X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Forg%2Fvamsas%2Fobjects%2Fcore%2FVAMSAS.java;h=28ee85908b7e81ae4cd484257d6bf985a60c68e6;hb=349c4a3b6842fd54d791e0a92728dba294b30488;hp=12a81f2b9286bfb930238180d56e85b5142cdc9f;hpb=a54f7d71affe4e9cd7a7b0f6137e44f5b82b7a9d;p=vamsas.git

diff --git a/src/org/vamsas/objects/core/VAMSAS.java b/src/org/vamsas/objects/core/VAMSAS.java
index 12a81f2..28ee859 100644
--- a/src/org/vamsas/objects/core/VAMSAS.java
+++ b/src/org/vamsas/objects/core/VAMSAS.java
@@ -43,14 +43,14 @@ implements java.io.Serializable
     private java.lang.String _id;
 
     /**
-     * Field _dendroList
+     * Field _treeList
      */
-    private java.util.Vector _dendroList;
+    private java.util.Vector _treeList;
 
     /**
-     * Field _sequenceSetList
+     * Field _dataSetList
      */
-    private java.util.Vector _sequenceSetList;
+    private java.util.Vector _dataSetList;
 
 
       //----------------/
@@ -60,8 +60,8 @@ implements java.io.Serializable
     public VAMSAS() 
      {
         super();
-        _dendroList = new Vector();
-        _sequenceSetList = new Vector();
+        _treeList = new Vector();
+        _dataSetList = new Vector();
     } //-- org.vamsas.objects.core.VAMSAS()
 
 
@@ -70,82 +70,82 @@ implements java.io.Serializable
     //-----------/
 
     /**
-     * Method addDendro
+     * Method addDataSet
      * 
      * 
      * 
-     * @param vDendro
+     * @param vDataSet
      */
-    public void addDendro(org.vamsas.objects.core.Dendro vDendro)
+    public void addDataSet(org.vamsas.objects.core.DataSet vDataSet)
         throws java.lang.IndexOutOfBoundsException
     {
-        _dendroList.addElement(vDendro);
-    } //-- void addDendro(org.vamsas.objects.core.Dendro) 
+        _dataSetList.addElement(vDataSet);
+    } //-- void addDataSet(org.vamsas.objects.core.DataSet) 
 
     /**
-     * Method addDendro
+     * Method addDataSet
      * 
      * 
      * 
      * @param index
-     * @param vDendro
+     * @param vDataSet
      */
-    public void addDendro(int index, org.vamsas.objects.core.Dendro vDendro)
+    public void addDataSet(int index, org.vamsas.objects.core.DataSet vDataSet)
         throws java.lang.IndexOutOfBoundsException
     {
-        _dendroList.insertElementAt(vDendro, index);
-    } //-- void addDendro(int, org.vamsas.objects.core.Dendro) 
+        _dataSetList.insertElementAt(vDataSet, index);
+    } //-- void addDataSet(int, org.vamsas.objects.core.DataSet) 
 
     /**
-     * Method addSequenceSet
+     * Method addTree
      * 
      * 
      * 
-     * @param vSequenceSet
+     * @param vTree
      */
-    public void addSequenceSet(org.vamsas.objects.core.SequenceSet vSequenceSet)
+    public void addTree(org.vamsas.objects.core.Tree vTree)
         throws java.lang.IndexOutOfBoundsException
     {
-        _sequenceSetList.addElement(vSequenceSet);
-    } //-- void addSequenceSet(org.vamsas.objects.core.SequenceSet) 
+        _treeList.addElement(vTree);
+    } //-- void addTree(org.vamsas.objects.core.Tree) 
 
     /**
-     * Method addSequenceSet
+     * Method addTree
      * 
      * 
      * 
      * @param index
-     * @param vSequenceSet
+     * @param vTree
      */
-    public void addSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet)
+    public void addTree(int index, org.vamsas.objects.core.Tree vTree)
         throws java.lang.IndexOutOfBoundsException
     {
-        _sequenceSetList.insertElementAt(vSequenceSet, index);
-    } //-- void addSequenceSet(int, org.vamsas.objects.core.SequenceSet) 
+        _treeList.insertElementAt(vTree, index);
+    } //-- void addTree(int, org.vamsas.objects.core.Tree) 
 
     /**
-     * Method enumerateDendro
+     * Method enumerateDataSet
      * 
      * 
      * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateDendro()
+    public java.util.Enumeration enumerateDataSet()
     {
-        return _dendroList.elements();
-    } //-- java.util.Enumeration enumerateDendro() 
+        return _dataSetList.elements();
+    } //-- java.util.Enumeration enumerateDataSet() 
 
     /**
-     * Method enumerateSequenceSet
+     * Method enumerateTree
      * 
      * 
      * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateSequenceSet()
+    public java.util.Enumeration enumerateTree()
     {
-        return _sequenceSetList.elements();
-    } //-- java.util.Enumeration enumerateSequenceSet() 
+        return _treeList.elements();
+    } //-- java.util.Enumeration enumerateTree() 
 
     /**
      * Note: hashCode() has not been overriden
@@ -171,19 +171,19 @@ implements java.io.Serializable
             }
             else if (temp._id != null)
                 return false;
-            if (this._dendroList != null) {
-                if (temp._dendroList == null) return false;
-                else if (!(this._dendroList.equals(temp._dendroList))) 
+            if (this._treeList != null) {
+                if (temp._treeList == null) return false;
+                else if (!(this._treeList.equals(temp._treeList))) 
                     return false;
             }
-            else if (temp._dendroList != null)
+            else if (temp._treeList != null)
                 return false;
-            if (this._sequenceSetList != null) {
-                if (temp._sequenceSetList == null) return false;
-                else if (!(this._sequenceSetList.equals(temp._sequenceSetList))) 
+            if (this._dataSetList != null) {
+                if (temp._dataSetList == null) return false;
+                else if (!(this._dataSetList.equals(temp._dataSetList))) 
                     return false;
             }
-            else if (temp._sequenceSetList != null)
+            else if (temp._dataSetList != null)
                 return false;
             return true;
         }
@@ -191,52 +191,52 @@ implements java.io.Serializable
     } //-- boolean equals(java.lang.Object) 
 
     /**
-     * Method getDendro
+     * Method getDataSet
      * 
      * 
      * 
      * @param index
-     * @return Dendro
+     * @return DataSet
      */
-    public org.vamsas.objects.core.Dendro getDendro(int index)
+    public org.vamsas.objects.core.DataSet getDataSet(int index)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _dendroList.size())) {
-            throw new IndexOutOfBoundsException("getDendro: Index value '"+index+"' not in range [0.."+_dendroList.size()+ "]");
+        if ((index < 0) || (index > _dataSetList.size())) {
+            throw new IndexOutOfBoundsException("getDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
         }
         
-        return (org.vamsas.objects.core.Dendro) _dendroList.elementAt(index);
-    } //-- org.vamsas.objects.core.Dendro getDendro(int) 
+        return (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
+    } //-- org.vamsas.objects.core.DataSet getDataSet(int) 
 
     /**
-     * Method getDendro
+     * Method getDataSet
      * 
      * 
      * 
-     * @return Dendro
+     * @return DataSet
      */
-    public org.vamsas.objects.core.Dendro[] getDendro()
+    public org.vamsas.objects.core.DataSet[] getDataSet()
     {
-        int size = _dendroList.size();
-        org.vamsas.objects.core.Dendro[] mArray = new org.vamsas.objects.core.Dendro[size];
+        int size = _dataSetList.size();
+        org.vamsas.objects.core.DataSet[] mArray = new org.vamsas.objects.core.DataSet[size];
         for (int index = 0; index < size; index++) {
-            mArray[index] = (org.vamsas.objects.core.Dendro) _dendroList.elementAt(index);
+            mArray[index] = (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
         }
         return mArray;
-    } //-- org.vamsas.objects.core.Dendro[] getDendro() 
+    } //-- org.vamsas.objects.core.DataSet[] getDataSet() 
 
     /**
-     * Method getDendroCount
+     * Method getDataSetCount
      * 
      * 
      * 
      * @return int
      */
-    public int getDendroCount()
+    public int getDataSetCount()
     {
-        return _dendroList.size();
-    } //-- int getDendroCount() 
+        return _dataSetList.size();
+    } //-- int getDataSetCount() 
 
     /**
      * Returns the value of field 'id'.
@@ -250,52 +250,52 @@ implements java.io.Serializable
     } //-- java.lang.String getId() 
 
     /**
-     * Method getSequenceSet
+     * Method getTree
      * 
      * 
      * 
      * @param index
-     * @return SequenceSet
+     * @return Tree
      */
-    public org.vamsas.objects.core.SequenceSet getSequenceSet(int index)
+    public org.vamsas.objects.core.Tree getTree(int index)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _sequenceSetList.size())) {
-            throw new IndexOutOfBoundsException("getSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]");
+        if ((index < 0) || (index > _treeList.size())) {
+            throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
         }
         
-        return (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
-    } //-- org.vamsas.objects.core.SequenceSet getSequenceSet(int) 
+        return (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
+    } //-- org.vamsas.objects.core.Tree getTree(int) 
 
     /**
-     * Method getSequenceSet
+     * Method getTree
      * 
      * 
      * 
-     * @return SequenceSet
+     * @return Tree
      */
-    public org.vamsas.objects.core.SequenceSet[] getSequenceSet()
+    public org.vamsas.objects.core.Tree[] getTree()
     {
-        int size = _sequenceSetList.size();
-        org.vamsas.objects.core.SequenceSet[] mArray = new org.vamsas.objects.core.SequenceSet[size];
+        int size = _treeList.size();
+        org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
         for (int index = 0; index < size; index++) {
-            mArray[index] = (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
+            mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
         }
         return mArray;
-    } //-- org.vamsas.objects.core.SequenceSet[] getSequenceSet() 
+    } //-- org.vamsas.objects.core.Tree[] getTree() 
 
     /**
-     * Method getSequenceSetCount
+     * Method getTreeCount
      * 
      * 
      * 
      * @return int
      */
-    public int getSequenceSetCount()
+    public int getTreeCount()
     {
-        return _sequenceSetList.size();
-    } //-- int getSequenceSetCount() 
+        return _treeList.size();
+    } //-- int getTreeCount() 
 
     /**
      * Method isValid
@@ -344,86 +344,86 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
-     * Method removeAllDendro
+     * Method removeAllDataSet
      * 
      */
-    public void removeAllDendro()
+    public void removeAllDataSet()
     {
-        _dendroList.removeAllElements();
-    } //-- void removeAllDendro() 
+        _dataSetList.removeAllElements();
+    } //-- void removeAllDataSet() 
 
     /**
-     * Method removeAllSequenceSet
+     * Method removeAllTree
      * 
      */
-    public void removeAllSequenceSet()
+    public void removeAllTree()
     {
-        _sequenceSetList.removeAllElements();
-    } //-- void removeAllSequenceSet() 
+        _treeList.removeAllElements();
+    } //-- void removeAllTree() 
 
     /**
-     * Method removeDendro
+     * Method removeDataSet
      * 
      * 
      * 
      * @param index
-     * @return Dendro
+     * @return DataSet
      */
-    public org.vamsas.objects.core.Dendro removeDendro(int index)
+    public org.vamsas.objects.core.DataSet removeDataSet(int index)
     {
-        java.lang.Object obj = _dendroList.elementAt(index);
-        _dendroList.removeElementAt(index);
-        return (org.vamsas.objects.core.Dendro) obj;
-    } //-- org.vamsas.objects.core.Dendro removeDendro(int) 
+        java.lang.Object obj = _dataSetList.elementAt(index);
+        _dataSetList.removeElementAt(index);
+        return (org.vamsas.objects.core.DataSet) obj;
+    } //-- org.vamsas.objects.core.DataSet removeDataSet(int) 
 
     /**
-     * Method removeSequenceSet
+     * Method removeTree
      * 
      * 
      * 
      * @param index
-     * @return SequenceSet
+     * @return Tree
      */
-    public org.vamsas.objects.core.SequenceSet removeSequenceSet(int index)
+    public org.vamsas.objects.core.Tree removeTree(int index)
     {
-        java.lang.Object obj = _sequenceSetList.elementAt(index);
-        _sequenceSetList.removeElementAt(index);
-        return (org.vamsas.objects.core.SequenceSet) obj;
-    } //-- org.vamsas.objects.core.SequenceSet removeSequenceSet(int) 
+        java.lang.Object obj = _treeList.elementAt(index);
+        _treeList.removeElementAt(index);
+        return (org.vamsas.objects.core.Tree) obj;
+    } //-- org.vamsas.objects.core.Tree removeTree(int) 
 
     /**
-     * Method setDendro
+     * Method setDataSet
      * 
      * 
      * 
      * @param index
-     * @param vDendro
+     * @param vDataSet
      */
-    public void setDendro(int index, org.vamsas.objects.core.Dendro vDendro)
+    public void setDataSet(int index, org.vamsas.objects.core.DataSet vDataSet)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _dendroList.size())) {
-            throw new IndexOutOfBoundsException("setDendro: Index value '"+index+"' not in range [0.."+_dendroList.size()+ "]");
+        if ((index < 0) || (index > _dataSetList.size())) {
+            throw new IndexOutOfBoundsException("setDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
         }
-        _dendroList.setElementAt(vDendro, index);
-    } //-- void setDendro(int, org.vamsas.objects.core.Dendro) 
+        _dataSetList.setElementAt(vDataSet, index);
+    } //-- void setDataSet(int, org.vamsas.objects.core.DataSet) 
 
     /**
-     * Method setDendro
+     * Method setDataSet
      * 
      * 
      * 
-     * @param dendroArray
+     * @param dataSetArray
      */
-    public void setDendro(org.vamsas.objects.core.Dendro[] dendroArray)
+    public void setDataSet(org.vamsas.objects.core.DataSet[] dataSetArray)
     {
         //-- copy array
-        _dendroList.removeAllElements();
-        for (int i = 0; i < dendroArray.length; i++) {
-            _dendroList.addElement(dendroArray[i]);
+        _dataSetList.removeAllElements();
+        for (int i = 0; i < dataSetArray.length; i++) {
+            _dataSetList.addElement(dataSetArray[i]);
         }
-    } //-- void setDendro(org.vamsas.objects.core.Dendro) 
+    } //-- void setDataSet(org.vamsas.objects.core.DataSet) 
 
     /**
      * Sets the value of field 'id'.
@@ -436,38 +436,38 @@ implements java.io.Serializable
     } //-- void setId(java.lang.String) 
 
     /**
-     * Method setSequenceSet
+     * Method setTree
      * 
      * 
      * 
      * @param index
-     * @param vSequenceSet
+     * @param vTree
      */
-    public void setSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet)
+    public void setTree(int index, org.vamsas.objects.core.Tree vTree)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _sequenceSetList.size())) {
-            throw new IndexOutOfBoundsException("setSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]");
+        if ((index < 0) || (index > _treeList.size())) {
+            throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
         }
-        _sequenceSetList.setElementAt(vSequenceSet, index);
-    } //-- void setSequenceSet(int, org.vamsas.objects.core.SequenceSet) 
+        _treeList.setElementAt(vTree, index);
+    } //-- void setTree(int, org.vamsas.objects.core.Tree) 
 
     /**
-     * Method setSequenceSet
+     * Method setTree
      * 
      * 
      * 
-     * @param sequenceSetArray
+     * @param treeArray
      */
-    public void setSequenceSet(org.vamsas.objects.core.SequenceSet[] sequenceSetArray)
+    public void setTree(org.vamsas.objects.core.Tree[] treeArray)
     {
         //-- copy array
-        _sequenceSetList.removeAllElements();
-        for (int i = 0; i < sequenceSetArray.length; i++) {
-            _sequenceSetList.addElement(sequenceSetArray[i]);
+        _treeList.removeAllElements();
+        for (int i = 0; i < treeArray.length; i++) {
+            _treeList.addElement(treeArray[i]);
         }
-    } //-- void setSequenceSet(org.vamsas.objects.core.SequenceSet) 
+    } //-- void setTree(org.vamsas.objects.core.Tree) 
 
     /**
      * Method unmarshal