/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, 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 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.
- *
- * 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
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-// ---------------------------------/
-// - Imported classes and packages -/
-// ---------------------------------/
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @param vAlignment
* @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 addAlignment(final Alignment vAlignment)
throws java.lang.IndexOutOfBoundsException
* @param index
* @param vAlignment
* @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 addAlignment(final int index, final Alignment vAlignment)
throws java.lang.IndexOutOfBoundsException
*
* @param vSequenceSet
* @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 addSequenceSet(final SequenceSet vSequenceSet)
throws java.lang.IndexOutOfBoundsException
* @param index
* @param vSequenceSet
* @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 addSequenceSet(final int index, final SequenceSet vSequenceSet)
+ public void addSequenceSet(final int index,
+ final SequenceSet vSequenceSet)
throws java.lang.IndexOutOfBoundsException
{
this._sequenceSetList.add(index, vSequenceSet);
*
* @param vTree
* @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 addTree(final java.lang.String vTree)
throws java.lang.IndexOutOfBoundsException
* @param index
* @param vTree
* @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 addTree(final int index, final java.lang.String vTree)
throws java.lang.IndexOutOfBoundsException
*
* @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 Alignment at the given index
*/
public Alignment getAlignment(final int index)
// check bounds for index
if (index < 0 || index >= this._alignmentList.size())
{
- throw new IndexOutOfBoundsException("getAlignment: Index value '"
- + index + "' not in range [0.."
- + (this._alignmentList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getAlignment: Index value '" + index + "' not in range [0.."
+ + (this._alignmentList.size() - 1) + "]");
}
return (Alignment) _alignmentList.get(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 SequenceSet at the given index
*/
public SequenceSet getSequenceSet(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 java.lang.String at the given index
*/
public java.lang.String getTree(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 removeAllAlignment()
{
this._alignmentList.clear();
}
/**
- */
+ */
public void removeAllSequenceSet()
{
this._sequenceSetList.clear();
}
/**
- */
+ */
public void removeAllTree()
{
this._treeList.clear();
* @param index
* @param vAlignment
* @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 setAlignment(final int index, final Alignment vAlignment)
throws java.lang.IndexOutOfBoundsException
// check bounds for index
if (index < 0 || index >= this._alignmentList.size())
{
- throw new IndexOutOfBoundsException("setAlignment: Index value '"
- + index + "' not in range [0.."
- + (this._alignmentList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setAlignment: Index value '" + index + "' not in range [0.."
+ + (this._alignmentList.size() - 1) + "]");
}
this._alignmentList.set(index, vAlignment);
* @param index
* @param vSequenceSet
* @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 setSequenceSet(final int index, final SequenceSet vSequenceSet)
+ public void setSequenceSet(final int index,
+ final SequenceSet vSequenceSet)
throws java.lang.IndexOutOfBoundsException
{
// check bounds for index
* @param index
* @param vTree
* @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 setTree(final int index, final java.lang.String vTree)
throws java.lang.IndexOutOfBoundsException
*
* @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.VAMSAS
*/
- public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader)
+ public static jalview.binding.VAMSAS unmarshal(
+ final java.io.Reader reader)
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(
- jalview.binding.VAMSAS.class, reader);
+ return (jalview.binding.VAMSAS) Unmarshaller
+ .unmarshal(jalview.binding.VAMSAS.class, reader);
}
/**
*
*
* @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