/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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
+ * This file is part of Jalview.\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
+ * Jalview 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 3 of the License, or (at your option) any later version.\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
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.schemabinding.version2;\r
\r
-// ---------------------------------/\r
-// - Imported classes and packages -/\r
-// ---------------------------------/\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
* \r
* @param vJGroup\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void addJGroup(final jalview.schemabinding.version2.JGroup vJGroup)\r
throws java.lang.IndexOutOfBoundsException\r
* @param index\r
* @param vJGroup\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void addJGroup(final int index,\r
final jalview.schemabinding.version2.JGroup vJGroup)\r
* \r
* @param vJSeq\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void addJSeq(final jalview.schemabinding.version2.JSeq vJSeq)\r
throws java.lang.IndexOutOfBoundsException\r
* @param index\r
* @param vJSeq\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void addJSeq(final int index,\r
final jalview.schemabinding.version2.JSeq vJSeq)\r
* \r
* @param vTree\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void addTree(final jalview.schemabinding.version2.Tree vTree)\r
throws java.lang.IndexOutOfBoundsException\r
* @param index\r
* @param vTree\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void addTree(final int index,\r
final jalview.schemabinding.version2.Tree vTree)\r
* \r
* @param vUserColours\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void addUserColours(\r
final jalview.schemabinding.version2.UserColours vUserColours)\r
* @param index\r
* @param vUserColours\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void addUserColours(final int index,\r
final jalview.schemabinding.version2.UserColours vUserColours)\r
* \r
* @param vViewport\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void addViewport(\r
final jalview.schemabinding.version2.Viewport vViewport)\r
* @param index\r
* @param vViewport\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void addViewport(final int index,\r
final jalview.schemabinding.version2.Viewport vViewport)\r
* \r
* @param index\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
* @return the value of the jalview.schemabinding.version2.JGroup at the given\r
* index\r
*/\r
* \r
* @param index\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
* @return the value of the jalview.schemabinding.version2.JSeq at the given\r
* index\r
*/\r
* \r
* @param index\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
* @return the value of the jalview.schemabinding.version2.Tree at the given\r
* index\r
*/\r
* \r
* @param index\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
* @return the value of the jalview.schemabinding.version2.UserColours at the\r
* given index\r
*/\r
* \r
* @param index\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
* @return the value of the jalview.schemabinding.version2.Viewport at the\r
* given index\r
*/\r
* \r
* @param out\r
* @throws org.exolab.castor.xml.MarshalException\r
- * if object is null or if any SAXException is thrown during\r
- * marshaling\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
* @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the\r
- * schema\r
+ * if this object is an invalid instance according to the schema\r
*/\r
public void marshal(final java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException,\r
* \r
* @param handler\r
* @throws java.io.IOException\r
- * if an IOException occurs during marshaling\r
+ * if an IOException occurs during marshaling\r
* @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the\r
- * schema\r
+ * if this object is an invalid instance according to the schema\r
* @throws org.exolab.castor.xml.MarshalException\r
- * if object is null or if any SAXException is thrown during\r
- * marshaling\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
*/\r
public void marshal(final org.xml.sax.ContentHandler handler)\r
throws java.io.IOException,\r
}\r
\r
/**\r
- */\r
+ */\r
public void removeAllJGroup()\r
{\r
this._JGroupList.clear();\r
}\r
\r
/**\r
- */\r
+ */\r
public void removeAllJSeq()\r
{\r
this._JSeqList.clear();\r
}\r
\r
/**\r
- */\r
+ */\r
public void removeAllTree()\r
{\r
this._treeList.clear();\r
}\r
\r
/**\r
- */\r
+ */\r
public void removeAllUserColours()\r
{\r
this._userColoursList.clear();\r
}\r
\r
/**\r
- */\r
+ */\r
public void removeAllViewport()\r
{\r
this._viewportList.clear();\r
* Sets the value of field 'featureSettings'.\r
* \r
* @param featureSettings\r
- * the value of field 'featureSettings'.\r
+ * the value of field 'featureSettings'.\r
*/\r
public void setFeatureSettings(\r
final jalview.schemabinding.version2.FeatureSettings featureSettings)\r
* @param index\r
* @param vJGroup\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void setJGroup(final int index,\r
final jalview.schemabinding.version2.JGroup vJGroup)\r
* @param index\r
* @param vJSeq\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void setJSeq(final int index,\r
final jalview.schemabinding.version2.JSeq vJSeq)\r
* @param index\r
* @param vTree\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void setTree(final int index,\r
final jalview.schemabinding.version2.Tree vTree)\r
* @param index\r
* @param vUserColours\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void setUserColours(final int index,\r
final jalview.schemabinding.version2.UserColours vUserColours)\r
* @param index\r
* @param vViewport\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void setViewport(final int index,\r
final jalview.schemabinding.version2.Viewport vViewport)\r
* \r
* @param reader\r
* @throws org.exolab.castor.xml.MarshalException\r
- * if object is null or if any SAXException is thrown during\r
- * marshaling\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
* @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the\r
- * schema\r
+ * if this object is an invalid instance according to the schema\r
* @return the unmarshaled jalview.schemabinding.version2.JalviewModelSequence\r
*/\r
public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(\r
* \r
* \r
* @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the\r
- * schema\r
+ * if this object is an invalid instance according to the schema\r
*/\r
public void validate() throws org.exolab.castor.xml.ValidationException\r
{\r
git://source.jalview.org / jalview.git / blobdiff