/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.binding;
-// ---------------------------------/
-// - Imported classes and packages -/
-// ---------------------------------/
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @param vAnnotation
* @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
+ * if the index given is outside the bounds of the collection
*/
public void addAnnotation(final jalview.binding.Annotation vAnnotation)
throws java.lang.IndexOutOfBoundsException
* @param index
* @param vAnnotation
* @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
+ * if the index given is outside the bounds of the collection
*/
public void addAnnotation(final int index,
final jalview.binding.Annotation vAnnotation)
*
* @param vSequence
* @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
+ * if the index given is outside the bounds of the collection
*/
public void addSequence(final jalview.binding.Sequence vSequence)
throws java.lang.IndexOutOfBoundsException
* @param index
* @param vSequence
* @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
+ * if the index given is outside the bounds of the collection
*/
public void addSequence(final int index,
final jalview.binding.Sequence vSequence)
}
/**
- */
+ */
public void deleteAligned()
{
this._has_aligned = false;
*
* @param index
* @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
+ * if the index given is outside the bounds of the collection
* @return the value of the jalview.binding.Annotation at the given index
*/
public jalview.binding.Annotation getAnnotation(final int index)
*
* @param index
* @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
+ * if the index given is outside the bounds of the collection
* @return the value of the jalview.binding.Sequence at the given index
*/
public jalview.binding.Sequence getSequence(final int index)
*
* @param out
* @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
+ * if object is null or if any SAXException is thrown during
+ * marshaling
* @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the
- * schema
+ * if this object is an invalid instance according to the schema
*/
public void marshal(final java.io.Writer out)
throws org.exolab.castor.xml.MarshalException,
*
* @param handler
* @throws java.io.IOException
- * if an IOException occurs during marshaling
+ * if an IOException occurs during marshaling
* @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the
- * schema
+ * if this object is an invalid instance according to the schema
* @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
+ * if object is null or if any SAXException is thrown during
+ * marshaling
*/
public void marshal(final org.xml.sax.ContentHandler handler)
throws java.io.IOException,
}
/**
- */
+ */
public void removeAllAnnotation()
{
this._annotationList.clear();
}
/**
- */
+ */
public void removeAllSequence()
{
this._sequenceList.clear();
* Sets the value of field 'aligned'.
*
* @param aligned
- * the value of field 'aligned'.
+ * the value of field 'aligned'.
*/
public void setAligned(final boolean aligned)
{
* @param index
* @param vAnnotation
* @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
+ * if the index given is outside the bounds of the collection
*/
public void setAnnotation(final int index,
final jalview.binding.Annotation vAnnotation)
* Sets the value of field 'gapChar'.
*
* @param gapChar
- * the value of field 'gapChar'.
+ * the value of field 'gapChar'.
*/
public void setGapChar(final java.lang.String gapChar)
{
* @param index
* @param vSequence
* @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
+ * if the index given is outside the bounds of the collection
*/
public void setSequence(final int index,
final jalview.binding.Sequence vSequence)
*
* @param reader
* @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
+ * if object is null or if any SAXException is thrown during
+ * marshaling
* @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the
- * schema
+ * if this object is an invalid instance according to the schema
* @return the unmarshaled jalview.binding.SequenceSet
*/
public static jalview.binding.SequenceSet unmarshal(
*
*
* @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the
- * schema
+ * if this object is an invalid instance according to the schema
*/
public void validate() throws org.exolab.castor.xml.ValidationException
{
git://source.jalview.org / jalview.git / blobdiff