X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=d0a0f11e28a5cc9f93d5f54991a2c879ee08c816;hb=fbc92d8f171f75002890bfa0ea1f436f7125d3b5;hp=62e05d0c365cda273965a7661b47b47fc6c2d565;hpb=f6a8570a72a975e9e967d98a64907476bddd8baa;p=jalview.git
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 62e05d0..d0a0f11 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -18,24 +18,6 @@
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
- */
package jalview.gui;
import jalview.analysis.AlignmentUtils;
@@ -419,10 +401,11 @@ public class AlignViewport extends AlignmentViewport implements
* @param align
* DOCUMENT ME!
*/
+ @Override
public void setAlignment(AlignmentI align)
{
replaceMappings(align);
- this.alignment = align;
+ super.setAlignment(align);
}
/**
@@ -675,7 +658,8 @@ public class AlignViewport extends AlignmentViewport implements
List choosenSeqs = new ArrayList();
for (SequenceI sq : alignment.getSequences())
{
- Vector pdbRefEntries = sq.getDatasetSequence().getAllPDBEntries();
+ Vector pdbRefEntries = sq.getDatasetSequence()
+ .getAllPDBEntries();
if (pdbRefEntries == null)
{
continue;
@@ -707,7 +691,8 @@ public class AlignViewport extends AlignmentViewport implements
}
}
}
- seqvectors.add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
+ seqvectors
+ .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
}
return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
}