Various Additions included in KEGGtranslator v2 Release.

src/de/zbit/kegg/gui/TranslatorBioPAXPanel.java

@@ -48,7 +48,7 @@
  * @author Clemens Wrzodek
  * @version $Rev$
  */
-public class TranslatorBioPAXPanel extends TranslatorGraphLayerPanel<Model>{
+public class TranslatorBioPAXPanel extends TranslatorGraphLayerPanel<Model> {
 
   private static final long serialVersionUID = -6585611929238639630L;
 
@@ -129,6 +129,14 @@ public boolean isAllowedToSaveAsGraphFormats() {
     return false;
   }
 
+  /* (non-Javadoc)
+   * @see de.zbit.graph.gui.TranslatorGraphLayerPanel#isDetailPanelAvailable()
+   */
+  @Override
+  public boolean isDetailPanelAvailable() {
+    return false;
+  }
+
   /* (non-Javadoc)
    * @see de.zbit.kegg.gui.TranslatorGraphLayerPanel#updateDetailPanel(javax.swing.JScrollPane, y.view.HitInfo)
    */

src/de/zbit/kegg/gui/TranslatorGraphPanel.java

@@ -108,7 +108,13 @@ protected boolean writeRealDocumentToFileUnchecked(File file, String format)
     throws Exception {
     return ((KEGG2yGraph)getTranslator()).writeToFile(document, file.getPath(), format);
   }
-
-
+
+  /* (non-Javadoc)
+   * @see de.zbit.graph.gui.TranslatorGraphLayerPanel#isDetailPanelAvailable()
+   */
+  @Override
+  public boolean isDetailPanelAvailable() {
+    return false;
+  }
 
 }

src/de/zbit/kegg/gui/TranslatorSBGNPanel.java

@@ -118,4 +118,13 @@ protected boolean writeRealDocumentToFileUnchecked(File file, String format)
     throws Exception {
     return ((KEGG2SBGN)getTranslator()).writeToFile(document, file.getPath());
   }
+
+  /* (non-Javadoc)
+   * @see de.zbit.graph.gui.TranslatorGraphLayerPanel#isDetailPanelAvailable()
+   */
+  @Override
+  public boolean isDetailPanelAvailable() {
+    return false;
+  }
+
 }

src/de/zbit/kegg/io/KEGG2BioPAX.java

@@ -277,6 +277,9 @@ public BioPAXElement createXRef(IdentifierDatabases db, String id, int type) {
         instantiate = relationshipXref.class;
       } else if (type==3) {
         instantiate = publicationXref.class;
+      } else {
+        // we can NOT instantiate xref.class
+        instantiate = relationshipXref.class;
       }
 
       xr = model.addNew(instantiate, uri);
@@ -293,6 +296,9 @@ public BioPAXElement createXRef(IdentifierDatabases db, String id, int type) {
         instantiate = RelationshipXref.class;
       } else if (type==3) {
         instantiate = PublicationXref.class;
+      } else {
+        // we can NOT instantiate Xref.class
+        instantiate = RelationshipXref.class;
       }
 
       xr = model.addNew(instantiate, uri);

src/de/zbit/kegg/io/KEGG2BioPAX_level2.java

@@ -113,7 +113,7 @@ protected BioPAXElement createPathwayInstance(Pathway p) {
     // Parse Kegg Pathway information
     boolean isKEGGPathway = DatabaseIdentifiers.checkID(DatabaseIdentifiers.IdentifierDatabases.KEGG_Pathway, p.getNameForMIRIAM());
     if (isKEGGPathway) {
-      xref xr = (xref)createXRef(IdentifierDatabases.KEGG_Pathway, p.getNameForMIRIAM());
+      xref xr = (xref)createXRef(IdentifierDatabases.KEGG_Pathway, p.getNameForMIRIAM(), 1);
       if (xr!=null) {
         pathway.addXREF(xr);
       }

src/de/zbit/kegg/io/KEGG2BioPAX_level3.java

@@ -55,7 +55,6 @@
 import org.biopax.paxtools.model.level3.SmallMolecule;
 import org.biopax.paxtools.model.level3.SmallMoleculeReference;
 import org.biopax.paxtools.model.level3.Stoichiometry;
-import org.biopax.paxtools.model.level3.UnificationXref;
 import org.biopax.paxtools.model.level3.XReferrable;
 import org.biopax.paxtools.model.level3.Xref;
 
@@ -307,7 +306,7 @@ protected BioPAXElement createPathwayInstance(Pathway p) {
     // Parse Kegg Pathway information
     boolean isKEGGPathway = DatabaseIdentifiers.checkID(DatabaseIdentifiers.IdentifierDatabases.KEGG_Pathway, p.getNameForMIRIAM());
     if (isKEGGPathway) {
-      Xref xr = (Xref)createXRef(IdentifierDatabases.KEGG_Pathway, p.getNameForMIRIAM());
+      Xref xr = (Xref)createXRef(IdentifierDatabases.KEGG_Pathway, p.getNameForMIRIAM(), 1);
       if (xr!=null) {
         pathway.addXref(xr);
       }
@@ -474,6 +473,16 @@ public BioPAXElement addKGMLRelation(Relation r, Pathway p) {
       return null;
     }
 
+//    // Relations should prefarably translated, using the EntityReferences
+//    if (qOne instanceof SimplePhysicalEntity && 
+//        ((SimplePhysicalEntity)qOne).getEntityReference()!=null ) {
+//      qOne = ((SimplePhysicalEntity)qOne).getEntityReference();
+//    }
+//    if (qTwo instanceof SimplePhysicalEntity && 
+//        ((SimplePhysicalEntity)qTwo).getEntityReference()!=null ) {
+//      qTwo = ((SimplePhysicalEntity)qTwo).getEntityReference();
+//    }
+
     // Most relations have a left and right side => conversion as default
     Class<? extends BioPAXElement> instantiate = Conversion.class;
 

src/de/zbit/kegg/io/KEGG2SBMLqual.java

@@ -38,6 +38,7 @@
 import org.sbml.jsbml.ext.groups.Group;
 import org.sbml.jsbml.ext.qual.Input;
 import org.sbml.jsbml.ext.qual.InputTransitionEffect;
+import org.sbml.jsbml.ext.qual.Output;
 import org.sbml.jsbml.ext.qual.OutputTransitionEffect;
 import org.sbml.jsbml.ext.qual.QualConstant;
 import org.sbml.jsbml.ext.qual.QualitativeModel;
@@ -93,6 +94,13 @@ public class KEGG2SBMLqual extends KEGG2jSBML {
    */
   private boolean considerReactions = false;
 
+  /**
+   * All transitions that are added to the model.
+   * Identified as "inputQualitativeSpecies ouptutQualitativeSpecies [SBOterm]",
+   * used to check for duplicates.
+   */
+  private Set<String> containedTransitions = new HashSet<String>();
+
 
   /**
    * @param document
@@ -242,7 +250,7 @@ public Transition addKGMLRelation(Relation r, Pathway p, QualitativeModel qualMo
     in.setMetaId("meta_" + in.getId());
 
     // Output
-    t.createOutput(NameToSId("out"), qTwo.getId(), OutputTransitionEffect.assignmentLevel); //TODO: is this correct?    
+    Output out = t.createOutput(NameToSId("out"), qTwo.getId(), OutputTransitionEffect.assignmentLevel); //TODO: is this correct?    
 
     //XXX: "function term" is intentionally not set in KEGG2X (info not provided).
 
@@ -327,6 +335,13 @@ public Transition addKGMLRelation(Relation r, Pathway p, QualitativeModel qualMo
       t.addCVTerm(cv);
     }
 
+    // Don't att same relations twice
+    String transitionIdentifier = in.getQualitativeSpecies() + " " + out.getQualitativeSpecies() + " " + (t.isSetSBOTerm() ? t.getSBOTermID():"");
+    if (!containedTransitions.add(transitionIdentifier)) {
+      qualModel.getListOfTransitions().remove(t);
+      t=null;
+    }
+
     return t;
   }
 

src/de/zbit/kegg/io/KEGG2jSBML.java

@@ -219,7 +219,8 @@ public void setUseGroupsExtension(boolean b) {
 
   /** Load the default preferences from the SBPreferences object. */
   private void loadPreferences() {
-    addCellDesignerAnnots = KEGGtranslatorOptions.CELLDESIGNER_ANNOTATIONS.getValue(prefs);
+    // CellDeisnger annotations are not supported anymore!
+    //addCellDesignerAnnots = KEGGtranslatorOptions.CELLDESIGNER_ANNOTATIONS.getValue(prefs);
     addLayoutExtension = KEGGtranslatorOptions.ADD_LAYOUT_EXTENSION.getValue(prefs);
     useGroupsExtension = KEGGtranslatorOptions.USE_GROUPS_EXTENSION.getValue(prefs);
   }