import/export of sbml supports z-index

CHANGELOG

@@ -48,6 +48,8 @@ minerva (13.1.0~alpha.0) unstable; urgency=low
   * Small improvement: allow admin to disable CORS check (#802)
   * Small improvement: TransparencyZoomLevelVisibility parameter renamed to
     SemanticZoomLevelTransparency (#801)
+  * Small improvement: export/import from SBML support z-index in LAYOUT 
+    extension
   * Bug fix: progress bar of gene genome mapping upload is refreshing properly
     (#728)
   * Bug fix: when editing project Disease and Organism could not be removed

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

@@ -301,7 +301,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
   }
 
   private void createCircleLineEnding(LineEnding result) {
-    BoundingBox boundingBox = createBoundingBox(-2, 0, 4, 4);
+    BoundingBox boundingBox = createBoundingBox(-2, 0, 4, 4, 0);
     result.getGroup().setFill(getColorDefinition(Color.WHITE).getId());
     result.setBoundingBox(boundingBox);
     Ellipse ellipse = new Ellipse();
@@ -317,7 +317,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
   }
 
   private void createOpenLineEnding(LineEnding result) {
-    BoundingBox boundingBox = createBoundingBox(-12, -6, 12, 12);
+    BoundingBox boundingBox = createBoundingBox(-12, -6, 12, 12, 0);
     result.setBoundingBox(boundingBox);
     Polygon polygon = new Polygon();
     polygon.addElement(createRenderPoint(0, 0));
@@ -328,7 +328,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
   }
 
   private void createDiamondLineEnding(LineEnding result) {
-    BoundingBox boundingBox = createBoundingBox(-18, -6, 18, 12);
+    BoundingBox boundingBox = createBoundingBox(-18, -6, 18, 12, 0);
     result.setBoundingBox(boundingBox);
     result.getGroup().setFill(getColorDefinition(Color.WHITE).getId());
     Polygon polygon = new Polygon();
@@ -341,7 +341,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
   }
 
   private void createCrossBarLineEnding(LineEnding result) {
-    BoundingBox boundingBox = createBoundingBox(0, -6, 1, 12);
+    BoundingBox boundingBox = createBoundingBox(0, -6, 1, 12, 0);
     result.setBoundingBox(boundingBox);
     Polygon crossBar = new Polygon();
     crossBar.addElement(createRenderPoint(0, 0));
@@ -355,7 +355,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
   }
 
   private void createFullLineEnding(LineEnding result) {
-    BoundingBox boundingBox = createBoundingBox(-12, -6, 12, 12);
+    BoundingBox boundingBox = createBoundingBox(-12, -6, 12, 12, 0);
     result.setBoundingBox(boundingBox);
     result.getGroup().setFill(getColorDefinition(Color.BLACK).getId());
     Polygon polygon = new Polygon();
@@ -367,7 +367,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
   }
 
   private void createBlankCrossBarLineEnding(LineEnding result) {
-    BoundingBox boundingBox = createBoundingBox(-18, -6, 18, 12);
+    BoundingBox boundingBox = createBoundingBox(-18, -6, 18, 12, 0);
     result.setBoundingBox(boundingBox);
     result.getGroup().setFill(getColorDefinition(Color.WHITE).getId());
     Polygon polygon = new Polygon();
@@ -397,10 +397,10 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
     return result;
   }
 
-  protected BoundingBox createBoundingBox(double x, double y, double w, double h) {
+  protected BoundingBox createBoundingBox(double x, double y, int z, double w, double h) {
     BoundingBox boundingBox = new BoundingBox();
 
-    boundingBox.setPosition(new Point(x, y));
+    boundingBox.setPosition(new Point(x, y, z));
     Dimensions dimensions = new Dimensions();
 
     dimensions.setWidth(w);

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

@@ -39,13 +39,14 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
   protected void assignLayoutToGlyph(T element, AbstractReferenceGlyph speciesGlyph) {
     BoundingBox boundingBox = new BoundingBox();
 
-    boundingBox.setPosition(new Point(element.getX(), element.getY()));
+    boundingBox.setPosition(new Point(element.getX(), element.getY(), element.getZ()));
     Dimensions dimensions = new Dimensions();
     dimensions.setWidth(element.getWidth());
     dimensions.setHeight(element.getHeight());
     boundingBox.setDimensions(dimensions);
     speciesGlyph.setBoundingBox(boundingBox);
 
+
     if (isExtensionEnabled(SbmlExtension.RENDER)) {
       LocalStyle style = createStyle(element);
 

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

@@ -74,7 +74,7 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
       if (style != null) {
         applyStyleToElement(source, style);
       }
-      
+
       used.add(source.getElementId());
       AbstractReferenceGlyph glyph = idGlyphPair.getRight();
       if (glyph.getId() == null || glyph.getId().equals("")) {
@@ -104,6 +104,9 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
     elementWithLayout.setElementId(glyph.getId());
     elementWithLayout.setX(glyph.getBoundingBox().getPosition().getX());
     elementWithLayout.setY(glyph.getBoundingBox().getPosition().getY());
+    if (glyph.getBoundingBox().getPosition().isSetZ()) {
+      elementWithLayout.setZ((int) glyph.getBoundingBox().getPosition().getZ());
+    }
     elementWithLayout.setWidth(glyph.getBoundingBox().getDimensions().getWidth());
     elementWithLayout.setHeight(glyph.getBoundingBox().getDimensions().getHeight());
 

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

@@ -22,6 +22,7 @@ import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.ConverterException;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.ZIndexPopulator;
 import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentParser;
 import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionParser;
 import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParser;
@@ -200,6 +201,7 @@ public class SbmlParser extends Converter {
     } catch (CommandExecutionException e) {
       throw new InvalidInputDataExecption("Problem with generating layout", e);
     }
+    new ZIndexPopulator().populateZIndex(model);
   }
 
   private void updateModifierTypes(Reaction reaction) {

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java

@@ -136,7 +136,7 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
     if (element.getElementId().equals("default")) {
       BoundingBox boundingBox = new BoundingBox();
 
-      boundingBox.setPosition(new Point(element.getX(), element.getY()));
+      boundingBox.setPosition(new Point(element.getX(), element.getY(), 0));
       Dimensions dimensions = new Dimensions();
 
       if (getMinervaModel().getWidth() != null) {
@@ -151,7 +151,7 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
       Point2D point = element.getNamePoint();
       double width = element.getWidth() - (point.getX() - element.getX());
       double height = element.getHeight() - (point.getY() - element.getY());
-      textGlyph.setBoundingBox(createBoundingBox(point.getX(), point.getY(), width, height));
+      textGlyph.setBoundingBox(createBoundingBox(point.getX(), point.getY(), element.getZ() + 1, width, height));
       textGlyph.setReference(speciesGlyph.getId());
 
       if (isExtensionEnabled(SbmlExtension.RENDER)) {

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

@@ -10,7 +10,6 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import lcsb.mapviewer.common.XmlParser;
 import org.apache.log4j.Logger;
 import org.sbml.jsbml.ASTNode;
 import org.sbml.jsbml.KineticLaw;
@@ -20,6 +19,7 @@ import org.sbml.jsbml.SimpleSpeciesReference;
 import org.sbml.jsbml.Species;
 import org.sbml.jsbml.SpeciesReference;
 import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
+import org.sbml.jsbml.ext.layout.BoundingBox;
 import org.sbml.jsbml.ext.layout.Curve;
 import org.sbml.jsbml.ext.layout.LineSegment;
 import org.sbml.jsbml.ext.layout.Point;
@@ -33,6 +33,7 @@ import org.sbml.jsbml.ext.render.RenderGroup;
 import org.w3c.dom.Node;
 
 import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityExporter;
 import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
@@ -55,7 +56,6 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
   /**
    * Default class logger.
    */
-  @SuppressWarnings("unused")
   private static Logger logger = Logger.getLogger(SbmlReactionExporter.class);
 
   private SbmlBioEntityExporter<lcsb.mapviewer.model.map.species.Species, Species> speciesExporter;
@@ -295,6 +295,13 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     if (isExtensionEnabled(SbmlExtension.RENDER)) {
       assignStyleToGlyph(reactionGlyph, createStyle(reaction));
     }
+    if (reactionGlyph.getBoundingBox()==null) {
+      reactionGlyph.setBoundingBox(new BoundingBox());
+    }
+    if (reactionGlyph.getBoundingBox().getPosition()==null) {
+      reactionGlyph.getBoundingBox().setPosition(new Point());
+    }
+    reactionGlyph.getBoundingBox().getPosition().setZ(reaction.getZ());
 
   }
 

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

@@ -117,6 +117,12 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
         Reaction reactionWithLayout = source.copy();
         // getId doesn't have to be unique, therefore we concatenate with reaction
         reactionWithLayout.setIdReaction(glyph.getReaction() + "__" + glyph.getId());
+        
+        //z index
+        if (glyph.getBoundingBox() != null && glyph.getBoundingBox().getPosition() != null
+            && glyph.getBoundingBox().getPosition().isSetZ()) {
+          reactionWithLayout.setZ((int) glyph.getBoundingBox().getPosition().getZ());
+        }
         for (SpeciesReferenceGlyph speciesRefernceGlyph : glyph.getListOfSpeciesReferenceGlyphs()) {
           SpeciesGlyph speciesGlyph = getLayout().getSpeciesGlyph(speciesRefernceGlyph.getSpeciesGlyph());
           ReactionNode minervaNode = null;

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

@@ -545,7 +545,8 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     }
     TextGlyph textGlyph = getLayout().createTextGlyph("text_" + element.getElementId(), element.getName());
     textGlyph
-        .setBoundingBox(createBoundingBox(element.getX(), element.getY(), element.getWidth(), element.getHeight()));
+        .setBoundingBox(createBoundingBox(element.getX(), element.getY(), element.getZ() + 1, element.getWidth(),
+            element.getHeight()));
     textGlyph.setReference(speciesGlyph.getId());
 
     if (isExtensionEnabled(SbmlExtension.RENDER)) {
@@ -601,7 +602,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     double x = mr.getPosition().getX() - width / 2;
     double y = mr.getPosition().getY() - height / 2;
     BoundingBox boundingBox = new BoundingBox();
-    boundingBox.setPosition(new Point(x, y));
+    boundingBox.setPosition(new Point(x, y, mr.getSpecies().getZ() + 1));
     Dimensions dimensions = new Dimensions();
     dimensions.setWidth(width);
     dimensions.setHeight(height);

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

@@ -19,11 +19,10 @@ import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelComparator;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Species;
 
 @RunWith(Parameterized.class)
-public class ElementPropertiesExport {
+public class ElementPropertiesExport extends SbmlTestFunctions {
 
   static Logger logger = Logger.getLogger(ElementPropertiesExport.class.getName());
 
@@ -37,21 +36,21 @@ public class ElementPropertiesExport {
   public static Collection<Object[]> data() throws IOException {
     Collection<Object[]> data = new ArrayList<>();
 
-    data.add(createTestEntry("Empty", createElement()));
+    data.add(createTestEntry("Empty", createProtein()));
 
-    Species element = createElement();
+    Species element = createProtein();
     element.setInitialConcentration(1.0);
     data.add(createTestEntry("Initial concentration", element));
 
-    element = createElement();
+    element = createProtein();
     element.setInitialAmount(2.0);
     data.add(createTestEntry("Initial amount", element));
 
-    element = createElement();
+    element = createProtein();
     element.setBoundaryCondition(true);
     data.add(createTestEntry("Boundary condition", element));
 
-    element = createElement();
+    element = createProtein();
     element.setConstant(true);
     data.add(createTestEntry("Constatnt", element));
 
@@ -67,15 +66,6 @@ public class ElementPropertiesExport {
     return new Object[] { string, result };
   }
 
-  private static Species createElement() {
-    Species element = new GenericProtein("id");
-    element.setX(10);
-    element.setY(10);
-    element.setWidth(1000);
-    element.setHeight(30);
-    return element;
-  }
-
   @Test
   public void createModelTest() throws Exception {
     try {

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

@@ -19,11 +19,10 @@ import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelComparator;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Species;
 
 @RunWith(Parameterized.class)
-public class ElementPropertiesExportToLayoutTest {
+public class ElementPropertiesExportToLayoutTest extends SbmlTestFunctions {
 
   static Logger logger = Logger.getLogger(ElementPropertiesExportToLayoutTest.class.getName());
 
@@ -37,9 +36,9 @@ public class ElementPropertiesExportToLayoutTest {
   public static Collection<Object[]> data() throws IOException {
     Collection<Object[]> data = new ArrayList<>();
 
-    data.add(createTestEntry("Empty", createElement()));
+    data.add(createTestEntry("Empty", createProtein()));
 
-    Species element = createElement();
+    Species element = createProtein();
     element.setFontSize(40);
     data.add(createTestEntry("Font size", element));
 
@@ -55,15 +54,6 @@ public class ElementPropertiesExportToLayoutTest {
     return new Object[] { string, result };
   }
 
-  private static Species createElement() {
-    Species element = new GenericProtein("id");
-    element.setX(10);
-    element.setY(10);
-    element.setWidth(1000);
-    element.setHeight(30);
-    return element;
-  }
-
   @Test
   public void createModelTest() throws Exception {
     try {

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

@@ -20,11 +20,10 @@ import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelComparator;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Species;
 
 @RunWith(Parameterized.class)
-public class ElementPropertiesExportToMultiTest {
+public class ElementPropertiesExportToMultiTest extends SbmlTestFunctions {
 
   static Logger logger = Logger.getLogger(ElementPropertiesExportToMultiTest.class.getName());
 
@@ -38,45 +37,45 @@ public class ElementPropertiesExportToMultiTest {
   public static Collection<Object[]> data() throws IOException {
     Collection<Object[]> data = new ArrayList<>();
 
-    data.add(createTestEntry("Empty", createElement()));
+    data.add(createTestEntry("Empty", createProtein()));
 
-    Species element = createElement();
+    Species element = createProtein();
     element.setAbbreviation("xyz");
     data.add(createTestEntry("Abbreviation", element));
 
-    element = createElement();
+    element = createProtein();
     element.setFormerSymbols(Arrays.asList(new String[] { "symbol 1", "s2" }));
     data.add(createTestEntry("Former Symbols", element));
 
-    element = createElement();
+    element = createProtein();
     element.setFormula("C2H5OH");
     data.add(createTestEntry("Formula", element));
 
-    element = createElement();
+    element = createProtein();
     element.setFullName("Amazing element");
     data.add(createTestEntry("Full name", element));
 
-    element = createElement();
+    element = createProtein();
     element.setHomodimer(4);
     data.add(createTestEntry("Homodimer", element));
 
-    element = createElement();
+    element = createProtein();
     element.setCharge(5);
     data.add(createTestEntry("Charge", element));
 
-    element = createElement();
+    element = createProtein();
     element.setHypothetical(true);
     data.add(createTestEntry("Hypothetical", element));
 
-    element = createElement();
+    element = createProtein();
     element.setActivity(true);
     data.add(createTestEntry("Activity", element));
 
-    element = createElement();
+    element = createProtein();
     element.setSymbol("H2O");
     data.add(createTestEntry("Symbol", element));
 
-    element = createElement();
+    element = createProtein();
     element.setSynonyms(Arrays.asList(new String[] { "syn 1", "s2" }));
     data.add(createTestEntry("Synonyms", element));
 
@@ -92,15 +91,6 @@ public class ElementPropertiesExportToMultiTest {
     return new Object[] { string, result };
   }
 
-  private static Species createElement() {
-    Species element = new GenericProtein("id");
-    element.setX(10);
-    element.setY(10);
-    element.setWidth(1000);
-    element.setHeight(30);
-    return element;
-  }
-
   @Test
   public void createModelTest() throws Exception {
     try {

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

@@ -15,8 +15,6 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
 
 public class SbmlExporterFromCellDesignerTest extends SbmlTestFunctions {
   Logger logger = Logger.getLogger(SbmlExporterFromCellDesignerTest.class);
-  SbmlParser parser = new SbmlParser();
-  SbmlExporter exporter = new SbmlExporter();
 
   CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
 
@@ -51,14 +49,4 @@ public class SbmlExporterFromCellDesignerTest extends SbmlTestFunctions {
     }
   }
 
-  private Model getModelAfterSerializing(Model originalModel) throws Exception {
-    String xml = exporter.toXml(originalModel);
-    // logger.debug(xml);
-    ByteArrayInputStream stream = new ByteArrayInputStream(xml.getBytes("UTF-8"));
-    Model result = parser.createModel(new ConverterParams().inputStream(stream));
-    // showImage(originalModel);
-    // showImage(result);
-    return result;
-  }
-
 }

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

@@ -8,7 +8,6 @@ import static org.junit.Assert.assertTrue;
 import java.awt.Color;
 import java.awt.geom.Line2D;
 import java.awt.geom.Point2D;
-import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.lang.reflect.Modifier;
 import java.util.Arrays;
@@ -30,17 +29,13 @@ import lcsb.mapviewer.common.comparator.LineComparator;
 import lcsb.mapviewer.common.comparator.ListComparator;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelComparator;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Species;
@@ -50,13 +45,11 @@ import lcsb.mapviewer.model.map.species.field.Residue;
 
 public class SbmlExporterTest extends SbmlTestFunctions {
   Logger logger = Logger.getLogger(SbmlExporterTest.class);
-  SbmlParser parser = new SbmlParser();
-  SbmlExporter exporter;
 
   ModelComparator comparator = new ModelComparator();
 
   public SbmlExporterTest() {
-    exporter = new SbmlExporter();
+    exporter.setProvideDefaults(false);
   }
 
   @Test
@@ -82,16 +75,6 @@ public class SbmlExporterTest extends SbmlTestFunctions {
     return getModelAfterSerializing(originalModel);
   }
 
-  private Model getModelAfterSerializing(Model originalModel) throws Exception {
-    exporter.setProvideDefaults(false);
-    String xml = exporter.toXml(originalModel);
-    ByteArrayInputStream stream = new ByteArrayInputStream(xml.getBytes("UTF-8"));
-    Model result = parser.createModel(new ConverterParams().inputStream(stream));
-    // showImage(originalModel);
-    // showImage(result);
-    return result;
-  }
-
   @Test
   public void testExportSpecies() throws Exception {
     Model model = getModelAfterSerializing("testFiles/layoutExample/SpeciesGlyph_Example_level2_level3.xml");
@@ -188,31 +171,13 @@ public class SbmlExporterTest extends SbmlTestFunctions {
 
   private Model createModelWithReaction() {
     Model model = createEmptyModel();
-    GenericProtein p1 = new GenericProtein("s1");
-    p1.setWidth(100);
-    p1.setHeight(20);
-    p1.setX(10);
+    GenericProtein p1 = createProtein();
     p1.setY(10);
     model.addElement(p1);
-    GenericProtein p2 = new GenericProtein("s2");
-    p2.setWidth(100);
-    p2.setHeight(20);
-    p2.setX(10);
+    GenericProtein p2 = createProtein();
     p2.setY(50);
     model.addElement(p2);
-    Reaction reaction = new StateTransitionReaction();
-    Reactant reactant = new Reactant(p1);
-    Product product = new Product(p2);
-    PolylineData reactantLine = new PolylineData();
-    reactantLine.addPoint(new Point2D.Double(50, 20));
-    reactantLine.addPoint(new Point2D.Double(50, 30));
-    reactant.setLine(reactantLine);
-    PolylineData productLine = new PolylineData();
-    productLine.addPoint(new Point2D.Double(50, 40));
-    productLine.addPoint(new Point2D.Double(50, 60));
-    product.setLine(productLine);
-    reaction.addReactant(reactant);
-    reaction.addProduct(product);
+    Reaction reaction = createReaction(p1, p2);
     model.addReaction(reaction);
     return model;
   }
@@ -344,6 +309,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
         element.setWidth(10);
         element.setY(10);
         element.setHeight(10);
+        element.setZ(127);
         model.addElement(element);
         Model deserializedModel = getModelAfterSerializing(model);
 
@@ -480,12 +446,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
   public void testMultiExtensionProteinStateInTypes() throws Exception {
     String structuralState = "xxx";
     Model model = createEmptyModel();
-    GenericProtein element = new GenericProtein("id");
-    element.setName("test name");
-    element.setX(10);
-    element.setWidth(10);
-    element.setY(10);
-    element.setHeight(10);
+    GenericProtein element = createProtein();
     element.setStructuralState(structuralState);
     model.addElement(element);
     org.sbml.jsbml.Model sbmlModel = exporter.toSbmlDocument(model).getModel();
@@ -509,20 +470,10 @@ public class SbmlExporterTest extends SbmlTestFunctions {
   public void testMultiExtensionProteinStateSuplicateInTypes() throws Exception {
     String structuralState = "xxx";
     Model model = createEmptyModel();
-    GenericProtein element = new GenericProtein("id");
-    element.setName("test name");
-    element.setX(10);
-    element.setWidth(10);
-    element.setY(10);
-    element.setHeight(10);
+    GenericProtein element = createProtein();
     element.setStructuralState(structuralState);
     model.addElement(element);
-    element = new GenericProtein("id2");
-    element.setName("test name");
-    element.setX(10);