Simplified schema

[jalview.git] / src / jalview / schemabinding / version2 / VAMSAS.java

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