JAL-207 pairwise alignment sequence contexts propergation bugfix

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

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index d3f7a93..5a3b56c 100644 (file)
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -20,15 +20,21 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Panel;
+import java.awt.ScrollPane;
+import java.awt.TextArea;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Vector;
+
 public class PairwiseAlignPanel extends Panel implements ActionListener
 {
   Vector sequences = new Vector();
@@ -89,13 +95,8 @@ public class PairwiseAlignPanel extends Panel implements ActionListener
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
-        seq = new Sequence(as.getS1().getName(), as.getAStr1(), as.getS1()
-                .getStart(), as.getS1().getEnd());
-        sequences.addElement(seq);
-
-        seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2()
-                .getStart(), as.getS2().getEnd());
-        sequences.addElement(seq);
+        sequences.add(as.getAlignedSeq1());
+        sequences.add(as.getAlignedSeq1());
       }
     }
 
@@ -164,7 +165,8 @@ public class PairwiseAlignPanel extends Panel implements ActionListener
     textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
     textarea.setText("");
     viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
-    viewInEditorButton.setLabel(MessageManager.getString("label.view_alignment_editor"));
+    viewInEditorButton.setLabel(MessageManager
+            .getString("label.view_alignment_editor"));
     viewInEditorButton.addActionListener(this);
     this.add(scrollPane, BorderLayout.CENTER);
     scrollPane.add(textarea);