-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
- this._treeList = new java.util.Vector();\r
- this._sequenceSetList = new java.util.Vector();\r
- }\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vSequenceSet\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * 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
- this._sequenceSetList.addElement(vSequenceSet);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSequenceSet\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addSequenceSet(\r
- final int index,\r
- final jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._sequenceSetList.add(index, vSequenceSet);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addTree(\r
- final java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._treeList.addElement(vTree);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addTree(\r
- final int index,\r
- final java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._treeList.add(index, vTree);\r
- }\r
-\r
- /**\r
- * Method enumerateSequenceSet.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.SequenceSet 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 if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the\r
- * jalview.schemabinding.version2.SequenceSet at the given index\r
- */\r
- public jalview.schemabinding.version2.SequenceSet getSequenceSet(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._sequenceSetList.size()) {\r
- throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.get(index);\r
- }\r
-\r
- /**\r
- * Method getSequenceSet.Returns the contents of the collection\r
- * in an Array. <p>Note: Just in case the collection contents\r
- * are changing in another thread, we pass a 0-length Array of\r
- * the correct type into the API call. This way we <i>know</i>\r
- * that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.SequenceSet[] getSequenceSet(\r
- ) {\r
- jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];\r
- return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList.toArray(array);\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
+ {\r
+ throw new IndexOutOfBoundsException("getSequenceSet: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._sequenceSetList.size() - 1) + "]");\r