JAL-207 pairwise alignment context patch

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index dcddf88..82f0120 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -20,14 +20,16 @@
  */
 package jalview.gui;
 
-import java.util.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+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 java.awt.event.ActionEvent;
+import java.util.Vector;
+
 /**
  * DOCUMENT ME!
  * 
@@ -97,12 +99,12 @@ 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());
+        seq = new Sequence(as.getAlignedSeq1().getName(), as.getAStr1(), as
+                .getAlignedSeq1().getStart(), as.getAlignedSeq1().getEnd());
         sequences.add(seq);
 
-        seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2()
-                .getStart(), as.getS2().getEnd());
+        seq = new Sequence(as.getAlignedSeq2().getName(), as.getAStr2(), as
+                .getAlignedSeq2().getStart(), as.getAlignedSeq2().getEnd());
         sequences.add(seq);
       }
     }