/*\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
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.binding;\r
-\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
\r
-import org.xml.sax.ContentHandler;\r
+package jalview.binding;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
+\r
import java.io.IOException;\r
import java.io.Reader;\r
import java.io.Serializable;\r
import java.io.Writer;\r
-\r
import java.util.Enumeration;\r
import java.util.Vector;\r
-\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 implements java.io.Serializable {\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.util.Vector _sequenceSetList;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
+\r
public VAMSAS() {\r
super();\r
_alignmentList = new Vector();\r
_treeList = new Vector();\r
_sequenceSetList = new Vector();\r
- }\r
- //-- jalview.binding.VAMSAS()\r
- //-----------/\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_alignmentList.addElement(vAlignment);\r
- }\r
- //-- void addAlignment(jalview.binding.Alignment)\r
+ } //-- void addAlignment(jalview.binding.Alignment) \r
\r
/**\r
* Method addAlignment\r
- *\r
- *\r
- *\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_alignmentList.insertElementAt(vAlignment, index);\r
- }\r
- //-- void addAlignment(int, jalview.binding.Alignment)\r
+ } //-- void addAlignment(int, jalview.binding.Alignment) \r
\r
/**\r
* Method addSequenceSet\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param vSequenceSet\r
*/\r
public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_sequenceSetList.addElement(vSequenceSet);\r
- }\r
- //-- void addSequenceSet(jalview.binding.SequenceSet)\r
+ } //-- void addSequenceSet(jalview.binding.SequenceSet) \r
\r
/**\r
* Method addSequenceSet\r
- *\r
- *\r
- *\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
+ public void addSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_sequenceSetList.insertElementAt(vSequenceSet, index);\r
- }\r
- //-- void addSequenceSet(int, jalview.binding.SequenceSet)\r
+ } //-- void addSequenceSet(int, jalview.binding.SequenceSet) \r
\r
/**\r
* Method addTree\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param vTree\r
*/\r
public void addTree(java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_treeList.addElement(vTree);\r
- }\r
- //-- void addTree(java.lang.String)\r
+ } //-- void addTree(java.lang.String) \r
\r
/**\r
* Method addTree\r
- *\r
- *\r
- *\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_treeList.insertElementAt(vTree, index);\r
- }\r
- //-- void addTree(int, java.lang.String)\r
+ } //-- void addTree(int, java.lang.String) \r
\r
/**\r
* Method enumerateAlignment\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateAlignment() {\r
+ public java.util.Enumeration enumerateAlignment()\r
+ {\r
return _alignmentList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateAlignment()\r
+ } //-- java.util.Enumeration enumerateAlignment() \r
\r
/**\r
* Method enumerateSequenceSet\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateSequenceSet() {\r
+ public java.util.Enumeration enumerateSequenceSet()\r
+ {\r
return _sequenceSetList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateSequenceSet()\r
+ } //-- java.util.Enumeration enumerateSequenceSet() \r
\r
/**\r
* Method enumerateTree\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateTree() {\r
+ public java.util.Enumeration enumerateTree()\r
+ {\r
return _treeList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateTree()\r
+ } //-- java.util.Enumeration enumerateTree() \r
\r
/**\r
* Method getAlignment\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Alignment\r
*/\r
public jalview.binding.Alignment getAlignment(int index)\r
- throws java.lang.IndexOutOfBoundsException {\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
+ \r
return (jalview.binding.Alignment) _alignmentList.elementAt(index);\r
- }\r
- //-- jalview.binding.Alignment getAlignment(int)\r
+ } //-- jalview.binding.Alignment getAlignment(int) \r
\r
/**\r
* Method getAlignment\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Alignment\r
*/\r
- public jalview.binding.Alignment[] getAlignment() {\r
+ public jalview.binding.Alignment[] getAlignment()\r
+ {\r
int size = _alignmentList.size();\r
jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.Alignment[] getAlignment()\r
+ } //-- jalview.binding.Alignment[] getAlignment() \r
\r
/**\r
* Method getAlignmentCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getAlignmentCount() {\r
+ public int getAlignmentCount()\r
+ {\r
return _alignmentList.size();\r
- }\r
- //-- int getAlignmentCount()\r
+ } //-- int getAlignmentCount() \r
\r
/**\r
* Method getSequenceSet\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return SequenceSet\r
*/\r
public jalview.binding.SequenceSet getSequenceSet(int index)\r
- throws java.lang.IndexOutOfBoundsException {\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
+ \r
return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
- }\r
- //-- jalview.binding.SequenceSet getSequenceSet(int)\r
+ } //-- jalview.binding.SequenceSet getSequenceSet(int) \r
\r
/**\r
* Method getSequenceSet\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return SequenceSet\r
*/\r
- public jalview.binding.SequenceSet[] getSequenceSet() {\r
+ public jalview.binding.SequenceSet[] getSequenceSet()\r
+ {\r
int size = _sequenceSetList.size();\r
jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.SequenceSet[] getSequenceSet()\r
+ } //-- jalview.binding.SequenceSet[] getSequenceSet() \r
\r
/**\r
* Method getSequenceSetCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getSequenceSetCount() {\r
+ public int getSequenceSetCount()\r
+ {\r
return _sequenceSetList.size();\r
- }\r
- //-- int getSequenceSetCount()\r
+ } //-- int getSequenceSetCount() \r
\r
/**\r
* Method getTree\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return String\r
*/\r
public java.lang.String getTree(int index)\r
- throws java.lang.IndexOutOfBoundsException {\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
- }\r
- //-- java.lang.String getTree(int)\r
+ \r
+ return (String)_treeList.elementAt(index);\r
+ } //-- java.lang.String getTree(int) \r
\r
/**\r
* Method getTree\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return String\r
*/\r
- public java.lang.String[] getTree() {\r
+ public java.lang.String[] getTree()\r
+ {\r
int size = _treeList.size();\r
java.lang.String[] mArray = new java.lang.String[size];\r
-\r
for (int index = 0; index < size; index++) {\r
- mArray[index] = (String) _treeList.elementAt(index);\r
+ mArray[index] = (String)_treeList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- java.lang.String[] getTree()\r
+ } //-- java.lang.String[] getTree() \r
\r
/**\r
* Method getTreeCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getTreeCount() {\r
+ public int getTreeCount()\r
+ {\r
return _treeList.size();\r
- }\r
- //-- int getTreeCount()\r
+ } //-- int getTreeCount() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean isValid() {\r
+ public boolean isValid()\r
+ {\r
try {\r
validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
-\r
return true;\r
- }\r
- //-- boolean isValid()\r
+ } //-- boolean isValid() \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
Marshaller.marshal(this, out);\r
- }\r
- //-- void marshal(java.io.Writer)\r
+ } //-- void marshal(java.io.Writer) \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
Marshaller.marshal(this, handler);\r
- }\r
- //-- void marshal(org.xml.sax.ContentHandler)\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Method removeAlignment\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Alignment\r
*/\r
- public jalview.binding.Alignment removeAlignment(int index) {\r
+ public jalview.binding.Alignment removeAlignment(int index)\r
+ {\r
java.lang.Object obj = _alignmentList.elementAt(index);\r
_alignmentList.removeElementAt(index);\r
-\r
return (jalview.binding.Alignment) obj;\r
- }\r
- //-- jalview.binding.Alignment removeAlignment(int)\r
+ } //-- jalview.binding.Alignment removeAlignment(int) \r
\r
/**\r
* Method removeAllAlignment\r
- *\r
+ * \r
*/\r
- public void removeAllAlignment() {\r
+ public void removeAllAlignment()\r
+ {\r
_alignmentList.removeAllElements();\r
- }\r
- //-- void removeAllAlignment()\r
+ } //-- void removeAllAlignment() \r
\r
/**\r
* Method removeAllSequenceSet\r
- *\r
+ * \r
*/\r
- public void removeAllSequenceSet() {\r
+ public void removeAllSequenceSet()\r
+ {\r
_sequenceSetList.removeAllElements();\r
- }\r
- //-- void removeAllSequenceSet()\r
+ } //-- void removeAllSequenceSet() \r
\r
/**\r
* Method removeAllTree\r
- *\r
+ * \r
*/\r
- public void removeAllTree() {\r
+ public void removeAllTree()\r
+ {\r
_treeList.removeAllElements();\r
- }\r
- //-- void removeAllTree()\r
+ } //-- void removeAllTree() \r
\r
/**\r
* Method removeSequenceSet\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return SequenceSet\r
*/\r
- public jalview.binding.SequenceSet removeSequenceSet(int index) {\r
+ public jalview.binding.SequenceSet removeSequenceSet(int index)\r
+ {\r
java.lang.Object obj = _sequenceSetList.elementAt(index);\r
_sequenceSetList.removeElementAt(index);\r
-\r
return (jalview.binding.SequenceSet) obj;\r
- }\r
- //-- jalview.binding.SequenceSet removeSequenceSet(int)\r
+ } //-- jalview.binding.SequenceSet removeSequenceSet(int) \r
\r
/**\r
* Method removeTree\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return String\r
*/\r
- public java.lang.String removeTree(int index) {\r
+ public java.lang.String removeTree(int index)\r
+ {\r
java.lang.Object obj = _treeList.elementAt(index);\r
_treeList.removeElementAt(index);\r
-\r
- return (String) obj;\r
- }\r
- //-- java.lang.String removeTree(int)\r
+ return (String)obj;\r
+ } //-- java.lang.String removeTree(int) \r
\r
/**\r
* Method setAlignment\r
- *\r
- *\r
- *\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _alignmentList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_alignmentList.setElementAt(vAlignment, index);\r
- }\r
- //-- void setAlignment(int, jalview.binding.Alignment)\r
+ } //-- void setAlignment(int, jalview.binding.Alignment) \r
\r
/**\r
* Method setAlignment\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param alignmentArray\r
*/\r
- public void setAlignment(jalview.binding.Alignment[] alignmentArray) {\r
+ public void setAlignment(jalview.binding.Alignment[] alignmentArray)\r
+ {\r
//-- copy array\r
_alignmentList.removeAllElements();\r
-\r
for (int i = 0; i < alignmentArray.length; i++) {\r
_alignmentList.addElement(alignmentArray[i]);\r
}\r
- }\r
- //-- void setAlignment(jalview.binding.Alignment)\r
+ } //-- void setAlignment(jalview.binding.Alignment) \r
\r
/**\r
* Method setSequenceSet\r
- *\r
- *\r
- *\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
+ 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
-\r
_sequenceSetList.setElementAt(vSequenceSet, index);\r
- }\r
- //-- void setSequenceSet(int, jalview.binding.SequenceSet)\r
+ } //-- void setSequenceSet(int, jalview.binding.SequenceSet) \r
\r
/**\r
* Method setSequenceSet\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param sequenceSetArray\r
*/\r
- public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray) {\r
+ public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray)\r
+ {\r
//-- copy array\r
_sequenceSetList.removeAllElements();\r
-\r
for (int i = 0; i < sequenceSetArray.length; i++) {\r
_sequenceSetList.addElement(sequenceSetArray[i]);\r
}\r
- }\r
- //-- void setSequenceSet(jalview.binding.SequenceSet)\r
+ } //-- void setSequenceSet(jalview.binding.SequenceSet) \r
\r
/**\r
* Method setTree\r
- *\r
- *\r
- *\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
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _treeList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_treeList.setElementAt(vTree, index);\r
- }\r
- //-- void setTree(int, java.lang.String)\r
+ } //-- void setTree(int, java.lang.String) \r
\r
/**\r
* Method setTree\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param treeArray\r
*/\r
- public void setTree(java.lang.String[] treeArray) {\r
+ public void setTree(java.lang.String[] treeArray)\r
+ {\r
//-- copy array\r
_treeList.removeAllElements();\r
-\r
for (int i = 0; i < treeArray.length; i++) {\r
_treeList.addElement(treeArray[i]);\r
}\r
- }\r
- //-- void setTree(java.lang.String)\r
+ } //-- void setTree(java.lang.String) \r
\r
/**\r
* Method unmarshal\r
- *\r
- *\r
- *\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
- return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.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
*/\r
- public void validate() throws org.exolab.castor.xml.ValidationException {\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
- }\r
- //-- void validate()\r
+ } //-- void validate() \r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff