X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=53d118b33a3f612a113bd89983006dedede00920;hb=abd0918cc633b946cfea588ef4b4d666edf9fc8b;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 <http://www.gnu.org/licenses/>.
  * 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<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
       for (SequenceI sq : alignment.getSequences())
       {
-        Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence().getAllPDBEntries();
+        Vector<PDBEntry> 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())
     {