X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=c9285dd853ea1d05264c153a186dc5e88e6d8917;hb=04b6d995eb9395cb4107b28119fff413d8bacafd;hp=55cf2ccb95004792c97b9677d850cbf326143d0c;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 55cf2cc..c9285dd 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -31,16 +31,16 @@ public class PairwiseAlignPanel
     extends GPairwiseAlignPanel
 {
   Vector sequences = new Vector();
-  AlignViewport av;
+  AlignmentPanel ap;
 
-  public PairwiseAlignPanel(AlignViewport av)
+  public PairwiseAlignPanel(AlignmentPanel ap)
   {
     super();
-    this.av = av;
-    float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().
+    this.ap = ap;
+    float scores[][] = new float[ap.av.alignment.getHeight()][ap.av.alignment.
         getHeight()];
     double totscore = 0;
-    int count = av.getSelectionGroup().getSize();
+    int count = ap.av.getSelectionGroup().getSize();
 
     int acount = 0;
     for (int i = 1; i < count; i++)
@@ -48,8 +48,8 @@ public class PairwiseAlignPanel
       for (int j = 0; j < i; j++)
       {
         acount++;
-        AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),
-                                   av.getSelectionGroup().getSequenceAt(j),
+        AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i),
+                                   ap.av.getSelectionGroup().getSequenceAt(j),
                                    "pep");
 
         as.calcScoreMatrix();
@@ -88,10 +88,9 @@ public class PairwiseAlignPanel
       seq[i] = (Sequence) sequences.elementAt(i);
     }
 
-    AlignFrame af = new AlignFrame(new Alignment(seq));
-    jalview.bin.JalviewLite.addFrame(af, "Pairwise Aligned Sequences",
-                                     AlignFrame.NEW_WINDOW_WIDTH,
-                                     AlignFrame.NEW_WINDOW_HEIGHT);
+    AlignFrame af = new AlignFrame(new Alignment(seq),
+                                   ap.alignFrame.applet,
+                                   "Pairwise Aligned Sequences");
 
   }