/*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
\r
package jalview.binding;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
\r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class VAMSAS.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class VAMSAS\r
- implements java.io.Serializable\r
-{\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\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
- /**\r
- * Field _sequenceSetList\r
- */\r
- private java.util.Vector _sequenceSetList;\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public VAMSAS()\r
- {\r
- super();\r
- _alignmentList = new Vector();\r
- _treeList = new Vector();\r
- _sequenceSetList = new Vector();\r
- } //-- jalview.binding.VAMSAS()\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addAlignment\r
- *\r
- *\r
- *\r
- * @param vAlignment\r
- */\r
- public void addAlignment(jalview.binding.Alignment vAlignment)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _alignmentList.addElement(vAlignment);\r
- } //-- void addAlignment(jalview.binding.Alignment)\r
-\r
- /**\r
- * Method addAlignment\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vAlignment\r
- */\r
- public void addAlignment(int index, jalview.binding.Alignment vAlignment)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _alignmentList.insertElementAt(vAlignment, index);\r
- } //-- void addAlignment(int, jalview.binding.Alignment)\r
-\r
- /**\r
- * Method addSequenceSet\r
- *\r
- *\r
- *\r
- * @param vSequenceSet\r
- */\r
- public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceSetList.addElement(vSequenceSet);\r
- } //-- void addSequenceSet(jalview.binding.SequenceSet)\r
-\r
- /**\r
- * Method addSequenceSet\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vSequenceSet\r
- */\r
- public void addSequenceSet(int index,\r
- jalview.binding.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceSetList.insertElementAt(vSequenceSet, index);\r
- } //-- void addSequenceSet(int, jalview.binding.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 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
- *\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 getAlignment\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Alignment\r
- */\r
- public jalview.binding.Alignment getAlignment(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _alignmentList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.binding.Alignment) _alignmentList.elementAt(index);\r
- } //-- jalview.binding.Alignment getAlignment(int)\r
-\r
- /**\r
- * Method getAlignment\r
- *\r
- *\r
- *\r
- * @return Alignment\r
- */\r
- public jalview.binding.Alignment[] getAlignment()\r
- {\r
- int size = _alignmentList.size();\r
- jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(\r
- index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.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
- *\r
- * @param index\r
- * @return SequenceSet\r
- */\r
- public jalview.binding.SequenceSet getSequenceSet(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _sequenceSetList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
- } //-- jalview.binding.SequenceSet getSequenceSet(int)\r
-\r
- /**\r
- * Method getSequenceSet\r
- *\r
- *\r
- *\r
- * @return SequenceSet\r
- */\r
- public jalview.binding.SequenceSet[] getSequenceSet()\r
- {\r
- int size = _sequenceSetList.size();\r
- jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(\r
- index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.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
- {\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
- {\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
- {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\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,\r
- 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,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
-\r
- Marshaller.marshal(this, handler);\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.binding.Alignment removeAlignment(int index)\r
- {\r
- java.lang.Object obj = _alignmentList.elementAt(index);\r
- _alignmentList.removeElementAt(index);\r
- return (jalview.binding.Alignment) obj;\r
- } //-- jalview.binding.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
- public void removeAllSequenceSet()\r
- {\r
- _sequenceSetList.removeAllElements();\r
- } //-- void removeAllSequenceSet()\r
-\r
- /**\r
- * Method removeAllTree\r
- *\r
- */\r
- public void removeAllTree()\r
- {\r
- _treeList.removeAllElements();\r
- } //-- void removeAllTree()\r
-\r
- /**\r
- * Method removeSequenceSet\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return SequenceSet\r
- */\r
- public jalview.binding.SequenceSet removeSequenceSet(int index)\r
- {\r
- java.lang.Object obj = _sequenceSetList.elementAt(index);\r
- _sequenceSetList.removeElementAt(index);\r
- return (jalview.binding.SequenceSet) obj;\r
- } //-- jalview.binding.SequenceSet removeSequenceSet(int)\r
-\r
- /**\r
- * Method removeTree\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return String\r
- */\r
- public java.lang.String removeTree(int index)\r
- {\r
- java.lang.Object obj = _treeList.elementAt(index);\r
- _treeList.removeElementAt(index);\r
- return (String) obj;\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.binding.Alignment vAlignment)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _alignmentList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _alignmentList.setElementAt(vAlignment, index);\r
- } //-- void setAlignment(int, jalview.binding.Alignment)\r
-\r
- /**\r
- * Method setAlignment\r
- *\r
- *\r
- *\r
- * @param alignmentArray\r
- */\r
- public void setAlignment(jalview.binding.Alignment[] alignmentArray)\r
- {\r
- //-- copy array\r
- _alignmentList.removeAllElements();\r
- for (int i = 0; i < alignmentArray.length; i++)\r
- {\r
- _alignmentList.addElement(alignmentArray[i]);\r
- }\r
- } //-- void setAlignment(jalview.binding.Alignment)\r
-\r
- /**\r
- * Method setSequenceSet\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vSequenceSet\r
- */\r
- public void setSequenceSet(int index,\r
- jalview.binding.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _sequenceSetList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _sequenceSetList.setElementAt(vSequenceSet, index);\r
- } //-- void setSequenceSet(int, jalview.binding.SequenceSet)\r
-\r
- /**\r
- * Method setSequenceSet\r
- *\r
- *\r
- *\r
- * @param sequenceSetArray\r
- */\r
- public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray)\r
- {\r
- //-- copy array\r
- _sequenceSetList.removeAllElements();\r
- for (int i = 0; i < sequenceSetArray.length; i++)\r
- {\r
- _sequenceSetList.addElement(sequenceSetArray[i]);\r
- }\r
- } //-- void setSequenceSet(jalview.binding.SequenceSet)\r
-\r
- /**\r
- * Method setTree\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vTree\r
- */\r
- public void setTree(int index, java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _treeList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _treeList.setElementAt(vTree, index);\r
- } //-- void setTree(int, java.lang.String)\r
-\r
- /**\r
- * Method setTree\r
- *\r
- *\r
- *\r
- * @param treeArray\r
- */\r
- public void setTree(java.lang.String[] treeArray)\r
- {\r
- //-- copy array\r
- _treeList.removeAllElements();\r
- for (int i = 0; i < treeArray.length; i++)\r
- {\r
- _treeList.addElement(treeArray[i]);\r
- }\r
- } //-- void setTree(java.lang.String)\r
-\r
- /**\r
- * Method unmarshal\r
- *\r
- *\r
- *\r
- * @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.\r
- VAMSAS.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
- /**\r
- * Method validate\r
- *\r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
- Validator();\r
- validator.validate(this);\r
- } //-- void validate()\r
+public class VAMSAS implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\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
+ /**\r
+ * Field _sequenceSetList\r
+ */\r
+ private java.util.Vector _sequenceSetList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public VAMSAS() {\r
+ super();\r
+ _alignmentList = new Vector();\r
+ _treeList = new Vector();\r
+ _sequenceSetList = new Vector();\r
+ } //-- jalview.binding.VAMSAS()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addAlignment\r
+ * \r
+ * \r
+ * \r
+ * @param vAlignment\r
+ */\r
+ public void addAlignment(jalview.binding.Alignment vAlignment)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _alignmentList.addElement(vAlignment);\r
+ } //-- void addAlignment(jalview.binding.Alignment) \r
+\r
+ /**\r
+ * Method addAlignment\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlignment\r
+ */\r
+ public void addAlignment(int index, jalview.binding.Alignment vAlignment)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _alignmentList.insertElementAt(vAlignment, index);\r
+ } //-- void addAlignment(int, jalview.binding.Alignment) \r
+\r
+ /**\r
+ * Method addSequenceSet\r
+ * \r
+ * \r
+ * \r
+ * @param vSequenceSet\r
+ */\r
+ public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _sequenceSetList.addElement(vSequenceSet);\r
+ } //-- void addSequenceSet(jalview.binding.SequenceSet) \r
+\r
+ /**\r
+ * Method addSequenceSet\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequenceSet\r
+ */\r
+ public void addSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _sequenceSetList.insertElementAt(vSequenceSet, index);\r
+ } //-- void addSequenceSet(int, jalview.binding.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 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
+ * \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 getAlignment\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Alignment\r
+ */\r
+ public jalview.binding.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.binding.Alignment) _alignmentList.elementAt(index);\r
+ } //-- jalview.binding.Alignment getAlignment(int) \r
+\r
+ /**\r
+ * Method getAlignment\r
+ * \r
+ * \r
+ * \r
+ * @return Alignment\r
+ */\r
+ public jalview.binding.Alignment[] getAlignment()\r
+ {\r
+ int size = _alignmentList.size();\r
+ jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.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
+ * \r
+ * @param index\r
+ * @return SequenceSet\r
+ */\r
+ public jalview.binding.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.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
+ } //-- jalview.binding.SequenceSet getSequenceSet(int) \r
+\r
+ /**\r
+ * Method getSequenceSet\r
+ * \r
+ * \r
+ * \r
+ * @return SequenceSet\r
+ */\r
+ public jalview.binding.SequenceSet[] getSequenceSet()\r
+ {\r
+ int size = _sequenceSetList.size();\r
+ jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.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 removeAlignment\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Alignment\r
+ */\r
+ public jalview.binding.Alignment removeAlignment(int index)\r
+ {\r
+ java.lang.Object obj = _alignmentList.elementAt(index);\r
+ _alignmentList.removeElementAt(index);\r
+ return (jalview.binding.Alignment) obj;\r
+ } //-- jalview.binding.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
+ public void removeAllSequenceSet()\r
+ {\r
+ _sequenceSetList.removeAllElements();\r
+ } //-- void removeAllSequenceSet() \r
+\r
+ /**\r
+ * Method removeAllTree\r
+ * \r
+ */\r
+ public void removeAllTree()\r
+ {\r
+ _treeList.removeAllElements();\r
+ } //-- void removeAllTree() \r
+\r
+ /**\r
+ * Method removeSequenceSet\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return SequenceSet\r
+ */\r
+ public jalview.binding.SequenceSet removeSequenceSet(int index)\r
+ {\r
+ java.lang.Object obj = _sequenceSetList.elementAt(index);\r
+ _sequenceSetList.removeElementAt(index);\r
+ return (jalview.binding.SequenceSet) obj;\r
+ } //-- jalview.binding.SequenceSet removeSequenceSet(int) \r
+\r
+ /**\r
+ * Method removeTree\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return String\r
+ */\r
+ public java.lang.String removeTree(int index)\r
+ {\r
+ java.lang.Object obj = _treeList.elementAt(index);\r
+ _treeList.removeElementAt(index);\r
+ return (String)obj;\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.binding.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.binding.Alignment) \r
+\r
+ /**\r
+ * Method setAlignment\r
+ * \r
+ * \r
+ * \r
+ * @param alignmentArray\r
+ */\r
+ public void setAlignment(jalview.binding.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.binding.Alignment) \r
+\r
+ /**\r
+ * Method setSequenceSet\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequenceSet\r
+ */\r
+ public void setSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _sequenceSetList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _sequenceSetList.setElementAt(vSequenceSet, index);\r
+ } //-- void setSequenceSet(int, jalview.binding.SequenceSet) \r
+\r
+ /**\r
+ * Method setSequenceSet\r
+ * \r
+ * \r
+ * \r
+ * @param sequenceSetArray\r
+ */\r
+ public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray)\r
+ {\r
+ //-- copy array\r
+ _sequenceSetList.removeAllElements();\r
+ for (int i = 0; i < sequenceSetArray.length; i++) {\r
+ _sequenceSetList.addElement(sequenceSetArray[i]);\r
+ }\r
+ } //-- void setSequenceSet(jalview.binding.SequenceSet) \r
+\r
+ /**\r
+ * Method setTree\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\r
+ */\r
+ public void setTree(int index, java.lang.String vTree)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _treeList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _treeList.setElementAt(vTree, index);\r
+ } //-- void setTree(int, java.lang.String) \r
+\r
+ /**\r
+ * Method setTree\r
+ * \r
+ * \r
+ * \r
+ * @param treeArray\r
+ */\r
+ public void setTree(java.lang.String[] treeArray)\r
+ {\r
+ //-- copy array\r
+ _treeList.removeAllElements();\r
+ for (int i = 0; i < treeArray.length; i++) {\r
+ _treeList.addElement(treeArray[i]);\r
+ }\r
+ } //-- void setTree(java.lang.String) \r
+\r
+ /**\r
+ * Method unmarshal\r
+ * \r
+ * \r
+ * \r
+ * @param reader\r
+ * @return Object\r
+ */\r
+ public static java.lang.Object unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+ /**\r
+ * Method validate\r
+ * \r
+ */\r
+ public void validate()\r
+ throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
\r
}\r