-public class VAMSAS\r
- 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
- _treeList = new Vector();\r
- _sequenceSetList = new Vector();\r
- } //-- jalview.schemabinding.version2.VAMSAS()\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\r
- 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,\r
- jalview.schemabinding.version2.SequenceSet\r
- 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
+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
+ {\r
+ return _sequenceSetList.size();\r
+ } //-- int getSequenceSetCount() \r
+\r
+ /**\r
+ * Method getTree\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return String\r
+ */\r
+ public java.lang.String getTree(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _treeList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (String)_treeList.elementAt(index);\r
+ } //-- java.lang.String getTree(int) \r
+\r
+ /**\r
+ * Method getTree\r
+ * \r
+ * \r
+ * \r
+ * @return String\r
+ */\r
+ public java.lang.String[] getTree()\r
+ {\r
+ int size = _treeList.size();\r
+ java.lang.String[] mArray = new java.lang.String[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (String)_treeList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- java.lang.String[] getTree() \r
+\r
+ /**\r
+ * Method getTreeCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getTreeCount()\r
+ {\r
+ return _treeList.size();\r
+ } //-- int getTreeCount() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid() \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param out\r
+ */\r
+ public void marshal(java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer) \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param handler\r
+ */\r
+ public void marshal(org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Method removeAllSequenceSet\r
+ * \r
+ */\r
+ public void removeAllSequenceSet()\r