Modified output on stdout for similarity matrix.

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 972d4f5..76f4eb5 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -17,40 +17,47 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     {\r
       super();\r
       this.av = av;\r
-      float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()];\r
+      Vector selsubset = new Vector();\r
+      for (int i=0, j=av.getSelectionGroup().getSize(); i<j; i++)\r
+        if (av.getAlignment().getSequences().contains(av.getSelectionGroup().getSequenceAt(i)))\r
+          selsubset.add(av.getSelectionGroup().getSequenceAt(i));\r
+      float scores[][] = new float[selsubset.size()][selsubset.size()];\r
       double totscore = 0;\r
-      int count = av.getSelectionGroup().getSize();\r
+      int count = selsubset.size();\r
 \r
       int acount = 0;\r
-        for (int i = 1; i < count; i++)\r
+      for (int i = 1; i < count; i++)\r
+      {\r
+        for (int j = 0; j < i; j++)\r
         {\r
-          for (int j = 0; j < i; j++)\r
-          {\r
-            acount++;\r
-            AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),\r
-                                       av.getSelectionGroup().getSequenceAt(j),"pep");\r
-\r
-            as.calcScoreMatrix();\r
-            as.traceAlignment();\r
-            as.printAlignment();\r
-            scores[i][j] = (float)as.getMaxScore()/(float)as.getASeq1().length;\r
-            totscore = totscore + scores[i][j];\r
-\r
-            textarea.append(as.getOutput());\r
-            sequences.add( new Sequence( as.getS1().getName(), as.getAStr1()) );\r
-            sequences.add( new Sequence( as.getS2().getName(), as.getAStr2()) );\r
-\r
-\r
-          }\r
+          acount++;\r
+          AlignSeq as = new AlignSeq( (SequenceI) selsubset.elementAt(i),\r
+                                     (SequenceI) selsubset.elementAt(j), "pep");\r
+          as.calcScoreMatrix();\r
+          as.traceAlignment();\r
+          as.printAlignment();\r
+          scores[i][j] = (float) as.getMaxScore() /\r
+              (float) as.getASeq1().length;\r
+          totscore = totscore + scores[i][j];\r
+\r
+          textarea.append(as.getOutput());\r
+          sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));\r
+          sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));\r
         }\r
+      }\r
+      if (count > 2)\r
+      {\r
+        System.out.println("Pairwise alignment scaled similarity score matrix\n");\r
+        for (int i = 0; i < count;i++)\r
+          jalview.util.Format.print(System.out, "%s \n", (""+i)+" "+((SequenceI) selsubset.elementAt(i)).getName());\r
+        System.out.println("\n");\r
+        for (int i = 0; i < count;i++)\r
+          for (int j = 0; j < i; j++)\r
+            jalview.util.Format.print(System.out,"%7.3f",scores[i][j]/totscore);\r
+        System.out.println("\n");\r
 \r
-        if (count > 2)\r
-        {\r
-          for (int i = 0; i < count;i++)\r
-            for (int j = 0; j < i; j++)\r
-              jalview.util.Format.print(System.out,"%7.3f",scores[i][j]/totscore);\r
-        }\r
       }\r
+    }\r
 \r
 \r
   protected void viewInEditorButton_actionPerformed(ActionEvent e)\r