X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=d0b0c986e7bae3c1c8f2b1df8b8a3380830f0d55;hb=23d3cb8d0e4c227224587135f41132d436dc1178;hp=910a20678eafa1cd40d13e730b546b77be6e7bc1;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 910a206..d0b0c98 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -28,7 +28,7 @@ import jalview.datamodel.*;
 import java.awt.*;
 
 public class PairwiseAlignPanel
-    extends Panel
+    extends Panel implements ActionListener
 {
   Vector sequences = new Vector();
   AlignmentPanel ap;
@@ -47,9 +47,10 @@ public class PairwiseAlignPanel
     float scores[][] = new float[ap.av.alignment.getHeight()][ap.av.alignment.
         getHeight()];
     double totscore = 0;
-    int count = ap.av.getSelectionGroup().getSize();
+    int count = ap.av.getSelectionGroup().getSize(false);
 
     int acount = 0;
+    Sequence seq;
     for (int i = 1; i < count; i++)
     {
       for (int j = 0; j < i; j++)
@@ -66,9 +67,19 @@ public class PairwiseAlignPanel
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
-        sequences.addElement(new Sequence(as.getS1().getName(), as.getAStr1()));
-        sequences.addElement(new Sequence(as.getS2().getName(), as.getAStr2()));
 
+        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);
       }
     }
 
@@ -85,7 +96,13 @@ public class PairwiseAlignPanel
     }
   }
 
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)
+  public void actionPerformed(ActionEvent evt)
+  {
+    if(evt.getSource()==viewInEditorButton)
+      viewInEditorButton_actionPerformed();
+  }
+
+  protected void viewInEditorButton_actionPerformed()
   {
 
     Sequence[] seq = new Sequence[sequences.size()];
@@ -97,7 +114,8 @@ public class PairwiseAlignPanel
 
     new AlignFrame(new Alignment(seq),
                                    ap.alignFrame.applet,
-                                   "Pairwise Aligned Sequences");
+                                   "Pairwise Aligned Sequences",
+                                   false);
 
   }
   protected ScrollPane scrollPane = new ScrollPane();
@@ -112,11 +130,7 @@ public class PairwiseAlignPanel
       textarea.setText("");
       viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
       viewInEditorButton.setLabel("View in alignment editor");
-      viewInEditorButton.addActionListener(new java.awt.event.ActionListener() {
-              public void actionPerformed(ActionEvent e) {
-                  viewInEditorButton_actionPerformed(e);
-              }
-          });
+      viewInEditorButton.addActionListener(this);
       this.add(scrollPane, BorderLayout.CENTER);
       scrollPane.add(textarea);
       this.add(jPanel1, BorderLayout.SOUTH);