Use propertyListener for alignment edits

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

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 55cf2cc..0ff2708 100755 (executable)
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -31,16 +31,16 @@ public class PairwiseAlignPanel
     extends GPairwiseAlignPanel\r
 {\r
   Vector sequences = new Vector();\r
-  AlignViewport av;\r
+  AlignmentPanel ap;\r
 \r
-  public PairwiseAlignPanel(AlignViewport av)\r
+  public PairwiseAlignPanel(AlignmentPanel ap)\r
   {\r
     super();\r
-    this.av = av;\r
-    float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().\r
+    this.ap = ap;\r
+    float scores[][] = new float[ap.av.alignment.getHeight()][ap.av.alignment.\r
         getHeight()];\r
     double totscore = 0;\r
-    int count = av.getSelectionGroup().getSize();\r
+    int count = ap.av.getSelectionGroup().getSize();\r
 \r
     int acount = 0;\r
     for (int i = 1; i < count; i++)\r
@@ -48,8 +48,8 @@ public class PairwiseAlignPanel
       for (int j = 0; j < i; j++)\r
       {\r
         acount++;\r
-        AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),\r
-                                   av.getSelectionGroup().getSequenceAt(j),\r
+        AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i),\r
+                                   ap.av.getSelectionGroup().getSequenceAt(j),\r
                                    "pep");\r
 \r
         as.calcScoreMatrix();\r
@@ -88,7 +88,7 @@ public class PairwiseAlignPanel
       seq[i] = (Sequence) sequences.elementAt(i);\r
     }\r
 \r
-    AlignFrame af = new AlignFrame(new Alignment(seq));\r
+    AlignFrame af = new AlignFrame(new Alignment(seq), ap.alignFrame.applet);\r
     jalview.bin.JalviewLite.addFrame(af, "Pairwise Aligned Sequences",\r
                                      AlignFrame.NEW_WINDOW_WIDTH,\r
                                      AlignFrame.NEW_WINDOW_HEIGHT);\r