Revision: 17506
          http://sourceforge.net/p/gate/code/17506
Author:   markagreenwood
Date:     2014-03-03 13:45:23 +0000 (Mon, 03 Mar 2014)
Log Message:
-----------
supress the deprecation warnings as we know we are using deprecated calls as 
there is no workable replacement

Modified Paths:
--------------
    gate/trunk/plugins/Ontology_Tools/src/com/ontotext/gate/vr/ClassNode.java
    gate/trunk/plugins/Ontology_Tools/src/com/ontotext/gate/vr/Gaze.java

Modified: 
gate/trunk/plugins/Ontology_Tools/src/com/ontotext/gate/vr/ClassNode.java
===================================================================
--- gate/trunk/plugins/Ontology_Tools/src/com/ontotext/gate/vr/ClassNode.java   
2014-03-03 13:24:38 UTC (rev 17505)
+++ gate/trunk/plugins/Ontology_Tools/src/com/ontotext/gate/vr/ClassNode.java   
2014-03-03 13:45:23 UTC (rev 17506)
@@ -9,373 +9,434 @@
 import java.net.URL;
 
 /** Represents a single class node from the visualized ontology */
-public class ClassNode
-    implements IFolder,Transferable,Cloneable, Serializable
-{
+public class ClassNode implements IFolder, Transferable, Cloneable,
+               Serializable {
 
-  private static final long serialVersionUID = 3258128055154063414L;
+       private static final long serialVersionUID = 3258128055154063414L;
 
-  /** flavor used for drag and drop */
-  final public static DataFlavor CLASS_NODE_FLAVOR =
-    new DataFlavor(ClassNode.class, "Class Node");
+       /** flavor used for drag and drop */
+       final public static DataFlavor CLASS_NODE_FLAVOR = new DataFlavor(
+                       ClassNode.class, "Class Node");
 
-  static DataFlavor flavors[] = {CLASS_NODE_FLAVOR};
+       static DataFlavor flavors[] = { CLASS_NODE_FLAVOR };
 
-  private String name;
-  private Vector<ClassNode> children = new Vector<ClassNode>();
-  private Object source;
+       private String name;
+       private Vector<ClassNode> children = new Vector<ClassNode>();
+       private Object source;
 
-  /**
-   * create a structure representing the class hierarchy of an ontology
-   * 
-   * @return the root node of the structure
-   */
-  public static ClassNode createRootNode(Ontology o) {
-    return createRootNode(o, false, false);
-  }
+       /**
+        * create a structure representing the class hierarchy of an ontology
+        * 
+        * @return the root node of the structure
+        */
+       public static ClassNode createRootNode(Ontology o) {
+               return createRootNode(o, false, false);
+       }
 
-  public static ClassNode createRootNode(Ontology o, boolean includeInstances, 
boolean includeAnonymousClasses) {
-    if (null == o)
-      throw new gate.util.LazyProgrammerException("ontology is null.");
+       public static ClassNode createRootNode(Ontology o,
+                       boolean includeInstances, boolean 
includeAnonymousClasses) {
+               if (null == o)
+                       throw new gate.util.LazyProgrammerException("ontology 
is null.");
 
-    ClassNode root = new ClassNode(o);
-    Iterator<OClass> itops = o.getOClasses(true).iterator();
-    Vector<ClassNode> kids = new Vector<ClassNode>();
-    if(includeAnonymousClasses) {
-      while (itops.hasNext()) {
-        ClassNode node = new ClassNode(itops.next());
-        kids.add(node);
-      } // while
-    } else {
-      while (itops.hasNext()) {
-        OClass aClass = itops.next();
-        if(aClass instanceof AnonymousClass) {
-          continue;
-        }
-        ClassNode node = new ClassNode(aClass);
-        kids.add(node);
-      } // while
-    }
+               ClassNode root = new ClassNode(o);
+               Iterator<OClass> itops = o.getOClasses(true).iterator();
+               Vector<ClassNode> kids = new Vector<ClassNode>();
+               if (includeAnonymousClasses) {
+                       while (itops.hasNext()) {
+                               ClassNode node = new ClassNode(itops.next());
+                               kids.add(node);
+                       } // while
+               } else {
+                       while (itops.hasNext()) {
+                               OClass aClass = itops.next();
+                               if (aClass instanceof AnonymousClass) {
+                                       continue;
+                               }
+                               ClassNode node = new ClassNode(aClass);
+                               kids.add(node);
+                       } // while
+               }
 
-    root.source = o;
-    root.setChildren(kids);
-    Vector<ClassNode> parents = kids;
-    Vector<ClassNode> allKids;
-    do {
-      allKids = new Vector<ClassNode>();
-      for ( int i= 0 ; i < parents.size() ; i++ ) {
-        ClassNode parent = parents.get(i);
-        kids = new Vector<ClassNode>();
+               root.source = o;
+               root.setChildren(kids);
+               Vector<ClassNode> parents = kids;
+               Vector<ClassNode> allKids;
+               do {
+                       allKids = new Vector<ClassNode>();
+                       for (int i = 0; i < parents.size(); i++) {
+                               ClassNode parent = parents.get(i);
+                               kids = new Vector<ClassNode>();
 
-        //skip this one if it's an instance
-        if(parent.getSource() instanceof OInstance)
-          continue;
+                               // skip this one if it's an instance
+                               if (parent.getSource() instanceof OInstance)
+                                       continue;
 
-        OClass ocl = (OClass) parent.getSource();
+                               OClass ocl = (OClass) parent.getSource();
 
-        //if we include instances, then get them too
-        if (includeInstances && (o instanceof Ontology)) {
-          Ontology kb = (Ontology) o;
-          Set<OInstance> instances = kb.getOInstances(ocl, 
OConstants.Closure.DIRECT_CLOSURE);
-          if (instances != null && !instances.isEmpty()) {
-            Iterator<OInstance> insti = instances.iterator();
-            while (insti.hasNext())
-              kids.add(new ClassNode(insti.next()));
-          }
-        }
+                               // if we include instances, then get them too
+                               if (includeInstances && (o instanceof 
Ontology)) {
+                                       Ontology kb = (Ontology) o;
+                                       Set<OInstance> instances = 
kb.getOInstances(ocl,
+                                                       
OConstants.Closure.DIRECT_CLOSURE);
+                                       if (instances != null && 
!instances.isEmpty()) {
+                                               Iterator<OInstance> insti = 
instances.iterator();
+                                               while (insti.hasNext())
+                                                       kids.add(new 
ClassNode(insti.next()));
+                                       }
+                               }
 
-        if (0 == ocl.getSubClasses(OConstants.Closure.DIRECT_CLOSURE).size()) {
-          if (!kids.isEmpty())
-            //add the instances as children, but do not add them for future
-            //traversal to allKids
-            parent.setChildren(kids);
-          continue;
-        }  // if 0 children
+                               if (0 == 
ocl.getSubClasses(OConstants.Closure.DIRECT_CLOSURE)
+                                               .size()) {
+                                       if (!kids.isEmpty())
+                                               // add the instances as 
children, but do not add them
+                                               // for future
+                                               // traversal to allKids
+                                               parent.setChildren(kids);
+                                       continue;
+                               } // if 0 children
 
-        Iterator<OClass> kidsi = 
ocl.getSubClasses(OConstants.Closure.DIRECT_CLOSURE).iterator();
+                               Iterator<OClass> kidsi = ocl.getSubClasses(
+                                               
OConstants.Closure.DIRECT_CLOSURE).iterator();
 
-        while ( kidsi.hasNext()) {
-          OClass aClass = kidsi.next();
-          if(!includeAnonymousClasses && aClass instanceof AnonymousClass) 
continue;
-          kids.add(new ClassNode(aClass));
-        } // while kidsi
-        parent.setChildren(kids);
-        allKids.addAll(kids);
+                               while (kidsi.hasNext()) {
+                                       OClass aClass = kidsi.next();
+                                       if (!includeAnonymousClasses
+                                                       && aClass instanceof 
AnonymousClass)
+                                               continue;
+                                       kids.add(new ClassNode(aClass));
+                               } // while kidsi
+                               parent.setChildren(kids);
+                               allKids.addAll(kids);
 
-      }   // for i
-      parents = allKids;
-    } while (0 < allKids.size());
+                       } // for i
+                       parents = allKids;
+               } while (0 < allKids.size());
 
-    return root;
-  }//createRootNode()
+               return root;
+       }// createRootNode()
 
-  /** Creates a structure representing the class hierarchy of an ontology
-   *  and the gazetteerLists mapped to it.
-   *  @param o an ontology
-   *  @param mapping mapping definition
-   *  @param nameVsNode : this is actually a return value: should be
-   *  initialized before passing to this method and afterwards one can find a 
mapping
-   *  of class names vs class nodes there.
-   *  @return the root node of the structure
-   */
-  public static ClassNode createRootNode(Ontology o, MappingDefinition 
mapping, Map<String, ClassNode> nameVsNode) {
-    if (null == o || null == nameVsNode || null == mapping)
-      throw new gate.util.LazyProgrammerException("mapping, nameVsNode or 
ontology-o is null.");
-    ClassNode root = new ClassNode(o);
-    Iterator<OClass> itops = o.getOClasses(true).iterator();
-    Vector<ClassNode> kids = new Vector<ClassNode>();
-    while (itops.hasNext()) {
-      ClassNode node = new ClassNode(itops.next());
-      nameVsNode.put(node.toString(),node);
-      kids.add(node);
-    } // while
+       /**
+        * Creates a structure representing the class hierarchy of an ontology 
and
+        * the gazetteerLists mapped to it.
+        * 
+        * @param o
+        *            an ontology
+        * @param mapping
+        *            mapping definition
+        * @param nameVsNode
+        *            : this is actually a return value: should be initialized
+        *            before passing to this method and afterwards one can find 
a
+        *            mapping of class names vs class nodes there.
+        * @return the root node of the structure
+        */
+       @SuppressWarnings("deprecation")
+       public static ClassNode createRootNode(Ontology o,
+                       MappingDefinition mapping, Map<String, ClassNode> 
nameVsNode) {
+               if (null == o || null == nameVsNode || null == mapping)
+                       throw new gate.util.LazyProgrammerException(
+                                       "mapping, nameVsNode or ontology-o is 
null.");
+               ClassNode root = new ClassNode(o);
+               Iterator<OClass> itops = o.getOClasses(true).iterator();
+               Vector<ClassNode> kids = new Vector<ClassNode>();
+               while (itops.hasNext()) {
+                       ClassNode node = new ClassNode(itops.next());
+                       nameVsNode.put(node.toString(), node);
+                       kids.add(node);
+               } // while
 
-    root.source = o;
-    root.setChildren(kids);
-    Vector<ClassNode> parents = kids;
-    Vector<ClassNode> allKids;
-    do {
-      allKids = new Vector<ClassNode>();
-      for ( int i= 0 ; i < parents.size() ; i++ ) {
-        ClassNode parent = parents.get(i);
+               root.source = o;
+               root.setChildren(kids);
+               Vector<ClassNode> parents = kids;
+               Vector<ClassNode> allKids;
+               do {
+                       allKids = new Vector<ClassNode>();
+                       for (int i = 0; i < parents.size(); i++) {
+                               ClassNode parent = parents.get(i);
 
-        OClass ocl = (OClass) parent.getSource();
-        if (0 == ocl.getSubClasses(OConstants.Closure.DIRECT_CLOSURE).size()) {
-          continue;
-        }  // if 0 children
+                               OClass ocl = (OClass) parent.getSource();
+                               if (0 == 
ocl.getSubClasses(OConstants.Closure.DIRECT_CLOSURE)
+                                               .size()) {
+                                       continue;
+                               } // if 0 children
 
-        Iterator<OClass> kidsi = 
ocl.getSubClasses(OConstants.Closure.DIRECT_CLOSURE).iterator();
+                               Iterator<OClass> kidsi = ocl.getSubClasses(
+                                               
OConstants.Closure.DIRECT_CLOSURE).iterator();
 
-        kids = new Vector<ClassNode>();
-        while ( kidsi.hasNext()) {
-          ClassNode cn = new ClassNode(kidsi.next());
-          kids.add(cn);
-          nameVsNode.put(cn.toString(),cn);
-        } // while kidsi
-        parent.setChildren(kids);
-        allKids.addAll(kids);
+                               kids = new Vector<ClassNode>();
+                               while (kidsi.hasNext()) {
+                                       ClassNode cn = new 
ClassNode(kidsi.next());
+                                       kids.add(cn);
+                                       nameVsNode.put(cn.toString(), cn);
+                               } // while kidsi
+                               parent.setChildren(kids);
+                               allKids.addAll(kids);
 
-      }   // for i
-      parents = allKids;
-    } while (0 < allKids.size());
+                       } // for i
+                       parents = allKids;
+               } while (0 < allKids.size());
 
-    // display mapping
-    Iterator<MappingNode> inodes = mapping.iterator();
-    MappingNode mn;
-    while (inodes.hasNext()) {
-      mn = inodes.next();
-      URL turl = null;
-      try { turl = new URL(mn.getOntologyID());
-      } catch (java.net.MalformedURLException x) {
-      }
-      if ( null != turl ){
-        Ontology o2 = null;
-        try { o2 = OntologyUtilities.getOntology(turl);
-        } catch (gate.creole.ResourceInstantiationException x) {
-        }
-        if ( o2 != null && o2.equals(o) ) {
-          ClassNode cmn = new ClassNode(mn);
-          ClassNode cn = nameVsNode.get(mn.getClassID());
-          if (null!= cn) {
-            cn.children.add(cn.children.size(),cmn);
-          }
-        }// if from the same ontology
-      } // turl != null
-    }// while inodes
+               // display mapping
+               Iterator<MappingNode> inodes = mapping.iterator();
+               MappingNode mn;
+               while (inodes.hasNext()) {
+                       mn = inodes.next();
+                       URL turl = null;
+                       try {
+                               turl = new URL(mn.getOntologyID());
+                       } catch (java.net.MalformedURLException x) {
+                       }
+                       if (null != turl) {
+                               Ontology o2 = null;
+                               try {
+                                       o2 = 
OntologyUtilities.getOntology(turl);
+                               } catch 
(gate.creole.ResourceInstantiationException x) {
+                               }
+                               if (o2 != null && o2.equals(o)) {
+                                       ClassNode cmn = new ClassNode(mn);
+                                       ClassNode cn = 
nameVsNode.get(mn.getClassID());
+                                       if (null != cn) {
+                                               
cn.children.add(cn.children.size(), cmn);
+                                       }
+                               }// if from the same ontology
+                       } // turl != null
+               }// while inodes
 
+               return root;
+       }// createRootNode()
 
-    return root;
-  }//createRootNode()
+       /**
+        * Constructs a root class node from an ontology
+        * 
+        * @param o
+        *            the ontology
+        */
+       public ClassNode(Ontology o) {
+               name = o.getName();
+       }
 
-  /**Constructs a root class node from an ontology
-   * @param o the ontology    */
-  public ClassNode(Ontology o) {
-    name = o.getName();
-  }
+       /**
+        * Constructs a class node given an ontology class
+        * 
+        * @param clas
+        *            ontology class
+        */
+       public ClassNode(OClass clas) {
+               name = clas.getName();
+               source = clas;
+       }
 
-  /**Constructs a class node given an ontology class
-   * @param clas ontology class   */
-  public ClassNode(OClass clas) {
-    name = clas.getName();
-    source = clas;
-  }
+       /**
+        * Constructs a class node given an ontology instance
+        * 
+        * @param instance
+        *            ontology instance
+        */
+       public ClassNode(OInstance instance) {
+               name = instance.getName();
+               source = instance;
+       }
 
-  /**Constructs a class node given an ontology instance
-   * @param instance ontology instance   */
-  public ClassNode(OInstance instance) {
-    name = instance.getName();
-    source = instance;
-  }
+       /**
+        * Constructs a class node given a mapping node
+        * 
+        * @param mapNode
+        *            mapping node
+        */
+       public ClassNode(MappingNode mapNode) {
+               name = mapNode.getList();
+               source = mapNode;
+       }
 
-  /**
-   * Constructs a class node given a mapping node
-   * @param mapNode mapping node    */
-  public ClassNode(MappingNode mapNode) {
-    name = mapNode.getList();
-    source = mapNode;
-  }
+       public int getIndexOfChild(Object child) {
+               return children.indexOf(child);
+       }
 
-  public int getIndexOfChild(Object child) {
-    return children.indexOf(child);
-  }
+       public Iterator<ClassNode> getChildren() {
+               return children.iterator();
+       }
 
-  public Iterator<ClassNode> getChildren() {
-    return children.iterator();
-  }
+       public void setChildren(Vector<ClassNode> chldrn) {
+               children = chldrn;
+       }
 
-  public void setChildren(Vector<ClassNode> chldrn ) {
-    children = chldrn;
-  }
+       public Vector<ClassNode> children() {
+               return children;
+       }
 
-  public Vector<ClassNode> children() {
-    return children;
-  }
+       public String toString() {
+               return name;
+       }
 
-  public String toString() {
-    return name;
-  }
+       public int getChildCount() {
+               return children.size();
+       }
 
-  public int getChildCount() {
-    return children.size();
-  }
+       public IFolder getChild(int index) {
+               return children.get(index);
+       }
 
-  public IFolder getChild(int index) {
-    return children.get(index);
-  }
+       @Override
+       public int hashCode() {
+               final int prime = 31;
+               int result = 1;
+               result = prime * result + ((source == null) ? 0 : 
source.hashCode());
+               return result;
+       }
 
-  @Override
-  public int hashCode() {
-    final int prime = 31;
-    int result = 1;
-    result = prime * result + ((source == null) ? 0 : source.hashCode());
-    return result;
-  }
+       @Override
+       public boolean equals(Object obj) {
+               if (this == obj)
+                       return true;
+               if (obj == null)
+                       return false;
+               if (getClass() != obj.getClass())
+                       return false;
+               ClassNode other = (ClassNode) obj;
+               if (source == null) {
+                       if (other.source != null)
+                               return false;
+               } else if (!source.equals(other.source))
+                       return false;
+               return true;
+       }
 
-  @Override
-  public boolean equals(Object obj) {
-    if(this == obj) return true;
-    if(obj == null) return false;
-    if(getClass() != obj.getClass()) return false;
-    ClassNode other = (ClassNode)obj;
-    if(source == null) {
-      if(other.source != null) return false;
-    } else if(!source.equals(other.source)) return false;
-    return true;
-  }
+       /**
+        * Gets the Source object
+        * 
+        * @return the source object e.g. an gate.creole.TClass or a
+        *         gate.creole.Ontology
+        */
+       public Object getSource() {
+               return source;
+       }
 
-  /**Gets the Source object
-   * @return the source object e.g. an gate.creole.TClass
-   * or a gate.creole.Ontology   */
-  public Object getSource(){
-    return source;
-  }
+       /**
+        * Sets the source object
+        * 
+        * @param o
+        *            the source object to be set
+        */
+       public void setSource(Object o) {
+               source = o;
+       }
 
-  /**Sets the source object
-   * @param o the source object to be set   */
-  public void setSource(Object o)  {
-    source = o;
-  }
+       /**
+        * Renames this class node
+        * 
+        * @param newName
+        *            the new name of the node
+        */
+       public void rename(String newName) {
+               name = newName;
+       }
 
-  /**Renames this class node
-   * @param newName the new name of the node   */
-  public void rename(String newName) {
-    name = newName;
-  }
+       /**
+        * Removes a sub class
+        * 
+        * @param sub
+        *            the sub class to be removed
+        */
+       public void removeSubNode(ClassNode sub) {
+               if (children.contains(sub)) {
+                       children.remove(sub);
+                       Object source = this.getSource();
+                       if (source instanceof OClass) {
+                               OClass c = (OClass) source;
+                               if (sub.getSource() instanceof OClass)
+                                       c.removeSubClass((OClass) 
sub.getSource());
+                               else if (sub.getSource() instanceof OInstance
+                                               && c.getOntology() instanceof 
Ontology)
+                                       ((Ontology) c.getOntology())
+                                                       
.removeOInstance((OInstance) sub.getSource());
+                       } else if (source instanceof Ontology) {
+                               Ontology o = (Ontology) source;
+                               o.removeOClass((OClass) sub.getSource());
+                       } else if (source instanceof OInstance) {
+                               // cannot remove anything from an instance
+                               return;
+                       } else {
+                               throw new GateRuntimeException(
+                                               "Can not remove a sub node from 
a classnode.\n"
+                                                               + "The source 
is neither an Ontology neither TClass");
+                       } // else
+               } // if contains
+       } // removeSubNode
 
-  /**Removes a sub class
-   * @param sub the sub class to be removed*/
-  public void removeSubNode(ClassNode sub) {
-    if ( children.contains(sub) ) {
-      children.remove(sub);
-      Object source = this.getSource();
-      if (source instanceof OClass) {
-        OClass c = (OClass) source;
-        if (sub.getSource() instanceof OClass)
-          c.removeSubClass((OClass)sub.getSource());
-        else if (sub.getSource() instanceof OInstance &&
-                 c.getOntology() instanceof Ontology)
-          ((Ontology)c.getOntology()).removeOInstance((OInstance) 
sub.getSource());
-      } else if ( source instanceof Ontology) {
-          Ontology o = (Ontology) source;
-          o.removeOClass((OClass)sub.getSource());
-        } else if (source instanceof OInstance) {
-          //cannot remove anything from an instance
-          return;
-        } else {
-          throw new GateRuntimeException(
-          "Can not remove a sub node from a classnode.\n"
-          +"The source is neither an Ontology neither TClass");
-        } // else
-    } // if contains
-  } // removeSubNode
+       /**
+        * Adds a sub node
+        * 
+        * @param sub
+        *            the sub node to be added
+        */
+       public void addSubNode(ClassNode sub) {
+               if (!children.contains(sub)) {
+                       Object source = this.getSource();
+                       if (source instanceof OClass) {
+                               OClass c = (OClass) source;
+                               if (!(sub.getSource() instanceof OClass)
+                                               && !(sub.getSource() instanceof 
OInstance))
+                                       throw new GateRuntimeException(
+                                                       "The sub node's source 
is not an instance of TClass or OInstance");
+                               if (sub.getSource() instanceof OClass) {
+                                       OClass sc = (OClass) sub.getSource();
+                                       c.addSubClass(sc);
+                                       // this code originally used the 
deprecated method
+                                       // addOClass(URI, byte)
+                                       // with the byte constant indicating a 
class, without
+                                       // checking for
+                                       // sc not being an anonymous class.
+                                       c.getOntology().addOClass((OURI) 
sc.getONodeID());
+                                       children.add(sub);
+                               }
+                               if (sub.getSource() instanceof OInstance
+                                               && c.getOntology() instanceof 
Ontology) {
+                                       OInstance inst = (OInstance) 
sub.getSource();
+                                       if (!((Ontology) 
c.getOntology()).containsOInstance(inst
+                                                       .getOURI())) {
+                                               Iterator<OClass> instClasses = 
inst.getOClasses(
+                                                               
OConstants.Closure.DIRECT_CLOSURE).iterator();
+                                               while (instClasses.hasNext()) {
+                                                       ((Ontology) 
c.getOntology()).addOInstance(
+                                                                       
inst.getOURI(), instClasses.next());
+                                               }
+                                       }
 
-  /**Adds a sub node
-   * @param sub the sub node to be added    */
-  public void addSubNode(ClassNode sub) {
-    if ( ! children.contains(sub) )  {
-      Object source = this.getSource();
-      if ( source instanceof OClass) {
-        OClass c = (OClass)source; 
-        if (!(sub.getSource() instanceof OClass) &&
-            !(sub.getSource() instanceof OInstance))
-          throw new GateRuntimeException(
-          "The sub node's source is not an instance of TClass or OInstance");
-        if (sub.getSource() instanceof OClass) {
-          OClass sc = (OClass) sub.getSource();
-          c.addSubClass(sc);
-          // this code originally used the deprecated method addOClass(URI, 
byte)
-          // with the byte constant indicating a class, without checking for
-          // sc not being an anonymous class. 
-          c.getOntology().addOClass((OURI)sc.getONodeID());
-          children.add(sub);
-        }
-        if (sub.getSource() instanceof OInstance &&
-            c.getOntology() instanceof Ontology){
-          OInstance inst = (OInstance) sub.getSource();
-          if(!((Ontology)c.getOntology()).containsOInstance(inst.getOURI())) {
-            Iterator<OClass> instClasses =
-                    
inst.getOClasses(OConstants.Closure.DIRECT_CLOSURE).iterator();
-            while(instClasses.hasNext()) {
-              ((Ontology)c.getOntology()).addOInstance(inst.getOURI(), 
instClasses.next());
-            }
-          }
-          
-          children.add(sub);
-        }
+                                       children.add(sub);
+                               }
 
-      } else {
-        if (source instanceof Ontology) {
-            Ontology o = (Ontology) source;
-          if (!(sub.getSource() instanceof OClass))
-            throw new GateRuntimeException("The sub node's source is not an 
instance of TClass");
-          OClass sc = (OClass)sub.getSource();
-          o.addOClass((OURI)sc.getONodeID());
-          children.add(sub);
-        } else  {
-          throw new GateRuntimeException(
-          "cannot add a sub node to something which "
-          +"is neither an Ontology neither an TClass");
-        } // else
-      } // else
-    } // if ! contains
-  } // addSubNode()
+                       } else {
+                               if (source instanceof Ontology) {
+                                       Ontology o = (Ontology) source;
+                                       if (!(sub.getSource() instanceof 
OClass))
+                                               throw new GateRuntimeException(
+                                                               "The sub node's 
source is not an instance of TClass");
+                                       OClass sc = (OClass) sub.getSource();
+                                       o.addOClass((OURI) sc.getONodeID());
+                                       children.add(sub);
+                               } else {
+                                       throw new GateRuntimeException(
+                                                       "cannot add a sub node 
to something which "
+                                                                       + "is 
neither an Ontology neither an TClass");
+                               } // else
+                       } // else
+               } // if ! contains
+       } // addSubNode()
 
-  /*--- Transferable interface implementation ---*/
-  public boolean isDataFlavorSupported(DataFlavor df) {
-    return df.equals(CLASS_NODE_FLAVOR);
-  }
+       /*--- Transferable interface implementation ---*/
+       public boolean isDataFlavorSupported(DataFlavor df) {
+               return df.equals(CLASS_NODE_FLAVOR);
+       }
 
-  public Object getTransferData(DataFlavor df)
-      throws UnsupportedFlavorException, IOException {
-    if (df.equals(CLASS_NODE_FLAVOR)) {
-      return this;
-    }
-    else throw new UnsupportedFlavorException(df);
-  }
+       public Object getTransferData(DataFlavor df)
+                       throws UnsupportedFlavorException, IOException {
+               if (df.equals(CLASS_NODE_FLAVOR)) {
+                       return this;
+               } else
+                       throw new UnsupportedFlavorException(df);
+       }
 
-  public DataFlavor[] getTransferDataFlavors() {
-    return flavors;
-  }
+       public DataFlavor[] getTransferDataFlavors() {
+               return flavors;
+       }
 
-
 } // class ClassNode
\ No newline at end of file

Modified: gate/trunk/plugins/Ontology_Tools/src/com/ontotext/gate/vr/Gaze.java
===================================================================
--- gate/trunk/plugins/Ontology_Tools/src/com/ontotext/gate/vr/Gaze.java        
2014-03-03 13:24:38 UTC (rev 17505)
+++ gate/trunk/plugins/Ontology_Tools/src/com/ontotext/gate/vr/Gaze.java        
2014-03-03 13:45:23 UTC (rev 17506)
@@ -398,6 +398,7 @@
     /* add list selection listener to the mapping definition list component*/
     mappingList.addListSelectionListener(
       new ListSelectionListener () {
+        @SuppressWarnings("deprecation")
         public void valueChanged(ListSelectionEvent e) {
           if (0 < mappingList.getModel().getSize()) {
             Object obj = mappingList.getModel().getElementAt(

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