X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FVAMSAS.java;h=03633d62f1091fbe83e2679a8e836ad180ffc7e2;hb=77dd1ea813b06b331614520a8b3d561435f27880;hp=9550690d83bf1f0b22d7739a77d108207ee2629a;hpb=65df62f4b048a1615d32ea2c3576082ad2b63af8;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java
index 9550690..03633d6 100755
--- a/src/jalview/schemabinding/version2/VAMSAS.java
+++ b/src/jalview/schemabinding/version2/VAMSAS.java
@@ -36,11 +36,6 @@ public class VAMSAS implements java.io.Serializable {
     //--------------------------/
 
     /**
-     * Field _alignmentList
-     */
-    private java.util.Vector _alignmentList;
-
-    /**
      * Field _treeList
      */
     private java.util.Vector _treeList;
@@ -57,7 +52,6 @@ public class VAMSAS implements java.io.Serializable {
 
     public VAMSAS() {
         super();
-        _alignmentList = new Vector();
         _treeList = new Vector();
         _sequenceSetList = new Vector();
     } //-- jalview.schemabinding.version2.VAMSAS()
@@ -68,33 +62,6 @@ public class VAMSAS implements java.io.Serializable {
     //-----------/
 
     /**
-     * Method addAlignment
-     * 
-     * 
-     * 
-     * @param vAlignment
-     */
-    public void addAlignment(jalview.schemabinding.version2.Alignment vAlignment)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _alignmentList.addElement(vAlignment);
-    } //-- void addAlignment(jalview.schemabinding.version2.Alignment) 
-
-    /**
-     * Method addAlignment
-     * 
-     * 
-     * 
-     * @param index
-     * @param vAlignment
-     */
-    public void addAlignment(int index, jalview.schemabinding.version2.Alignment vAlignment)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _alignmentList.insertElementAt(vAlignment, index);
-    } //-- void addAlignment(int, jalview.schemabinding.version2.Alignment) 
-
-    /**
      * Method addSequenceSet
      * 
      * 
@@ -149,18 +116,6 @@ public class VAMSAS implements java.io.Serializable {
     } //-- void addTree(int, java.lang.String) 
 
     /**
-     * Method enumerateAlignment
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateAlignment()
-    {
-        return _alignmentList.elements();
-    } //-- java.util.Enumeration enumerateAlignment() 
-
-    /**
      * Method enumerateSequenceSet
      * 
      * 
@@ -185,54 +140,6 @@ public class VAMSAS implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateTree() 
 
     /**
-     * Method getAlignment
-     * 
-     * 
-     * 
-     * @param index
-     * @return Alignment
-     */
-    public jalview.schemabinding.version2.Alignment getAlignment(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _alignmentList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.Alignment) _alignmentList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Alignment getAlignment(int) 
-
-    /**
-     * Method getAlignment
-     * 
-     * 
-     * 
-     * @return Alignment
-     */
-    public jalview.schemabinding.version2.Alignment[] getAlignment()
-    {
-        int size = _alignmentList.size();
-        jalview.schemabinding.version2.Alignment[] mArray = new jalview.schemabinding.version2.Alignment[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Alignment) _alignmentList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Alignment[] getAlignment() 
-
-    /**
-     * Method getAlignmentCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getAlignmentCount()
-    {
-        return _alignmentList.size();
-    } //-- int getAlignmentCount() 
-
-    /**
      * Method getSequenceSet
      * 
      * 
@@ -375,30 +282,6 @@ public class VAMSAS implements java.io.Serializable {
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
-     * Method removeAlignment
-     * 
-     * 
-     * 
-     * @param index
-     * @return Alignment
-     */
-    public jalview.schemabinding.version2.Alignment removeAlignment(int index)
-    {
-        java.lang.Object obj = _alignmentList.elementAt(index);
-        _alignmentList.removeElementAt(index);
-        return (jalview.schemabinding.version2.Alignment) obj;
-    } //-- jalview.schemabinding.version2.Alignment removeAlignment(int) 
-
-    /**
-     * Method removeAllAlignment
-     * 
-     */
-    public void removeAllAlignment()
-    {
-        _alignmentList.removeAllElements();
-    } //-- void removeAllAlignment() 
-
-    /**
      * Method removeAllSequenceSet
      * 
      */
@@ -447,40 +330,6 @@ public class VAMSAS implements java.io.Serializable {
     } //-- java.lang.String removeTree(int) 
 
     /**
-     * Method setAlignment
-     * 
-     * 
-     * 
-     * @param index
-     * @param vAlignment
-     */
-    public void setAlignment(int index, jalview.schemabinding.version2.Alignment vAlignment)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _alignmentList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _alignmentList.setElementAt(vAlignment, index);
-    } //-- void setAlignment(int, jalview.schemabinding.version2.Alignment) 
-
-    /**
-     * Method setAlignment
-     * 
-     * 
-     * 
-     * @param alignmentArray
-     */
-    public void setAlignment(jalview.schemabinding.version2.Alignment[] alignmentArray)
-    {
-        //-- copy array
-        _alignmentList.removeAllElements();
-        for (int i = 0; i < alignmentArray.length; i++) {
-            _alignmentList.addElement(alignmentArray[i]);
-        }
-    } //-- void setAlignment(jalview.schemabinding.version2.Alignment) 
-
-    /**
      * Method setSequenceSet
      * 
      *