X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=53d118b33a3f612a113bd89983006dedede00920;hb=7dc7fb2a35c435d825bc91c5ae60ec6073419a69;hp=d4d2054953611af16b01374513ceb7dc378c6dcf;hpb=8b27085fa7fc5f2877e078421284c2636b85b8c6;p=jalview.git
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index d4d2054..53d118b 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;
@@ -55,6 +37,7 @@ import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
@@ -419,10 +402,11 @@ 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 +659,8 @@ 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 +692,8 @@ 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()][]);
}
@@ -890,9 +876,9 @@ public class AlignViewport extends AlignmentViewport implements
MessageManager.getString("label.new_window"), };
final String question = JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.open_split_window?"));
- int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
+ int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
MessageManager.getString("label.open_split_window"),
- JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
if (response != 1 && response != 2)
@@ -1057,7 +1043,7 @@ public class AlignViewport extends AlignmentViewport implements
* there is no complement, or it is not following highlights, or no mapping
* is found, the result will be empty.
*/
- SearchResults sr = new SearchResults();
+ SearchResultsI sr = new SearchResults();
int verticalOffset = findComplementScrollTarget(sr);
if (!sr.isEmpty())
{