X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Fobjects%2Fcore%2FVAMSAS.java;h=28ee85908b7e81ae4cd484257d6bf985a60c68e6;hb=31a237800ee9c6a324426645d395ae32db885a8e;hp=0cd3f56014663a8605c46bcf4ea2ff50a59f56dd;hpb=074762e534ccb9623b6b67e5670644afb651aa7a;p=vamsas.git

diff --git a/src/org/vamsas/objects/core/VAMSAS.java b/src/org/vamsas/objects/core/VAMSAS.java
index 0cd3f56..28ee859 100644
--- a/src/org/vamsas/objects/core/VAMSAS.java
+++ b/src/org/vamsas/objects/core/VAMSAS.java
@@ -48,9 +48,9 @@ implements java.io.Serializable
     private java.util.Vector _treeList;
 
     /**
-     * Field _sequenceSetList
+     * Field _dataSetList
      */
-    private java.util.Vector _sequenceSetList;
+    private java.util.Vector _dataSetList;
 
 
       //----------------/
@@ -61,7 +61,7 @@ implements java.io.Serializable
      {
         super();
         _treeList = new Vector();
-        _sequenceSetList = new Vector();
+        _dataSetList = new Vector();
     } //-- org.vamsas.objects.core.VAMSAS()
 
 
@@ -70,31 +70,31 @@ implements java.io.Serializable
     //-----------/
 
     /**
-     * Method addSequenceSet
+     * Method addDataSet
      * 
      * 
      * 
-     * @param vSequenceSet
+     * @param vDataSet
      */
-    public void addSequenceSet(org.vamsas.objects.core.SequenceSet vSequenceSet)
+    public void addDataSet(org.vamsas.objects.core.DataSet vDataSet)
         throws java.lang.IndexOutOfBoundsException
     {
-        _sequenceSetList.addElement(vSequenceSet);
-    } //-- void addSequenceSet(org.vamsas.objects.core.SequenceSet) 
+        _dataSetList.addElement(vDataSet);
+    } //-- void addDataSet(org.vamsas.objects.core.DataSet) 
 
     /**
-     * Method addSequenceSet
+     * Method addDataSet
      * 
      * 
      * 
      * @param index
-     * @param vSequenceSet
+     * @param vDataSet
      */
-    public void addSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet)
+    public void addDataSet(int index, org.vamsas.objects.core.DataSet vDataSet)
         throws java.lang.IndexOutOfBoundsException
     {
-        _sequenceSetList.insertElementAt(vSequenceSet, index);
-    } //-- void addSequenceSet(int, org.vamsas.objects.core.SequenceSet) 
+        _dataSetList.insertElementAt(vDataSet, index);
+    } //-- void addDataSet(int, org.vamsas.objects.core.DataSet) 
 
     /**
      * Method addTree
@@ -124,16 +124,16 @@ implements java.io.Serializable
     } //-- void addTree(int, org.vamsas.objects.core.Tree) 
 
     /**
-     * Method enumerateSequenceSet
+     * Method enumerateDataSet
      * 
      * 
      * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateSequenceSet()
+    public java.util.Enumeration enumerateDataSet()
     {
-        return _sequenceSetList.elements();
-    } //-- java.util.Enumeration enumerateSequenceSet() 
+        return _dataSetList.elements();
+    } //-- java.util.Enumeration enumerateDataSet() 
 
     /**
      * Method enumerateTree
@@ -178,12 +178,12 @@ implements java.io.Serializable
             }
             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;
         }
@@ -191,63 +191,63 @@ implements java.io.Serializable
     } //-- boolean equals(java.lang.Object) 
 
     /**
-     * Returns the value of field 'id'.
-     * 
-     * @return String
-     * @return the value of field 'id'.
-     */
-    public java.lang.String getId()
-    {
-        return this._id;
-    } //-- java.lang.String getId() 
-
-    /**
-     * Method getSequenceSet
+     * Method getDataSet
      * 
      * 
      * 
      * @param index
-     * @return SequenceSet
+     * @return DataSet
      */
-    public org.vamsas.objects.core.SequenceSet getSequenceSet(int index)
+    public org.vamsas.objects.core.DataSet getDataSet(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 > _dataSetList.size())) {
+            throw new IndexOutOfBoundsException("getDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
         }
         
-        return (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
-    } //-- org.vamsas.objects.core.SequenceSet getSequenceSet(int) 
+        return (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
+    } //-- org.vamsas.objects.core.DataSet getDataSet(int) 
 
     /**
-     * Method getSequenceSet
+     * Method getDataSet
      * 
      * 
      * 
-     * @return SequenceSet
+     * @return DataSet
      */
-    public org.vamsas.objects.core.SequenceSet[] getSequenceSet()
+    public org.vamsas.objects.core.DataSet[] getDataSet()
     {
-        int size = _sequenceSetList.size();
-        org.vamsas.objects.core.SequenceSet[] mArray = new org.vamsas.objects.core.SequenceSet[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.SequenceSet) _sequenceSetList.elementAt(index);
+            mArray[index] = (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
         }
         return mArray;
-    } //-- org.vamsas.objects.core.SequenceSet[] getSequenceSet() 
+    } //-- org.vamsas.objects.core.DataSet[] getDataSet() 
 
     /**
-     * Method getSequenceSetCount
+     * Method getDataSetCount
      * 
      * 
      * 
      * @return int
      */
-    public int getSequenceSetCount()
+    public int getDataSetCount()
     {
-        return _sequenceSetList.size();
-    } //-- int getSequenceSetCount() 
+        return _dataSetList.size();
+    } //-- int getDataSetCount() 
+
+    /**
+     * Returns the value of field 'id'.
+     * 
+     * @return String
+     * @return the value of field 'id'.
+     */
+    public java.lang.String getId()
+    {
+        return this._id;
+    } //-- java.lang.String getId() 
 
     /**
      * Method getTree
@@ -344,13 +344,13 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
-     * Method removeAllSequenceSet
+     * Method removeAllDataSet
      * 
      */
-    public void removeAllSequenceSet()
+    public void removeAllDataSet()
     {
-        _sequenceSetList.removeAllElements();
-    } //-- void removeAllSequenceSet() 
+        _dataSetList.removeAllElements();
+    } //-- void removeAllDataSet() 
 
     /**
      * Method removeAllTree
@@ -362,19 +362,19 @@ implements java.io.Serializable
     } //-- void removeAllTree() 
 
     /**
-     * Method removeSequenceSet
+     * Method removeDataSet
      * 
      * 
      * 
      * @param index
-     * @return SequenceSet
+     * @return DataSet
      */
-    public org.vamsas.objects.core.SequenceSet removeSequenceSet(int index)
+    public org.vamsas.objects.core.DataSet removeDataSet(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 = _dataSetList.elementAt(index);
+        _dataSetList.removeElementAt(index);
+        return (org.vamsas.objects.core.DataSet) obj;
+    } //-- org.vamsas.objects.core.DataSet removeDataSet(int) 
 
     /**
      * Method removeTree
@@ -392,48 +392,48 @@ implements java.io.Serializable
     } //-- org.vamsas.objects.core.Tree removeTree(int) 
 
     /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(java.lang.String id)
-    {
-        this._id = id;
-    } //-- void setId(java.lang.String) 
-
-    /**
-     * Method setSequenceSet
+     * Method setDataSet
      * 
      * 
      * 
      * @param index
-     * @param vSequenceSet
+     * @param vDataSet
      */
-    public void setSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet)
+    public void setDataSet(int index, org.vamsas.objects.core.DataSet vDataSet)
         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 > _dataSetList.size())) {
+            throw new IndexOutOfBoundsException("setDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
         }
-        _sequenceSetList.setElementAt(vSequenceSet, index);
-    } //-- void setSequenceSet(int, org.vamsas.objects.core.SequenceSet) 
+        _dataSetList.setElementAt(vDataSet, index);
+    } //-- void setDataSet(int, org.vamsas.objects.core.DataSet) 
 
     /**
-     * Method setSequenceSet
+     * Method setDataSet
      * 
      * 
      * 
-     * @param sequenceSetArray
+     * @param dataSetArray
      */
-    public void setSequenceSet(org.vamsas.objects.core.SequenceSet[] sequenceSetArray)
+    public void setDataSet(org.vamsas.objects.core.DataSet[] dataSetArray)
     {
         //-- copy array
-        _sequenceSetList.removeAllElements();
-        for (int i = 0; i < sequenceSetArray.length; i++) {
-            _sequenceSetList.addElement(sequenceSetArray[i]);
+        _dataSetList.removeAllElements();
+        for (int i = 0; i < dataSetArray.length; i++) {
+            _dataSetList.addElement(dataSetArray[i]);
         }
-    } //-- void setSequenceSet(org.vamsas.objects.core.SequenceSet) 
+    } //-- void setDataSet(org.vamsas.objects.core.DataSet) 
+
+    /**
+     * Sets the value of field 'id'.
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(java.lang.String id)
+    {
+        this._id = id;
+    } //-- void setId(java.lang.String) 
 
     /**
      * Method setTree