no need to send consensus

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

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index c771693..972d4f5 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -19,7 +19,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
       this.av = av;\r
       float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()];\r
       double totscore = 0;\r
-      int count = av.getSelection().size();\r
+      int count = av.getSelectionGroup().getSize();\r
 \r
       int acount = 0;\r
         for (int i = 1; i < count; i++)\r
@@ -27,8 +27,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
           for (int j = 0; j < i; j++)\r
           {\r
             acount++;\r
-            AlignSeq as = new AlignSeq(av.getSelection().sequenceAt(i),av.getSelection().sequenceAt(j),"pep");\r
-            //tf.status.setText("Aligning " + as.getS1().getName() + " and " + as.getS2().getName() + " (" + acount + "/" + (count*(count-1)/2) + ")");\r
+            AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),\r
+                                       av.getSelectionGroup().getSequenceAt(j),"pep");\r
 \r
             as.calcScoreMatrix();\r
             as.traceAlignment();\r
@@ -37,8 +37,9 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
             totscore = totscore + scores[i][j];\r
 \r
             textarea.append(as.getOutput());\r
-            sequences.add( as.getS1() );\r
-            sequences.add( as.getS2() );\r
+            sequences.add( new Sequence( as.getS1().getName(), as.getAStr1()) );\r
+            sequences.add( new Sequence( as.getS2().getName(), as.getAStr2()) );\r
+\r
 \r
           }\r
         }\r
@@ -62,11 +63,9 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 \r
 \r
       AlignFrame af = new AlignFrame(new Alignment(seq));\r
-      int newHeight = seq.length * af.viewport.getCharHeight() + 200;\r
-      if(newHeight>500)\r
-        newHeight=500;\r
-\r
-      Desktop.addInternalFrame(af, "Pairwise Aligned Sequences", 700,newHeight);\r
+      Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",\r
+                               AlignFrame.NEW_WINDOW_WIDTH,\r
+                               AlignFrame.NEW_WINDOW_HEIGHT);\r
 \r
   }\r
 \r