obo-svn-commit Mailing List for Open Biomedical Ontologies (Page 169)

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Revision: 440
          http://svn.sourceforge.net/obo/?rev=440&view=rev
Author:   mgibson
Date:     2007-03-30 13:00:40 -0700 (Fri, 30 Mar 2007)

Log Message:
-----------
well alright - so its not spiffy yet but now can do 2 differentia in post comp
- its currently hard wired to allow for up to 2 - no more - can do 1
eventually i want to add a button where the user can ask for more diff fields
- as many as they want

also this is writing out at the moment - to syn & tab - but not reading in
properly - i need johns post comp parser for that and i dont think hes at work
at the moment as hes not responding to my pleas

Modified Paths:
--------------
    phenote/trunk/conf/human.cfg
    phenote/trunk/src/java/phenote/datamodel/OboUtil.java
    phenote/trunk/src/java/phenote/datamodel/OntologyManager.java
    phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
    phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
    phenote/trunk/src/java/phenote/gui/field/PostCompGui.java
    phenote/trunk/src/java/phenote/gui/field/RelationCompList.java
    phenote/trunk/src/java/phenote/gui/field/TermCompList.java
    phenote/trunk/src/java/phenote/main/PhenoteVersion.java

Modified: phenote/trunk/conf/human.cfg
===================================================================

--- phenote/trunk/conf/human.cfg	2007-03-30 16:24:52 UTC (rev 439)
+++ phenote/trunk/conf/human.cfg	2007-03-30 20:00:40 UTC (rev 440)
@@ -3,6 +3,8 @@
 
   <dataadapter name="phenosyntax" enable="true"/>
   <dataadapter name="phenoxml" enable="true"/>
+  <dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter"
+                enable="true"/>
 
   <log config-file="conf/log4j-standalone.xml" />
 

Modified: phenote/trunk/src/java/phenote/datamodel/OboUtil.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/OboUtil.java	2007-03-30 16:24:52 UTC (rev 439)
+++ phenote/trunk/src/java/phenote/datamodel/OboUtil.java	2007-03-30 20:00:40 UTC (rev 440)
@@ -8,28 +8,72 @@
 import org.geneontology.oboedit.datamodel.impl.OBORestrictionImpl;
 
 
-// or should this go in datamodel?
+/** changing this from static to non-static so can build post comp object from
+    multiple rel-diffs */
 
 public class OboUtil {
 
+  private OBOClass postCompTerm;
+  private String id;
+  private String name;
+  private boolean hasRelAndDiff=false;
+
+
+  /** used by OntologyManager */
   public static OBOClass makePostCompTerm(OBOClass genus, OBOProperty rel,
                                           OBOClass diff) {
     String nm = pcString(genus.getName(),rel.getName(),diff.getName());
     String id = pcString(genus.getID(),rel.getName(),diff.getID());
-    OBOClass postComp = new OBOClassImpl(nm,id);
+    OBOClass postCompTerm = new OBOClassImpl(nm,id);
     OBOProperty ISA = OBOProperty.IS_A;
-    OBORestrictionImpl gRel = new OBORestrictionImpl(postComp,ISA,genus);
+    OBORestrictionImpl gRel = new OBORestrictionImpl(postCompTerm,ISA,genus);
     gRel.setCompletes(true); // post comp flag
-    postComp.addParent(gRel);
-    OBORestrictionImpl dRel = new OBORestrictionImpl(postComp,rel,diff);
+    postCompTerm.addParent(gRel);
+    OBORestrictionImpl dRel = new OBORestrictionImpl(postCompTerm,rel,diff);
     dRel.setCompletes(true); // post comp
-    postComp.addParent(dRel);
-    return postComp;
+    postCompTerm.addParent(dRel);
+    return postCompTerm;
   }
+
+  public static OboUtil initPostCompTerm(OBOClass genus) {
+    OboUtil ou = new OboUtil();
+    ou.addGenus(genus);
+    return ou;
+  }
+
+  private void addGenus(OBOClass genus) {
+    id = genus.getID();
+    name = genus.getName();
+    postCompTerm = new OBOClassImpl(name,id);
+    OBOProperty ISA = OBOProperty.IS_A;
+    OBORestrictionImpl gRel = new OBORestrictionImpl(postCompTerm,ISA,genus);
+    gRel.setCompletes(true); // post comp flag
+    postCompTerm.addParent(gRel);
+  }
+
+  public void addRelDiff(OBOProperty rel,OBOClass diff) {
+    OBORestrictionImpl dRel = new OBORestrictionImpl(postCompTerm,rel,diff);
+    dRel.setCompletes(true); // post comp
+    postCompTerm.addParent(dRel);
+    name += relDiffString(rel.getName(),diff.getName());
+    postCompTerm.setName(name);
+    id += relDiffString(rel.getName(),diff.getID());
+    // just for now
+    ((OBOClassImpl)postCompTerm).setID(id);
+    hasRelAndDiff = true;
+  }
+
+  public boolean hasRelAndDiff() { return hasRelAndDiff; }
+
+  public OBOClass getPostCompTerm() { return postCompTerm; }
+
   private static String pcString(String g, String r, String d) {
     // for now hard wire to part_of
-    return g+"^"+r+"("+d+")";
+    return g + relDiffString(r,d);
   }
 
+  private static String relDiffString(String r, String d) {
+    return "^"+r+"("+d+")";
+  }
 
 }

Modified: phenote/trunk/src/java/phenote/datamodel/OntologyManager.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/OntologyManager.java	2007-03-30 16:24:52 UTC (rev 439)
+++ phenote/trunk/src/java/phenote/datamodel/OntologyManager.java	2007-03-30 20:00:40 UTC (rev 440)
@@ -12,8 +12,8 @@
 import org.geneontology.oboedit.datamodel.OBOProperty;
 import org.geneontology.oboedit.datamodel.impl.OBOPropertyImpl;
 
-import phenote.datamodel.CharFieldEnum;
-import phenote.datamodel.OboUtil;
+//import phenote.datamodel.CharFieldEnum;
+//import phenote.datamodel.OboUtil;
 
 /** Manages all of the ontology. Eventually will get config info (xml? OntologyConfig?)
     and set itself up from that. Should there be an ontology package - whats funny
@@ -121,7 +121,8 @@
     return id.contains("^");
   }
 
-  /** parse string GO:123^part_of(AO:345) into post comp obo class */
+  /** parse string GO:123^part_of(AO:345) into post comp obo class 
+      This will be replaced with obo edits post comp parse utility */
   OBOClass getPostComp(String id) throws TermNotFoundException {
     Pattern pat = Pattern.compile("([^\\^]+)\\^([^\\(]*)\\(([^\\)]*)\\)");
     Matcher m = pat.matcher(id);

Modified: phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-03-30 16:24:52 UTC (rev 439)
+++ phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-03-30 20:00:40 UTC (rev 440)
@@ -130,6 +130,8 @@
 
   protected CompListSearcher getCompListSearcher() { return compListSearcher; }
 
+  protected AbstractAutoCompList getCompList() { return this; }
+
   //void setOntology(Ontology o) { ontology = o; }
 
   //void setSearchParams(SearchParamsI sp) { searchParams = sp; }

Modified: phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java	2007-03-30 16:24:52 UTC (rev 439)
+++ phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java	2007-03-30 20:00:40 UTC (rev 440)
@@ -270,14 +270,14 @@
   }
 
   /** for testing and internal use */
-  AbstractAutoCompList getCompList() {
-    if (!isCompList())
-      return null;
-    if (isRelationshipList())
-      return getRelComp();
-    return getTermComp();
-    //return comboBox;
-  }
+  AbstractAutoCompList getCompList() { return null; } // overridden
+//     if (!isCompList())
+//       return null;
+//     if (isRelationshipList())
+//       return getRelComp();
+//     return getTermComp();
+//     //return comboBox;
+//   }
 
   // hasOntology? overridded by AbstractAutoCompList
   boolean isCompList() { return false; }// isCompList; }
@@ -292,10 +292,10 @@
     return null; // overridden by TermCompList
   }
 
-  private RelationCompList getRelComp() {
-    //return relCompList;
-    return null; // overridden
-  }
+//   private RelationCompList getRelComp() {
+//     //return relCompList;
+//     return null; // overridden
+//   }
 
   // hardwired in term & rel subclasses now
 //   void enableTermInfoListening(boolean enable) {
@@ -465,12 +465,13 @@
     //else textField.setText(term.getName()); // shouldnt happen
   }
 
-  /** for auto combos (ontol) for relationships (post comp rel) */
-  void setRel(OBOProperty rel) {
-    if (!isCompList() || !isRelationshipList()) return; // ex???
-    getRelComp().setRel(rel);
-    //else textField.setText(rel.getName()); // shouldnt actually happen
-  }
+  /** for auto combos (ontol) for relationships (post comp rel)
+   overriddedn by RelationCompList */
+  void setRel(OBOProperty rel) {}
+//     if (!isCompList() || !isRelationshipList()) return; // ex???
+//     getRelComp().setRel(rel);
+//     //else textField.setText(rel.getName()); // shouldnt actually happen
+//   }
 
   CharFieldEnum getCharFieldEnum() { return charField.getCharFieldEnum(); }
   protected CharField getCharField() { return charField; }
@@ -502,19 +503,25 @@
 //     }
 //   }
 
+  static class CharFieldGuiEx extends Exception {
+    protected CharFieldGuiEx(String m) { super(m); }
+  }
+
   /** should define a CharFieldGuiEx! */
-  OBOClass getCurrentOboClass() throws Exception {
+  OBOClass getCurrentOboClass() throws CharFieldGuiEx {
     //if (!isCompList() || isRelationshipList)
-    if (!isTermCompList())
-      throw new Exception("Field has no OBO Class");
-    return null; // overridden by term comp list
+    //if (!isTermCompList())
+    // overridden by term comp list
+    throw new CharFieldGuiEx("Field has no OBO Class");
+      //return null; 
     //return getTermComp().getCurrentOboClass(); // throws Ex
   }
 
-  OBOProperty getCurrentRelation() throws Exception {
-    if (!isCompList() || !isRelationshipList())
-      throw new Exception("Field has no Relation");
-    return getRelComp().getCurrentRelation(); // throws Ex
+  /** overridden by RelationCompList */
+  OBOProperty getCurrentRelation() throws CharFieldGuiEx {
+    //if (!isCompList() || !isRelationshipList())
+    throw new CharFieldGuiEx("Field has no Relation");
+    //return getRelComp().getCurrentRelation(); // throws Ex
   }
 
   protected boolean isTermCompList() {

Modified: phenote/trunk/src/java/phenote/gui/field/PostCompGui.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/PostCompGui.java	2007-03-30 16:24:52 UTC (rev 439)
+++ phenote/trunk/src/java/phenote/gui/field/PostCompGui.java	2007-03-30 20:00:40 UTC (rev 440)
@@ -1,7 +1,8 @@
 package phenote.gui.field;
 
+import java.util.ArrayList;
+import java.util.List;
 import java.awt.Dimension;
-import java.util.List;
 import java.awt.BorderLayout;
 import java.awt.Frame;
 import java.awt.GridBagLayout;
@@ -45,45 +46,89 @@
 
   private CharField charField;
   private JDialog dialog;
+  // eventually with embedding this will be a TermGui
   private CharFieldGui genusField;
   //private RelationshipFieldGui relField; ??
-  private CharFieldGui relField;
-  private CharFieldGui diffField;
+  //private CharFieldGui relField;
+  //private CharFieldGui diffField;
+  private List<RelDiffGui> relDiffGuis = new ArrayList<RelDiffGui>(3);
+  private SearchParamsI searchParams;
+  private FieldPanel compFieldPanel;
 
   PostCompGui(CharField charField,SearchParamsI searchParams) {
     this.charField = charField;
-    init(searchParams);
+    this.searchParams = searchParams;
+    init();
   }
 
-  private void init(SearchParamsI searchParams) {
+  private class RelDiffGui {
+    private CharFieldGui relField;
+    // with embedded/recurse this will be a TermGui...
+    private CharFieldGui diffField;
+    private RelDiffGui() {
+      CharField relChar = new CharField(CharFieldEnum.RELATIONSHIP);
+      Ontology o = charField.getPostCompRelOntol();
+      relChar.addOntology(o);
+      relField = CharFieldGui.makeRelationList(relChar,searchParams);//"Relationship"?
+      compFieldPanel.addCharFieldGuiToPanel(relField);
+      diffField = CharFieldGui.makePostCompTermList(charField,searchParams,"Differentia");
+      compFieldPanel.addCharFieldGuiToPanel(diffField);
+    }
+    private void setRelDiffModel(RelDiffModel rd) {
+//       try { rd.relField.setRel(getRel(currentTerm)); } catch (Exception e){}
+      relField.setRel(rd.rel);
+      diffField.setOboClass(rd.diff);
+      diffField.setOntologyChooserFromTerm(rd.diff);
+    }
+  }
+
+  private class RelDiffModel {
+    private OBOProperty rel;
+    private OBOClass diff;
+    private RelDiffModel(OBORestriction link) {
+      rel = link.getType();
+      diff = (OBOClass)link.getParent();
+    }
+  }
+
+
+  private void init() {
     // dialog wont be focusable if owner is not showing or something like that
     Frame owner = Phenote.getPhenote().getFrame();
     dialog = new JDialog(owner,charField.getName()+" Post Composition");
-    FieldPanel compFieldPanel = new FieldPanel(false,false); // (searchParams)?
+    compFieldPanel = new FieldPanel(false,false); // (searchParams)?
     compFieldPanel.setSearchParams(searchParams);
     
-    // false - dont edit model, false - no post comp button
-    //genusField = new CharFieldGui(charField,compFieldPanel,"Genus",false,false);
+    // MAIN GENUS TERM
     genusField = CharFieldGui.makePostCompTermList(charField,searchParams,"Genus");
     compFieldPanel.addCharFieldGuiToPanel(genusField);
 
-    // Relationship?? stripped down ontology? hmmmmmm...
-    CharField relChar = new CharField(CharFieldEnum.RELATIONSHIP);
-    // Ontology o = OntologyManager.getRelationshipOntology() ?? getRelCharField?
-    Ontology o = charField.getPostCompRelOntol();
-    relChar.addOntology(o);
-    //relField = new CharFieldGui(relChar,compFieldPanel,"Relationship",false,false);
-    relField = CharFieldGui.makeRelationList(relChar,searchParams); // "Relationship"?
-    compFieldPanel.addCharFieldGuiToPanel(relField);
-    //relField.enableTermInfoListening(false); // turn off term info for rels
-    // relField = new RelFieldGui(relChar,compTermPanel,"Relationship");
-    // relField = new RelationshipFieldGui(compFieldPanel);
+    // REL-DIFFS
+    addRelDiffGui();
 
-    // when recurse put in flag for comp button
-    diffField = CharFieldGui.makePostCompTermList(charField,searchParams,"Differentia");
-    compFieldPanel.addCharFieldGuiToPanel(diffField);
-    //new CharFieldGui(charField,compFieldPanel,"Differentia",false,false);
+    // HARDWIRE 2ND REL&DIFF FOR NOW eventually put in refine button to add more diffs
+    addRelDiffGui();
 
+//     // Relationship?? stripped down ontology? hmmmmmm...
+//     CharField relChar = new CharField(CharFieldEnum.RELATIONSHIP);
+//     // Ontology o = OntologyManager.getRelationshipOntology() ?? getRelCharField?
+//     Ontology o = charField.getPostCompRelOntol();
+//     relChar.addOntology(o);
+//     //relField = new CharFieldGui(relChar,compFieldPanel,"Relationship",false,false);
+//     relField = CharFieldGui.makeRelationList(relChar,searchParams); // "Relationship"?
+//     compFieldPanel.addCharFieldGuiToPanel(relField);
+//     //relField.enableTermInfoListening(false); // turn off term info for rels
+//     // relField = new RelFieldGui(relChar,compTermPanel,"Relationship");
+//     // relField = new RelationshipFieldGui(compFieldPanel);
+
+//     // when recurse put in flag for comp button
+//     diffField = CharFieldGui.makePostCompTermList(charField,searchParams,"Differentia");
+//     compFieldPanel.addCharFieldGuiToPanel(diffField);
+//     //new CharFieldGui(charField,compFieldPanel,"Differentia",false,false);
+
+    
+
+
     setGuiFromSelectedModel();
 
     // override FieldPanel preferred size which will set window size
@@ -98,6 +143,10 @@
     SelectionManager.inst().addCharSelectionListener(new CompCharSelectListener());
   }
 
+  private void addRelDiffGui() {
+    relDiffGuis.add(new RelDiffGui());
+  }
+
   private void setGuiFromSelectedModel() {
     OBOClass currentTerm = getModelTerm();
     if (currentTerm == null) return;
@@ -106,13 +155,28 @@
     genusField.setOboClass(getGenusTerm(currentTerm));
     // should this happen automatically from setOboClass or is that a burden/inefficiency
     genusField.setOntologyChooserFromTerm(getGenusTerm(currentTerm));
-    //if (modelHasDiff(currentTerm))
-    try { relField.setRel(getRel(currentTerm)); } catch (Exception e){}
+    //if (modelHasDiff(currentTerm)) // should query if temp or real post comp??
+    
     try {
-      diffField.setOboClass(getDiffTerm(currentTerm));
-      diffField.setOntologyChooserFromTerm(getDiffTerm(currentTerm));
-    } 
-    catch (Exception e) {} // throws if no diff term
+      List<RelDiffModel>diffs = getRelDiffs(currentTerm);
+      
+      for (int i=0; i<diffs.size(); i++) {
+        // check that have enough guis for diffs
+        if (i >= relDiffGuis.size()) addRelDiffGui();
+        relDiffGuis.get(i).setRelDiffModel(diffs.get(i));
+      }
+    }
+    catch (CompEx e) { log().debug("get rel diffs failed "+e); }
+
+
+//     for (RelDiffGui rd : relDiffGuis) {
+//       try { rd.relField.setRel(getRel(currentTerm)); } catch (Exception e){}
+//       try {
+//         rd.diffField.setOboClass(getDiffTerm(currentTerm));
+//         rd.diffField.setOntologyChooserFromTerm(getDiffTerm(currentTerm));
+//       } 
+//       catch (Exception e) {} // throws if no diff term
+//     }
     
   }
 
@@ -161,29 +225,54 @@
     return term;
   }
 
+  private class CompEx extends Exception {
+    private CompEx() {}
+    private CompEx(String m) { super(m); }
+  }
+
+  private List<RelDiffModel> getRelDiffs(OBOClass term) throws CompEx {
+    if (!isPostCompTerm(term)) throw new CompEx();
+    List<RelDiffModel>diffs = new ArrayList<RelDiffModel>(4);
+    for (Object o : term.getParents()) {
+      OBORestriction r = (OBORestriction)o;
+      if (isLinkToDiff(r)) {
+        diffs.add(new RelDiffModel(r));
+      }
+      //return r;
+    }
+    if (diffs.isEmpty()) throw new CompEx(); // none found
+    return diffs;
+  }
+
+  private boolean isLinkToDiff(OBORestriction r) {
+    return r.completes() && r.getType() != OBOProperty.IS_A;
+  }
+
   /** Throws exception if no diff term - for now only returning one diff term
       can there be more than one */
-  private OBOClass getDiffTerm(OBOClass term) throws Exception {
+  private OBOClass getDiffTerm(OBOClass term) throws CompEx {
     OBORestriction link = getDiffLink(term); // throws Ex
     return (OBOClass)link.getParent(); // check downcast?
   }
 
   /** If term is post comp return obo property relationship for differentia 
       otherwise thorws exception */
-  private OBOProperty getRel(OBOClass term) throws Exception {
-    return getDiffLink(term).getType(); // thorws ex
+  private OBOProperty getRel(OBOClass term) throws CompEx {
+    return getDiffLink(term).getType(); // throws ex
   }
 
   /** return the oboRestriction link between term and its differentia 
-      exception if there is none. */
-  private OBORestriction getDiffLink(OBOClass term) throws Exception {
-    if (!isPostCompTerm(term)) throw new Exception();
+      exception if there is none. 
+      This assumes that there is only one diff - no longer true! 
+      should make specific ex*/
+  private OBORestriction getDiffLink(OBOClass term) throws CompEx {
+    if (!isPostCompTerm(term)) throw new CompEx();
     for (Object o : term.getParents()) {
       OBORestriction r = (OBORestriction)o;
       if (r.completes() && r.getType() != OBOProperty.IS_A)
         return r;
     }
-    throw new Exception(); // none found
+    throw new CompEx(); // none found
   }
 
   private void addButtons() {
@@ -208,7 +297,7 @@
       try {
         OBOClass pc = makePostCompTerm();
         commitTerm(pc);
-      } catch (Exception ex) {
+      } catch (CompEx ex) {
         String m = "Post composition not fully filled in ";
         if (ex.getMessage()!=null) m+=ex.getMessage();
         log().debug(m); // ??
@@ -219,14 +308,28 @@
     }
   }
 
-  private OBOClass makePostCompTerm() throws Exception {
-    // check that we have a valid genus & differentia
-    OBOClass genusTerm = genusField.getCurrentOboClass(); // throws Ex
-    OBOClass diffTerm = diffField.getCurrentOboClass(); // throws Ex
-//     // eventually get from obo relationship?
-    //OBOProperty partOf = new OBOPropertyImpl("OBO_REL:part_of","part_of");
-    OBOProperty rel = relField.getCurrentRelation();
-    return OboUtil.makePostCompTerm(genusTerm,rel,diffTerm);
+  private OBOClass makePostCompTerm() throws CompEx {
+    try {
+      // check that we have a valid genus & differentia
+      OBOClass genusTerm;
+      try { genusTerm = genusField.getCurrentOboClass(); }
+      catch (CharFieldGui.CharFieldGuiEx e) { throw new CompEx("Genus is unspecified"); }
+      OboUtil oboUtil = OboUtil.initPostCompTerm(genusTerm);
+      for (RelDiffGui rd : relDiffGuis) {
+        // check if filled in both rel & diff
+        try {
+          OBOProperty rel = rd.relField.getCurrentRelation(); // throws ex
+          OBOClass diffTerm = rd.diffField.getCurrentOboClass(); // throws Ex
+          oboUtil.addRelDiff(rel,diffTerm);
+        }
+        catch (CharFieldGui.CharFieldGuiEx e) {} // try next diff
+      }
+      //return OboUtil.makePostCompTerm(genusTerm,rel,diffTerm);
+      //if we didnt get a complete comp - genus rel diff - then throw ex
+      if (!oboUtil.hasRelAndDiff()) throw new CompEx("Missing relation or diff");
+      return oboUtil.getPostCompTerm();
+    }
+    catch (Exception e) { throw new CompEx(e.getMessage()); }
   }
 
   private void commitTerm(OBOClass postComp) {

Modified: phenote/trunk/src/java/phenote/gui/field/RelationCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/RelationCompList.java	2007-03-30 16:24:52 UTC (rev 439)
+++ phenote/trunk/src/java/phenote/gui/field/RelationCompList.java	2007-03-30 20:00:40 UTC (rev 440)
@@ -70,10 +70,10 @@
   /** Throws exception if there isnt a current relation - for relation lists
       (post comp), if the user
       has typed something that isnt yet a rel - hasnt selected a rel */
-  OBOProperty getCurrentRelation() throws Exception {
-    if (currentRel == null) throw new Exception("relation is null");
+  OBOProperty getCurrentRelation() throws CharFieldGuiEx {
+    if (currentRel == null) throw new CharFieldGuiEx("relation is null");
     if (!currentRel.getName().equals(getText()))
-      throw new Exception("(relation "+currentRel.getName()+" and input "+getText()+
+      throw new CharFieldGuiEx("(relation "+currentRel.getName()+" and input "+getText()+
                           " dont match)");
     return currentRel;
     

Modified: phenote/trunk/src/java/phenote/gui/field/TermCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/TermCompList.java	2007-03-30 16:24:52 UTC (rev 439)
+++ phenote/trunk/src/java/phenote/gui/field/TermCompList.java	2007-03-30 20:00:40 UTC (rev 440)
@@ -179,10 +179,10 @@
 
   /** Throws exception if there isnt a current obo class, if the user
       has typed something that isnt yet a term - hasnt selected a term */
-  OBOClass getCurrentOboClass() throws Exception {
-    if (currentOboClass == null) throw new Exception("term is null");
+  OBOClass getCurrentOboClass() throws CharFieldGuiEx {
+    if (currentOboClass == null) throw new CharFieldGuiEx("term is null");
     if (!currentOboClass.getName().equals(getText()))
-      throw new Exception("(obo class "+currentOboClass+" and input "+getText()+
+      throw new CharFieldGuiEx("(obo class "+currentOboClass+" and input "+getText()+
                           " dont match)");
     return currentOboClass;
   }

Modified: phenote/trunk/src/java/phenote/main/PhenoteVersion.java
===================================================================
--- phenote/trunk/src/java/phenote/main/PhenoteVersion.java	2007-03-30 16:24:52 UTC (rev 439)
+++ phenote/trunk/src/java/phenote/main/PhenoteVersion.java	2007-03-30 20:00:40 UTC (rev 440)
@@ -6,7 +6,7 @@
   
   //private static final float MAJOR_VERSION_NUM = 0.8f;
   //private static final float SUB_VERSION_NUM = .3f;
-  private static final String VERSION = "1.1.3 release"; // ??
+  private static final String VERSION = "1.2-beta1"; // ??
   // type is "dev" or "release" 
   //private static final String type = " dev"; // "release"
   


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