//--------------------------/\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
\r
public VAMSAS() {\r
super();\r
- _alignmentList = new Vector();\r
_treeList = new Vector();\r
_sequenceSetList = new Vector();\r
} //-- jalview.schemabinding.version2.VAMSAS()\r
//-----------/\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
} //-- 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
} //-- 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
} //-- 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
} //-- 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