/*\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
+/*\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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class JalviewModelSequence.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class JalviewModelSequence implements java.io.Serializable {\r
\r
/**\r
* Method addJGroup\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vJGroup\r
*/\r
public void addJGroup(jalview.binding.JGroup vJGroup)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_JGroupList.addElement(vJGroup);\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
throws java.lang.IndexOutOfBoundsException\r
{\r
_JGroupList.insertElementAt(vJGroup, index);\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
{\r
_JSeqList.addElement(vJSeq);\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
throws java.lang.IndexOutOfBoundsException\r
{\r
_JSeqList.insertElementAt(vJSeq, index);\r
- } //-- void addJSeq(int, jalview.binding.JSeq) \r
+ } //-- void addJSeq(int, jalview.binding.JSeq)\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
{\r
_userColoursList.addElement(vUserColours);\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
throws java.lang.IndexOutOfBoundsException\r
{\r
_userColoursList.insertElementAt(vUserColours, index);\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
{\r
_viewportList.addElement(vViewport);\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
throws java.lang.IndexOutOfBoundsException\r
{\r
_viewportList.insertElementAt(vViewport, index);\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
{\r
return _JGroupList.elements();\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
{\r
return _JSeqList.elements();\r
- } //-- java.util.Enumeration enumerateJSeq() \r
+ } //-- java.util.Enumeration enumerateJSeq()\r
\r
/**\r
* Method enumerateUserColours\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateUserColours()\r
{\r
return _userColoursList.elements();\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
{\r
return _viewportList.elements();\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
if ((index < 0) || (index > _JGroupList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.JGroup) _JGroupList.elementAt(index);\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
mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
}\r
return mArray;\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
{\r
return _JGroupList.size();\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
if ((index < 0) || (index > _JSeqList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.JSeq) _JSeqList.elementAt(index);\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
mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
}\r
return mArray;\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
{\r
return _JSeqList.size();\r
- } //-- int getJSeqCount() \r
+ } //-- int getJSeqCount()\r
\r
/**\r
* Method getUserColours\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return UserColours\r
*/\r
if ((index < 0) || (index > _userColoursList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.UserColours) _userColoursList.elementAt(index);\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
mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
}\r
return mArray;\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
{\r
return _userColoursList.size();\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
if ((index < 0) || (index > _viewportList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.Viewport) _viewportList.elementAt(index);\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
mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index);\r
}\r
return mArray;\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
{\r
return _viewportList.size();\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
return false;\r
}\r
return true;\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, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\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, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\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
{\r
_JGroupList.removeAllElements();\r
- } //-- void removeAllJGroup() \r
+ } //-- void removeAllJGroup()\r
\r
/**\r
* Method removeAllJSeq\r
- * \r
+ *\r
*/\r
public void removeAllJSeq()\r
{\r
_JSeqList.removeAllElements();\r
- } //-- void removeAllJSeq() \r
+ } //-- void removeAllJSeq()\r
\r
/**\r
* Method removeAllUserColours\r
- * \r
+ *\r
*/\r
public void removeAllUserColours()\r
{\r
_userColoursList.removeAllElements();\r
- } //-- void removeAllUserColours() \r
+ } //-- void removeAllUserColours()\r
\r
/**\r
* Method removeAllViewport\r
- * \r
+ *\r
*/\r
public void removeAllViewport()\r
{\r
_viewportList.removeAllElements();\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
java.lang.Object obj = _JGroupList.elementAt(index);\r
_JGroupList.removeElementAt(index);\r
return (jalview.binding.JGroup) obj;\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
java.lang.Object obj = _JSeqList.elementAt(index);\r
_JSeqList.removeElementAt(index);\r
return (jalview.binding.JSeq) obj;\r
- } //-- jalview.binding.JSeq removeJSeq(int) \r
+ } //-- jalview.binding.JSeq removeJSeq(int)\r
\r
/**\r
* Method removeUserColours\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return UserColours\r
*/\r
java.lang.Object obj = _userColoursList.elementAt(index);\r
_userColoursList.removeElementAt(index);\r
return (jalview.binding.UserColours) obj;\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
java.lang.Object obj = _viewportList.elementAt(index);\r
_viewportList.removeElementAt(index);\r
return (jalview.binding.Viewport) obj;\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
throw new IndexOutOfBoundsException();\r
}\r
_JGroupList.setElementAt(vJGroup, index);\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
for (int i = 0; i < JGroupArray.length; i++) {\r
_JGroupList.addElement(JGroupArray[i]);\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
throw new IndexOutOfBoundsException();\r
}\r
_JSeqList.setElementAt(vJSeq, index);\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
for (int i = 0; i < JSeqArray.length; i++) {\r
_JSeqList.addElement(JSeqArray[i]);\r
}\r
- } //-- void setJSeq(jalview.binding.JSeq) \r
+ } //-- void setJSeq(jalview.binding.JSeq)\r
\r
/**\r
* Method setUserColours\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vUserColours\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_userColoursList.setElementAt(vUserColours, index);\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
for (int i = 0; i < userColoursArray.length; i++) {\r
_userColoursList.addElement(userColoursArray[i]);\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
throw new IndexOutOfBoundsException();\r
}\r
_viewportList.setElementAt(vViewport, index);\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
for (int i = 0; i < viewportArray.length; i++) {\r
_viewportList.addElement(viewportArray[i]);\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
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
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \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
+ } //-- void validate()\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff