-public class VAMSAS implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _treeList\r
- */\r
- private java.util.Vector _treeList;\r
-\r
- /**\r
- * Field _sequenceSetList\r
- */\r
- private java.util.Vector _sequenceSetList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public VAMSAS() {\r
- super();\r
- _treeList = new Vector();\r
- _sequenceSetList = new Vector();\r
- } //-- jalview.schemabinding.version2.VAMSAS()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addSequenceSet\r
- * \r
- * \r
- * \r
- * @param vSequenceSet\r
- */\r
- public void addSequenceSet(jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceSetList.addElement(vSequenceSet);\r
- } //-- void addSequenceSet(jalview.schemabinding.version2.SequenceSet) \r
-\r
- /**\r
- * Method addSequenceSet\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vSequenceSet\r
- */\r
- public void addSequenceSet(int index, jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceSetList.insertElementAt(vSequenceSet, index);\r
- } //-- void addSequenceSet(int, jalview.schemabinding.version2.SequenceSet) \r
-\r
- /**\r
- * Method addTree\r
- * \r
- * \r
- * \r
- * @param vTree\r
- */\r
- public void addTree(java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.addElement(vTree);\r
- } //-- void addTree(java.lang.String) \r
-\r
- /**\r
- * Method addTree\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- */\r
- public void addTree(int index, java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.insertElementAt(vTree, index);\r
- } //-- void addTree(int, java.lang.String) \r
-\r
- /**\r
- * Method enumerateSequenceSet\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateSequenceSet()\r
- {\r
- return _sequenceSetList.elements();\r
- } //-- java.util.Enumeration enumerateSequenceSet() \r
-\r
- /**\r
- * Method enumerateTree\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateTree()\r
- {\r
- return _treeList.elements();\r
- } //-- java.util.Enumeration enumerateTree() \r
-\r
- /**\r
- * Method getSequenceSet\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return SequenceSet\r
- */\r
- public jalview.schemabinding.version2.SequenceSet getSequenceSet(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _sequenceSetList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.SequenceSet getSequenceSet(int) \r
-\r
- /**\r
- * Method getSequenceSet\r
- * \r
- * \r
- * \r
- * @return SequenceSet\r
- */\r
- public jalview.schemabinding.version2.SequenceSet[] getSequenceSet()\r
- {\r
- int size = _sequenceSetList.size();\r
- jalview.schemabinding.version2.SequenceSet[] mArray = new jalview.schemabinding.version2.SequenceSet[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.SequenceSet[] getSequenceSet() \r
-\r
- /**\r
- * Method getSequenceSetCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getSequenceSetCount()\r
+public class VAMSAS implements java.io.Serializable\r
+{\r
+\r
+ // --------------------------/\r
+ // - Class/Member Variables -/\r
+ // --------------------------/\r
+\r
+ /**\r
+ * Field _treeList.\r
+ */\r
+ private java.util.Vector _treeList;\r
+\r
+ /**\r
+ * Field _sequenceSetList.\r
+ */\r
+ private java.util.Vector _sequenceSetList;\r
+\r
+ // ----------------/\r
+ // - Constructors -/\r
+ // ----------------/\r
+\r
+ public VAMSAS()\r
+ {\r
+ super();\r
+ this._treeList = new java.util.Vector();\r
+ this._sequenceSetList = new java.util.Vector();\r
+ }\r
+\r
+ // -----------/\r
+ // - Methods -/\r
+ // -----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSequenceSet\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addSequenceSet(\r
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._sequenceSetList.addElement(vSequenceSet);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequenceSet\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addSequenceSet(final int index,\r
+ final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._sequenceSetList.add(index, vSequenceSet);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addTree(final java.lang.String vTree)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._treeList.addElement(vTree);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addTree(final int index, final java.lang.String vTree)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._treeList.add(index, vTree);\r
+ }\r
+\r
+ /**\r
+ * Method enumerateSequenceSet.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.SequenceSet\r
+ * elements\r
+ */\r
+ public java.util.Enumeration enumerateSequenceSet()\r
+ {\r
+ return this._sequenceSetList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateTree.\r
+ * \r
+ * @return an Enumeration over all java.lang.String elements\r
+ */\r
+ public java.util.Enumeration enumerateTree()\r
+ {\r
+ return this._treeList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method getSequenceSet.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the jalview.schemabinding.version2.SequenceSet at the\r
+ * given index\r
+ */\r
+ public jalview.schemabinding.version2.SequenceSet getSequenceSet(\r
+ final int index) throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceSetList.size())\r