/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * 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 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
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * 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.gui;
import java.util.*;
+import java.util.List;
import java.awt.*;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
/**
* DOCUMENT ME!
- *
+ *
* @param comp
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param al
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public static void Register(Component comp, String seqSetId)
{
if (validateSequences && comp instanceof AlignmentPanel
&& source instanceof AlignmentPanel)
{
- validateSequences(((AlignmentPanel) source).av.alignment,
- ((AlignmentPanel) comp).av.alignment);
+ validateSequences(((AlignmentPanel) source).av.getAlignment(),
+ ((AlignmentPanel) comp).av.getAlignment());
}
if (comp instanceof AlignmentPanel && alignmentChanged)
{
if (i < comp.getHeight())
{
- comp.getSequences().insertElementAt(a1[i], i);
+ // TODO: the following does not trigger any recalculation of height/etc, or maintain the dataset
+ if (comp.getDataset()!=source.getDataset())
+ {
+ // raise an implementation warning here - not sure if this situation will ever occur
+ System.err.println("IMPLEMENTATION PROBLEM: DATASET out of sync due to an insert whilst calling PaintRefresher.validateSequences(AlignmentI, ALignmentI)");
+ }
+ List<SequenceI> alsq;
+ synchronized (alsq=comp.getSequences()) {
+ alsq.add(i, a1[i]);
+ }
}
else
{
static AlignmentPanel[] getAssociatedPanels(String id)
{
+ if (components==null) { return new AlignmentPanel[0]; };
Vector comps = (Vector) components.get(id);
+ if (comps==null) { return new AlignmentPanel[0]; };
Vector tmp = new Vector();
int i, iSize = comps.size();
for (i = 0; i < iSize; i++)
{
if (comps.elementAt(i) instanceof AlignmentPanel)
{
- tmp.addElement(((AlignmentPanel) comps.elementAt(i)));
+ tmp.addElement(comps.elementAt(i));
}
}
AlignmentPanel[] result = new AlignmentPanel[tmp.size()];