diff --git a/CHANGELOG b/CHANGELOG
index 7470a35bba857a34e0550e4366d72126a3f662bd..62513c844ef7692fabbb3186a95e2aab3328c31e 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,4 +1,5 @@
minerva (18.1.0) stable; urgency=medium
+ * Small improvement: SBGN-ML import/export is processing notes (#2192)
* Small improvement: support for links that should be opened immediately
(#2189)
* Bug fix: don't create duplicated refresh jobs (#2165)
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
index 1aedbdef808958c52e258be2bc1e29f01b78d56d..4b5055a8bafc34481a8eebe161b633502907b3a5 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
@@ -6,7 +6,7 @@ import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.graphics.bioentity.reaction.ReactionConverter;
-import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
+import lcsb.mapviewer.converter.model.sbgnml.parser.NotesConverter;
import lcsb.mapviewer.model.LogMarker;
import lcsb.mapviewer.model.ProjectLogEntryType;
import lcsb.mapviewer.model.graphics.ArrowType;
@@ -168,6 +168,8 @@ public class SbgnmlXmlExporter {
private final ColorParser colorParser = new ColorParser();
+ private final NotesConverter notesConverter = new NotesConverter();
+
private final XmlAnnotationParser xap = new XmlAnnotationParser(new ArrayList<>(), true);
private final java.util.Map<Element, String> exportElementIds = new HashMap<>();
@@ -253,25 +255,7 @@ public class SbgnmlXmlExporter {
throw new ConverterException("Problem with providing render information");
}
- try {
- final StringBuilder notes = new StringBuilder();
- notes.append("<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>");
- if (model.getNotes() != null) {
- notes.append(new CommonXmlParser().getNotesXmlContent(model.getNotes()));
- }
- notes.append("</body></html>");
-
- final DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
- dbf.setNamespaceAware(true);
- final DocumentBuilder db;
- db = dbf.newDocumentBuilder();
- final Document doc = db.parse(new ByteArrayInputStream(notes.toString().getBytes()));
-
- map.setNotes(new SBGNBase.Notes());
- map.getNotes().getAny().add((org.w3c.dom.Element) (doc.getFirstChild()));
- } catch (final Exception e) {
- logger.warn("Problem with processing notes");
- }
+ map.setNotes(notesConverter.createNotesNode(model.getNotes()));
sbgnData.getMap().add(map);
return sbgnData;
@@ -289,6 +273,7 @@ public class SbgnmlXmlExporter {
newGlyph.setId(elementId);
newGlyph.setClazz(getGlyphClazzFromElement(element).getClazz());
newGlyph.setLabel(getGlyphLabelFromAlias(element));
+ newGlyph.setNotes(notesConverter.createNotesNode(element.getNotes()));
final Bbox bbox = new Bbox();
bbox.setX(element.getX().floatValue());
@@ -449,7 +434,7 @@ public class SbgnmlXmlExporter {
glyph.setClazz(GlyphClazz.STATE_VARIABLE.getClazz());
final Glyph.State state = new Glyph.State();
- if (structuralState.getName().indexOf("@") >= 0) {
+ if (structuralState.getName().contains("@")) {
state.setValue(structuralState.getName().substring(0, structuralState.getName().indexOf("@")));
state.setVariable(structuralState.getName().substring(structuralState.getName().indexOf("@") + 1));
} else {
@@ -685,14 +670,14 @@ public class SbgnmlXmlExporter {
}
if (species instanceof TruncatedProtein) {
- if (!uoiText.equals("")) {
+ if (!uoiText.isEmpty()) {
uoiText = uoiText.concat("; ");
}
uoiText = uoiText.concat("ct:truncatedProtein");
}
if ((species.getStateLabel() != null) && (species.getStatePrefix() != null)) {
- if (!uoiText.equals("")) {
+ if (!uoiText.isEmpty()) {
uoiText = uoiText.concat("; ");
}
if (!species.getStatePrefix().equals("free input")) {
@@ -703,26 +688,26 @@ public class SbgnmlXmlExporter {
if (!uoiText.contains("ct:")) {
if (species instanceof Rna) {
- if (!uoiText.equals("")) {
+ if (!uoiText.isEmpty()) {
uoiText = uoiText.concat("; ");
}
uoiText = uoiText.concat("ct:RNA");
}
if (species instanceof AntisenseRna) {
- if (!uoiText.equals("")) {
+ if (!uoiText.isEmpty()) {
uoiText = uoiText.concat("; ");
}
uoiText = uoiText.concat("ct:antisenseRNA");
}
if (species instanceof Gene) {
- if (!uoiText.equals("")) {
+ if (!uoiText.isEmpty()) {
uoiText = uoiText.concat("; ");
}
uoiText = uoiText.concat("ct:gene");
}
}
- if (!uoiText.equals("")) {
+ if (!uoiText.isEmpty()) {
uoiGlyph = new Glyph();
uoiGlyph.setClazz(GlyphClazz.UNIT_OF_INFORMATION.getClazz());
uoiGlyph.setId(species.getElementId().concat("uoi"));
@@ -1031,7 +1016,7 @@ public class SbgnmlXmlExporter {
*
* @param reaction the reaction to extract arcs from
* @param glyphList list of all glyphs in the map; used only for parsing operators
- * @return set of all arcs used in the reaction
+ * @return list of all arcs used in the reaction
*/
private List<Arc> getArcsFromReaction(final Reaction reaction, final List<Glyph> glyphList) {
final List<Arc> arcList = new ArrayList<>();
@@ -1179,13 +1164,13 @@ public class SbgnmlXmlExporter {
final DoubleComparator doubleComparator = new DoubleComparator();
for (int i = 1; i < arcPoints.size() - 1; i++) {
final Point2D nextPoint = arcPoints.get(i);
- if ((doubleComparator.compare(nextPoint.getX(), new Double(start.getX())) == 0)
- && (doubleComparator.compare(nextPoint.getY(), new Double(start.getY())) == 0)) {
+ if ((doubleComparator.compare(nextPoint.getX(), (double) start.getX()) == 0)
+ && (doubleComparator.compare(nextPoint.getY(), (double) start.getY()) == 0)) {
arc.getNext().clear();
continue;
}
- if ((doubleComparator.compare(nextPoint.getX(), new Double(end.getX())) == 0)
- && (doubleComparator.compare(nextPoint.getY(), new Double(end.getY())) == 0)) {
+ if ((doubleComparator.compare(nextPoint.getX(), (double) end.getX()) == 0)
+ && (doubleComparator.compare(nextPoint.getY(), (double) end.getY()) == 0)) {
break;
}
final Next next = new Next();
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
index fbeac9272faf24244a4e9bd629a81bb6b78beff5..6e5728d44676d05f5b77857e814edb9125603865 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
@@ -1,38 +1,12 @@
package lcsb.mapviewer.converter.model.sbgnml;
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.sbgn.GlyphClazz;
-import org.sbgn.RenderUtil;
-import org.sbgn.SbgnUtil;
-import org.sbgn.bindings.Arc;
-import org.sbgn.bindings.Arc.End;
-import org.sbgn.bindings.Arc.Next;
-import org.sbgn.bindings.Arc.Start;
-import org.sbgn.bindings.Bbox;
-import org.sbgn.bindings.Glyph;
-import org.sbgn.bindings.Map;
-import org.sbgn.bindings.RenderInformation;
-import org.sbgn.bindings.Sbgn;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.ZIndexPopulator;
import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.sbgnml.parser.ElementParser;
+import lcsb.mapviewer.converter.model.sbgnml.parser.NotesConverter;
import lcsb.mapviewer.converter.model.sbgnml.parser.ReactionParser;
import lcsb.mapviewer.converter.model.sbgnml.parser.RenderParser;
import lcsb.mapviewer.converter.model.sbgnml.structures.Process;
@@ -48,24 +22,43 @@ 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 org.apache.commons.io.FilenameUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.sbgn.GlyphClazz;
+import org.sbgn.RenderUtil;
+import org.sbgn.SbgnUtil;
+import org.sbgn.bindings.Arc;
+import org.sbgn.bindings.Arc.End;
+import org.sbgn.bindings.Arc.Next;
+import org.sbgn.bindings.Arc.Start;
+import org.sbgn.bindings.Bbox;
+import org.sbgn.bindings.Glyph;
+import org.sbgn.bindings.Map;
+import org.sbgn.bindings.RenderInformation;
+import org.sbgn.bindings.Sbgn;
+import org.w3c.dom.Node;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
/**
* This class is a parser for SBGN-ML files.
- *
- * @author Michał Kuźma
*
+ * @author Michał Kuźma
*/
public class SbgnmlXmlParser {
/**
* Default class logger.
*/
- private Logger logger = LogManager.getLogger();
+ private final Logger logger = LogManager.getLogger();
/**
* List of all arcs that should be translated as activity flow reactions.
*/
- private List<Arc> activityFlowArcs = new ArrayList<>();
+ private final List<Arc> activityFlowArcs = new ArrayList<>();
private Model model;
@@ -77,17 +70,15 @@ public class SbgnmlXmlParser {
private ReactionParser reactionParser;
+ private final NotesConverter notesConverter = new NotesConverter();
+
/**
* Method used to create a model from SBGN-ML file.
*
- * @param filename
- * The filename of the input file.
- * @param inputSbgnmlFile
- * the input file.
- *
+ * @param filename The filename of the input file.
+ * @param inputSbgnmlFile the input file.
* @return valid model parsed from the file
- * @throws InvalidInputDataExecption
- * thrown when input file is invalid
+ * @throws InvalidInputDataExecption thrown when input file is invalid
*/
public Model createModel(final String filename, final File inputSbgnmlFile) throws InvalidInputDataExecption {
@@ -126,23 +117,7 @@ public class SbgnmlXmlParser {
elementParser = new ElementParser(renderParser, model);
reactionParser = new ReactionParser(renderParser, model);
- RestAnnotationParser rap = new RestAnnotationParser();
-
- if (map.getNotes() != null && map.getNotes().getAny().size() > 0) {
- try {
- String notes = "<notes>" + XmlParser.nodeToString(map.getNotes().getAny().get(0).getParentNode(), true)
- + "</notes>";
- DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
- dbf.setNamespaceAware(true);
- DocumentBuilder db;
- db = dbf.newDocumentBuilder();
- Document doc = db.parse(new ByteArrayInputStream(notes.getBytes()));
-
- model.setNotes(rap.getNotes(doc.getFirstChild()));
- } catch (final Exception e) {
- logger.warn("Problem with extracting map notes", e);
- }
- }
+ model.setNotes(notesConverter.parseNotes(map.getNotes()));
elementParser.adjustSizeOfElements(map);
@@ -225,11 +200,9 @@ public class SbgnmlXmlParser {
/**
* Method used to compute height and width of the model.
- *
- * @param map
- * Map parsed from SBGN-ML file
- * @param model
- * Model to be updated
+ *
+ * @param map Map parsed from SBGN-ML file
+ * @param model Model to be updated
*/
private void setModelSize(final Map map, final Model model) {
if (map.getBbox() != null) {
@@ -351,11 +324,9 @@ public class SbgnmlXmlParser {
/**
* Finds a compartment where element should be located (base on the
* coordinates).
- *
- * @param child
- * {@link Element} for which we want to find compartment
- * @param model
- * {@link Model} where we look for a compartment
+ *
+ * @param child {@link Element} for which we want to find compartment
+ * @param model {@link Model} where we look for a compartment
* @return parent {@link Compartment}
*/
private Compartment findParentCompartment(final Element child, final Model model) {
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ElementParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ElementParser.java
index 20aa6fdb5e4691a4715c6b2cb1d7981f54f22333..f74070706e28562b5aeb33c41bd92ef39b2c735d 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ElementParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ElementParser.java
@@ -72,6 +72,8 @@ public class ElementParser extends GlyphParser {
private final Model model;
+ private final NotesConverter notesConverter = new NotesConverter();
+
public ElementParser(final RenderParser renderParser, final Model model) {
this.renderParser = renderParser;
this.model = model;
@@ -246,6 +248,7 @@ public class ElementParser extends GlyphParser {
element.setName("");
}
+ element.setNotes(notesConverter.parseNotes(g.getNotes()));
if (element instanceof Species) {
final Species newSpecies = (Species) element;
// Add species to parent complex if there is one
@@ -448,8 +451,6 @@ public class ElementParser extends GlyphParser {
* Method used to parse state variable.
*
* @param stateVariable unit of information glyph from sbgn-ml file
- * @throws Exception Exception is thrown if state variable is parsed for species other
- * than Protein
*/
private Residue stateVariableToResidue(final Glyph stateVariable) {
if (stateVariable.getState() != null && (stateVariable.getState().getVariable() == null
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/NotesConverter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/NotesConverter.java
new file mode 100644
index 0000000000000000000000000000000000000000..4db5742a0d245cab88137dbd7cc21491f6429335
--- /dev/null
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/NotesConverter.java
@@ -0,0 +1,62 @@
+package lcsb.mapviewer.converter.model.sbgnml.parser;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.sbgn.bindings.SBGNBase;
+import org.w3c.dom.Document;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import java.io.ByteArrayInputStream;
+
+public class NotesConverter {
+
+ private final Logger logger = LogManager.getLogger();
+
+ private final RestAnnotationParser rap = new RestAnnotationParser();
+
+ public SBGNBase.Notes createNotesNode(final String notes) {
+ SBGNBase.Notes result = new SBGNBase.Notes();
+ try {
+ final StringBuilder notesXml = new StringBuilder();
+ notesXml.append("<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>");
+ if (notes != null) {
+ notesXml.append(new CommonXmlParser().getNotesXmlContent(notes));
+ }
+ notesXml.append("</body></html>");
+
+ final DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+ dbf.setNamespaceAware(true);
+ final DocumentBuilder db;
+ db = dbf.newDocumentBuilder();
+ final Document doc = db.parse(new ByteArrayInputStream(notesXml.toString().getBytes()));
+
+ result.getAny().add((org.w3c.dom.Element) (doc.getFirstChild()));
+ } catch (final Exception e) {
+ logger.warn("Problem with processing notes");
+ }
+ return result;
+ }
+
+ public String parseNotes(final SBGNBase.Notes notesNode) {
+ if (notesNode != null && !notesNode.getAny().isEmpty()) {
+ try {
+ String notes = "<notes>" + XmlParser.nodeToString(notesNode.getAny().get(0).getParentNode(), true)
+ + "</notes>";
+ DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+ dbf.setNamespaceAware(true);
+ DocumentBuilder db;
+ db = dbf.newDocumentBuilder();
+ Document doc = db.parse(new ByteArrayInputStream(notes.getBytes()));
+
+ return rap.getNotes(doc.getFirstChild());
+ } catch (final Exception e) {
+ logger.warn("Problem with extracting map notes", e);
+ }
+ }
+ return "";
+ }
+}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java
index be2f8bb72001771afb63b3f6f5ff7ff598d31385..6918f2e1086564087266e08376c876539ef378ff 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java
@@ -1,20 +1,5 @@
package lcsb.mapviewer.converter.model.sbgnml;
-import java.awt.Color;
-import java.awt.Desktop;
-import java.awt.geom.Point2D;
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.nio.charset.StandardCharsets;
-import java.nio.file.Files;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.junit.Rule;
-import org.sbgn.GlyphClazz;
-import org.sbgn.bindings.Bbox;
-import org.sbgn.bindings.Glyph;
-
import lcsb.mapviewer.common.tests.TestUtils;
import lcsb.mapviewer.common.tests.UnitTestFailedWatcher;
import lcsb.mapviewer.converter.Converter;
@@ -35,23 +20,36 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.StructuralState;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.Rule;
+import org.sbgn.GlyphClazz;
+import org.sbgn.bindings.Bbox;
+import org.sbgn.bindings.Glyph;
+
+import java.awt.Color;
+import java.awt.Desktop;
+import java.awt.geom.Point2D;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
public class SbgnmlTestFunctions extends TestUtils {
protected static Logger logger = LogManager.getLogger();
-
+ private static int counter = 0;
+ private final Converter sbgnmlConverter = new SbgnmlXmlConverter();
@Rule
public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
- private static int counter = 0;
-
protected void showImage(final Model model) throws Exception {
String dir = Files.createTempDirectory("sbml-temp-images-dir").toFile().getAbsolutePath();
AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().height(model.getHeight())
.width(model.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model);
NormalImageGenerator nig = new PngImageGenerator(params);
- String pathWithouExtension = dir + "/" + model.getName();
- String pngFilePath = pathWithouExtension.concat(".png");
+ String pathWithoutExtension = dir + "/" + model.getName();
+ String pngFilePath = pathWithoutExtension.concat(".png");
nig.saveToFile(pngFilePath);
Desktop.getDesktop().open(new File(pngFilePath));
}
@@ -114,8 +112,6 @@ public class SbgnmlTestFunctions extends TestUtils {
return structuralState;
}
- private Converter sbgnmlConverter = new SbgnmlXmlConverter();
-
protected Model serializeAndCleanOverSbgn(final Model model) throws InconsistentModelException, ConverterException, InvalidInputDataExecption {
String sbgn = sbgnmlConverter.model2String(model);
// logger.debug(sbgn);
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
index 6db64a2a48370df28d1727e259fd2de15baec58c..582c6d4977d6c950b404148a6abbe2ef5cd51ba3 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
@@ -1,19 +1,5 @@
package lcsb.mapviewer.converter.model.sbgnml;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-import java.io.File;
-import java.io.PrintWriter;
-
-import org.junit.Test;
-import org.sbgn.ArcClazz;
-import org.sbgn.GlyphClazz;
-import org.sbgn.SbgnUtil;
-
import lcsb.mapviewer.common.geometry.PointTransformation;
import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.model.graphics.PolylineData;
@@ -29,6 +15,19 @@ import lcsb.mapviewer.model.map.species.Drug;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.modelutils.map.ElementUtils;
+import org.junit.Test;
+import org.sbgn.ArcClazz;
+import org.sbgn.GlyphClazz;
+import org.sbgn.SbgnUtil;
+
+import java.awt.geom.Point2D;
+import java.io.File;
+import java.io.PrintWriter;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
@@ -68,7 +67,7 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
private static Reaction createReaction(final Class<? extends Reaction> clazz) throws Exception {
- Reaction reaction = clazz.getConstructor(String.class).newInstance(new Object[] { "re" + (counter++) });
+ Reaction reaction = clazz.getConstructor(String.class).newInstance("re" + (counter++));
Ion ion = createIon(counter++);
Ion ion2 = createIon(counter);
@@ -138,6 +137,19 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
assertEquals(0, new ModelComparator().compare(model, model2));
}
+ @Test
+ public void importExportNotes() throws Exception {
+ GenericProtein protein = createProtein();
+ protein.setNotes("hello world");
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(2000);
+ model.setHeight(2000);
+ model.addElement(protein);
+
+ Model model2 = serializeAndCleanOverSbgn(model);
+ assertEquals(0, new ModelComparator().compare(model, model2));
+ }
+
@Test
public void testExportWithWarning() throws Exception {
Converter sbgnmlConverter = new SbgnmlXmlConverter();