export of species type added

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

 package lcsb.mapviewer.converter.model.sbml.species;
 
-import java.util.HashSet;
-import java.util.Set;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.apache.log4j.Logger;
 
@@ -18,6 +18,7 @@ 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.Species;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
 import lcsb.mapviewer.model.map.species.Unknown;
 
 public enum SBOTermSpeciesType {
@@ -27,6 +28,7 @@ public enum SBOTermSpeciesType {
   DRUG(Drug.class, new String[] { "SBO:0000298" }), //
   GENE(Gene.class, new String[] { "SBO:0000243" }), //
   GENERIC_PROTEIN(GenericProtein.class, new String[] { "SBO:0000252" }), //
+  TRUNCATED_PROTEIN(TruncatedProtein.class, new String[] {}, new String[] { "SBO:0000252" }), //
   ION(Ion.class, new String[] { "SBO:0000327" }), //
   ION_CHANNEL(IonChannelProtein.class, new String[] { "SBO:0000284" }), //
   PHENOTYPE(Phenotype.class, new String[] { "SBO:0000358" }), //
@@ -37,7 +39,8 @@ public enum SBOTermSpeciesType {
   ;
 
   private static Logger logger = Logger.getLogger(SBOTermSpeciesType.class);
-  private Set<String> sboTerms = new HashSet<>();
+  private List<String> sboTerms = new ArrayList<>();
+  private List<String> exportSboTerms = new ArrayList<>();
   Class<? extends Species> clazz;
 
   private SBOTermSpeciesType(Class<? extends Species> clazz, String[] inputSboTerms) {
@@ -47,6 +50,16 @@ public enum SBOTermSpeciesType {
     }
   }
 
+  private SBOTermSpeciesType(Class<? extends Species> clazz, String[] inputSboTerms, String[] outputSboTerms) {
+    this.clazz = clazz;
+    for (String string : inputSboTerms) {
+      sboTerms.add(string);
+    }
+    for (String string : outputSboTerms) {
+      exportSboTerms.add(string);
+    }
+  }
+
   public static Class<? extends Species> getTypeSBOTerm(String sboTerm) {
     if (sboTerm == null || sboTerm.isEmpty()) {
       return SimpleMolecule.class;
@@ -65,4 +78,25 @@ public enum SBOTermSpeciesType {
     }
     return result;
   }
+
+  public static String getTermByType(Class<? extends Species> clazz) {
+    for (SBOTermSpeciesType term : values()) {
+      if (clazz.equals(term.clazz)) {
+        return term.getSBO();
+      }
+    }
+    logger.warn("Cannot find SBO term for class: " + clazz);
+    return null;
+  }
+
+  private String getSBO() {
+    if (sboTerms.size() != 0) {
+      return sboTerms.get(0);
+    }
+    if (exportSboTerms.size() != 0) {
+      return exportSboTerms.get(0);
+    }
+    logger.warn("Cannot find SBO term for class: " + clazz);
+    return null;
+  }
 }

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

@@ -24,6 +24,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
   @Override
   public org.sbml.jsbml.Species createSbmlElement(Species element) throws InconsistentModelException {
     org.sbml.jsbml.Species result = getSbmlModel().createSpecies("species_" + (getNextId()));
+    result.setSBOTerm(SBOTermSpeciesType.getTermByType(element.getClass()));
     if (element.getCompartment() != null) {
       result.setCompartment(compartmentExporter.getSbmlElement(element.getCompartment(), null));
     }