multi species type is exported

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

@@ -14,6 +14,7 @@ import org.apache.log4j.Logger;
 import org.sbml.jsbml.Model;
 import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
 import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.multi.MultiModelPlugin;
 import org.sbml.jsbml.ext.render.ColorDefinition;
 import org.sbml.jsbml.ext.render.LocalRenderInformation;
 import org.sbml.jsbml.ext.render.LocalStyle;
@@ -151,6 +152,10 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
     return null;
   }
 
+  protected MultiModelPlugin getMultiPlugin() {
+    return (MultiModelPlugin) sbmlModel.getExtension("multi");
+  }
+
   protected lcsb.mapviewer.model.map.model.Model getMinervaModel() {
     return minervaModel;
   }

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

@@ -6,6 +6,8 @@ import java.util.List;
 import org.apache.log4j.Logger;
 import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
 import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.multi.MultiSpeciesPlugin;
+import org.sbml.jsbml.ext.multi.MultiSpeciesType;
 import org.sbml.jsbml.ext.render.LocalStyle;
 
 import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
@@ -15,13 +17,13 @@ import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.species.Species;
 
 public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.jsbml.Species> {
-  
+
   /**
    * Default class logger.
    */
   @SuppressWarnings("unused")
   private static Logger logger = Logger.getLogger(SbmlSpeciesExporter.class);
-  
+
   private SbmlCompartmentExporter compartmentExporter;
 
   public SbmlSpeciesExporter(Layout layout,
@@ -49,9 +51,20 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     if (element.getConstant() != null) {
       result.setConstant(element.getConstant());
     }
+    if (isExtensionEnabled(SbmlExtension.MULTI)) {
+      MultiSpeciesPlugin multiExtension = new MultiSpeciesPlugin(result);
+      multiExtension.setSpeciesType(getMultiSpeciesType(element));
+      result.addExtension("multi", multiExtension);
+    }
     return result;
   }
 
+  private String getMultiSpeciesType(Species element) {
+    MultiSpeciesType speciesType = getMultiPlugin()
+        .getSpeciesType("minerva_species_type_" + element.getClass().getSimpleName());
+    return speciesType.getId();
+  }
+
   @Override
   protected AbstractReferenceGlyph createElementGlyph(String sbmlElementId, String glyphId) {
     AbstractReferenceGlyph speciesGlyph = getLayout().createSpeciesGlyph(glyphId, sbmlElementId);

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

@@ -21,6 +21,7 @@ import org.junit.Test;
 import org.reflections.Reflections;
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.ext.multi.MultiModelPlugin;
+import org.sbml.jsbml.ext.multi.MultiSpeciesPlugin;
 import org.sbml.jsbml.ext.multi.MultiSpeciesType;
 import org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue;
 import org.sbml.jsbml.ext.multi.SpeciesFeatureType;
@@ -537,4 +538,35 @@ public class SbmlExporterTest {
     }
   }
 
+  @Test
+  public void testMultiExtensionTypeDefinition() 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);
+    element.setStructuralState(structuralState);
+    model.addElement(element);
+    org.sbml.jsbml.Model sbmlModel = exporter.toSbmlDocument(model).getModel();
+
+    MultiModelPlugin multiPlugin = (MultiModelPlugin) sbmlModel.getExtension("multi");
+
+    org.sbml.jsbml.Species sbmlSpecies = sbmlModel.getSpecies(0);
+    MultiSpeciesPlugin speciesExtension = (MultiSpeciesPlugin) sbmlSpecies.getExtension("multi");
+    assertNotNull("Multi extension not defined for species", speciesExtension);
+    String speciesTypeString = speciesExtension.getSpeciesType();
+
+    MultiSpeciesType speciesType = null;
+    for (MultiSpeciesType type : multiPlugin.getListOfSpeciesTypes()) {
+      if (type.getId().equals(speciesTypeString)) {
+        speciesType = type;
+      }
+    }
+    assertNotNull("Species type is not set in multi extension", speciesType);
+
+  }
+
 }