we want to have detailed information
+ */
+CustomMap.prototype.retrieveOverlayDetailDataForElement = function(element,
+ general) {
+ if (general === undefined) {
+ logger.warn("general param is undefined!");
+ general = [];
+ }
+ for ( var overlayName in this.overlayCollections) {
+ if (this.overlayCollections.hasOwnProperty(overlayName)) {
+ var overlay = this.overlayCollections[overlayName];
+
+ var generalRequest = general[overlayName];
+ if (generalRequest === undefined) {
+ logger.warn(
+ "No information about general overlay request for overlay: ",
+ overlayName);
+ generalRequest = false;
+ }
+ generalRequest = generalRequest || !overlay.allowSearchById();
+
+ if (overlay.allowGeneralSearch() || overlay.allowSearchById()) {
+ if (overlay.isMissingDetailData(element, generalRequest)) {
+ ServerConnector.sendOverlayDetailDataRequest(overlayName, element,
+ generalRequest);
+ }
+ }
+ }
+ }
+};
+
+/**
+ * Updates info window identified by element given as a parameter.
+ *
+ * @param identifiedElement
+ * element for which info window should be updated
+ */
+CustomMap.prototype.updateInfoWindowForIdentifiedElement = function(
+ identifiedElement) {
+ var infoWindow = this.getInfoWindowForIdentifiedElement(identifiedElement);
+ if (infoWindow == null) {
+ return;
+ } else {
+ infoWindow.update();
+ }
+};
+
+/**
+ * Returns data from all {@link OverlayCollection} for a given alias.
+ *
+ * @param alias
+ * {@link Alias} for which overlay data will be returned
+ * @param general
+ * if true then all elements will be returned, if false then only
+ * ones availble right now in the overlay
+ * @returns data from all {@link OverlayCollection} for a given alias
+ */
+CustomMap.prototype.getOverlayDataForAlias = function(alias, general) {
+ var identifiedElement = new IdentifiedElement(alias);
+ return this.getOverlayDataForIdentifiedElement(identifiedElement, general);
+};
+
+/**
+ * Returns data from all {@link OverlayCollection} for a given reaction.
+ *
+ * @param reaction
+ * {@link Reaction} for which overlay data will be returned
+ * @param general
+ * if true then all elements will be returned, if false then only
+ * ones availble right now in the overlay
+ * @returns data from all {@link OverlayCollection} for a given alias
+ */
+CustomMap.prototype.getOverlayDataForReaction = function(reaction, general) {
+ var identifiedElement = new IdentifiedElement(reaction);
+ return this.getOverlayDataForIdentifiedElement(identifiedElement, general);
+};
+
+/**
+ * Returns data from all {@link OverlayCollection} for a given {@link PointData}
+ *
+ * @param point
+ * {@link PointData} for which overlay data will be returned
+ * @returns data from all {@link OverlayCollection} for a given
+ * {@link PointData}
+ */
+CustomMap.prototype.getOverlayDataForPoint = function(point, general) {
+ var identifiedElement = new IdentifiedElement(point);
+ return this.getOverlayDataForIdentifiedElement(identifiedElement, general);
+};
+
+/**
+ * Returns data from all {@link OverlayCollection} for element identified by the
+ * parameter
+ *
+ * @param identifiedElement
+ * {@link IdentifiedElement} for which overlay data will be returned
+ * @returns data from all {@link OverlayCollection} for a given
+ * {@link IdentifiedElement}
+ */
+CustomMap.prototype.getOverlayDataForIdentifiedElement = function(
+ identifiedElement, general) {
+ if (general === undefined) {
+ logger.warn("general parameter must be defined");
+ general = [];
+ }
+ var result = [];
+ for ( var overlayName in this.overlayCollections) {
+ if (this.overlayCollections.hasOwnProperty(overlayName)) {
+ var overlay = this.overlayCollections[overlayName];
+ if (overlay.allowGeneralSearch() || overlay.allowSearchById()) {
+ var generalFlag = general[overlay.getName()];
+ if (generalFlag === undefined) {
+ logger.warn("General flag for overlay: " + overlay.getName()
+ + " is not defined, assuming false");
+ generalFlag = false;
+ }
+ result.push({
+ overlay : overlay,
+ data : overlay.getDetailDataByIdentifiedElement(identifiedElement,
+ !overlay.allowSearchById() || generalFlag)
+ });
+ }
+ }
+ }
+ return result;
+};
+
+/**
+ * Returns {@link AbstractInfoWindow} for element identified by the parameter.
+ *
+ * @param identifiedElement
+ * {@link IdentifiedElement} that determines for which element we
+ * want {@link AbstractInfoWindow}
+ * @returns {@link AbstractInfoWindow} for element identified by the parameter
+ */
+CustomMap.prototype.getInfoWindowForIdentifiedElement = function(
+ identifiedElement) {
+ var model = this.getSubmodelById(identifiedElement.modelId);
+ var infoWindow = null;
+ if (identifiedElement.type == "ALIAS") {
+ infoWindow = model.getAliasInfoWindowById(identifiedElement.getId());
+ } else if (identifiedElement.type == "POINT") {
+ infoWindow = model.getPointInfoWindowById(identifiedElement.getId());
+ } else if (identifiedElement.type == "REACTION") {
+ infoWindow = model.getReactionInfoWindowById(identifiedElement.getId());
+ } else {
+ logger.error("Unknown type of IdentifiedElement: ", identifiedElement);
+ }
+ return infoWindow;
+};
+
+CustomMap.prototype.getActiveSubmapId = function() {
+ return this._activeSubmapId;
+};
+
+CustomMap.prototype.setActiveSubmapId = function(submapId) {
+ this._activeSubmapId = submapId;
+};
+
+CustomMap.prototype.updateAliasesForLayout = function(layoutId, jsonAliases) {
+ logger.debug("Updating aliases for layout: " + layoutId);
+
+ // init layout data
+ if (this.mapModel.getLayoutDataById(layoutId) == null) {
+ this.mapModel.initLayoutData(layoutId);
+ for (var i = 0; i < this.submaps.length; i++) {
+ this.submaps[i].mapModel.initLayoutData(layoutId);
+ }
+ }
+
+ var aliases = JSON.parse(jsonAliases);
+ for (var i = 0; i < aliases.length; i++) {
+ var alias = aliases[i];
+ var model = this.getSubmodelById(alias.modelId);
+ if (model != 'undefined' && model != null) {
+ model.mapModel.updateAliasForLayout(layoutId, alias);
+ model.getAliasInfoWindowById(alias.idObject).update();
+ } else {
+ logger.warn("Unknown model: " + alias.modelId);
+ }
+ }
+
+ this.retrieveMissingAliases();
+};
+
+CustomMap.prototype.getReferenceGenome = function(type, version) {
+ var result = null;
+ if (this._referenceGenome[type] == null) {
+ this._referenceGenome[type] = [];
+ }
+ if (this._referenceGenome[type][version] == null) {
+ ServerConnector.sendReferenceGenomeDetailRequest(type, version);
+ this._referenceGenome[type][version] = new ReferenceGenome(null);
+ return null;
+ } else {
+ return this._referenceGenome[type][version];
+ }
+};
+
+CustomMap.prototype.updateReferenceGenome = function(type, version, jsonObj) {
+ if (this._referenceGenome[type] == null) {
+ this._referenceGenome[type] = [];
+ }
+ this._referenceGenome[type][version] = new ReferenceGenome(jsonObj);
+ this.refreshInfoWindows();
+}
diff --git a/web/src/main/webapp/resources/js/GuiConnector.js b/web/src/main/webapp/resources/js/GuiConnector.js
index e5bb74b28a6e5df625236a55eea75af9c4364e28..85503c34d5cf8985fc0827f01f23de2e297914ad 100644
--- a/web/src/main/webapp/resources/js/GuiConnector.js
+++ b/web/src/main/webapp/resources/js/GuiConnector.js
@@ -1,302 +1,302 @@
-/**
- * This static global object contains set of functions that returns/set data in
- * the Gui (html).
- */
-GuiConnector = new Object();
-
-/**
- * Flag informing if the context menu is visible or not.
- */
-GuiConnector.contextMenuVisible = false;
-
-/**
- * Flag informing if selection menu is visible or not. Selection menu is
- * available when selcting polygon on the map and right clicking on it.
- */
-GuiConnector.selectionMenuVisible = false;
-
-/**
- * X coordinate of the mouse in a browser.
- */
-GuiConnector.xPos = 0;
-
-/**
- * Y coordinate of the mouse in a browser.
- */
-GuiConnector.yPos = 0;
-
-/**
- * List of GET params passed via url.
- */
-GuiConnector.getParams = [];
-
-// find GuiConnector.getParams
-document.location.search.replace(/\??(?:([^=]+)=([^&]*)&?)/g, function() {
- function decode(s) {
- return decodeURIComponent(s.split("+").join(" "));
- }
- GuiConnector.getParams[decode(arguments[1])] = decode(arguments[2]);
-});
-
-/**
- * Initialize navigation for left panel tab.
- */
-$(document)
- .ready(
- function() {
- GuiConnector.leftPanelTabNavi = new TabNavi("tabView", {
- top : "17px"
- });
- GuiConnector.searchTabNavi = new TabNavi("tabView:mainForm:dTable", {
- hideRemaining : false,
- tabSize : 1,
- top : "5px"
- });
- GuiConnector.drugTabNavi = new TabNavi(
- "tabView:drugForm:drugResults", {
- hideRemaining : false,
- tabSize : 1,
- top : "5px"
- });
- if (document.getElementById("tabView:chemicalForm:chemicalResults") != null) {
- GuiConnector.chemicalTabNavi = new TabNavi(
- "tabView:chemicalForm:chemicalResults", {
- hideRemaining : false,
- tabSize : 1,
- top : "5px"
- });
- }
- GuiConnector.miRnaTabNavi = new TabNavi(
- "tabView:miRNAForm:miRNAResults", {
- hideRemaining : false,
- tabSize : 1,
- top : "5px"
- });
- });
-
-/**
- * Returns name of the file with LCSB logo.
- *
- * @param bigLogo
- * {@link Boolean} value determining if we want to have big logo or
- * small one
- */
-GuiConnector.getLcsbLogoImg = function(bigLogo) {
- if (bigLogo) {
- return 'lcsb_logo_mid.png';
- } else {
- return 'lcsb_logo.png';
- }
-};
-
-/**
- * Returns name of the file with image that should be presented when we are
- * wainting for data to be loaded.
- */
-GuiConnector.getLoadingImg = function() {
- return "icons/ajax-loader.gif";
-};
-
-/**
- * Returns home directory for images in the application.
- */
-GuiConnector.getImgPrefix = function() {
- return "resources/images/";
-};
-
-/**
- * Returns main google maps div tag placed on the webpage.
- */
-GuiConnector.getGoogleMapElement = function() {
- return document.getElementById(ServerConnector.formIdentifier
- + ":gmapElement");
-};
-
-/**
- * Shows main google map (by default map is hidden, because it doesn't point to
- * our data from the beginning).
- */
-GuiConnector.showGoogleMap = function() {
- GuiConnector.getGoogleMapElement().style.visibility = "visible";
-};
-
-/**
- * Shows legend.
- */
-GuiConnector.showLegend = function() {
- document.getElementById(ServerConnector.formIdentifier + ':legend').style.display = "block";
-};
-
-/**
- * Hides legend.
- */
-GuiConnector.hideLegend = function() {
- document.getElementById(ServerConnector.formIdentifier + ':legend').style.display = "none";
-};
-
-/**
- * Hides right click menu.
- */
-GuiConnector.hideRightClickMenu = function() {
- $(PrimeFaces.escapeClientId(ServerConnector.formIdentifier + ':contextMenu'))
- .hide();
- this.contextMenuVisible = false;
-};
-
-/**
- * Returns <code>true</code> if right click menu is visible,
- * <code>false</code> otherwise.
- */
-GuiConnector.isRightMenuVisible = function() {
- return this.contextMenuVisible;
-};
-
-/**
- * Shows right click menu.
- */
-GuiConnector.showRightClickMenu = function(x, y) {
- $(PrimeFaces.escapeClientId(ServerConnector.formIdentifier + ':contextMenu'))
- .css({
- top : y + 'px',
- left : x + 'px'
- }).show();
- this.contextMenuVisible = true;
-
- if (this.isSelectionMenuVisible) {
- this.hideSelectionMenu();
- }
-};
-
-/**
- * Hides selection menu.
- *
- * @see selectionMenuVisible
- */
-GuiConnector.hideSelectionMenu = function() {
- $(
- PrimeFaces.escapeClientId(ServerConnector.formIdentifier
- + ':selectionContextMenu')).hide();
- this.selectionMenuVisible = false;
-};
-
-/**
- * Returns <code>true</code> when selection menu is visible,
- * <code>false</code> otherwise.
- *
- * @see selectionMenuVisible
- */
-GuiConnector.isSelectionMenuVisible = function() {
- return this.selectionMenuVisible;
-};
-
-/**
- * Shows selection menu.
- *
- * @see selectionMenuVisible
- */
-GuiConnector.showSelectionMenu = function(x, y) {
- $(
- PrimeFaces.escapeClientId(ServerConnector.formIdentifier
- + ':selectionContextMenu')).css({
- top : y + 'px',
- left : x + 'px'
- }).show();
- this.selectionMenuVisible = true;
-
- if (this.isRightMenuVisible()) {
- this.hideRightClickMenu();
- }
-};
-
-/**
- * Gets html div where overview images should be visualized.
- *
- */
-GuiConnector.getOverviewHtmlTag = function() {
- return document.getElementById(ServerConnector.formIdentifier
- + ':overviewDialog');
-};
-
-/**
- * Updates coordinates of the mouse in the browser.
- */
-GuiConnector.updateMouseCoordinates = function(x, y) {
- this.xPos = x;
- this.yPos = y;
-};
-
-// forser browser to update mouse coordinates whenever mouse move
-jQuery(document).ready(function() {
- $(document).mousemove(function(e) {
- GuiConnector.updateMouseCoordinates(e.pageX, e.pageY);
- });
-});
-
-/**
- * Return html tag for submap visualization.
- *
- * @param id
- * identifier of the submodel
- */
-GuiConnector.getHtmlTagForSubmodelId = function(id) {
- return document.getElementById('_gmapForm:submodelDialog' + id);
-};
-
-/**
- * Returns js Primefaces object for submap visualization.
- *
- * @param id
- * identifier of the submodel
- */
-GuiConnector.getJsPopupForSubmodelId = function(id) {
- return window['submodelDialog' + id];
-};
-
-/**
- * Opens popup for submap visualization.
- *
- * @param id
- * identifier of the submodel
- */
-GuiConnector.openDialog = function(id) {
- var jsVar = GuiConnector.getJsPopupForSubmodelId(id);
- if (jsVar != null) {
- var htmlTag = GuiConnector.getHtmlTagForSubmodelId(id);
- customMap.openSubmodel(id, htmlTag, jsVar);
- }
- return false;
-};
-
-GuiConnector.referenceToHtml = function(reference) {
- if (reference.summary != null && reference.summary != "") {
- var result = '<div title="' + reference.summary + '">';
- result += '<a href="' + reference.link + '" target="_blank">'
- + reference.name + "</a>";
- // + reference.name + "(" + reference.type + ")</a>";
- result += "</div>";
- return result;
- } else {
- var result = '<div><a href="' + reference.link + '" target="_blank">'
- + reference.name + "</a></div>";
- // + reference.name + "(" + reference.type + ")</a></div>";
- return result;
- }
-};
-
-GuiConnector.openSearchPanel = function() {
- $('a[href$="#tabView:searchTab"]').click();
-};
-
-/**
- * Opens window that informs user data data is being loaded from server.
- */
-GuiConnector.openLoadingDialog = function() {
- PF('loadingDlg').show();
-};
-
-/**
- * Closes window that informs user data data is being loaded from server.
- */
-GuiConnector.closeLoadingDialog = function() {
- PF('loadingDlg').hide();
-};
+/**
+ * This static global object contains set of functions that returns/set data in
+ * the Gui (html).
+ */
+GuiConnector = new Object();
+
+/**
+ * Flag informing if the context menu is visible or not.
+ */
+GuiConnector.contextMenuVisible = false;
+
+/**
+ * Flag informing if selection menu is visible or not. Selection menu is
+ * available when selcting polygon on the map and right clicking on it.
+ */
+GuiConnector.selectionMenuVisible = false;
+
+/**
+ * X coordinate of the mouse in a browser.
+ */
+GuiConnector.xPos = 0;
+
+/**
+ * Y coordinate of the mouse in a browser.
+ */
+GuiConnector.yPos = 0;
+
+/**
+ * List of GET params passed via url.
+ */
+GuiConnector.getParams = [];
+
+// find GuiConnector.getParams
+document.location.search.replace(/\??(?:([^=]+)=([^&]*)&?)/g, function() {
+ function decode(s) {
+ return decodeURIComponent(s.split("+").join(" "));
+ }
+ GuiConnector.getParams[decode(arguments[1])] = decode(arguments[2]);
+});
+
+/**
+ * Initialize navigation for left panel tab.
+ */
+$(document)
+ .ready(
+ function() {
+ GuiConnector.leftPanelTabNavi = new TabNavi("tabView", {
+ top : "17px"
+ });
+ GuiConnector.searchTabNavi = new TabNavi("tabView:mainForm:dTable", {
+ hideRemaining : false,
+ tabSize : 1,
+ top : "5px"
+ });
+ GuiConnector.drugTabNavi = new TabNavi(
+ "tabView:drugForm:drugResults", {
+ hideRemaining : false,
+ tabSize : 1,
+ top : "5px"
+ });
+ if (document.getElementById("tabView:chemicalForm:chemicalResults") != null) {
+ GuiConnector.chemicalTabNavi = new TabNavi(
+ "tabView:chemicalForm:chemicalResults", {
+ hideRemaining : false,
+ tabSize : 1,
+ top : "5px"
+ });
+ }
+ GuiConnector.miRnaTabNavi = new TabNavi(
+ "tabView:miRNAForm:miRNAResults", {
+ hideRemaining : false,
+ tabSize : 1,
+ top : "5px"
+ });
+ });
+
+/**
+ * Returns name of the file with LCSB logo.
+ *
+ * @param bigLogo
+ * {@link Boolean} value determining if we want to have big logo or
+ * small one
+ */
+GuiConnector.getLcsbLogoImg = function(bigLogo) {
+ if (bigLogo) {
+ return 'lcsb_logo_mid.png';
+ } else {
+ return 'lcsb_logo.png';
+ }
+};
+
+/**
+ * Returns name of the file with image that should be presented when we are
+ * wainting for data to be loaded.
+ */
+GuiConnector.getLoadingImg = function() {
+ return "icons/ajax-loader.gif";
+};
+
+/**
+ * Returns home directory for images in the application.
+ */
+GuiConnector.getImgPrefix = function() {
+ return "resources/images/";
+};
+
+/**
+ * Returns main google maps div tag placed on the webpage.
+ */
+GuiConnector.getGoogleMapElement = function() {
+ return document.getElementById(ServerConnector.formIdentifier
+ + ":gmapElement");
+};
+
+/**
+ * Shows main google map (by default map is hidden, because it doesn't point to
+ * our data from the beginning).
+ */
+GuiConnector.showGoogleMap = function() {
+ GuiConnector.getGoogleMapElement().style.visibility = "visible";
+};
+
+/**
+ * Shows legend.
+ */
+GuiConnector.showLegend = function() {
+ document.getElementById(ServerConnector.formIdentifier + ':legend').style.display = "block";
+};
+
+/**
+ * Hides legend.
+ */
+GuiConnector.hideLegend = function() {
+ document.getElementById(ServerConnector.formIdentifier + ':legend').style.display = "none";
+};
+
+/**
+ * Hides right click menu.
+ */
+GuiConnector.hideRightClickMenu = function() {
+ $(PrimeFaces.escapeClientId(ServerConnector.formIdentifier + ':contextMenu'))
+ .hide();
+ this.contextMenuVisible = false;
+};
+
+/**
+ * Returns <code>true</code> if right click menu is visible,
+ * <code>false</code> otherwise.
+ */
+GuiConnector.isRightMenuVisible = function() {
+ return this.contextMenuVisible;
+};
+
+/**
+ * Shows right click menu.
+ */
+GuiConnector.showRightClickMenu = function(x, y) {
+ $(PrimeFaces.escapeClientId(ServerConnector.formIdentifier + ':contextMenu'))
+ .css({
+ top : y + 'px',
+ left : x + 'px'
+ }).show();
+ this.contextMenuVisible = true;
+
+ if (this.isSelectionMenuVisible) {
+ this.hideSelectionMenu();
+ }
+};
+
+/**
+ * Hides selection menu.
+ *
+ * @see selectionMenuVisible
+ */
+GuiConnector.hideSelectionMenu = function() {
+ $(
+ PrimeFaces.escapeClientId(ServerConnector.formIdentifier
+ + ':selectionContextMenu')).hide();
+ this.selectionMenuVisible = false;
+};
+
+/**
+ * Returns <code>true</code> when selection menu is visible,
+ * <code>false</code> otherwise.
+ *
+ * @see selectionMenuVisible
+ */
+GuiConnector.isSelectionMenuVisible = function() {
+ return this.selectionMenuVisible;
+};
+
+/**
+ * Shows selection menu.
+ *
+ * @see selectionMenuVisible
+ */
+GuiConnector.showSelectionMenu = function(x, y) {
+ $(
+ PrimeFaces.escapeClientId(ServerConnector.formIdentifier
+ + ':selectionContextMenu')).css({
+ top : y + 'px',
+ left : x + 'px'
+ }).show();
+ this.selectionMenuVisible = true;
+
+ if (this.isRightMenuVisible()) {
+ this.hideRightClickMenu();
+ }
+};
+
+/**
+ * Gets html div where overview images should be visualized.
+ *
+ */
+GuiConnector.getOverviewHtmlTag = function() {
+ return document.getElementById(ServerConnector.formIdentifier
+ + ':overviewDialog');
+};
+
+/**
+ * Updates coordinates of the mouse in the browser.
+ */
+GuiConnector.updateMouseCoordinates = function(x, y) {
+ this.xPos = x;
+ this.yPos = y;
+};
+
+// forser browser to update mouse coordinates whenever mouse move
+jQuery(document).ready(function() {
+ $(document).mousemove(function(e) {
+ GuiConnector.updateMouseCoordinates(e.pageX, e.pageY);
+ });
+});
+
+/**
+ * Return html tag for submap visualization.
+ *
+ * @param id
+ * identifier of the submodel
+ */
+GuiConnector.getHtmlTagForSubmodelId = function(id) {
+ return document.getElementById('_gmapForm:submodelDialog' + id);
+};
+
+/**
+ * Returns js Primefaces object for submap visualization.
+ *
+ * @param id
+ * identifier of the submodel
+ */
+GuiConnector.getJsPopupForSubmodelId = function(id) {
+ return window['submodelDialog' + id];
+};
+
+/**
+ * Opens popup for submap visualization.
+ *
+ * @param id
+ * identifier of the submodel
+ */
+GuiConnector.openDialog = function(id) {
+ var jsVar = GuiConnector.getJsPopupForSubmodelId(id);
+ if (jsVar != null) {
+ var htmlTag = GuiConnector.getHtmlTagForSubmodelId(id);
+ customMap.openSubmodel(id, htmlTag, jsVar);
+ }
+ return false;
+};
+
+GuiConnector.referenceToHtml = function(reference) {
+ if (reference.summary != null && reference.summary != "") {
+ var result = '<div title="' + reference.summary + '">';
+ result += '<a href="' + reference.link + '" target="_blank">'
+ + reference.name + "</a>";
+ // + reference.name + "(" + reference.type + ")</a>";
+ result += "</div>";
+ return result;
+ } else {
+ var result = '<div><a href="' + reference.link + '" target="_blank">'
+ + reference.name + "</a></div>";
+ // + reference.name + "(" + reference.type + ")</a></div>";
+ return result;
+ }
+};
+
+GuiConnector.openSearchPanel = function() {
+ $('a[href$="#tabView:searchTab"]').click();
+};
+
+/**
+ * Opens window that informs user data data is being loaded from server.
+ */
+GuiConnector.openLoadingDialog = function() {
+ PF('loadingDlg').show();
+};
+
+/**
+ * Closes window that informs user data data is being loaded from server.
+ */
+GuiConnector.closeLoadingDialog = function() {
+ PF('loadingDlg').hide();
+};
diff --git a/web/src/main/webapp/resources/js/ReactionOverlay.js b/web/src/main/webapp/resources/js/ReactionOverlay.js
index d35b5c3490dd4ae572d3cbbbf83129817100ade2..c0b144caa2a6c783aed09c80bcc1d86073a29885 100644
--- a/web/src/main/webapp/resources/js/ReactionOverlay.js
+++ b/web/src/main/webapp/resources/js/ReactionOverlay.js
@@ -15,6 +15,9 @@
* the same time)
*/
function ReactionOverlay(layoutReaction, reactionData, map, customized, id) {
+ // call super constructor
+ AbstractOverlayElement.call();
+
this.color = "#FF0000";
this.width = 5.0;
// list of google map objects associated with the reaction (like lines)
@@ -30,7 +33,7 @@ function ReactionOverlay(layoutReaction, reactionData, map, customized, id) {
if (layoutReaction.width) {
this.width = layoutReaction.width;
}
- this.color = intToColorString(layoutReaction.color.value);
+ this.color = this.overlayToColor(layoutReaction);
}
if (reactionData != null) {
@@ -44,6 +47,10 @@ function ReactionOverlay(layoutReaction, reactionData, map, customized, id) {
};
+ReactionOverlay.prototype = Object.create(AbstractOverlayElement.prototype);
+ReactionOverlay.prototype.constructor = ReactionOverlay;
+
+
/**
* Returns {@link google.maps.Bounds bounds} of all google maps elements
* included in the object.
diff --git a/web/src/main/webapp/resources/js/ServerConnector.js b/web/src/main/webapp/resources/js/ServerConnector.js
index ac913103206f21e64e7224318dffd645b18f0e88..bd1646dc904e5dadb5fa340f8e68f231f03603bf 100644
--- a/web/src/main/webapp/resources/js/ServerConnector.js
+++ b/web/src/main/webapp/resources/js/ServerConnector.js
@@ -1,1025 +1,1046 @@
-/**
- * This object contains methods that will communicate with server.
- */
-ServerConnector = new Object();
-
-/**
- * List of {@link OverlayCollection} that was added to the server connector. It
- * describes list of all overlays that communicate with server.
- */
-ServerConnector._overlays = [];
-
-/**
- * Associative array with methods that should be used for comunication of the
- * {@link OverlayCollection} from _overlays field.
- */
-ServerConnector._overlayMethods = [];
-
-/**
- * Form where fields passed to/from server are stored.
- */
-ServerConnector.formIdentifier = "_gmapForm";
-
-/**
- * Variable describing when was last transmition of data (location of the map,
- * zoom level, etc.) to the server session.
- */
-ServerConnector.lastActualization = 0;
-
-ServerConnector._customMap = null;
-
-/**
- * Number of requests send to server about AliasLayout data.
- */
-ServerConnector._waitingForAliasLayoutData = 0;
-ServerConnector._waitingForAliasLayoutDataByLayoutId = [];
-
-ServerConnector._waitingFullAliasLayoutData = 0;
-ServerConnector._waitingFullAliasLayoutDataById = [];
-
-/**
- * Number of requests send to server about AliasData data.
- */
-ServerConnector._waitingForAliasData = 0;
-ServerConnector._waitingForAliasDataByAliasId = [];
-
-/**
- * Number of requests send to server about ReactionLayout data.
- */
-ServerConnector._waitingForReactionLayoutData = 0;
-ServerConnector._waitingForReactionLayoutDataByLayoutId = [];
-
-/**
- * Number of requests send to server about ReactionData data.
- */
-ServerConnector._waitingForReactionData = 0;
-ServerConnector._waitingForReactionDataByReactionId = [];
-
-/**
- * Get name of the file that should be used as logo.
- */
-ServerConnector.getLogoImg = function() {
- return document.getElementById('logoImg').value;
-};
-
-/**
- * Get link to the website that should be accessed when clicking on
- * {@link ServerConnector.getLogoImg}.
- */
-ServerConnector.getLogoLink = function() {
- return document.getElementById('logoLink').value;
-};
-
-/**
- * Get zoom level of the {@link CustomMap} at which it was last browsed.
- */
-ServerConnector.getZoomLevel = function() {
- return document.getElementById(ServerConnector.formIdentifier + ':zoomLevel').value;
-};
-
-/**
- * Set zoom level for {@link CustomMap} on the server side.
- */
-ServerConnector.setZoomLevel = function(value) {
- document.getElementById(ServerConnector.formIdentifier + ':zoomLevel').value = ""
- + value;
-};
-
-/**
- * Set x coordinate for {@link CustomMap} on the server side.
- */
-ServerConnector.setCenterCoordinateX = function(value) {
- document
- .getElementById(ServerConnector.formIdentifier + ':centerCoordinateX').value = ""
- + value;
-};
-
-/**
- * Get x coordinate of the {@link CustomMap} at which it was last browsed.
- */
-ServerConnector.getCenterCoordinateX = function() {
- var result = parseFloat(document
- .getElementById(ServerConnector.formIdentifier + ':centerCoordinateX').value);
- return result;
-};
-
-/**
- * Set y coordinate for {@link CustomMap} on the server side.
- */
-ServerConnector.setCenterCoordinateY = function(value) {
- document
- .getElementById(ServerConnector.formIdentifier + ':centerCoordinateY').value = ""
- + value;
-};
-
-/**
- * Get y coordinate of the {@link CustomMap} at which it was last browsed.
- */
-ServerConnector.getCenterCoordinateY = function() {
- var result = parseFloat(document
- .getElementById(ServerConnector.formIdentifier + ':centerCoordinateY').value);
- return result;
-};
-
-/**
- * Set layout that is currently browsed for {@link CustomMap} on the server
- * side.
- */
-ServerConnector.setSelectedLayout = function(value) {
- document.getElementById(ServerConnector.formIdentifier + ':selectedLayout').value = ""
- + value;
-};
-/**
- * Sets list of layouts visualized by javascript.
- */
-ServerConnector.setVisibleLayouts = function(value) {
- document.getElementById(ServerConnector.formIdentifier + ':visibleLayouts').value = value;
-}
-
-/**
- * Get layout of the {@link CustomMap} which was last browsed.
- */
-ServerConnector.getSelectedLayout = function() {
- return document.getElementById(ServerConnector.formIdentifier
- + ':selectedLayout').value;
-};
-
-/**
- * Sends data about coordinates/zoom level etc. to the server. Method checks if
- * the transmition is not done to often (at most once per second)
- */
-ServerConnector.actualizeSessionData = function(value) {
- var timestamp = new Date().getTime();
- // we send the data with at least 1 second time distance
- if (timestamp > ServerConnector.lastActualization) {
- ServerConnector.lastActualization = timestamp + 1000;
- setTimeout(function() {
- ServerConnector.actualizeParams();
- }, 1000);
- }
-};
-
-/**
- * Sends data about coordinates/zoom level etc. to the server. Sending is
- * performed immediatelly.
- *
- * @see ServerConnector.actualizeSessionData
- */
-ServerConnector.actualizeParams = function() {
- actualizeParams();
-};
-
-/**
- * Sets search query that will be handled by server.
- */
-ServerConnector.setSearchQuery = function(value) {
- document.getElementById(ServerConnector.formIdentifier + ':mapParam').value = ""
- + value;
-};
-
-/**
- * Sets data mining query that will be handled by server.
- */
-ServerConnector.setDataMiningQuery = function(value) {
- document.getElementById(ServerConnector.formIdentifier
- + ':missingConnectionParam').value = "" + value;
-};
-
-/**
- * Sets drug search query that will be handled by server.
- */
-ServerConnector.setDrugQuery = function(value) {
- document.getElementById(ServerConnector.formIdentifier + ':drugParam').value = ""
- + value;
-};
-
-/**
- * Sets comment query that will be handled by server.
- */
-ServerConnector.setCommentQuery = function(value) {
- logger.error("ServerConnector.setCommentQuery: Not implemented");
- document.getElementById(ServerConnector.formIdentifier + ':commentParam').value = ""
- + value;
-};
-
-/**
- * Sets selected polygon. This might be in futer used oto extract/analyze data
- * in the polygon by the server side.
- */
-ServerConnector.setSelectedPolygon = function(value) {
- document.getElementById(ServerConnector.formIdentifier + ':selectedPolygon').value = ""
- + value;
- document.getElementById(ServerConnector.formIdentifier
- + ':selectedDrugPolygon').value = "" + value;
-};
-
-/**
- * Sets identifier of the model where selected polygon (@see
- * ServerConnector.setSelectedPolygon) was selected.
- */
-ServerConnector.setExportModelId = function(value) {
- document.getElementById(ServerConnector.formIdentifier + ':exportModelId').value = ""
- + value;
-};
-
-/**
- * Sets flag marking if the comments are visible or not.
- */
-ServerConnector.setShowComments = function(value) {
- _setShowComments([ {
- name : 'showComments',
- value : value
- } ]);
-};
-
-/**
- * Search for similar data mining entries on the map.
- */
-ServerConnector.showSimilarDataMining = function(param) {
- document.getElementById(ServerConnector.formIdentifier + ':geneName').value = ""
- + param;
- searchMissingConnections();
-};
-
-/**
- * Ask server to send list of aliases that were highlighted in the layout with a
- * given identifier.
- *
- * @param identifier
- * of the layout
- */
-ServerConnector.retreiveActiveAliasesForLayout = function(identifier) {
- this.setWaitingForAliasLayoutData(parseInt(identifier), true);
- _retreiveActiveAliasesForLayout([ {
- name : 'layoutId',
- value : identifier
- } ]);
-};
-
-ServerConnector.retreiveFullAliasesForLayout = function(layoutId, aliasId, modelId) {
- this.setWaitingForFullAliasLayoutData(parseInt(layoutId),parseInt(aliasId), true);
- _retreiveFullAliasesForLayout([ {
- name : 'layoutId',
- value : layoutId,
- }, {
- name : 'ids',
- value : JSON.stringify([[modelId, aliasId]]),
- },
- ]);
-};
-
-/**
- * Ask server to send list of reactions that were highlighted in the layout with
- * a given identifier.
- *
- * @param identifier
- * of the layout
- */
-ServerConnector.retreiveActiveReactionsForLayout = function(identifier) {
- this.setWaitingForReactionLayoutData(parseInt(identifier), true);
- _retreiveActiveReactionsForLayout([ {
- name : 'layoutId',
- value : identifier
- } ]);
-};
-
-/**
- * Ask server to send list of light information about aliases.
- *
- * @param ids
- * list of alias identifiers, every identifier is an array with two
- * values: modelId, aliasId
- */
-ServerConnector.retreiveLightAliases = function(ids) {
- for (var i = 0; i < ids.length; i++) {
- this.setWaitingForAliasData(parseInt(ids[i][1]), true);
- }
- _retreiveLightAliases([ {
- name : 'ids',
- value : JSON.stringify(ids)
- } ]);
-};
-
-/**
- * Ask server to send list of full information about aliases.
- *
- * @param ids
- * list of alias identifiers, every identifier is an array with two
- * values: modelId, aliasId
- */
-ServerConnector.retreiveFullAliases = function(ids) {
- _retreiveFullAliases([ {
- name : 'ids',
- value : JSON.stringify(ids)
- } ]);
-};
-
-/**
- * Ask server to send list of light information about reactions.
- *
- * @param ids
- * list of reaction identifiers, every identifier is an array with
- * two values: modelId, reactionId
- */
-ServerConnector.retreiveLightReactions = function(ids) {
- for (var i = 0; i < ids.length; i++) {
- this.setWaitingForReactionData(parseInt(ids[i][1]), true);
- }
- _retreiveLightReactions([ {
- name : 'ids',
- value : JSON.stringify(ids)
- } ]);
-};
-
-/**
- * Sends request to server to refresh data for overlay with a given name.
- *
- * @param overlayName
- * name of the overlay
- */
-ServerConnector.sendRefreshRequest = function(overlayName) {
- var functions = ServerConnector._overlayMethods[overlayName];
- if (functions != null) {
- var refreshFunction = functions.refreshFunction;
- if (refreshFunction != null) {
- refreshFunction();
- } else {
- logger.warn("Refresh function for " + overlayName + " doesn't exist");
- }
- } else {
- logger.warn("[Refresh function] Unknown overlay: ", overlayName);
- }
-};
-
-/**
- * Adds {@link OverlayCollection} to ServerConnector.
- */
-ServerConnector.addOverlayCollection = function(overlay) {
- if (ServerConnector._overlayMethods[overlay.name] != null) {
- if (ServerConnector._overlays[overlay.name] != null) {
- logger.warn("Overlay with name " + overlay.name + " already added");
- return;
- }
- ServerConnector._overlays[overlay.name] = overlay;
- if (ServerConnector._overlayMethods[overlay.name].initFunction != null) {
- ServerConnector._overlayMethods[overlay.name].initFunction();
- } else {
- logger.warn("Cannot initialize overlay: " + overlay);
- }
- } else {
- logger.warn("Unknown overlay: ", overlay);
- }
-};
-
-/**
- * Method that should be called by server to update data in overlay.
- *
- * @param overlayName
- * name of overlay for which the data is sent
- * @param data
- * new data for overlay
- * @param fitBounds
- * should the map call fitBounds after update
- */
-ServerConnector.updateOverlayCollection = function(overlayName, data, fitBounds) {
- logger.debug("Updating: " + overlayName);
- var overlay = ServerConnector._overlays[overlayName];
- if (overlay != null) {
- overlay.updateOverlays(data, fitBounds);
- } else {
- logger.warn("Overlay " + overlayName
- + " cannot be updated. It doesn't exist");
- }
-}
-
-/**
- * Name of the overlay for 'search' overlay.
- */
-ServerConnector.SEARCH_OVERLAY_NAME = 'search';
-
-/**
- * Name of the overlay for 'data mining' overlay.
- */
-ServerConnector.DATA_MINING_OVERLAY_NAME = 'missingConnection';
-
-/**
- * Name of the overlay for 'drug' overlay.
- */
-ServerConnector.DRUG_OVERLAY_NAME = 'drug';
-
-/**
- * Name of the overlay for 'chemical' overlay.
- */
-ServerConnector.CHEMICAL_OVERLAY_NAME = 'chemical';
-
-/**
- * Name of the overlay for 'comment' overlay.
- */
-ServerConnector.COMMENT_OVERLAY_NAME = 'comment';
-
-/**
- * Name of the overlay for 'mirna' overlay.
- */
-ServerConnector.MI_RNA_OVERLAY_NAME = 'mirna';
-
-/**
- * Register 'search' overlay on the server.
- */
-ServerConnector.registerSearchOverlay = function() {
- _registerSearchOverlayCollection([ {
- name : "overlayName",
- value : ServerConnector.SEARCH_OVERLAY_NAME,
- } ]);
-};
-
-/**
- * Sends request to the server to refresh data in 'search' overlay.
- */
-ServerConnector.refreshSearchOverlay = function() {
- _refreshSearchOverlayCollection();
-};
-
-/**
- * Clear data related to 'search' overlay..
- */
-ServerConnector.clearSearchOverlay = function() {
- _clearSearchOverlayCollection();
-};
-
-/**
- * Register 'data mining' overlay on the server.
- */
-ServerConnector.registerDataMiningOverlay = function() {
- _registerMissingConnectionOverlayCollection([ {
- name : "overlayName",
- value : ServerConnector.DATA_MINING_OVERLAY_NAME,
- } ]);
-};
-
-/**
- * Sends request to the server to refresh data in 'data mining' overlay.
- */
-ServerConnector.refreshDataMiningOverlay = function() {
- _refreshMissingConnectionOverlayCollection();
-};
-
-/**
- * Clear data related to 'data mining' overlay.
- */
-ServerConnector.clearDataMiningOverlay = function() {
- _clearMissingConnectionOverlayCollection();
-};
-
-/**
- * Register 'drug' overlay on the server.
- */
-ServerConnector.registerDrugOverlay = function() {
- _registerDrugOverlayCollection([ {
- name : "overlayName",
- value : ServerConnector.DRUG_OVERLAY_NAME,
- } ]);
-};
-
-ServerConnector.requestDrugDetailDataFunction = function(identfiedElement, id) {
- logger.debug("Requesting drug details: ", identfiedElement, id);
- _requestDrugDetailDataFunction([ {
- name : "searchResultIdentifier",
- value : id,
- }, {
- name : "objectIdentifier",
- value : identfiedElement.getId(),
- }, {
- name : "modelIdentifier",
- value : identfiedElement.getModelId(),
- }, {
- name : "type",
- value : identfiedElement.getType(),
- } ]);
-};
-ServerConnector.requestCommentDetailDataFunction = function(identfiedElement,
- id) {
- _requestCommentDetailDataFunction([ {
- name : "searchResultIdentifier",
- value : id,
- }, {
- name : "objectIdentifier",
- value : identfiedElement.getId(),
- }, {
- name : "modelIdentifier",
- value : identfiedElement.getModelId(),
- }, {
- name : "type",
- value : identfiedElement.getType(),
- } ]);
-};
-
-/**
- * Sends request to the server to refresh data in 'drug' overlay.
- */
-ServerConnector.refreshDrugOverlay = function() {
- _refreshDrugOverlayCollection();
-};
-
-/**
- * Clear data related to 'drug' overlay.
- */
-ServerConnector.clearDrugOverlay = function() {
- _clearDrugOverlayCollection();
-};
-
-ServerConnector.registerChemicalOverlay = function() {
- _registerChemicalOverlayCollection([ {
- name : "overlayName",
- value : ServerConnector.CHEMICAL_OVERLAY_NAME,
- } ]);
-};
-
-ServerConnector.requestChemicalDetailDataFunction = function(identfiedElement,
- id) {
- _requestChemicalDetailDataFunction([ {
- name : "searchResultIdentifier",
- value : id,
- }, {
- name : "objectIdentifier",
- value : identfiedElement.getId(),
- }, {
- name : "modelIdentifier",
- value : identfiedElement.getModelId(),
- }, {
- name : "type",
- value : identfiedElement.getType(),
- } ]);
-};
-
-/**
- * Sends request to the server to refresh data in 'drug' overlay.
- */
-ServerConnector.refreshChemicalOverlay = function() {
- _refreshChemicalOverlayCollection();
-};
-
-/**
- * Clear data related to 'chemical' overlay.
- */
-ServerConnector.clearChemicalOverlay = function() {
- _clearChemicalOverlayCollection();
-};
-
-/**
- * Register 'comment' overlay on the server.
- */
-ServerConnector.registerCommentOverlay = function() {
- _registerCommentOverlayCollection([ {
- name : "overlayName",
- value : ServerConnector.COMMENT_OVERLAY_NAME,
- } ]);
-};
-
-/**
- * Sends request to the server to refresh data in 'comment' overlay.
- */
-ServerConnector.refreshCommentOverlay = function() {
- _refreshCommentOverlayCollection();
-};
-
-/**
- * Clear data related to 'comment' overlay.
- */
-ServerConnector.clearCommentOverlay = function() {
- _clearCommentOverlayCollection();
-};
-
-/**
- * Clear data related to 'data mining' overlay.
- */
-ServerConnector.clearDataMiningOverlay = function() {
- _clearMissingConnectionOverlayCollection();
-};
-
-/**
- * Register 'drug' overlay on the server.
- */
-ServerConnector.registerMiRnaOverlay = function() {
- _registerMiRnaOverlayCollection([ {
- name : "overlayName",
- value : ServerConnector.MI_RNA_OVERLAY_NAME,
- } ]);
-};
-
-ServerConnector.requestMiRnaDetailDataFunction = function(identfiedElement, id) {
- _requestMiRnaDetailDataFunction([ {
- name : "searchResultIdentifier",
- value : id,
- }, {
- name : "objectIdentifier",
- value : identfiedElement.getId(),
- }, {
- name : "modelIdentifier",
- value : identfiedElement.getModelId(),
- }, {
- name : "type",
- value : identfiedElement.getType(),
- } ]);
-};
-
-/**
- * Sends request to the server to refresh data in 'drug' overlay.
- */
-ServerConnector.refreshMiRnaOverlay = function() {
- _refreshMiRnaOverlayCollection();
-};
-
-/**
- * Clear data related to 'mirna' overlay.
- */
-ServerConnector.clearMiRnaOverlay = function() {
- _clearMiRnaOverlayCollection();
-};
-
-/**
- * Define pack of methods for 'search' overlay.
- */
-ServerConnector._overlayMethods[ServerConnector.SEARCH_OVERLAY_NAME] = {
- initFunction : ServerConnector.registerSearchOverlay,
- refreshFunction : ServerConnector.refreshSearchOverlay,
- clearFunction : ServerConnector.clearSearchOverlay,
-};
-
-/**
- * Define pack of methods for 'data minig' overlay.
- */
-ServerConnector._overlayMethods[ServerConnector.DATA_MINING_OVERLAY_NAME] = {
- initFunction : ServerConnector.registerDataMiningOverlay,
- refreshFunction : ServerConnector.refreshDataMiningOverlay,
- clearFunction : ServerConnector.clearDataMiningOverlay,
-};
-
-/**
- * Define pack of methods for 'drug' overlay.
- */
-ServerConnector._overlayMethods[ServerConnector.DRUG_OVERLAY_NAME] = {
- initFunction : ServerConnector.registerDrugOverlay,
- refreshFunction : ServerConnector.refreshDrugOverlay,
- clearFunction : ServerConnector.clearDrugOverlay,
- requestDetailDataFunction : ServerConnector.requestDrugDetailDataFunction,
-};
-
-/**
- * Define pack of methods for 'chemical' overlay.
- */
-ServerConnector._overlayMethods[ServerConnector.CHEMICAL_OVERLAY_NAME] = {
- initFunction : ServerConnector.registerChemicalOverlay,
- refreshFunction : ServerConnector.refreshChemicalOverlay,
- clearFunction : ServerConnector.clearChemicalOverlay,
- requestDetailDataFunction : ServerConnector.requestChemicalDetailDataFunction,
-};
-
-/**
- * Define pack of methods for 'comment' overlay.
- */
-ServerConnector._overlayMethods[ServerConnector.COMMENT_OVERLAY_NAME] = {
- initFunction : ServerConnector.registerCommentOverlay,
- refreshFunction : ServerConnector.refreshCommentOverlay,
- clearFunction : ServerConnector.clearCommentOverlay,
- requestDetailDataFunction : ServerConnector.requestCommentDetailDataFunction,
-};
-
-ServerConnector._overlayMethods[ServerConnector.MI_RNA_OVERLAY_NAME] = {
- initFunction : ServerConnector.registerMiRnaOverlay,
- refreshFunction : ServerConnector.refreshMiRnaOverlay,
- clearFunction : ServerConnector.clearMiRnaOverlay,
- requestDetailDataFunction : ServerConnector.requestMiRnaDetailDataFunction,
-};
-
-ServerConnector.sendClearRequest = function(overlayName) {
- var functions = ServerConnector._overlayMethods[overlayName];
- if (functions != null) {
- var clearFunction = functions.clearFunction;
- if (clearFunction != null) {
- clearFunction();
- } else {
- logger.warn("Clear function for " + overlayName + " doesn't exist");
- }
- } else {
- logger.warn("[Clear function] Unknown overlay: ", overlayName);
- }
-};
-
-ServerConnector.setOverlayResultIds = function(overlayName, ids) {
- var overlay = this._overlays[overlayName];
- if (overlay != null) {
- overlay.setResultsIds(ids);
- } else {
- logger.warn("Overlay '" + overlayName + "' doesn't exist");
- }
-};
-
-ServerConnector.sendOverlayDetailDataRequest = function(overlayName,
- identifiedElement, general) {
- var overlay = ServerConnector._overlays[overlayName];
- if (overlay == null) {
- logger.warn("Unknown overlay: " + overlayName);
- return;
- }
- var functions = ServerConnector._overlayMethods[overlayName];
- if (functions != null) {
- var requestDetailDataFunction = functions.requestDetailDataFunction;
- if (requestDetailDataFunction != null) {
- var missingData = overlay.getMissingDetailDataIds(identifiedElement,
- general);
- if (missingData.length == 0) {
- logger
- .warn(
- "request of missing data called for empty data set... overlay name = ",
- overlayName, "general: ", general);
- }
- for (var i = 0; i < missingData.length; i++) {
- requestDetailDataFunction(identifiedElement, missingData[i]);
- }
- } else {
- logger.warn("Request detail data function for " + overlayName
- + " doesn't exist");
- }
- } else {
- logger.warn("[Clear function] Unknown overlay: ", overlayName);
- }
-
-};
-
-ServerConnector.updateOverviewElementDetailData = function(overlayName,
- searchResultIdentifier, identifiedElement, data) {
- var overlay = this._overlays[overlayName];
- if (overlay != null) {
- overlay.updateOverviewElementDetailData(identifiedElement,
- searchResultIdentifier, data);
- } else {
- logger.warn("Overlay '" + overlayName + "' doesn't exist");
- }
-};
-
-/**
- * Returns <code>true</code> if we are waiting for any kind of data from
- * server, <code>false</code> otherwise.
- *
- * @returns {Boolean}: <code>true</code> if we are waiting for any kind of
- * data from server, <code>false</code> otherwise.
- */
-ServerConnector.isWaitingForData = function() {
- var result = (this._waitingForAliasLayoutData != 0) || //
- (this._waitingForAliasData != 0) || //
- (this._waitingForReactionLayoutData != 0) || //
- (this._waitingForReactionData != 0);
- return result;
-};
-
-/**
- * Sets waitingForAliasLayoutData flag that monitors if we are waiting for the
- * data about aliases in a layout from server.
- *
- * @param value
- * new value of the waitingForAliasLayoutData field
- */
-ServerConnector.setWaitingForAliasLayoutData = function(layoutId, value) {
- if (isInt(layoutId)) {
- var oldVal = this._waitingForAliasLayoutDataByLayoutId[layoutId];
- this._waitingForAliasLayoutDataByLayoutId[layoutId] = value;
- if (value === true) {
- if (oldVal !== true) {
- this._waitingForAliasLayoutData++;
- }
- } else if (value === false) {
- if (oldVal === true) {
- this._waitingForAliasLayoutData--;
- }
- } else {
- logger
- .error(
- "WaitingForAliasLayoutData value must be boolean, but found: ",
- value);
- }
- } else {
- logger.error(
- "WaitingForAliasLayoutData layoutId must be integer, but found: ",
- layoutId);
- }
-}
-
-ServerConnector.setWaitingForFullAliasLayoutData = function(layoutId, aliasId, value) {
- if (!isInt(layoutId)) {
- logger.error(
- "setWaitingForFullAliasLayoutData layoutId must be integer, but found: ",
- layoutId);
- }
- if (!isInt(aliasId)) {
- logger.error(
- "setWaitingForFullAliasLayoutData aliasId must be integer, but found: ",
- aliasId);
- }
-
- var oldVal = this._waitingFullAliasLayoutDataById[layoutId+"-"+aliasId];
- this._waitingFullAliasLayoutDataById[layoutId+"-"+aliasId] = value;
- if (value === true) {
- if (oldVal !== true) {
- this._waitingFullAliasLayoutData++;
- }
- } else if (value === false) {
- if (oldVal === true) {
- this._waitingFullAliasLayoutData--;
- }
- } else {
- logger
- .error(
- "setWaitingForFullAliasLayoutData value must be boolean, but found: ",
- value);
- }
-}
-
-ServerConnector.isWaitingForFullAliasLayoutData = function(layoutId, aliasId) {
- if (!isInt(layoutId)) {
- logger.error(
- "isWaitingForFullAliasLayoutData layoutId must be integer, but found: ",
- layoutId);
- }
- if (!isInt(aliasId)) {
- logger.error(
- "isWaitingForFullAliasLayoutData aliasId must be integer, but found: ",
- aliasId);
- }
-
- var val = this._waitingFullAliasLayoutDataById[layoutId+"-"+aliasId];
- if (val==null) {
- return false;
- }
- return val;
-}
-
-/**
- * Sets waitingForAliasData flag that monitors if we are waiting for the data
- * about aliases from server.
- *
- * @param value
- * new value of the waitingForAliasData field
- */
-ServerConnector.setWaitingForAliasData = function(aliasId, value) {
- if (isInt(aliasId)) {
- var oldVal = this._waitingForAliasDataByAliasId[aliasId];
- this._waitingForAliasDataByAliasId[aliasId] = value;
- if (value === true) {
- if (oldVal !== true) {
- this._waitingForAliasData++;
- }
- } else if (value === false) {
- if (oldVal === true) {
- this._waitingForAliasData--;
- }
- } else {
- logger.error("WaitingForAliasData value must be boolean, but found: ",
- value);
- }
- } else {
- logger.error("WaitingForAliasData aliasId must be integer, but found: ",
- aliasId);
- }
-};
-
-/**
- * Sets waitingForReactionLayoutData flag that monitors if we are waiting for
- * the data about reactions in a layout from server.
- *
- * @param value
- * new value of the waitingForReactionLayoutData field
- */
-ServerConnector.setWaitingForReactionLayoutData = function(layoutId, value) {
- if (isInt(layoutId)) {
- var oldVal = this._waitingForReactionLayoutDataByLayoutId[layoutId];
- this._waitingForReactionLayoutDataByLayoutId[layoutId] = value;
- if (value === true) {
- if (oldVal !== true) {
- this._waitingForReactionLayoutData++;
- }
- } else if (value === false) {
- if (oldVal === true) {
- this._waitingForReactionLayoutData--;
- }
- } else {
- logger.error(
- "WaitingForReactionLayoutData value must be boolean, but found: ",
- value);
- }
- } else {
- logger.error(
- "WaitingForReactionLayoutData layoutId must be integer, but found: ",
- layoutId);
- }
-};
-/**
- * Sets waitingForReactionData flag that monitors if we are waiting for the data
- * about reactions from server.
- *
- * @param value
- * new value of the waitingForReactionData field
- */
-ServerConnector.setWaitingForReactionData = function(reactionId, value) {
- if (isInt(reactionId)) {
- var oldVal = this._waitingForReactionDataByReactionId[reactionId];
- this._waitingForReactionDataByReactionId[reactionId] = value;
- if (value === true) {
- if (oldVal !== true) {
- this._waitingForReactionData++;
- }
- } else if (value === false) {
- if (oldVal === true) {
- this._waitingForReactionData--;
- }
- } else {
- logger.error("WaitingForReactionData value must be boolean, but found: ",
- value);
- }
- } else {
- logger.error(
- "WaitingForReactionData reactionId must be integer, but found: ",
- reactionId);
- }
-};
-
-ServerConnector.setCustomMap = function(customMap) {
- this._customMap = customMap;
-};
-
-ServerConnector.getCustomMap = function() {
- return this._customMap;
-};
-
-ServerConnector.addAliasesForLayout = function(layoutId, jsonAliases) {
- this.setWaitingForAliasLayoutData(parseInt(layoutId), false);
- this.getCustomMap().addAliasesForLayout(layoutId, jsonAliases);
-};
-
-ServerConnector.updateAliasesForLayout = function(layoutId, jsonAliases) {
- var arr = JSON.parse(jsonAliases);
- for (var i=0;i<arr.length;i++) {
- this.setWaitingForFullAliasLayoutData(parseInt(layoutId), parseInt(arr[i].idObject), false);
- }
- this.getCustomMap().updateAliasesForLayout(layoutId, jsonAliases);
-};
-
-ServerConnector.addAliases = function(aliases) {
- for (var i = 0; i < aliases.length; i++) {
- this.setWaitingForAliasData(parseInt(aliases[i].idObject), false);
- }
- this.getCustomMap().addAliases(aliases);
-};
-
-ServerConnector.addReactionsForLayout = function(layoutId, jsonReactions) {
- this.setWaitingForReactionLayoutData(parseInt(layoutId), false);
- this.getCustomMap().addReactionsForLayout(layoutId, jsonReactions);
-};
-
-ServerConnector.addReactions = function(jsonReactions) {
- var arr = JSON.parse(jsonReactions);
- for (var i = 0; i < arr.length; i++) {
- this.setWaitingForReactionData(parseInt(arr[i].idObject), false);
- }
- this.getCustomMap().addReactions(jsonReactions);
-};
-
-ServerConnector.searchByCoord = function(modelId, latLngCoordinates) {
- _searchByCoord([ {
- name : 'submodelId',
- value : modelId
- }, {
- name : 'latCoord',
- value : latLngCoordinates.lat()
- }, {
- name : 'lngCoord',
- value : latLngCoordinates.lng()
- } ]);
-};
-
-ServerConnector.requestUpdateCommentList = function(modelId, latLngCoordinates) {
- _updateCommentList([ {
- name : 'submodelId',
- value : modelId
- }, {
- name : 'latCoord',
- value : latLngCoordinates.lat()
- }, {
- name : 'lngCoord',
- value : latLngCoordinates.lng()
- } ]);
-};
-
-ServerConnector.sendReferenceGenomeDetailRequest = function(type, version) {
- logger.debug("Send request", type, version);
- _sendReferenceGenomeDetailRequest([ {
- name : 'type',
- value : type
- }, {
- name : 'version',
- value : version
- }]);
-};
-ServerConnector.updateReferenceGenomeData = function(organismId, type, version, jsonObj) {
- this.getCustomMap().updateReferenceGenome(type, version, jsonObj);
-};
-
+/**
+ * This object contains methods that will communicate with server.
+ */
+ServerConnector = new Object();
+
+/**
+ * List of {@link OverlayCollection} that was added to the server connector. It
+ * describes list of all overlays that communicate with server.
+ */
+ServerConnector._overlays = [];
+
+/**
+ * Associative array with methods that should be used for comunication of the
+ * {@link OverlayCollection} from _overlays field.
+ */
+ServerConnector._overlayMethods = [];
+
+/**
+ * Form where fields passed to/from server are stored.
+ */
+ServerConnector.formIdentifier = "_gmapForm";
+
+/**
+ * Variable describing when was last transmition of data (location of the map,
+ * zoom level, etc.) to the server session.
+ */
+ServerConnector.lastActualization = 0;
+
+ServerConnector._customMap = null;
+
+/**
+ * Number of requests send to server about AliasLayout data.
+ */
+ServerConnector._waitingForAliasLayoutData = 0;
+ServerConnector._waitingForAliasLayoutDataByLayoutId = [];
+
+ServerConnector._waitingFullAliasLayoutData = 0;
+ServerConnector._waitingFullAliasLayoutDataById = [];
+
+/**
+ * Number of requests send to server about AliasData data.
+ */
+ServerConnector._waitingForAliasData = 0;
+ServerConnector._waitingForAliasDataByAliasId = [];
+
+/**
+ * Number of requests send to server about ReactionLayout data.
+ */
+ServerConnector._waitingForReactionLayoutData = 0;
+ServerConnector._waitingForReactionLayoutDataByLayoutId = [];
+
+/**
+ * Number of requests send to server about ReactionData data.
+ */
+ServerConnector._waitingForReactionData = 0;
+ServerConnector._waitingForReactionDataByReactionId = [];
+
+/**
+ * Get name of the file that should be used as logo.
+ */
+ServerConnector.getLogoImg = function() {
+ return document.getElementById('logoImg').value;
+};
+
+/**
+ * Get link to the website that should be accessed when clicking on
+ * {@link ServerConnector.getLogoImg}.
+ */
+ServerConnector.getLogoLink = function() {
+ return document.getElementById('logoLink').value;
+};
+
+/**
+ * Get zoom level of the {@link CustomMap} at which it was last browsed.
+ */
+ServerConnector.getZoomLevel = function() {
+ return document.getElementById(ServerConnector.formIdentifier + ':zoomLevel').value;
+};
+
+/**
+ * Set zoom level for {@link CustomMap} on the server side.
+ */
+ServerConnector.setZoomLevel = function(value) {
+ document.getElementById(ServerConnector.formIdentifier + ':zoomLevel').value = ""
+ + value;
+};
+
+/**
+ * Set x coordinate for {@link CustomMap} on the server side.
+ */
+ServerConnector.setCenterCoordinateX = function(value) {
+ document
+ .getElementById(ServerConnector.formIdentifier + ':centerCoordinateX').value = ""
+ + value;
+};
+
+/**
+ * Get x coordinate of the {@link CustomMap} at which it was last browsed.
+ */
+ServerConnector.getCenterCoordinateX = function() {
+ var result = parseFloat(document
+ .getElementById(ServerConnector.formIdentifier + ':centerCoordinateX').value);
+ return result;
+};
+
+/**
+ * Set y coordinate for {@link CustomMap} on the server side.
+ */
+ServerConnector.setCenterCoordinateY = function(value) {
+ document
+ .getElementById(ServerConnector.formIdentifier + ':centerCoordinateY').value = ""
+ + value;
+};
+
+/**
+ * Get y coordinate of the {@link CustomMap} at which it was last browsed.
+ */
+ServerConnector.getCenterCoordinateY = function() {
+ var result = parseFloat(document
+ .getElementById(ServerConnector.formIdentifier + ':centerCoordinateY').value);
+ return result;
+};
+
+/**
+ * Set layout that is currently browsed for {@link CustomMap} on the server
+ * side.
+ */
+ServerConnector.setSelectedLayout = function(value) {
+ document.getElementById(ServerConnector.formIdentifier + ':selectedLayout').value = ""
+ + value;
+};
+/**
+ * Sets list of layouts visualized by javascript.
+ */
+ServerConnector.setVisibleLayouts = function(value) {
+ document.getElementById(ServerConnector.formIdentifier + ':visibleLayouts').value = value;
+}
+
+/**
+ * Get layout of the {@link CustomMap} which was last browsed.
+ */
+ServerConnector.getSelectedLayout = function() {
+ return document.getElementById(ServerConnector.formIdentifier
+ + ':selectedLayout').value;
+};
+
+/**
+ * Sends data about coordinates/zoom level etc. to the server. Method checks if
+ * the transmition is not done to often (at most once per second)
+ */
+ServerConnector.actualizeSessionData = function(value) {
+ var timestamp = new Date().getTime();
+ // we send the data with at least 1 second time distance
+ if (timestamp > ServerConnector.lastActualization) {
+ ServerConnector.lastActualization = timestamp + 1000;
+ setTimeout(function() {
+ ServerConnector.actualizeParams();
+ }, 1000);
+ }
+};
+
+/**
+ * Sends data about coordinates/zoom level etc. to the server. Sending is
+ * performed immediatelly.
+ *
+ * @see ServerConnector.actualizeSessionData
+ */
+ServerConnector.actualizeParams = function() {
+ actualizeParams();
+};
+
+/**
+ * Sets search query that will be handled by server.
+ */
+ServerConnector.setSearchQuery = function(value) {
+ document.getElementById(ServerConnector.formIdentifier + ':mapParam').value = ""
+ + value;
+};
+
+/**
+ * Sets data mining query that will be handled by server.
+ */
+ServerConnector.setDataMiningQuery = function(value) {
+ document.getElementById(ServerConnector.formIdentifier
+ + ':missingConnectionParam').value = "" + value;
+};
+
+/**
+ * Sets drug search query that will be handled by server.
+ */
+ServerConnector.setDrugQuery = function(value) {
+ document.getElementById(ServerConnector.formIdentifier + ':drugParam').value = ""
+ + value;
+};
+
+/**
+ * Sets comment query that will be handled by server.
+ */
+ServerConnector.setCommentQuery = function(value) {
+ logger.error("ServerConnector.setCommentQuery: Not implemented");
+ document.getElementById(ServerConnector.formIdentifier + ':commentParam').value = ""
+ + value;
+};
+
+/**
+ * Sets selected polygon. This might be in futer used oto extract/analyze data
+ * in the polygon by the server side.
+ */
+ServerConnector.setSelectedPolygon = function(value) {
+ document.getElementById(ServerConnector.formIdentifier + ':selectedPolygon').value = ""
+ + value;
+ document.getElementById(ServerConnector.formIdentifier
+ + ':selectedDrugPolygon').value = "" + value;
+};
+
+/**
+ * Sets identifier of the model where selected polygon (@see
+ * ServerConnector.setSelectedPolygon) was selected.
+ */
+ServerConnector.setExportModelId = function(value) {
+ document.getElementById(ServerConnector.formIdentifier + ':exportModelId').value = ""
+ + value;
+};
+
+/**
+ * Sets flag marking if the comments are visible or not.
+ */
+ServerConnector.setShowComments = function(value) {
+ _setShowComments([ {
+ name : 'showComments',
+ value : value
+ } ]);
+};
+
+/**
+ * Search for similar data mining entries on the map.
+ */
+ServerConnector.showSimilarDataMining = function(param) {
+ document.getElementById(ServerConnector.formIdentifier + ':geneName').value = ""
+ + param;
+ searchMissingConnections();
+};
+
+/**
+ * Ask server to send list of aliases that were highlighted in the layout with a
+ * given identifier.
+ *
+ * @param identifier
+ * of the layout
+ */
+ServerConnector.retreiveActiveAliasesForLayout = function(identifier) {
+ this.setWaitingForAliasLayoutData(parseInt(identifier), true);
+ _retreiveActiveAliasesForLayout([ {
+ name : 'layoutId',
+ value : identifier
+ } ]);
+};
+
+ServerConnector.retreiveFullAliasesForLayout = function(layoutId, aliasId, modelId) {
+ this.setWaitingForFullAliasLayoutData(parseInt(layoutId),parseInt(aliasId), true);
+ _retreiveFullAliasesForLayout([ {
+ name : 'layoutId',
+ value : layoutId,
+ }, {
+ name : 'ids',
+ value : JSON.stringify([[modelId, aliasId]]),
+ },
+ ]);
+};
+
+/**
+ * Ask server to send list of reactions that were highlighted in the layout with
+ * a given identifier.
+ *
+ * @param identifier
+ * of the layout
+ */
+ServerConnector.retreiveActiveReactionsForLayout = function(identifier) {
+ this.setWaitingForReactionLayoutData(parseInt(identifier), true);
+ _retreiveActiveReactionsForLayout([ {
+ name : 'layoutId',
+ value : identifier
+ } ]);
+};
+
+/**
+ * Ask server to send list of light information about aliases.
+ *
+ * @param ids
+ * list of alias identifiers, every identifier is an array with two
+ * values: modelId, aliasId
+ */
+ServerConnector.retreiveLightAliases = function(ids) {
+ for (var i = 0; i < ids.length; i++) {
+ this.setWaitingForAliasData(parseInt(ids[i][1]), true);
+ }
+ _retreiveLightAliases([ {
+ name : 'ids',
+ value : JSON.stringify(ids)
+ } ]);
+};
+
+/**
+ * Ask server to send list of full information about aliases.
+ *
+ * @param ids
+ * list of alias identifiers, every identifier is an array with two
+ * values: modelId, aliasId
+ */
+ServerConnector.retreiveFullAliases = function(ids) {
+ _retreiveFullAliases([ {
+ name : 'ids',
+ value : JSON.stringify(ids)
+ } ]);
+};
+
+/**
+ * Ask server to send list of light information about reactions.
+ *
+ * @param ids
+ * list of reaction identifiers, every identifier is an array with
+ * two values: modelId, reactionId
+ */
+ServerConnector.retreiveLightReactions = function(ids) {
+ for (var i = 0; i < ids.length; i++) {
+ this.setWaitingForReactionData(parseInt(ids[i][1]), true);
+ }
+ _retreiveLightReactions([ {
+ name : 'ids',
+ value : JSON.stringify(ids)
+ } ]);
+};
+
+/**
+ * Sends request to server to refresh data for overlay with a given name.
+ *
+ * @param overlayName
+ * name of the overlay
+ */
+ServerConnector.sendRefreshRequest = function(overlayName) {
+ var functions = ServerConnector._overlayMethods[overlayName];
+ if (functions != null) {
+ var refreshFunction = functions.refreshFunction;
+ if (refreshFunction != null) {
+ refreshFunction();
+ } else {
+ logger.warn("Refresh function for " + overlayName + " doesn't exist");
+ }
+ } else {
+ logger.warn("[Refresh function] Unknown overlay: ", overlayName);
+ }
+};
+
+/**
+ * Adds {@link OverlayCollection} to ServerConnector.
+ */
+ServerConnector.addOverlayCollection = function(overlay) {
+ if (ServerConnector._overlayMethods[overlay.name] != null) {
+ if (ServerConnector._overlays[overlay.name] != null) {
+ logger.warn("Overlay with name " + overlay.name + " already added");
+ return;
+ }
+ ServerConnector._overlays[overlay.name] = overlay;
+ if (ServerConnector._overlayMethods[overlay.name].initFunction != null) {
+ ServerConnector._overlayMethods[overlay.name].initFunction();
+ } else {
+ logger.warn("Cannot initialize overlay: " + overlay);
+ }
+ } else {
+ logger.warn("Unknown overlay: ", overlay);
+ }
+};
+
+/**
+ * Method that should be called by server to update data in overlay.
+ *
+ * @param overlayName
+ * name of overlay for which the data is sent
+ * @param data
+ * new data for overlay
+ * @param fitBounds
+ * should the map call fitBounds after update
+ */
+ServerConnector.updateOverlayCollection = function(overlayName, data, fitBounds) {
+ logger.debug("Updating: " + overlayName);
+ var overlay = ServerConnector._overlays[overlayName];
+ if (overlay != null) {
+ overlay.updateOverlays(data, fitBounds);
+ } else {
+ logger.warn("Overlay " + overlayName
+ + " cannot be updated. It doesn't exist");
+ }
+}
+
+/**
+ * Name of the overlay for 'search' overlay.
+ */
+ServerConnector.SEARCH_OVERLAY_NAME = 'search';
+
+/**
+ * Name of the overlay for 'data mining' overlay.
+ */
+ServerConnector.DATA_MINING_OVERLAY_NAME = 'missingConnection';
+
+/**
+ * Name of the overlay for 'drug' overlay.
+ */
+ServerConnector.DRUG_OVERLAY_NAME = 'drug';
+
+/**
+ * Name of the overlay for 'chemical' overlay.
+ */
+ServerConnector.CHEMICAL_OVERLAY_NAME = 'chemical';
+
+/**
+ * Name of the overlay for 'comment' overlay.
+ */
+ServerConnector.COMMENT_OVERLAY_NAME = 'comment';
+
+/**
+ * Name of the overlay for 'mirna' overlay.
+ */
+ServerConnector.MI_RNA_OVERLAY_NAME = 'mirna';
+
+/**
+ * Register 'search' overlay on the server.
+ */
+ServerConnector.registerSearchOverlay = function() {
+ _registerSearchOverlayCollection([ {
+ name : "overlayName",
+ value : ServerConnector.SEARCH_OVERLAY_NAME,
+ } ]);
+};
+
+/**
+ * Sends request to the server to refresh data in 'search' overlay.
+ */
+ServerConnector.refreshSearchOverlay = function() {
+ _refreshSearchOverlayCollection();
+};
+
+/**
+ * Clear data related to 'search' overlay..
+ */
+ServerConnector.clearSearchOverlay = function() {
+ _clearSearchOverlayCollection();
+};
+
+/**
+ * Register 'data mining' overlay on the server.
+ */
+ServerConnector.registerDataMiningOverlay = function() {
+ _registerMissingConnectionOverlayCollection([ {
+ name : "overlayName",
+ value : ServerConnector.DATA_MINING_OVERLAY_NAME,
+ } ]);
+};
+
+/**
+ * Sends request to the server to refresh data in 'data mining' overlay.
+ */
+ServerConnector.refreshDataMiningOverlay = function() {
+ _refreshMissingConnectionOverlayCollection();
+};
+
+/**
+ * Clear data related to 'data mining' overlay.
+ */
+ServerConnector.clearDataMiningOverlay = function() {
+ _clearMissingConnectionOverlayCollection();
+};
+
+/**
+ * Register 'drug' overlay on the server.
+ */
+ServerConnector.registerDrugOverlay = function() {
+ _registerDrugOverlayCollection([ {
+ name : "overlayName",
+ value : ServerConnector.DRUG_OVERLAY_NAME,
+ } ]);
+};
+
+ServerConnector.requestDrugDetailDataFunction = function(identfiedElement, id) {
+ logger.debug("Requesting drug details: ", identfiedElement, id);
+ _requestDrugDetailDataFunction([ {
+ name : "searchResultIdentifier",
+ value : id,
+ }, {
+ name : "objectIdentifier",
+ value : identfiedElement.getId(),
+ }, {
+ name : "modelIdentifier",
+ value : identfiedElement.getModelId(),
+ }, {
+ name : "type",
+ value : identfiedElement.getType(),
+ } ]);
+};
+ServerConnector.requestCommentDetailDataFunction = function(identfiedElement,
+ id) {
+ _requestCommentDetailDataFunction([ {
+ name : "searchResultIdentifier",
+ value : id,
+ }, {
+ name : "objectIdentifier",
+ value : identfiedElement.getId(),
+ }, {
+ name : "modelIdentifier",
+ value : identfiedElement.getModelId(),
+ }, {
+ name : "type",
+ value : identfiedElement.getType(),
+ } ]);
+};
+
+/**
+ * Sends request to the server to refresh data in 'drug' overlay.
+ */
+ServerConnector.refreshDrugOverlay = function() {
+ _refreshDrugOverlayCollection();
+};
+
+/**
+ * Clear data related to 'drug' overlay.
+ */
+ServerConnector.clearDrugOverlay = function() {
+ _clearDrugOverlayCollection();
+};
+
+ServerConnector.registerChemicalOverlay = function() {
+ _registerChemicalOverlayCollection([ {
+ name : "overlayName",
+ value : ServerConnector.CHEMICAL_OVERLAY_NAME,
+ } ]);
+};
+
+ServerConnector.requestChemicalDetailDataFunction = function(identfiedElement,
+ id) {
+ _requestChemicalDetailDataFunction([ {
+ name : "searchResultIdentifier",
+ value : id,
+ }, {
+ name : "objectIdentifier",
+ value : identfiedElement.getId(),
+ }, {
+ name : "modelIdentifier",
+ value : identfiedElement.getModelId(),
+ }, {
+ name : "type",
+ value : identfiedElement.getType(),
+ } ]);
+};
+
+/**
+ * Sends request to the server to refresh data in 'drug' overlay.
+ */
+ServerConnector.refreshChemicalOverlay = function() {
+ _refreshChemicalOverlayCollection();
+};
+
+/**
+ * Clear data related to 'chemical' overlay.
+ */
+ServerConnector.clearChemicalOverlay = function() {
+ _clearChemicalOverlayCollection();
+};
+
+/**
+ * Register 'comment' overlay on the server.
+ */
+ServerConnector.registerCommentOverlay = function() {
+ _registerCommentOverlayCollection([ {
+ name : "overlayName",
+ value : ServerConnector.COMMENT_OVERLAY_NAME,
+ } ]);
+};
+
+/**
+ * Sends request to the server to refresh data in 'comment' overlay.
+ */
+ServerConnector.refreshCommentOverlay = function() {
+ _refreshCommentOverlayCollection();
+};
+
+/**
+ * Clear data related to 'comment' overlay.
+ */
+ServerConnector.clearCommentOverlay = function() {
+ _clearCommentOverlayCollection();
+};
+
+/**
+ * Clear data related to 'data mining' overlay.
+ */
+ServerConnector.clearDataMiningOverlay = function() {
+ _clearMissingConnectionOverlayCollection();
+};
+
+/**
+ * Register 'drug' overlay on the server.
+ */
+ServerConnector.registerMiRnaOverlay = function() {
+ _registerMiRnaOverlayCollection([ {
+ name : "overlayName",
+ value : ServerConnector.MI_RNA_OVERLAY_NAME,
+ } ]);
+};
+
+ServerConnector.requestMiRnaDetailDataFunction = function(identfiedElement, id) {
+ _requestMiRnaDetailDataFunction([ {
+ name : "searchResultIdentifier",
+ value : id,
+ }, {
+ name : "objectIdentifier",
+ value : identfiedElement.getId(),
+ }, {
+ name : "modelIdentifier",
+ value : identfiedElement.getModelId(),
+ }, {
+ name : "type",
+ value : identfiedElement.getType(),
+ } ]);
+};
+
+/**
+ * Sends request to the server to refresh data in 'drug' overlay.
+ */
+ServerConnector.refreshMiRnaOverlay = function() {
+ _refreshMiRnaOverlayCollection();
+};
+
+/**
+ * Clear data related to 'mirna' overlay.
+ */
+ServerConnector.clearMiRnaOverlay = function() {
+ _clearMiRnaOverlayCollection();
+};
+
+/**
+ * Define pack of methods for 'search' overlay.
+ */
+ServerConnector._overlayMethods[ServerConnector.SEARCH_OVERLAY_NAME] = {
+ initFunction : ServerConnector.registerSearchOverlay,
+ refreshFunction : ServerConnector.refreshSearchOverlay,
+ clearFunction : ServerConnector.clearSearchOverlay,
+};
+
+/**
+ * Define pack of methods for 'data minig' overlay.
+ */
+ServerConnector._overlayMethods[ServerConnector.DATA_MINING_OVERLAY_NAME] = {
+ initFunction : ServerConnector.registerDataMiningOverlay,
+ refreshFunction : ServerConnector.refreshDataMiningOverlay,
+ clearFunction : ServerConnector.clearDataMiningOverlay,
+};
+
+/**
+ * Define pack of methods for 'drug' overlay.
+ */
+ServerConnector._overlayMethods[ServerConnector.DRUG_OVERLAY_NAME] = {
+ initFunction : ServerConnector.registerDrugOverlay,
+ refreshFunction : ServerConnector.refreshDrugOverlay,
+ clearFunction : ServerConnector.clearDrugOverlay,
+ requestDetailDataFunction : ServerConnector.requestDrugDetailDataFunction,
+};
+
+/**
+ * Define pack of methods for 'chemical' overlay.
+ */
+ServerConnector._overlayMethods[ServerConnector.CHEMICAL_OVERLAY_NAME] = {
+ initFunction : ServerConnector.registerChemicalOverlay,
+ refreshFunction : ServerConnector.refreshChemicalOverlay,
+ clearFunction : ServerConnector.clearChemicalOverlay,
+ requestDetailDataFunction : ServerConnector.requestChemicalDetailDataFunction,
+};
+
+/**
+ * Define pack of methods for 'comment' overlay.
+ */
+ServerConnector._overlayMethods[ServerConnector.COMMENT_OVERLAY_NAME] = {
+ initFunction : ServerConnector.registerCommentOverlay,
+ refreshFunction : ServerConnector.refreshCommentOverlay,
+ clearFunction : ServerConnector.clearCommentOverlay,
+ requestDetailDataFunction : ServerConnector.requestCommentDetailDataFunction,
+};
+
+ServerConnector._overlayMethods[ServerConnector.MI_RNA_OVERLAY_NAME] = {
+ initFunction : ServerConnector.registerMiRnaOverlay,
+ refreshFunction : ServerConnector.refreshMiRnaOverlay,
+ clearFunction : ServerConnector.clearMiRnaOverlay,
+ requestDetailDataFunction : ServerConnector.requestMiRnaDetailDataFunction,
+};
+
+ServerConnector.sendClearRequest = function(overlayName) {
+ var functions = ServerConnector._overlayMethods[overlayName];
+ if (functions != null) {
+ var clearFunction = functions.clearFunction;
+ if (clearFunction != null) {
+ clearFunction();
+ } else {
+ logger.warn("Clear function for " + overlayName + " doesn't exist");
+ }
+ } else {
+ logger.warn("[Clear function] Unknown overlay: ", overlayName);
+ }
+};
+
+ServerConnector.setOverlayResultIds = function(overlayName, ids) {
+ var overlay = this._overlays[overlayName];
+ if (overlay != null) {
+ overlay.setResultsIds(ids);
+ } else {
+ logger.warn("Overlay '" + overlayName + "' doesn't exist");
+ }
+};
+
+ServerConnector.sendOverlayDetailDataRequest = function(overlayName,
+ identifiedElement, general) {
+ var overlay = ServerConnector._overlays[overlayName];
+ if (overlay == null) {
+ logger.warn("Unknown overlay: " + overlayName);
+ return;
+ }
+ var functions = ServerConnector._overlayMethods[overlayName];
+ if (functions != null) {
+ var requestDetailDataFunction = functions.requestDetailDataFunction;
+ if (requestDetailDataFunction != null) {
+ var missingData = overlay.getMissingDetailDataIds(identifiedElement,
+ general);
+ if (missingData.length == 0) {
+ logger
+ .warn(
+ "request of missing data called for empty data set... overlay name = ",
+ overlayName, "general: ", general);
+ }
+ for (var i = 0; i < missingData.length; i++) {
+ requestDetailDataFunction(identifiedElement, missingData[i]);
+ }
+ } else {
+ logger.warn("Request detail data function for " + overlayName
+ + " doesn't exist");
+ }
+ } else {
+ logger.warn("[Clear function] Unknown overlay: ", overlayName);
+ }
+
+};
+
+ServerConnector.updateOverviewElementDetailData = function(overlayName,
+ searchResultIdentifier, identifiedElement, data) {
+ var overlay = this._overlays[overlayName];
+ if (overlay != null) {
+ overlay.updateOverviewElementDetailData(identifiedElement,
+ searchResultIdentifier, data);
+ } else {
+ logger.warn("Overlay '" + overlayName + "' doesn't exist");
+ }
+};
+
+/**
+ * Returns <code>true</code> if we are waiting for any kind of data from
+ * server, <code>false</code> otherwise.
+ *
+ * @returns {Boolean}: <code>true</code> if we are waiting for any kind of
+ * data from server, <code>false</code> otherwise.
+ */
+ServerConnector.isWaitingForData = function() {
+ var result = (this._waitingForAliasLayoutData != 0) || //
+ (this._waitingForAliasData != 0) || //
+ (this._waitingForReactionLayoutData != 0) || //
+ (this._waitingForReactionData != 0);
+ return result;
+};
+
+/**
+ * Sets waitingForAliasLayoutData flag that monitors if we are waiting for the
+ * data about aliases in a layout from server.
+ *
+ * @param value
+ * new value of the waitingForAliasLayoutData field
+ */
+ServerConnector.setWaitingForAliasLayoutData = function(layoutId, value) {
+ if (isInt(layoutId)) {
+ var oldVal = this._waitingForAliasLayoutDataByLayoutId[layoutId];
+ this._waitingForAliasLayoutDataByLayoutId[layoutId] = value;
+ if (value === true) {
+ if (oldVal !== true) {
+ this._waitingForAliasLayoutData++;
+ }
+ } else if (value === false) {
+ if (oldVal === true) {
+ this._waitingForAliasLayoutData--;
+ }
+ } else {
+ logger
+ .error(
+ "WaitingForAliasLayoutData value must be boolean, but found: ",
+ value);
+ }
+ } else {
+ logger.error(
+ "WaitingForAliasLayoutData layoutId must be integer, but found: ",
+ layoutId);
+ }
+}
+
+ServerConnector.setWaitingForFullAliasLayoutData = function(layoutId, aliasId, value) {
+ if (!isInt(layoutId)) {
+ logger.error(
+ "setWaitingForFullAliasLayoutData layoutId must be integer, but found: ",
+ layoutId);
+ }
+ if (!isInt(aliasId)) {
+ logger.error(
+ "setWaitingForFullAliasLayoutData aliasId must be integer, but found: ",
+ aliasId);
+ }
+
+ var oldVal = this._waitingFullAliasLayoutDataById[layoutId+"-"+aliasId];
+ this._waitingFullAliasLayoutDataById[layoutId+"-"+aliasId] = value;
+ if (value === true) {
+ if (oldVal !== true) {
+ this._waitingFullAliasLayoutData++;
+ }
+ } else if (value === false) {
+ if (oldVal === true) {
+ this._waitingFullAliasLayoutData--;
+ }
+ } else {
+ logger
+ .error(
+ "setWaitingForFullAliasLayoutData value must be boolean, but found: ",
+ value);
+ }
+}
+
+ServerConnector.isWaitingForFullAliasLayoutData = function(layoutId, aliasId) {
+ if (!isInt(layoutId)) {
+ logger.error(
+ "isWaitingForFullAliasLayoutData layoutId must be integer, but found: ",
+ layoutId);
+ }
+ if (!isInt(aliasId)) {
+ logger.error(
+ "isWaitingForFullAliasLayoutData aliasId must be integer, but found: ",
+ aliasId);
+ }
+
+ var val = this._waitingFullAliasLayoutDataById[layoutId+"-"+aliasId];
+ if (val==null) {
+ return false;
+ }
+ return val;
+}
+
+/**
+ * Sets waitingForAliasData flag that monitors if we are waiting for the data
+ * about aliases from server.
+ *
+ * @param value
+ * new value of the waitingForAliasData field
+ */
+ServerConnector.setWaitingForAliasData = function(aliasId, value) {
+ if (isInt(aliasId)) {
+ var oldVal = this._waitingForAliasDataByAliasId[aliasId];
+ this._waitingForAliasDataByAliasId[aliasId] = value;
+ if (value === true) {
+ if (oldVal !== true) {
+ this._waitingForAliasData++;
+ }
+ } else if (value === false) {
+ if (oldVal === true) {
+ this._waitingForAliasData--;
+ }
+ } else {
+ logger.error("WaitingForAliasData value must be boolean, but found: ",
+ value);
+ }
+ } else {
+ logger.error("WaitingForAliasData aliasId must be integer, but found: ",
+ aliasId);
+ }
+};
+
+/**
+ * Sets waitingForReactionLayoutData flag that monitors if we are waiting for
+ * the data about reactions in a layout from server.
+ *
+ * @param value
+ * new value of the waitingForReactionLayoutData field
+ */
+ServerConnector.setWaitingForReactionLayoutData = function(layoutId, value) {
+ if (isInt(layoutId)) {
+ var oldVal = this._waitingForReactionLayoutDataByLayoutId[layoutId];
+ this._waitingForReactionLayoutDataByLayoutId[layoutId] = value;
+ if (value === true) {
+ if (oldVal !== true) {
+ this._waitingForReactionLayoutData++;
+ }
+ } else if (value === false) {
+ if (oldVal === true) {
+ this._waitingForReactionLayoutData--;
+ }
+ } else {
+ logger.error(
+ "WaitingForReactionLayoutData value must be boolean, but found: ",
+ value);
+ }
+ } else {
+ logger.error(
+ "WaitingForReactionLayoutData layoutId must be integer, but found: ",
+ layoutId);
+ }
+};
+/**
+ * Sets waitingForReactionData flag that monitors if we are waiting for the data
+ * about reactions from server.
+ *
+ * @param value
+ * new value of the waitingForReactionData field
+ */
+ServerConnector.setWaitingForReactionData = function(reactionId, value) {
+ if (isInt(reactionId)) {
+ var oldVal = this._waitingForReactionDataByReactionId[reactionId];
+ this._waitingForReactionDataByReactionId[reactionId] = value;
+ if (value === true) {
+ if (oldVal !== true) {
+ this._waitingForReactionData++;
+ }
+ } else if (value === false) {
+ if (oldVal === true) {
+ this._waitingForReactionData--;
+ }
+ } else {
+ logger.error("WaitingForReactionData value must be boolean, but found: ",
+ value);
+ }
+ } else {
+ logger.error(
+ "WaitingForReactionData reactionId must be integer, but found: ",
+ reactionId);
+ }
+};
+
+ServerConnector.setCustomMap = function(customMap) {
+ this._customMap = customMap;
+};
+
+ServerConnector.getCustomMap = function() {
+ return this._customMap;
+};
+
+ServerConnector.addAliasesForLayout = function(layoutId, jsonAliases) {
+ this.setWaitingForAliasLayoutData(parseInt(layoutId), false);
+ this.getCustomMap().addAliasesForLayout(layoutId, jsonAliases);
+};
+
+ServerConnector.updateAliasesForLayout = function(layoutId, jsonAliases) {
+ var arr = JSON.parse(jsonAliases);
+ for (var i=0;i<arr.length;i++) {
+ this.setWaitingForFullAliasLayoutData(parseInt(layoutId), parseInt(arr[i].idObject), false);
+ }
+ this.getCustomMap().updateAliasesForLayout(layoutId, jsonAliases);
+};
+
+ServerConnector.addAliases = function(aliases) {
+ for (var i = 0; i < aliases.length; i++) {
+ this.setWaitingForAliasData(parseInt(aliases[i].idObject), false);
+ }
+ this.getCustomMap().addAliases(aliases);
+};
+
+ServerConnector.addReactionsForLayout = function(layoutId, jsonReactions) {
+ this.setWaitingForReactionLayoutData(parseInt(layoutId), false);
+ this.getCustomMap().addReactionsForLayout(layoutId, jsonReactions);
+};
+
+ServerConnector.addReactions = function(jsonReactions) {
+ var arr = JSON.parse(jsonReactions);
+ for (var i = 0; i < arr.length; i++) {
+ this.setWaitingForReactionData(parseInt(arr[i].idObject), false);
+ }
+ this.getCustomMap().addReactions(jsonReactions);
+};
+
+ServerConnector.searchByCoord = function(modelId, latLngCoordinates) {
+ _searchByCoord([ {
+ name : 'submodelId',
+ value : modelId
+ }, {
+ name : 'latCoord',
+ value : latLngCoordinates.lat()
+ }, {
+ name : 'lngCoord',
+ value : latLngCoordinates.lng()
+ } ]);
+};
+
+ServerConnector.requestUpdateCommentList = function(modelId, latLngCoordinates) {
+ _updateCommentList([ {
+ name : 'submodelId',
+ value : modelId
+ }, {
+ name : 'latCoord',
+ value : latLngCoordinates.lat()
+ }, {
+ name : 'lngCoord',
+ value : latLngCoordinates.lng()
+ } ]);
+};
+
+ServerConnector.sendReferenceGenomeDetailRequest = function(type, version) {
+ logger.debug("Send request", type, version);
+ _sendReferenceGenomeDetailRequest([ {
+ name : 'type',
+ value : type
+ }, {
+ name : 'version',
+ value : version
+ }]);
+};
+ServerConnector.updateReferenceGenomeData = function(organismId, type, version, jsonObj) {
+ this.getCustomMap().updateReferenceGenome(type, version, jsonObj);
+};
+
+ServerConnector.getMinOverlayColorInt = function() {
+ var color = document.getElementById("overlayConfigForm:userMinColor").value;
+ if (color=="") {
+ color = document.getElementById("overlayConfigForm:systemMinColor").value;
+ }
+ color = parseInt(color, 16);
+ var color = (color & 0xFFFFFF);
+ return color;
+};
+
+ServerConnector.getMaxOverlayColorInt = function() {
+ var color = document.getElementById("overlayConfigForm:userMaxColor").value;
+ if (color=="") {
+ color = document.getElementById("overlayConfigForm:systemMaxColor").value;
+ }
+ color = parseInt(color, 16);
+ var color = (color & 0xFFFFFF);
+ return color;
+};
+
+
diff --git a/web/src/test/java/lcsb/mapviewer/AllWebTests.java b/web/src/test/java/lcsb/mapviewer/AllWebTests.java
new file mode 100644
index 0000000000000000000000000000000000000000..c394dd619eb3f3fa9c10ec0ff7695787e7accc97
--- /dev/null
+++ b/web/src/test/java/lcsb/mapviewer/AllWebTests.java
@@ -0,0 +1,16 @@
+package lcsb.mapviewer;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.bean.AllBeanTests;
+import lcsb.mapviewer.validator.AllValidatorTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllBeanTests.class, //
+ AllValidatorTests.class,//
+})
+public class AllWebTests {
+
+}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/AbstractManagedBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/AbstractManagedBeanTest.java
index 2c2d3e525f8fd134aaca919705beb986b23dfa87..48b0cf4118c75e2f37da185a05f18776b994ac9e 100644
--- a/web/src/test/java/lcsb/mapviewer/bean/AbstractManagedBeanTest.java
+++ b/web/src/test/java/lcsb/mapviewer/bean/AbstractManagedBeanTest.java
@@ -1,117 +1,120 @@
-package lcsb.mapviewer.bean;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.events.Event;
-import lcsb.mapviewer.events.Listener;
-
-import org.apache.commons.lang3.mutable.MutableInt;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class AbstractManagedBeanTest {
-
- class AbstractManagedBeanMock extends AbstractManagedBean {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- public void clear() {
- }
-
- public void callMockEvent(String data) {
- callListeners(new EventMock(data));
- }
-
- @Override
- public void init() {
- // TODO Auto-generated method stub
-
- }
-
- };
-
- class EventMock extends Event {
- String data = "";
-
- public EventMock(String d) {
- data = d;
- }
- }
-
- AbstractManagedBeanMock mockBean;
-
- @Before
- public void setUp() throws Exception {
- mockBean = new AbstractManagedBeanMock();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testListeners() throws Exception {
- final MutableInt called = new MutableInt(0);
- try {
- Listener<EventMock> listener = new Listener<EventMock>(EventMock.class) {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(EventMock event) {
- called.add(1);
- }
- };
-
- mockBean.registerListener(listener);
- assertEquals(new MutableInt(0), called);
- mockBean.callMockEvent("hi");
- assertEquals(new MutableInt(1), called);
- mockBean.callMockEvent("hi2");
- assertEquals(new MutableInt(2), called);
- mockBean.unregisterListener(listener);
- mockBean.callMockEvent("hi3");
- assertEquals(new MutableInt(2), called);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveListeners() throws Exception {
- final MutableInt called = new MutableInt(0);
- try {
- Listener<EventMock> listener = new Listener<EventMock>(EventMock.class) {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(EventMock event) {
- called.add(1);
- }
- };
-
- try {
- mockBean.unregisterListener(listener);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.bean;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.mutable.MutableInt;
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.events.Event;
+import lcsb.mapviewer.events.Listener;
+
+public class AbstractManagedBeanTest {
+ Logger logger = Logger.getLogger(AbstractManagedBeanTest.class);
+
+ class AbstractManagedBeanMock extends AbstractManagedBean {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ public void clear() {
+ }
+
+ public void callMockEvent(String data) {
+ callListeners(new EventMock(data));
+ }
+
+ @Override
+ public void init() {
+ // TODO Auto-generated method stub
+
+ }
+
+ };
+
+ class EventMock extends Event {
+ String data = "";
+
+ public EventMock(String d) {
+ data = d;
+ }
+ }
+
+ AbstractManagedBeanMock mockBean;
+
+ @Before
+ public void setUp() throws Exception {
+ mockBean = new AbstractManagedBeanMock();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testListeners() throws Exception {
+ final MutableInt called = new MutableInt(0);
+ try {
+ Listener<EventMock> listener = new Listener<EventMock>(EventMock.class) {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ protected void handle(EventMock event) {
+ called.add(1);
+ }
+ };
+
+ mockBean.registerListener(listener);
+ assertEquals(new MutableInt(0), called);
+ mockBean.callMockEvent("hi");
+ assertEquals(new MutableInt(1), called);
+ mockBean.callMockEvent("hi2");
+ assertEquals(new MutableInt(2), called);
+ mockBean.unregisterListener(listener);
+ mockBean.callMockEvent("hi3");
+ assertEquals(new MutableInt(2), called);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemoveListeners() throws Exception {
+ final MutableInt called = new MutableInt(0);
+ try {
+ Listener<EventMock> listener = new Listener<EventMock>(EventMock.class) {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ protected void handle(EventMock event) {
+ called.add(1);
+ }
+ };
+
+ try {
+ mockBean.unregisterListener(listener);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/DrugBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/DrugBeanTest.java
index 21fbb10b623650d7cacc6e7394d19c2b69f2c5b3..f19ae4abf42f0a2f3953d7bb1460b78802ca4547 100644
--- a/web/src/test/java/lcsb/mapviewer/bean/DrugBeanTest.java
+++ b/web/src/test/java/lcsb/mapviewer/bean/DrugBeanTest.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.bean;
+import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import java.io.Serializable;
@@ -96,4 +97,15 @@ public class DrugBeanTest extends WebTestFunctions {
}
}
+ @Test
+ public void testFindDrug() throws Exception {
+ try {
+ drugBean.findDrug("levadopa; carbidopa");
+ assertEquals(2, drugBean.getResults().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/web/src/test/java/lcsb/mapviewer/validator/AllValidatorTests.java b/web/src/test/java/lcsb/mapviewer/validator/AllValidatorTests.java
new file mode 100644
index 0000000000000000000000000000000000000000..dd6e48a1eb63b7d82bfea487a32eea40b9d6162f
--- /dev/null
+++ b/web/src/test/java/lcsb/mapviewer/validator/AllValidatorTests.java
@@ -0,0 +1,11 @@
+package lcsb.mapviewer.validator;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ LoginValidatorTest.class })
+public class AllValidatorTests {
+
+}
diff --git a/web/src/test/java/lcsb/mapviewer/validator/LoginValidatorTest.java b/web/src/test/java/lcsb/mapviewer/validator/LoginValidatorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..a216753326f54d1d72112c0d1691ca7cedcc03ca
--- /dev/null
+++ b/web/src/test/java/lcsb/mapviewer/validator/LoginValidatorTest.java
@@ -0,0 +1,42 @@
+package lcsb.mapviewer.validator;
+
+import static org.junit.Assert.fail;
+
+import javax.faces.validator.ValidatorException;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class LoginValidatorTest {
+ LoginValidator validator = new LoginValidator();
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCorrect() {
+ validator.validate(null, null, "piotr.gawron");
+ }
+
+ @Test
+ public void testIncorrect() {
+ try {
+ validator.validate(null, null, "piotr gawron");
+ fail("Exception expected");
+ } catch (ValidatorException e) {
+
+ }
+ }
+
+}