/*\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 JalviewModelSequence.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
public class JalviewModelSequence 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 _userColoursList;\r
\r
+ /**\r
+ * Field _treeList\r
+ */\r
+ private java.util.Vector _treeList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
+\r
public JalviewModelSequence() {\r
super();\r
_JSeqList = new Vector();\r
_JGroupList = new Vector();\r
_viewportList = new Vector();\r
_userColoursList = new Vector();\r
- }\r
- //-- jalview.binding.JalviewModelSequence()\r
- //-----------/\r
+ _treeList = new Vector();\r
+ } //-- jalview.binding.JalviewModelSequence()\r
\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addJGroup\r
+ * \r
+ * \r
+ * \r
+ * @param vJGroup\r
+ */\r
public void addJGroup(jalview.binding.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_JGroupList.addElement(vJGroup);\r
- }\r
- //-- void addJGroup(jalview.binding.JGroup)\r
+ } //-- void addJGroup(jalview.binding.JGroup) \r
\r
/**\r
* Method addJGroup\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vJGroup\r
*/\r
public void addJGroup(int index, jalview.binding.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_JGroupList.insertElementAt(vJGroup, index);\r
- }\r
- //-- void addJGroup(int, jalview.binding.JGroup)\r
+ } //-- void addJGroup(int, jalview.binding.JGroup) \r
\r
/**\r
* Method addJSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param vJSeq\r
*/\r
public void addJSeq(jalview.binding.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_JSeqList.addElement(vJSeq);\r
- }\r
- //-- void addJSeq(jalview.binding.JSeq)\r
+ } //-- void addJSeq(jalview.binding.JSeq) \r
\r
/**\r
* Method addJSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vJSeq\r
*/\r
public void addJSeq(int index, jalview.binding.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_JSeqList.insertElementAt(vJSeq, index);\r
- }\r
- //-- void addJSeq(int, jalview.binding.JSeq)\r
+ } //-- void addJSeq(int, jalview.binding.JSeq) \r
+\r
+ /**\r
+ * Method addTree\r
+ * \r
+ * \r
+ * \r
+ * @param vTree\r
+ */\r
+ public void addTree(jalview.binding.Tree vTree)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _treeList.addElement(vTree);\r
+ } //-- void addTree(jalview.binding.Tree) \r
+\r
+ /**\r
+ * Method addTree\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\r
+ */\r
+ public void addTree(int index, jalview.binding.Tree vTree)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _treeList.insertElementAt(vTree, index);\r
+ } //-- void addTree(int, jalview.binding.Tree) \r
\r
/**\r
* Method addUserColours\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param vUserColours\r
*/\r
public void addUserColours(jalview.binding.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_userColoursList.addElement(vUserColours);\r
- }\r
- //-- void addUserColours(jalview.binding.UserColours)\r
+ } //-- void addUserColours(jalview.binding.UserColours) \r
\r
/**\r
* Method addUserColours\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vUserColours\r
*/\r
- public void addUserColours(int index,\r
- jalview.binding.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ public void addUserColours(int index, jalview.binding.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_userColoursList.insertElementAt(vUserColours, index);\r
- }\r
- //-- void addUserColours(int, jalview.binding.UserColours)\r
+ } //-- void addUserColours(int, jalview.binding.UserColours) \r
\r
/**\r
* Method addViewport\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param vViewport\r
*/\r
public void addViewport(jalview.binding.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_viewportList.addElement(vViewport);\r
- }\r
- //-- void addViewport(jalview.binding.Viewport)\r
+ } //-- void addViewport(jalview.binding.Viewport) \r
\r
/**\r
* Method addViewport\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vViewport\r
*/\r
public void addViewport(int index, jalview.binding.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_viewportList.insertElementAt(vViewport, index);\r
- }\r
- //-- void addViewport(int, jalview.binding.Viewport)\r
+ } //-- void addViewport(int, jalview.binding.Viewport) \r
\r
/**\r
* Method enumerateJGroup\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateJGroup() {\r
+ public java.util.Enumeration enumerateJGroup()\r
+ {\r
return _JGroupList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateJGroup()\r
+ } //-- java.util.Enumeration enumerateJGroup() \r
\r
/**\r
* Method enumerateJSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateJSeq() {\r
+ public java.util.Enumeration enumerateJSeq()\r
+ {\r
return _JSeqList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateJSeq()\r
+ } //-- java.util.Enumeration enumerateJSeq() \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 enumerateUserColours\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateUserColours() {\r
+ public java.util.Enumeration enumerateUserColours()\r
+ {\r
return _userColoursList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateUserColours()\r
+ } //-- java.util.Enumeration enumerateUserColours() \r
\r
/**\r
* Method enumerateViewport\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateViewport() {\r
+ public java.util.Enumeration enumerateViewport()\r
+ {\r
return _viewportList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateViewport()\r
+ } //-- java.util.Enumeration enumerateViewport() \r
\r
/**\r
* Method getJGroup\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return JGroup\r
*/\r
public jalview.binding.JGroup getJGroup(int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _JGroupList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
+ \r
return (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
- }\r
- //-- jalview.binding.JGroup getJGroup(int)\r
+ } //-- jalview.binding.JGroup getJGroup(int) \r
\r
/**\r
* Method getJGroup\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return JGroup\r
*/\r
- public jalview.binding.JGroup[] getJGroup() {\r
+ public jalview.binding.JGroup[] getJGroup()\r
+ {\r
int size = _JGroupList.size();\r
jalview.binding.JGroup[] mArray = new jalview.binding.JGroup[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.JGroup[] getJGroup()\r
+ } //-- jalview.binding.JGroup[] getJGroup() \r
\r
/**\r
* Method getJGroupCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getJGroupCount() {\r
+ public int getJGroupCount()\r
+ {\r
return _JGroupList.size();\r
- }\r
- //-- int getJGroupCount()\r
+ } //-- int getJGroupCount() \r
\r
/**\r
* Method getJSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return JSeq\r
*/\r
public jalview.binding.JSeq getJSeq(int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _JSeqList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
+ \r
return (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
- }\r
- //-- jalview.binding.JSeq getJSeq(int)\r
+ } //-- jalview.binding.JSeq getJSeq(int) \r
\r
/**\r
* Method getJSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return JSeq\r
*/\r
- public jalview.binding.JSeq[] getJSeq() {\r
+ public jalview.binding.JSeq[] getJSeq()\r
+ {\r
int size = _JSeqList.size();\r
jalview.binding.JSeq[] mArray = new jalview.binding.JSeq[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.JSeq[] getJSeq()\r
+ } //-- jalview.binding.JSeq[] getJSeq() \r
\r
/**\r
* Method getJSeqCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getJSeqCount() {\r
+ public int getJSeqCount()\r
+ {\r
return _JSeqList.size();\r
- }\r
- //-- int getJSeqCount()\r
+ } //-- int getJSeqCount() \r
+\r
+ /**\r
+ * Method getTree\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Tree\r
+ */\r
+ public jalview.binding.Tree 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 (jalview.binding.Tree) _treeList.elementAt(index);\r
+ } //-- jalview.binding.Tree getTree(int) \r
+\r
+ /**\r
+ * Method getTree\r
+ * \r
+ * \r
+ * \r
+ * @return Tree\r
+ */\r
+ public jalview.binding.Tree[] getTree()\r
+ {\r
+ int size = _treeList.size();\r
+ jalview.binding.Tree[] mArray = new jalview.binding.Tree[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.Tree) _treeList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.Tree[] 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 getUserColours\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return UserColours\r
*/\r
public jalview.binding.UserColours getUserColours(int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _userColoursList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
+ \r
return (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
- }\r
- //-- jalview.binding.UserColours getUserColours(int)\r
+ } //-- jalview.binding.UserColours getUserColours(int) \r
\r
/**\r
* Method getUserColours\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return UserColours\r
*/\r
- public jalview.binding.UserColours[] getUserColours() {\r
+ public jalview.binding.UserColours[] getUserColours()\r
+ {\r
int size = _userColoursList.size();\r
jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.UserColours[] getUserColours()\r
+ } //-- jalview.binding.UserColours[] getUserColours() \r
\r
/**\r
* Method getUserColoursCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getUserColoursCount() {\r
+ public int getUserColoursCount()\r
+ {\r
return _userColoursList.size();\r
- }\r
- //-- int getUserColoursCount()\r
+ } //-- int getUserColoursCount() \r
\r
/**\r
* Method getViewport\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Viewport\r
*/\r
public jalview.binding.Viewport getViewport(int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _viewportList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
+ \r
return (jalview.binding.Viewport) _viewportList.elementAt(index);\r
- }\r
- //-- jalview.binding.Viewport getViewport(int)\r
+ } //-- jalview.binding.Viewport getViewport(int) \r
\r
/**\r
* Method getViewport\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Viewport\r
*/\r
- public jalview.binding.Viewport[] getViewport() {\r
+ public jalview.binding.Viewport[] getViewport()\r
+ {\r
int size = _viewportList.size();\r
jalview.binding.Viewport[] mArray = new jalview.binding.Viewport[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.Viewport[] getViewport()\r
+ } //-- jalview.binding.Viewport[] getViewport() \r
\r
/**\r
* Method getViewportCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getViewportCount() {\r
+ public int getViewportCount()\r
+ {\r
return _viewportList.size();\r
- }\r
- //-- int getViewportCount()\r
+ } //-- int getViewportCount() \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 removeAllJGroup\r
- *\r
+ * \r
*/\r
- public void removeAllJGroup() {\r
+ public void removeAllJGroup()\r
+ {\r
_JGroupList.removeAllElements();\r
- }\r
- //-- void removeAllJGroup()\r
+ } //-- void removeAllJGroup() \r
\r
/**\r
* Method removeAllJSeq\r
- *\r
+ * \r
*/\r
- public void removeAllJSeq() {\r
+ public void removeAllJSeq()\r
+ {\r
_JSeqList.removeAllElements();\r
- }\r
- //-- void removeAllJSeq()\r
+ } //-- void removeAllJSeq() \r
+\r
+ /**\r
+ * Method removeAllTree\r
+ * \r
+ */\r
+ public void removeAllTree()\r
+ {\r
+ _treeList.removeAllElements();\r
+ } //-- void removeAllTree() \r
\r
/**\r
* Method removeAllUserColours\r
- *\r
+ * \r
*/\r
- public void removeAllUserColours() {\r
+ public void removeAllUserColours()\r
+ {\r
_userColoursList.removeAllElements();\r
- }\r
- //-- void removeAllUserColours()\r
+ } //-- void removeAllUserColours() \r
\r
/**\r
* Method removeAllViewport\r
- *\r
+ * \r
*/\r
- public void removeAllViewport() {\r
+ public void removeAllViewport()\r
+ {\r
_viewportList.removeAllElements();\r
- }\r
- //-- void removeAllViewport()\r
+ } //-- void removeAllViewport() \r
\r
/**\r
* Method removeJGroup\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return JGroup\r
*/\r
- public jalview.binding.JGroup removeJGroup(int index) {\r
+ public jalview.binding.JGroup removeJGroup(int index)\r
+ {\r
java.lang.Object obj = _JGroupList.elementAt(index);\r
_JGroupList.removeElementAt(index);\r
-\r
return (jalview.binding.JGroup) obj;\r
- }\r
- //-- jalview.binding.JGroup removeJGroup(int)\r
+ } //-- jalview.binding.JGroup removeJGroup(int) \r
\r
/**\r
* Method removeJSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return JSeq\r
*/\r
- public jalview.binding.JSeq removeJSeq(int index) {\r
+ public jalview.binding.JSeq removeJSeq(int index)\r
+ {\r
java.lang.Object obj = _JSeqList.elementAt(index);\r
_JSeqList.removeElementAt(index);\r
-\r
return (jalview.binding.JSeq) obj;\r
- }\r
- //-- jalview.binding.JSeq removeJSeq(int)\r
+ } //-- jalview.binding.JSeq removeJSeq(int) \r
+\r
+ /**\r
+ * Method removeTree\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Tree\r
+ */\r
+ public jalview.binding.Tree removeTree(int index)\r
+ {\r
+ java.lang.Object obj = _treeList.elementAt(index);\r
+ _treeList.removeElementAt(index);\r
+ return (jalview.binding.Tree) obj;\r
+ } //-- jalview.binding.Tree removeTree(int) \r
\r
/**\r
* Method removeUserColours\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return UserColours\r
*/\r
- public jalview.binding.UserColours removeUserColours(int index) {\r
+ public jalview.binding.UserColours removeUserColours(int index)\r
+ {\r
java.lang.Object obj = _userColoursList.elementAt(index);\r
_userColoursList.removeElementAt(index);\r
-\r
return (jalview.binding.UserColours) obj;\r
- }\r
- //-- jalview.binding.UserColours removeUserColours(int)\r
+ } //-- jalview.binding.UserColours removeUserColours(int) \r
\r
/**\r
* Method removeViewport\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Viewport\r
*/\r
- public jalview.binding.Viewport removeViewport(int index) {\r
+ public jalview.binding.Viewport removeViewport(int index)\r
+ {\r
java.lang.Object obj = _viewportList.elementAt(index);\r
_viewportList.removeElementAt(index);\r
-\r
return (jalview.binding.Viewport) obj;\r
- }\r
- //-- jalview.binding.Viewport removeViewport(int)\r
+ } //-- jalview.binding.Viewport removeViewport(int) \r
\r
/**\r
* Method setJGroup\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vJGroup\r
*/\r
public void setJGroup(int index, jalview.binding.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _JGroupList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_JGroupList.setElementAt(vJGroup, index);\r
- }\r
- //-- void setJGroup(int, jalview.binding.JGroup)\r
+ } //-- void setJGroup(int, jalview.binding.JGroup) \r
\r
/**\r
* Method setJGroup\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param JGroupArray\r
*/\r
- public void setJGroup(jalview.binding.JGroup[] JGroupArray) {\r
+ public void setJGroup(jalview.binding.JGroup[] JGroupArray)\r
+ {\r
//-- copy array\r
_JGroupList.removeAllElements();\r
-\r
for (int i = 0; i < JGroupArray.length; i++) {\r
_JGroupList.addElement(JGroupArray[i]);\r
}\r
- }\r
- //-- void setJGroup(jalview.binding.JGroup)\r
+ } //-- void setJGroup(jalview.binding.JGroup) \r
\r
/**\r
* Method setJSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vJSeq\r
*/\r
public void setJSeq(int index, jalview.binding.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _JSeqList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_JSeqList.setElementAt(vJSeq, index);\r
- }\r
- //-- void setJSeq(int, jalview.binding.JSeq)\r
+ } //-- void setJSeq(int, jalview.binding.JSeq) \r
\r
/**\r
* Method setJSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param JSeqArray\r
*/\r
- public void setJSeq(jalview.binding.JSeq[] JSeqArray) {\r
+ public void setJSeq(jalview.binding.JSeq[] JSeqArray)\r
+ {\r
//-- copy array\r
_JSeqList.removeAllElements();\r
-\r
for (int i = 0; i < JSeqArray.length; i++) {\r
_JSeqList.addElement(JSeqArray[i]);\r
}\r
- }\r
- //-- void setJSeq(jalview.binding.JSeq)\r
+ } //-- void setJSeq(jalview.binding.JSeq) \r
+\r
+ /**\r
+ * Method setTree\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\r
+ */\r
+ public void setTree(int index, jalview.binding.Tree 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, jalview.binding.Tree) \r
+\r
+ /**\r
+ * Method setTree\r
+ * \r
+ * \r
+ * \r
+ * @param treeArray\r
+ */\r
+ public void setTree(jalview.binding.Tree[] 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(jalview.binding.Tree) \r
\r
/**\r
* Method setUserColours\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vUserColours\r
*/\r
- public void setUserColours(int index,\r
- jalview.binding.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ public void setUserColours(int index, jalview.binding.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _userColoursList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_userColoursList.setElementAt(vUserColours, index);\r
- }\r
- //-- void setUserColours(int, jalview.binding.UserColours)\r
+ } //-- void setUserColours(int, jalview.binding.UserColours) \r
\r
/**\r
* Method setUserColours\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param userColoursArray\r
*/\r
- public void setUserColours(jalview.binding.UserColours[] userColoursArray) {\r
+ public void setUserColours(jalview.binding.UserColours[] userColoursArray)\r
+ {\r
//-- copy array\r
_userColoursList.removeAllElements();\r
-\r
for (int i = 0; i < userColoursArray.length; i++) {\r
_userColoursList.addElement(userColoursArray[i]);\r
}\r
- }\r
- //-- void setUserColours(jalview.binding.UserColours)\r
+ } //-- void setUserColours(jalview.binding.UserColours) \r
\r
/**\r
* Method setViewport\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vViewport\r
*/\r
public void setViewport(int index, jalview.binding.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _viewportList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_viewportList.setElementAt(vViewport, index);\r
- }\r
- //-- void setViewport(int, jalview.binding.Viewport)\r
+ } //-- void setViewport(int, jalview.binding.Viewport) \r
\r
/**\r
* Method setViewport\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param viewportArray\r
*/\r
- public void setViewport(jalview.binding.Viewport[] viewportArray) {\r
+ public void setViewport(jalview.binding.Viewport[] viewportArray)\r
+ {\r
//-- copy array\r
_viewportList.removeAllElements();\r
-\r
for (int i = 0; i < viewportArray.length; i++) {\r
_viewportList.addElement(viewportArray[i]);\r
}\r
- }\r
- //-- void setViewport(jalview.binding.Viewport)\r
+ } //-- void setViewport(jalview.binding.Viewport) \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.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.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.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.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