Last commit prior to working on Methods-Paper Revision.

- Added a invisible path2models option
- Shortened the BioPAX display name
- Fixed a bug that potentially causes spaces in BioPAX IDs (which is not allowed)
- Fixed the Controlled Vocabulary of BioPAX interactions to include childs of the MI:0190 branch
- Added MI-terms and getMITerm() methods and classes, e.g., in SBOMapping.java

src/de/zbit/kegg/Translator.java

@@ -35,6 +35,7 @@
 import de.zbit.Launcher;
 import de.zbit.gui.GUIOptions;
 import de.zbit.io.FileTools;
+import de.zbit.kegg.api.KeggInfos;
 import de.zbit.kegg.api.cache.KeggFunctionManagement;
 import de.zbit.kegg.api.cache.KeggInfoManagement;
 import de.zbit.kegg.ext.KEGGTranslatorPanelOptions;
@@ -74,6 +75,13 @@ public class Translator extends Launcher {
 	 * like the browser cache). Must be loaded upon start and saved upon exit.
 	 */  
   public final static String cacheFunctionFileName = "keggfc.dat";
+
+  /**
+   * Adjusts a few methods in KEGGtranslator to generate an ouput for
+   * the path2models project if true.
+   * <p><b>PLESE ALWAYS KEEP THE DEFAULT, INITIAL VALUE TO FALSE!</b>
+   */
+  public static boolean path2models = false;
 
 	/**
 	 * The {@link Logger} for this class.
@@ -333,14 +341,9 @@ public void commandLineMode(AppConf appConf) {
 		// Maybe adjust for path2models
 		SBPreferences prefs = SBPreferences.getPreferencesFor(KEGGtranslatorCommandLineOnlyOptions.class);
 		if (KEGGtranslatorCommandLineOnlyOptions.PATH2MODELS.getValue(props)) {
-		  /*  TODO:
-		   * 1) Set the required options
-		   * 2) Uncomment code in [KEGG] Pathway.java for 'getCompoundPreviewPicture()'
-		   * 3) Activate additional KEGG COMPOUND 2 ChEBI mapping in KeggInfos.java ('getChebi()'-method)
-		   */
+		  adjustForPath2Models();
 		}
 
-
 		// Make command-line options persistent
 		prefs.restoreDefaults(); // This is just used as an empty prefs-template.
 		try {
@@ -359,6 +362,47 @@ public void commandLineMode(AppConf appConf) {
 		}
 	}
 
+  /**
+   * Adjusts the current KEGGtranslator instances to create an outout
+   * for the path2models project.
+   */
+  public static void adjustForPath2Models() {
+    path2models = true;
+    KeggInfos.path2models = true;
+    /* 
+     * 1) Set the required options
+     * 2) Uncomment code in [KEGG] Pathway.java for 'getCompoundPreviewPicture()'
+     * 3) Activate additional KEGG COMPOUND 2 ChEBI mapping in KeggInfos.java ('getChebi()'-method)
+     */
+
+    KEGGtranslatorOptions.AUTOCOMPLETE_REACTIONS.setDefaultValue(Boolean.TRUE);
+    KEGGtranslatorOptions.USE_GROUPS_EXTENSION.setDefaultValue(Boolean.FALSE);
+    KEGGtranslatorOptions.REMOVE_ORPHANS.setDefaultValue(Boolean.FALSE);
+    KEGGtranslatorOptions.REMOVE_WHITE_GENE_NODES.setDefaultValue(Boolean.TRUE);
+    KEGGtranslatorOptions.SHOW_FORMULA_FOR_COMPOUNDS.setDefaultValue(Boolean.FALSE);
+    KEGGtranslatorOptions.REMOVE_PATHWAY_REFERENCES.setDefaultValue(Boolean.TRUE);
+    KEGGtranslatorOptions.CELLDESIGNER_ANNOTATIONS.setDefaultValue(Boolean.FALSE);
+    KEGGtranslatorOptions.ADD_LAYOUT_EXTENSION.setDefaultValue(Boolean.TRUE);
+    KEGGtranslatorOptions.CHECK_ATOM_BALANCE.setDefaultValue(Boolean.FALSE);
+
+    SBPreferences prefs = SBPreferences.getPreferencesFor(KEGGtranslatorOptions.class);
+    prefs.put(KEGGtranslatorOptions.AUTOCOMPLETE_REACTIONS, Boolean.TRUE);
+    prefs.put(KEGGtranslatorOptions.USE_GROUPS_EXTENSION, Boolean.FALSE);
+    prefs.put(KEGGtranslatorOptions.REMOVE_ORPHANS, Boolean.FALSE);
+    prefs.put(KEGGtranslatorOptions.REMOVE_WHITE_GENE_NODES, Boolean.TRUE);
+    prefs.put(KEGGtranslatorOptions.SHOW_FORMULA_FOR_COMPOUNDS, Boolean.FALSE);
+    prefs.put(KEGGtranslatorOptions.REMOVE_PATHWAY_REFERENCES, Boolean.TRUE);
+    prefs.put(KEGGtranslatorOptions.CELLDESIGNER_ANNOTATIONS, Boolean.FALSE);
+    prefs.put(KEGGtranslatorOptions.ADD_LAYOUT_EXTENSION, Boolean.TRUE);
+    prefs.put(KEGGtranslatorOptions.CHECK_ATOM_BALANCE, Boolean.FALSE);
+
+    try {
+      prefs.flush();
+    } catch (BackingStoreException e) {
+      log.log(Level.SEVERE, "Could not adjust KEGGtranslator options for path2models.", e);
+    }
+  }
+
 	/*
 	 * (non-Javadoc)
 	 * @see de.zbit.Launcher#getAppName()

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

@@ -805,22 +805,36 @@ protected String NameToSId(String name) {
      * letter ::= �a�..�z�,�A�..�Z� digit ::= �0�..�9� idChar ::= letter |
      * digit | �_� SId ::= ( letter | �_� ) idChar*
      */
-    String ret = "";
+    String ret;
     if (name == null || name.trim().length() == 0) {
       ret = incrementSIdSuffix("SId");
       SIds.add(ret);
     } else {
       name = name.trim();
+      StringBuilder ret2 = new StringBuilder(name.length()+4);
       char c = name.charAt(0);
+
       // Must start with letter or '_'.
-      if (!(isLetter(c) || c == '_')) ret = "SId_"; else ret = Character.toString(c);
+      if (!(isLetter(c) || c == '_')) {
+        ret2.append("SId_");
+      } else {
+        ret2.append(c);
+      }
+
       // May contain letters, digits or '_'
       for (int i = 1; i < name.length(); i++) {
         c = name.charAt(i);
-        if (c==' ') c='_'; // Replace spaces with "_"
-        if (isLetter(c) || Character.isDigit(c) || c == '_') ret += Character.toString(c);
+        if (c==' ') {
+          c='_'; // Replace spaces with "_"
+        }
+
+        if (isLetter(c) || Character.isDigit(c) || c == '_') {
+          ret2.append(c);
+        } // else: skip invalid characters
       }
+
       // Make unique
+      ret = ret2.toString();
       if (SIds.contains(ret)) ret = incrementSIdSuffix(ret);
       SIds.add(ret);
     }

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

@@ -91,6 +91,7 @@
 import de.zbit.util.EscapeChars;
 import de.zbit.util.Species;
 import de.zbit.util.Utils;
+import de.zbit.util.objectwrapper.ValuePair;
 
 /**
  * Abstract KEGG2BioPAX converter (also called KGML2BioPAX). This converter is
@@ -311,7 +312,8 @@ public BioPAXElement createXRef(IdentifierDatabases db, String id, int type) {
 
     return xr;
   }
-
+
+
   /**
    * Creates a biosource, corrsponding to the organism/species of
    * the input pathway <code>p</code>.
@@ -901,58 +903,79 @@ public void createPhysicalEntities(Pathway p) {
    * {@link openControlledVocabulary} for level 2.
    */
   protected BioPAXElement getInteractionVocuabulary(SubType st) {
-    String rfid = "#relation_subtype_" + st.getName();
+    String formattedName = st.getName().trim().replace(' ', '_').replace("/", "_or_");
+
+    String rfid = "#relation_subtype_" + formattedName;
     BioPAXElement voc=null;
     if (level == BioPAXLevel.L3) {
       voc = (InteractionVocabulary) model.getByID(rfid);
     } else if (level == BioPAXLevel.L2) {
       voc = (openControlledVocabulary) model.getByID(rfid);
     }
 
+    // Term is not yet available => create it.
     if (voc==null) {
+      // Convert to a term that is a child of 'MI:0190' (Molecular Interaction Ontology)
+      ValuePair<String, Integer> miTerm = SBOMapping.getMITerm(st.getName());
+      String termName = miTerm!=null?miTerm.getA():null;//formattedName;
 
       if (level == BioPAXLevel.L3) {
         voc = model.addNew(InteractionVocabulary.class, rfid);
         pathwayComponentCreated(voc);
-        ((InteractionVocabulary)voc).addTerm(st.getName());
+        if (termName!=null) {
+          ((InteractionVocabulary)voc).addTerm(termName);
+        }
+        ((InteractionVocabulary)voc).addComment(formattedName);// In all cases, add the original KEGG name
       } else if (level == BioPAXLevel.L2) {
         voc = model.addNew(openControlledVocabulary.class, rfid);
         pathwayComponentCreated(voc);
-        ((openControlledVocabulary)voc).addTERM(st.getName());
+        if (termName!=null) {
+          ((openControlledVocabulary)voc).addTERM(termName);
+        }
+        ((openControlledVocabulary)voc).addCOMMENT(formattedName);// In all cases, add the original KEGG name
       }
 
+
+      // Add additional XRefs to MI, SBO and GO
+      if (miTerm!=null && miTerm.getB()!=null && miTerm.getB()>0) {
+        BioPAXElement xr = createXRef(IdentifierDatabases.MI, Integer.toString(miTerm.getB()), 1);
+        addOntologyXRef(voc, xr, miTerm.getA());
+      }
 
       int sbo = SBOMapping.getSBOTerm(st.getName());
       if (sbo>0) {
         BioPAXElement xr = createXRef(IdentifierDatabases.SBO, Integer.toString(sbo), 1);
-        if (xr!=null) {
-          if (level == BioPAXLevel.L3) {
-            ((Xref) xr).addComment(st.getName());
-            ((org.biopax.paxtools.model.level3.XReferrable) voc).addXref((Xref) xr);
-          } else if (level == BioPAXLevel.L2) {
-            ((xref) xr).addCOMMENT(st.getName());
-            ((org.biopax.paxtools.model.level2.XReferrable) voc).addXREF((xref) xr);
-          }
-        }
+        addOntologyXRef(voc, xr, formattedName);
       }
 
       int go = SBOMapping.getGOTerm(st.getName());
       if (go>0) {
         BioPAXElement xr = createXRef(IdentifierDatabases.GeneOntology, Integer.toString(go), 1);
-        if (xr!=null) {
-          if (level == BioPAXLevel.L3) {
-            ((Xref) xr).addComment(st.getName());
-            ((org.biopax.paxtools.model.level3.XReferrable) voc).addXref((Xref) xr);
-          } else if (level == BioPAXLevel.L2) {
-            ((xref) xr).addCOMMENT(st.getName());
-            ((org.biopax.paxtools.model.level2.XReferrable) voc).addXREF((xref) xr);
-          }
-        }
+        addOntologyXRef(voc, xr, formattedName);
       }
     }
 
     return voc;
   }
+
+
+  /**
+   * @param xReferrableBPelement
+   * @param xRef
+   * @param formattedName
+   */
+  private void addOntologyXRef(BioPAXElement xReferrableBPelement,
+    BioPAXElement xRef, String formattedName) {
+    if (xRef!=null) {
+      if (level == BioPAXLevel.L3) {
+        ((Xref) xRef).addComment(formattedName);
+        ((org.biopax.paxtools.model.level3.XReferrable) xReferrableBPelement).addXref((Xref) xRef);
+      } else if (level == BioPAXLevel.L2) {
+        ((xref) xRef).addCOMMENT(formattedName);
+        ((org.biopax.paxtools.model.level2.XReferrable) xReferrableBPelement).addXREF((xref) xRef);
+      }
+    }
+  }
 
   /* (non-Javadoc)
    * @see de.zbit.kegg.io.KEGGtranslator#isGraphicalOutput()

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

@@ -187,7 +187,11 @@ public BioPAXElement addEntry(Entry entry, Pathway p) {
     if (fullName!=null) {
       ((Entity)element).setStandardName(fullName); // Graphics name
     }
-    ((Entity)element).setDisplayName(name); // Intelligent name
+    String displayName = name;
+    if (displayName.length()>20) {
+      displayName = displayName.substring(0, 16)+"...";
+    }
+    ((Entity)element).setDisplayName(displayName); // Intelligent name
     // ---
     addDataSources(element);
 
@@ -299,9 +303,14 @@ private void addDataSources(BioPAXElement element) {
   protected BioPAXElement createPathwayInstance(Pathway p) {
     pathway = model.addNew(org.biopax.paxtools.model.level3.Pathway.class, p.getName());
     pathway.addAvailability(String.format("This file has been generated by %s version %s", System.getProperty("app.name"), System.getProperty("app.version")));
-    pathway.addName(formatTextForHTMLnotes(p.getTitle()));
-    pathway.setDisplayName(formatTextForHTMLnotes(p.getTitle()));
-    pathway.setStandardName(formatTextForHTMLnotes(p.getTitle()));
+    String htmlName = formatTextForHTMLnotes(p.getTitle());
+    pathway.addName(htmlName);
+    String displayName = htmlName;
+    if (displayName.length()>20) {
+      displayName = displayName.substring(0, 16)+"...";
+    }
+    pathway.setDisplayName(displayName);
+    pathway.setStandardName(htmlName);
 
     // Parse Kegg Pathway information
     boolean isKEGGPathway = DatabaseIdentifiers.checkID(DatabaseIdentifiers.IdentifierDatabases.KEGG_Pathway, p.getNameForMIRIAM());
@@ -394,7 +403,11 @@ public BioPAXElement addKGMLReaction(Reaction r, Pathway p) {
 
 
     reaction.addName(r.getName());
-    reaction.setDisplayName(r.getName());
+    String displayName = r.getName();
+    if (displayName.length()>20) {
+      displayName = displayName.substring(0, 16)+"...";
+    }
+    reaction.setDisplayName(displayName);
     addDataSources(reaction);
 
     // Add all reaction components

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

@@ -915,7 +915,7 @@ public static void addMiriamURNs(Entry entry, SBase spec) {
           String ko_id_uc_t = ko_id.toUpperCase().trim();
           if (ko_id_uc_t.startsWith("CPD:")) {
             // KEGG and ChEBI provide picture for compounds (e.g., "C00118").
-            notes.append(Pathway.getCompoundPreviewPicture(ko_id_uc_t, infos));
+            notes.append(Pathway.getCompoundPreviewPicture(ko_id_uc_t, infos, Translator.path2models));
           }
         }
         if (entry.getType().equals(EntryType.map)) {

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

@@ -30,6 +30,7 @@
 import de.zbit.kegg.parser.pathway.ext.EntryExtended;
 import de.zbit.kegg.parser.pathway.ext.EntryTypeExtended;
 import de.zbit.util.StringUtil;
+import de.zbit.util.objectwrapper.ValuePair;
 
 /**
  * This static class defines how to map from certain
@@ -266,6 +267,62 @@ public static int getGOTerm(String subtype) {
     return ret;    
   }
 
+  /**
+   * Convert to a MI-term that is a child of 'MI:0190' (Molecular Interaction (PSI-MI)).
+   * @param subtype
+   * @return {@link ValuePair} with the term name and integer id. Or <code>NULL</code> if
+   * no MI term is available that matches the given input {@link SubType}. 
+   */
+  public static ValuePair<String, Integer> getMITerm(String subtype) {
+    if (subtype.equals(SubType.ASSOCIATION)) {
+      return new ValuePair<String, Integer>("association", 914); //MI:0914
+    } else if (subtype.equals(SubType.PHOSPHORYLATION)) {
+      return new ValuePair<String, Integer>("phosphorylation reaction", 217);
+    } else if (subtype.equals(SubType.DEPHOSPHORYLATION)) {
+      return new ValuePair<String, Integer>("dephosphorylation reaction", 203);
+    } else if (subtype.equals(SubType.UBIQUITINATION) ||
+        subtype.equalsIgnoreCase("ubiquination")) {
+      return new ValuePair<String, Integer>("ubiquitination reaction", 220);
+    } else if (subtype.equals(SubType.GLYCOSYLATION)) {
+      return new ValuePair<String, Integer>("glycosylation reaction", 559);
+    } else if (subtype.equals(SubType.METHYLATION)) {
+      return new ValuePair<String, Integer>("methylation reaction", 213);
+    } else if (subtype.equals(SubType.BINDING)) {
+      return new ValuePair<String, Integer>("covalent binding", 195);
+    } else if (subtype.equals(SubType.BINDING_ASSOCIATION)) {
+      return new ValuePair<String, Integer>("association", 914);
+    } else if (subtype.equals(SubType.COMPOUND) ||
+        subtype.equals(SubType.HIDDEN_COMPOUND)) {
+      return new ValuePair<String, Integer>("direct interaction", 407);
+
+//    } else if (subtype.equals(SubType.DEPHOSPHORYLATION)) {
+//      return new ValuePair<String, Integer>("dephosphorylation reaction", 203);
+//    } else if (subtype.equals(SubType.DEPHOSPHORYLATION)) {
+//      return new ValuePair<String, Integer>("dephosphorylation reaction", 203);
+//    } else if (subtype.equals(SubType.DEPHOSPHORYLATION)) {
+//      return new ValuePair<String, Integer>("dephosphorylation reaction", 203);
+//    } else if (subtype.equals(SubType.DEPHOSPHORYLATION)) {
+//      return new ValuePair<String, Integer>("dephosphorylation reaction", 203);
+//    } else if (subtype.equals(SubType.DEPHOSPHORYLATION)) {
+//      return new ValuePair<String, Integer>("dephosphorylation reaction", 203);
+    }
+    /* MISSING:
+     * EXPRESSION => positive genetic interaction / 935
+     * ACTIVATION => positive genetic interaction / 935
+     * REPRESSION => negative genetic interaction / 933
+     * INHIBITION => negative genetic interaction / 933
+     * 
+     * DISSOCIATION
+     * INDIRECT_EFFECT
+     * MISSING_INTERACTION
+     * STATE_CHANGE
+     * 
+     */
+
+    return null;
+  }
+
+
 
   /**
    * Formats an SBO term. E.g. "177" to "SBO:0000177".