export types contains structural state feature

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

@@ -18,6 +18,8 @@ import org.sbml.jsbml.ext.layout.Layout;
 import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
 import org.sbml.jsbml.ext.multi.MultiModelPlugin;
 import org.sbml.jsbml.ext.multi.MultiSpeciesType;
+import org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue;
+import org.sbml.jsbml.ext.multi.SpeciesFeatureType;
 import org.sbml.jsbml.ext.render.GlobalRenderInformation;
 import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
 
@@ -25,10 +27,13 @@ import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
 import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionExporter;
+import lcsb.mapviewer.converter.model.sbml.species.SBOTermSpeciesType;
 import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
 import lcsb.mapviewer.converter.model.sbml.units.SbmlUnitExporter;
 import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.species.Complex;
 import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Protein;
 import lcsb.mapviewer.model.map.species.Species;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
 
@@ -84,7 +89,7 @@ public class SbmlExporter {
     }
 
     if (usedExtensions.contains(SbmlExtension.MULTI)) {
-      createSbmlMultiPlugin(model, result);
+      createSbmlMultiPlugin(result);
     }
 
     SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model, usedExtensions);
@@ -140,7 +145,8 @@ public class SbmlExporter {
     return layout;
   }
 
-  public MultiModelPlugin createSbmlMultiPlugin(lcsb.mapviewer.model.map.model.Model model, Model result) {
+  @SuppressWarnings("unchecked")
+  protected MultiModelPlugin createSbmlMultiPlugin(Model result) {
     MultiModelPlugin multiPlugin = new MultiModelPlugin(result);
     result.addExtension("multi", multiPlugin);
     for (Class<? extends Element> clazz : new ElementUtils().getAvailableElementSubclasses()) {
@@ -148,7 +154,18 @@ public class SbmlExporter {
         MultiSpeciesType speciesType = new MultiSpeciesType();
         speciesType.setName(clazz.getSimpleName());
         speciesType.setId("minerva_species_type_" + clazz.getSimpleName());
+        if (Protein.class.isAssignableFrom(clazz) || Complex.class.isAssignableFrom(clazz)) {
+          SpeciesFeatureType feature = new SpeciesFeatureType();
+          feature.setName("Structural state");
+          feature.setId("minerva_structural_state_" + clazz.getSimpleName());
+          PossibleSpeciesFeatureValue featureEmptyValue = new PossibleSpeciesFeatureValue();
+          featureEmptyValue.setId("minerva_structural_state_" + clazz.getSimpleName() + "_empty");
+          featureEmptyValue.setName("");
+          feature.getListOfPossibleSpeciesFeatureValues().add(featureEmptyValue);
+          speciesType.getListOfSpeciesFeatureTypes().add(feature);
+        }
         multiPlugin.getListOfSpeciesTypes().add(speciesType);
+        speciesType.setSBOTerm(SBOTermSpeciesType.getTermByType((Class<? extends Species>) clazz));
       }
     }
     return multiPlugin;