Merge branch 'master' into structure-viewer

# Conflicts:
#	frontend-js/src/main/css/global.css

commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java

@@ -14,61 +14,64 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
  */
 public class ColorParser {
 
-	/**
-	 * Base of the hex representation.
-	 */
-	private static final int HEX_BASE										 = 16;
+  /**
+   * 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;
+  /**
+   * 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 red color in string 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 green color in string 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;
+  /**
+   * Where starts description of blue color in string 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));
-		}
-	}
+  /**
+   * 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));
+    }
+  }
 
-	/**
-	 * Converts color into list of atributes.
-	 * 
-	 * @param color color to convert
-	 * @return map with list of color attributes
-	 */
-	public Map<String, Object> colorToMap(Color color) {
-		Map<String, Object> result = new HashMap<>();
-		result.put("alpha", color.getAlpha());
-		result.put("rgb", color.getRGB());
-		return result;
-	}
+  /**
+   * Converts color into list of attributes.
+   * 
+   * @param color
+   *          color to convert
+   * @return map with list of color attributes
+   */
+  public Map<String, Object> colorToMap(Color color) {
+    Map<String, Object> result = new HashMap<>();
+    result.put("alpha", color.getAlpha());
+    result.put("rgb", color.getRGB());
+    return result;
+  }
 }

converter-sbml/.gitignore

+.settings/org.eclipse.wst.validation.prefs
+
 /bin/
 tmp.png
 tmp.xml

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java

@@ -15,8 +15,10 @@ import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
+import lcsb.mapviewer.converter.model.sbml.species.ElementColorEnum;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.species.Element;
 
 public class SbmlBioEntityParser extends XmlParser {
   Logger logger = Logger.getLogger(SbmlBioEntityParser.class);
@@ -55,6 +57,11 @@ public class SbmlBioEntityParser extends XmlParser {
     }
     String notes = extractNotes(sbmlElement);
     result.setNotes(notes);
+
+    if (result instanceof Element) {
+      Element element = (Element) result;
+      element.setColor(ElementColorEnum.getColorByClass(element.getClass()));
+    }
   }
 
   private String extractNotes(AbstractNamedSBase sbmlElement) throws InvalidInputDataExecption {

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java

@@ -7,6 +7,9 @@ import org.apache.log4j.Logger;
 
 import lcsb.mapviewer.model.map.modifier.Catalysis;
 import lcsb.mapviewer.model.map.modifier.Inhibition;
+import lcsb.mapviewer.model.map.modifier.Modulation;
+import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
+import lcsb.mapviewer.model.map.modifier.Trigger;
 import lcsb.mapviewer.model.map.modifier.UnknownCatalysis;
 import lcsb.mapviewer.model.map.modifier.UnknownInhibition;
 import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -14,6 +17,9 @@ import lcsb.mapviewer.model.map.reaction.Modifier;
 public enum SBOTermModifierType {
   CATALYSIS(Catalysis.class, new String[] { "SBO:0000013" }), //
   INHIBITION(Inhibition.class, new String[] { "SBO:0000537" }), //
+  MODULATION(Modulation.class, new String[] { "SBO:0000594" }), //
+  PHYSICAL_STIMULATION(PhysicalStimulation.class, new String[] { "SBO:0000459" }), //
+  TRIGGER(Trigger.class, new String[] { "SBO:0000461" }), //
   UNKNOWN_CATALYSIS(UnknownCatalysis.class, new String[] { "SBO:0000462" }), //
   UNKNOWN_INHIBITION(UnknownInhibition.class, new String[] { "SBO:0000536" }), //
   ;

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java

@@ -11,6 +11,9 @@ import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
 import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
 import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
 import lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction;
 import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
 import lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction;
 import lcsb.mapviewer.model.map.reaction.type.TranslationReaction;
@@ -18,22 +21,31 @@ import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
 import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
 import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction;
 import lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction;
 import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
 
 public enum SBOTermReactionType {
+  DISSOCIATION(DissociationReaction.class, new String[] { "SBO:0000180" }), //
+  HETERODIMER_ASSOCIATION(HeterodimerAssociationReaction.class, new String[] { "SBO:0000177" }), //
+  KNOWN_TRANSITION_OMITTED(KnownTransitionOmittedReaction.class, new String[] { "SBO:0000205" }), //
+  NEGATIVE_INFLUENCE(NegativeInfluenceReaction.class, new String[] { "SBO:0000407" }), //
+  POSITIVE_INFLUENCE(PositiveInfluenceReaction.class, new String[] { "SBO:0000171" }), //
+  REDUCED_MODULATION(ReducedModulationReaction.class, new String[] { "SBO:0000632" }), //
+  REDUCED_PHYSICAL_STIMULATION(ReducedPhysicalStimulationReaction.class, new String[] { "SBO:0000411" }), //
+  REDUCED_TRIGGER(ReducedTriggerReaction.class, new String[] { "SBO:0000461" }), //
   STATE_TRANSITION(StateTransitionReaction.class, new String[] { "SBO:0000176" }), //
   TRANSCRIPTION(TranscriptionReaction.class, new String[] { "SBO:0000183" }), //
   TRANSLATION(TranslationReaction.class, new String[] { "SBO:0000184" }), //
   TRANSPORT(TransportReaction.class, new String[] { "SBO:0000185" }), //
-  KNOWN_TRANSITION_OMITTED(KnownTransitionOmittedReaction.class, new String[] { "SBO:0000205" }), //
-  UNKNOWN_TRANSITION(UnknownTransitionReaction.class, new String[] { "SBO:0000396" }), //
-  HETERODIMER_ASSOCIATION(HeterodimerAssociationReaction.class, new String[] { "SBO:0000177" }), //
-  DISSOCIATION(DissociationReaction.class, new String[] { "SBO:0000180" }), //
   TRUNCATION(TruncationReaction.class, new String[] { "SBO:0000178" }), //
-  POSITIVE_INFLUENCE(PositiveInfluenceReaction.class, new String[] { "SBO:0000171" }), //
-  UNKNOWN_POSITIVE_INFLUENCE(UnknownPositiveInfluenceReaction.class, new String[] { "SBO:0000170" }), //
-  NEGATIVE_INFLUENCE(NegativeInfluenceReaction.class, new String[] { "SBO:0000407" }), //
   UNKNOWN_NEGATIVE_INFLUENCE(UnknownNegativeInfluenceReaction.class, new String[] { "SBO:0000169" }), //
+  UNKNOWN_POSITIVE_INFLUENCE(UnknownPositiveInfluenceReaction.class, new String[] { "SBO:0000172" }), //
+  UNKNOWN_REDUCED_MODULATION(UnknownReducedModulationReaction.class, new String[] { "SBO:0000631" }), //
+  UNKNOWN_REDUCED_PHYSICAL_STIMULATION(UnknownReducedPhysicalStimulationReaction.class, new String[] { "SBO:0000170" }), //
+  UNKNOWN_REDUCED_TRIGGER(UnknownReducedTriggerReaction.class, new String[] { "SBO:0000533" }), //
+  UNKNOWN_TRANSITION(UnknownTransitionReaction.class, new String[] { "SBO:0000396" }), //
   ;
 
   private static Logger logger = Logger.getLogger(SBOTermReactionType.class);
@@ -60,7 +72,7 @@ public enum SBOTermReactionType {
       }
     }
     if (result == null) {
-      logger.warn("Don't know how to handle SBOTerm " + sboTerm + " for modifier");
+      logger.warn("Don't know how to handle SBOTerm " + sboTerm + " for reaction");
       result = StateTransitionReaction.class;
     }
     return result;

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java

@@ -10,6 +10,7 @@ import org.apache.log4j.Logger;
 import org.sbml.jsbml.ASTNode;
 import org.sbml.jsbml.KineticLaw;
 import org.sbml.jsbml.LocalParameter;
+import org.sbml.jsbml.Model;
 import org.sbml.jsbml.SimpleSpeciesReference;
 import org.sbml.jsbml.Species;
 import org.sbml.jsbml.SpeciesReference;
@@ -63,7 +64,10 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     }
     result = getSbmlModel().createReaction(reactionId);
     result.setReversible(reaction.isReversible());
-    result.setSBOTerm(SBOTermReactionType.getTermByType(reaction.getClass()));
+    String sboTerm = SBOTermReactionType.getTermByType(reaction.getClass());
+    if (sboTerm != null) {
+      result.setSBOTerm(sboTerm);
+    }
     for (Product product : reaction.getProducts()) {
       Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(product.getElement().getElementId());
       SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
@@ -222,4 +226,9 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     return curve;
   }
 
+  @Override
+  protected void setSbmlModel(Model sbmlModel) {
+    super.setSbmlModel(sbmlModel);
+  }
+
 }

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/ElementColorEnum.java

+package lcsb.mapviewer.converter.model.sbml.species;
+
+import java.awt.Color;
+
+import lcsb.mapviewer.common.geometry.ColorParser;
+import lcsb.mapviewer.model.map.compartment.OvalCompartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+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;
+
+public enum ElementColorEnum {
+  ANTISENSE_RNA(AntisenseRna.class, "#ff6666"), //
+  COMPLEX(Complex.class, "#f7f7f7"), //
+  DEGRADED(Degraded.class, "#ffcccc"), //
+  DRUG(Drug.class, "#ff00ff"), //
+  ELEMENT(Element.class, "#000000"), //
+  GENE(Gene.class, "#ffff66"), //
+  GENERIC_PROTEIN(GenericProtein.class, "ccffcc"), //
+  TRUNCATED_PROTEIN(TruncatedProtein.class, "#ffcccc"), //
+  ION(Ion.class, "#9999ff"), //
+  ION_CHANNEL(IonChannelProtein.class, "#ccffff"), //
+  OVAL_COMPARTMENT(OvalCompartment.class, "#cccc00"), //
+  PHENOTYPE(Phenotype.class, "#cc99ff"), //
+  RECEPTOR(ReceptorProtein.class, "#ffffcc"), //
+  RNA(Rna.class, "#66ff66"), //
+  SIMPLE_MOLECULE(SimpleMolecule.class, "#ccff66"), //
+  SQUARE_COMPARTMENT(SquareCompartment.class, "#cccc00"), //
+  UNKNOWN(Unknown.class, "#cccccc"), //
+  ;
+
+  private Class<? extends Element> clazz;
+  private Color color;
+
+  ColorParser colorParser = new ColorParser();
+
+  private ElementColorEnum(Class<? extends Element> clazz, String color) {
+    this.clazz = clazz;
+    if (color != null) {
+      this.color = colorParser.parse(color);
+    }
+  }
+
+  public static Color getColorByClass(Class<? extends Element> clazz) {
+    Color result = null;
+    for (ElementColorEnum type : ElementColorEnum.values()) {
+      if (type.getClazz().equals(clazz)) {
+        result = type.getColor();
+      }
+    }
+    if (result == null) {
+      for (ElementColorEnum type : ElementColorEnum.values()) {
+        if (type.getClazz().isAssignableFrom(clazz)) {
+          result = type.getColor();
+        }
+      }
+    }
+    return result;
+  }
+
+  public Class<? extends Element> getClazz() {
+    return clazz;
+  }
+
+  public Color getColor() {
+    return color;
+  }
+
+}

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java

@@ -4,16 +4,16 @@ import org.junit.runner.RunWith;
 import org.junit.runners.Suite;
 import org.junit.runners.Suite.SuiteClasses;
 
-import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionParserTest;
+import lcsb.mapviewer.converter.model.sbml.reaction.AllSbmlReactionParserTests;
 import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParserTest;
 
 @RunWith(Suite.class)
-@SuiteClasses({ GenericSbmlParserTest.class, //
+@SuiteClasses({ AllSbmlReactionParserTests.class, //
+    GenericSbmlParserTest.class, //
     GenericSbmlToXmlParserTest.class, //
     SbmlExporterTest.class, //
     SbmlPareserForInvalidReactionTest.class, //
     SbmlParserTest.class, //
-    SbmlReactionParserTest.class, //
     SbmlSpeciesParserTest.class,//
 })
 public class AllSbmlConverterTests {

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/AllSbmlReactionParserTests.java

+package lcsb.mapviewer.converter.model.sbml.reaction;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ SbmlReactionExporterTest.class, //
+    SbmlReactionParserTest.class //
+})
+public class AllSbmlReactionParserTests {
+
+}

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java

+package lcsb.mapviewer.converter.model.sbml.reaction;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.Test;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.ext.layout.Dimensions;
+import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
+
+import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityExporter;
+import lcsb.mapviewer.converter.model.sbml.SbmlCompartmentExporter;
+import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.type.TriggerReaction;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class SbmlReactionExporterTest {
+
+  @Test
+  public void testTriggerReactionToSbml() throws InconsistentModelException {
+    ModelFullIndexed model = new ModelFullIndexed(null);
+
+    SbmlReactionExporter exporter = createExporter(model);
+    org.sbml.jsbml.Reaction result = exporter.createSbmlElement(new TriggerReaction());
+    assertNotNull(result);
+  }
+
+  private SbmlReactionExporter createExporter(ModelFullIndexed model) {
+    SBMLDocument doc = new SBMLDocument(3, 1);
+    Model result = doc.createModel(model.getIdModel());
+    result.setName(model.getName());
+    LayoutModelPlugin plugin = new LayoutModelPlugin(result);
+
+    Layout layout = new Layout();
+    Dimensions dimensions = new Dimensions();
+    if (model.getHeight() != null) {
+      dimensions.setHeight(model.getHeight());
+    } else {
+      dimensions.setHeight(640);
+    }
+    if (model.getWidth() != null) {
+      dimensions.setWidth(model.getWidth());
+    } else {
+      dimensions.setWidth(480);
+    }
+    layout.setDimensions(dimensions);
+    plugin.add(layout);
+    result.addExtension("layout", plugin);
+
+    SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model);
+    SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(layout, model,
+        compartmentExporter);
+
+    SbmlReactionExporter exporter = new SbmlReactionExporter(layout, model, speciesExporter, compartmentExporter);
+    exporter.setSbmlModel(result);
+    return exporter;
+  }
+
+}

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParserTest.java

@@ -151,10 +151,11 @@ public class SbmlReactionParserTest {
 
   @Test
   public void testParseUnknownPositiveInfluence() throws FileNotFoundException, InvalidInputDataExecption {
-    Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/unknown_positive_influence.xml"));
+    Model model = parser
+        .createModel(new ConverterParams().filename("testFiles/small/reaction/unknown_positive_influence.xml"));
     Reaction reaction = model.getReactions().iterator().next();
     assertNotNull(reaction);
-    assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+    assertTrue("Invalid class type: " + reaction.getClass(), reaction instanceof UnknownPositiveInfluenceReaction);
   }
 
   @Test
@@ -167,7 +168,8 @@ public class SbmlReactionParserTest {
 
   @Test
   public void testParseUnknownNegativeInfluence() throws FileNotFoundException, InvalidInputDataExecption {
-    Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/unknown_negative_influence.xml"));
+    Model model = parser
+        .createModel(new ConverterParams().filename("testFiles/small/reaction/unknown_negative_influence.xml"));
     Reaction reaction = model.getReactions().iterator().next();
     assertNotNull(reaction);
     assertTrue(reaction instanceof UnknownNegativeInfluenceReaction);

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java

 package lcsb.mapviewer.converter.model.sbml.species;
 
+import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
 
 import java.io.FileNotFoundException;
@@ -7,6 +8,7 @@ import java.io.FileNotFoundException;
 import org.apache.log4j.Logger;
 import org.junit.Test;
 
+import lcsb.mapviewer.common.geometry.ColorParser;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.converter.model.sbml.SbmlParser;
@@ -30,11 +32,14 @@ public class SbmlSpeciesParserTest {
   Logger logger = Logger.getLogger(SbmlSpeciesParserTest.class);
   SbmlParser parser = new SbmlParser();
 
+  ColorParser colorParser = new ColorParser();
+
   @Test
   public void testParseAntisenseRna() throws FileNotFoundException, InvalidInputDataExecption {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/small/antisense_rna.xml"));
     Element element = model.getElementByElementId("s1");
     assertTrue(element instanceof AntisenseRna);
+    assertEquals(ElementColorEnum.ANTISENSE_RNA.getColor(), element.getColor());
   }
 
   @Test
@@ -42,6 +47,7 @@ public class SbmlSpeciesParserTest {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/small/complex.xml"));
     Element element = model.getElementByElementId("s1");
     assertTrue(element instanceof Complex);
+    assertEquals(ElementColorEnum.COMPLEX.getColor(), element.getColor());
   }
 
   @Test
@@ -49,6 +55,7 @@ public class SbmlSpeciesParserTest {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/small/degraded.xml"));
     Element element = model.getElementByElementId("s1");
     assertTrue(element instanceof Degraded);
+    assertEquals(ElementColorEnum.DEGRADED.getColor(), element.getColor());
   }
 
   @Test
@@ -56,6 +63,7 @@ public class SbmlSpeciesParserTest {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/small/drug.xml"));
     Element element = model.getElementByElementId("s1");
     assertTrue(element instanceof Drug);
+    assertEquals(ElementColorEnum.DRUG.getColor(), element.getColor());
   }
 
   @Test
@@ -63,6 +71,7 @@ public class SbmlSpeciesParserTest {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/small/gene.xml"));
     Element element = model.getElementByElementId("s1");
     assertTrue(element instanceof Gene);
+    assertEquals(ElementColorEnum.GENE.getColor(), element.getColor());
   }
 
   @Test
@@ -70,6 +79,7 @@ public class SbmlSpeciesParserTest {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/small/generic_protein.xml"));
     Element element = model.getElementByElementId("s1");
     assertTrue(element instanceof GenericProtein);
+    assertEquals(ElementColorEnum.GENERIC_PROTEIN.getColor(), element.getColor());
   }
 
   @Test
@@ -77,6 +87,7 @@ public class SbmlSpeciesParserTest {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/small/ion_channel.xml"));
     Element element = model.getElementByElementId("s1");
     assertTrue(element instanceof IonChannelProtein);
+    assertEquals(ElementColorEnum.ION_CHANNEL.getColor(), element.getColor());
   }
 
   @Test
@@ -84,6 +95,7 @@ public class SbmlSpeciesParserTest {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/small/ion.xml"));
     Element element = model.getElementByElementId("s1");
     assertTrue(element instanceof Ion);
+    assertEquals(ElementColorEnum.ION.getColor(), element.getColor());
   }
 
   @Test
@@ -91,6 +103,7 @@ public class SbmlSpeciesParserTest {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/small/phenotype.xml"));
     Element element = model.getElementByElementId("s1");
     assertTrue(element instanceof Phenotype);
+    assertEquals(ElementColorEnum.PHENOTYPE.getColor(), element.getColor());
   }
 
   @Test
@@ -98,6 +111,7 @@ public class SbmlSpeciesParserTest {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/small/receptor.xml"));
     Element element = model.getElementByElementId("s1");
     assertTrue(element instanceof ReceptorProtein);
+    assertEquals(ElementColorEnum.RECEPTOR.getColor(), element.getColor());
   }
 
   @Test
@@ -105,6 +119,7 @@ public class SbmlSpeciesParserTest {