/*\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 2.5)\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 vFeatures\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 addFeatures(\r
final jalview.schemabinding.version2.Features vFeatures)\r
* @param index\r
* @param vFeatures\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 addFeatures(final int index,\r
final jalview.schemabinding.version2.Features vFeatures)\r
* \r
* @param vHiddenSequences\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 addHiddenSequences(final int vHiddenSequences)\r
throws java.lang.IndexOutOfBoundsException\r
* @param index\r
* @param vHiddenSequences\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 addHiddenSequences(final int index, final int vHiddenSequences)\r
throws java.lang.IndexOutOfBoundsException\r
* \r
* @param vPdbids\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 addPdbids(final jalview.schemabinding.version2.Pdbids vPdbids)\r
throws java.lang.IndexOutOfBoundsException\r
* @param index\r
* @param vPdbids\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 addPdbids(final int index,\r
final jalview.schemabinding.version2.Pdbids vPdbids)\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteColour()\r
{\r
this._has_colour = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteEnd()\r
{\r
this._has_end = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteHidden()\r
{\r
this._has_hidden = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteStart()\r
{\r
this._has_start = false;\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.Features 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 int at the given index\r
*/\r
public int getHiddenSequences(final int index)\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.Pdbids at the given\r
* 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 removeAllFeatures()\r
{\r
this._featuresList.clear();\r
}\r
\r
/**\r
- */\r
+ */\r
public void removeAllHiddenSequences()\r
{\r
this._hiddenSequencesList.clear();\r
}\r
\r
/**\r
- */\r
+ */\r
public void removeAllPdbids()\r
{\r
this._pdbidsList.clear();\r
* Sets the value of field 'colour'.\r
* \r
* @param colour\r
- * the value of field 'colour'.\r
+ * the value of field 'colour'.\r
*/\r
public void setColour(final int colour)\r
{\r
* Sets the value of field 'end'.\r
* \r
* @param end\r
- * the value of field 'end'.\r
+ * the value of field 'end'.\r
*/\r
public void setEnd(final int end)\r
{\r
* @param index\r
* @param vFeatures\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 setFeatures(final int index,\r
final jalview.schemabinding.version2.Features vFeatures)\r
* Sets the value of field 'hidden'.\r
* \r
* @param hidden\r
- * the value of field 'hidden'.\r
+ * the value of field 'hidden'.\r
*/\r
public void setHidden(final boolean hidden)\r
{\r
* @param index\r
* @param vHiddenSequences\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 setHiddenSequences(final int index, final int vHiddenSequences)\r
throws java.lang.IndexOutOfBoundsException\r
* Sets the value of field 'id'.\r
* \r
* @param id\r
- * the value of field 'id'.\r
+ * the value of field 'id'.\r
*/\r
public void setId(final java.lang.String id)\r
{\r
* @param index\r
* @param vPdbids\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 setPdbids(final int index,\r
final jalview.schemabinding.version2.Pdbids vPdbids)\r
* Sets the value of field 'start'.\r
* \r
* @param start\r
- * the value of field 'start'.\r
+ * the value of field 'start'.\r
*/\r
public void setStart(final int start)\r
{\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.JSeq\r
*/\r
public static jalview.schemabinding.version2.JSeq 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