X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=76f4eb50469f95179424ccea4054fa1605106bf2;hb=82e0c09533b4f568b50fdc290be58589cea3ebb6;hp=b85cb94a9dc9952fe37c0a0d1598a0c03923fa28;hpb=043de9819c2d780cdfa55dc0e278308e2c97aee1;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index b85cb94..76f4eb5 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -17,39 +17,47 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     {
       super();
       this.av = av;
-      float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()];
+      Vector selsubset = new Vector();
+      for (int i=0, j=av.getSelectionGroup().getSize(); i<j; i++)
+        if (av.getAlignment().getSequences().contains(av.getSelectionGroup().getSequenceAt(i)))
+          selsubset.add(av.getSelectionGroup().getSequenceAt(i));
+      float scores[][] = new float[selsubset.size()][selsubset.size()];
       double totscore = 0;
-      int count = av.getSelection().size();
+      int count = selsubset.size();
 
       int acount = 0;
-        for (int i = 1; i < count; i++)
+      for (int i = 1; i < count; i++)
+      {
+        for (int j = 0; j < i; j++)
         {
-          for (int j = 0; j < i; j++)
-          {
-            acount++;
-            AlignSeq as = new AlignSeq(av.getSelection().sequenceAt(i),av.getSelection().sequenceAt(j),"pep");
-
-            as.calcScoreMatrix();
-            as.traceAlignment();
-            as.printAlignment();
-            scores[i][j] = (float)as.getMaxScore()/(float)as.getASeq1().length;
-            totscore = totscore + scores[i][j];
-
-            textarea.append(as.getOutput());
-            sequences.add( new Sequence( as.getS1().getName(), as.getAStr1()) );
-            sequences.add( new Sequence( as.getS2().getName(), as.getAStr2()) );
-
-
-          }
+          acount++;
+          AlignSeq as = new AlignSeq( (SequenceI) selsubset.elementAt(i),
+                                     (SequenceI) selsubset.elementAt(j), "pep");
+          as.calcScoreMatrix();
+          as.traceAlignment();
+          as.printAlignment();
+          scores[i][j] = (float) as.getMaxScore() /
+              (float) as.getASeq1().length;
+          totscore = totscore + scores[i][j];
+
+          textarea.append(as.getOutput());
+          sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));
+          sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));
         }
+      }
+      if (count > 2)
+      {
+        System.out.println("Pairwise alignment scaled similarity score matrix\n");
+        for (int i = 0; i < count;i++)
+          jalview.util.Format.print(System.out, "%s \n", (""+i)+" "+((SequenceI) selsubset.elementAt(i)).getName());
+        System.out.println("\n");
+        for (int i = 0; i < count;i++)
+          for (int j = 0; j < i; j++)
+            jalview.util.Format.print(System.out,"%7.3f",scores[i][j]/totscore);
+        System.out.println("\n");
 
-        if (count > 2)
-        {
-          for (int i = 0; i < count;i++)
-            for (int j = 0; j < i; j++)
-              jalview.util.Format.print(System.out,"%7.3f",scores[i][j]/totscore);
-        }
       }
+    }
 
 
   protected void viewInEditorButton_actionPerformed(ActionEvent e)
@@ -62,11 +70,9 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
 
       AlignFrame af = new AlignFrame(new Alignment(seq));
-      int newHeight = seq.length * af.viewport.getCharHeight() + 200;
-      if(newHeight>500)
-        newHeight=500;
-
-      Desktop.addInternalFrame(af, "Pairwise Aligned Sequences", 700,newHeight);
+      Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
+                               AlignFrame.NEW_WINDOW_WIDTH,
+                               AlignFrame.NEW_WINDOW_HEIGHT);
 
   }