X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=b8a15d50bbc8fc2590bc9d0da972e882412e00e9;hb=3caa3405a5822c7248bab517b8d1a7776e0dc210;hp=e58dd76c133a376a6f3ab0b44947744519afc69c;hpb=621a628afc1f6ee7a2778b9d0ae2729b88fe5bfd;p=jalview.git

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index e58dd76..b8a15d5 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -42,21 +42,35 @@ public class PairwiseAlignPanel
     catch (Exception e)
     {
       e.printStackTrace();
-  }
+    }
     this.ap = ap;
-    float scores[][] = new float[ap.av.alignment.getHeight()][ap.av.alignment.
-        getHeight()];
+    sequences = new Vector();
+
+    SequenceI[] seqs;
+    String[] seqStrings = ap.av.getViewAsString(true);
+
+    if (ap.av.getSelectionGroup() == null)
+    {
+      seqs = ap.av.alignment.getSequencesArray();
+    }
+    else
+    {
+      seqs = ap.av.getSelectionGroup().getSequencesInOrder(ap.av.alignment);
+    }
+
+    float scores[][] = new float[seqs.length][seqs.length];
     double totscore = 0;
     int count = ap.av.getSelectionGroup().getSize(false);
 
     Sequence seq;
+
     for (int i = 1; i < count; i++)
     {
       for (int j = 0; j < i; j++)
       {
-        AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i),
-                                   ap.av.getSelectionGroup().getSequenceAt(j),
-                                   "pep");
+
+        AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
+                                   seqs[j], seqStrings[j], "pep");
 
         if (as.s1str.length() == 0 || as.s2str.length() == 0)
         {
@@ -65,29 +79,41 @@ public class PairwiseAlignPanel
 
         as.calcScoreMatrix();
         as.traceAlignment();
+
         as.printAlignment(System.out);
         scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
-
         seq = new Sequence(as.getS1().getName(),
                            as.getAStr1(),
-                           as.getS1().getStart(), as.getS1().getEnd()
+                           as.getS1().getStart(),
+                           as.getS1().getEnd()
             );
         sequences.addElement(seq);
 
         seq = new Sequence(as.getS2().getName(),
                            as.getAStr2(),
-                           as.getS2().getStart(), as.getS2().getEnd()
-            );
-
+                           as.getS2().getStart(),
+                           as.getS2().getEnd());
         sequences.addElement(seq);
       }
     }
 
     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) + " " +
+                                  seqs[i].getName());
+      }
+
+      System.out.println("\n");
+
       for (int i = 0; i < count; i++)
       {
         for (int j = 0; j < i; j++)
@@ -96,9 +122,10 @@ public class PairwiseAlignPanel
                                     scores[i][j] / totscore);
         }
       }
+
+      System.out.println("\n");
     }
   }
-
   public void actionPerformed(ActionEvent evt)
   {
     if(evt.getSource()==viewInEditorButton)
@@ -116,7 +143,7 @@ public class PairwiseAlignPanel
     }
 
     new AlignFrame(new Alignment(seq),
-                                   ap.alignFrame.applet,
+                                   ap.av.applet,
                                    "Pairwise Aligned Sequences",
                                    false);