JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / gui / PairwiseAlignPanel.java

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 15c8c70..22f1368 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,30 +1,35 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPairwiseAlignPanel;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+import java.awt.event.ActionEvent;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -35,7 +40,7 @@ import jalview.jbgui.*;
 public class PairwiseAlignPanel extends GPairwiseAlignPanel
 {
 
-  AlignViewport av;
+  AlignmentViewport av;
 
   Vector sequences;
 
@@ -43,9 +48,9 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
    * Creates a new PairwiseAlignPanel object.
    * 
    * @param av
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
-  public PairwiseAlignPanel(AlignViewport av)
+  public PairwiseAlignPanel(AlignmentViewport av)
   {
     super();
     this.av = av;
@@ -57,14 +62,14 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
     if (av.getSelectionGroup() == null)
     {
-      seqs = av.alignment.getSequencesArray();
+      seqs = av.getAlignment().getSequencesArray();
     }
     else
     {
-      seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+      seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
     }
 
-    String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA
+    String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA
             : AlignSeq.PEP;
 
     float[][] scores = new float[seqs.length][seqs.length];
@@ -95,13 +100,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
-        seq = new Sequence(as.getS1().getName(), as.getAStr1(), as.getS1()
-                .getStart(), as.getS1().getEnd());
-        sequences.add(seq);
-
-        seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2()
-                .getStart(), as.getS2().getEnd());
-        sequences.add(seq);
+        sequences.add(as.getAlignedSeq1());
+        sequences.add(as.getAlignedSeq2());
       }
     }
 
@@ -135,7 +135,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void viewInEditorButton_actionPerformed(ActionEvent e)
   {
@@ -149,7 +149,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     AlignFrame af = new AlignFrame(new Alignment(seq),
             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 
-    Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
+    Desktop.addInternalFrame(af,
+            MessageManager.getString("label.pairwise_aligned_sequences"),
             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
   }
 }