objects from refactored schema.

[vamsas.git] / src / org / vamsas / objects / core / SequenceSet.java

diff --git a/src/org/vamsas/objects/core/SequenceSet.java b/src/org/vamsas/objects/core/SequenceSet.java
index f41fdc0..816da66 100644 (file)
--- a/src/org/vamsas/objects/core/SequenceSet.java
+++ b/src/org/vamsas/objects/core/SequenceSet.java
@@ -73,9 +73,9 @@ implements java.io.Serializable
     private java.util.Vector _alignmentList;
 
     /**
-     * Field _tree
+     * Field _treeList
      */
-    private org.vamsas.objects.core.Tree _tree;
+    private java.util.Vector _treeList;
 
     /**
      * Field _provenance
@@ -93,6 +93,7 @@ implements java.io.Serializable
         _sequenceList = new Vector();
         _sequenceSetAnnotationsList = new Vector();
         _alignmentList = new Vector();
+        _treeList = new Vector();
     } //-- org.vamsas.objects.core.SequenceSet()
 
 
@@ -182,6 +183,33 @@ implements java.io.Serializable
     } //-- void addSequenceSetAnnotations(int, org.vamsas.objects.core.SequenceSetAnnotations) 
 
     /**
+     * Method addTree
+     * 
+     * 
+     * 
+     * @param vTree
+     */
+    public void addTree(org.vamsas.objects.core.Tree vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _treeList.addElement(vTree);
+    } //-- void addTree(org.vamsas.objects.core.Tree) 
+
+    /**
+     * Method addTree
+     * 
+     * 
+     * 
+     * @param index
+     * @param vTree
+     */
+    public void addTree(int index, org.vamsas.objects.core.Tree vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _treeList.insertElementAt(vTree, index);
+    } //-- void addTree(int, org.vamsas.objects.core.Tree) 
+
+    /**
      * Method deleteAligned
      * 
      */
@@ -227,6 +255,18 @@ implements java.io.Serializable
     } //-- java.util.Enumeration enumerateSequenceSetAnnotations() 
 
     /**
+     * Method enumerateTree
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateTree()
+    {
+        return _treeList.elements();
+    } //-- java.util.Enumeration enumerateTree() 
+
+    /**
      * Note: hashCode() has not been overriden
      * 
      * @param obj
@@ -282,12 +322,12 @@ implements java.io.Serializable
             }
             else if (temp._alignmentList != null)
                 return false;
-            if (this._tree != null) {
-                if (temp._tree == null) return false;
-                else if (!(this._tree.equals(temp._tree))) 
+            if (this._treeList != null) {
+                if (temp._treeList == null) return false;
+                else if (!(this._treeList.equals(temp._treeList))) 
                     return false;
             }
-            else if (temp._tree != null)
+            else if (temp._treeList != null)
                 return false;
             if (this._provenance != null) {
                 if (temp._provenance == null) return false;
@@ -490,15 +530,52 @@ implements java.io.Serializable
     } //-- int getSequenceSetAnnotationsCount() 
 
     /**
-     * Returns the value of field 'tree'.
+     * Method getTree
+     * 
+     * 
+     * 
+     * @param index
+     * @return Tree
+     */
+    public org.vamsas.objects.core.Tree getTree(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _treeList.size())) {
+            throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
+        }
+        
+        return (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
+    } //-- org.vamsas.objects.core.Tree getTree(int) 
+
+    /**
+     * Method getTree
+     * 
+     * 
      * 
      * @return Tree
-     * @return the value of field 'tree'.
      */
-    public org.vamsas.objects.core.Tree getTree()
+    public org.vamsas.objects.core.Tree[] getTree()
     {
-        return this._tree;
-    } //-- org.vamsas.objects.core.Tree getTree() 
+        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.Tree) _treeList.elementAt(index);
+        }
+        return mArray;
+    } //-- org.vamsas.objects.core.Tree[] getTree() 
+
+    /**
+     * Method getTreeCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getTreeCount()
+    {
+        return _treeList.size();
+    } //-- int getTreeCount() 
 
     /**
      * Method hasAligned
@@ -601,6 +678,15 @@ implements java.io.Serializable
     } //-- void removeAllSequenceSetAnnotations() 
 
     /**
+     * Method removeAllTree
+     * 
+     */
+    public void removeAllTree()
+    {
+        _treeList.removeAllElements();
+    } //-- void removeAllTree() 
+
+    /**
      * Method removeSequence
      * 
      * 
@@ -631,6 +717,21 @@ implements java.io.Serializable
     } //-- org.vamsas.objects.core.SequenceSetAnnotations removeSequenceSetAnnotations(int) 
 
     /**
+     * Method removeTree
+     * 
+     * 
+     * 
+     * @param index
+     * @return Tree
+     */
+    public org.vamsas.objects.core.Tree removeTree(int index)
+    {
+        java.lang.Object obj = _treeList.elementAt(index);
+        _treeList.removeElementAt(index);
+        return (org.vamsas.objects.core.Tree) obj;
+    } //-- org.vamsas.objects.core.Tree removeTree(int) 
+
+    /**
      * Sets the value of field 'aligned'.
      * 
      * @param aligned the value of field 'aligned'.
@@ -774,13 +875,37 @@ implements java.io.Serializable
     } //-- void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations) 
 
     /**
-     * Sets the value of field 'tree'.
+     * Method setTree
+     * 
+     * 
+     * 
+     * @param index
+     * @param vTree
+     */
+    public void setTree(int index, org.vamsas.objects.core.Tree vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _treeList.size())) {
+            throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
+        }
+        _treeList.setElementAt(vTree, index);
+    } //-- void setTree(int, org.vamsas.objects.core.Tree) 
+
+    /**
+     * Method setTree
+     * 
+     * 
      * 
-     * @param tree the value of field 'tree'.
+     * @param treeArray
      */
-    public void setTree(org.vamsas.objects.core.Tree tree)
+    public void setTree(org.vamsas.objects.core.Tree[] treeArray)
     {
-        this._tree = tree;
+        //-- copy array
+        _treeList.removeAllElements();
+        for (int i = 0; i < treeArray.length; i++) {
+            _treeList.addElement(treeArray[i]);
+        }
     } //-- void setTree(org.vamsas.objects.core.Tree) 
 
     /**