X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=248a54c4ba013bb37b28942ab6bd2b654341e975;hb=a4bc1a8625949ba5b82eeba56058d44c349a5bc9;hp=76c75cbfc78fc96f4e6ea84e4b21882a7b5a45d0;hpb=ce63216585308bf40dd3f8370c3af13e098a7a3b;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 76c75cb..248a54c 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -37,8 +37,9 @@ import java.util.*;
  */
 public class PairwiseAlignPanel extends GPairwiseAlignPanel
 {
-    Vector sequences = new Vector();
+
     AlignViewport av;
+    Vector sequences;
 
     /**
      * Creates a new PairwiseAlignPanel object.
@@ -50,34 +51,44 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         super();
         this.av = av;
 
-        Vector selsubset = new Vector();
+        sequences = new Vector();
+
+        SequenceI [] seqs;
+        String []  seqStrings = av.getViewAsString(true);
 
-        for (int i = 0, j = av.getSelectionGroup().getSize(); i < j; i++)
+        if(av.getSelectionGroup()==null)
         {
-            if (av.getAlignment().getSequences().contains(av.getSelectionGroup()
-                                                                .getSequenceAt(i)))
-            {
-                selsubset.add(av.getSelectionGroup().getSequenceAt(i));
-            }
+          seqs = av.alignment.getSequencesArray();
         }
+        else
+        {
+          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+        }
+
 
-        float[][] scores = new float[selsubset.size()][selsubset.size()];
+        float[][] scores = new float[seqs.length][seqs.length];
         double totscore = 0;
-        int count = selsubset.size();
+        int count = seqs.length;
 
-        int acount = 0;
         Sequence seq;
 
         for (int i = 1; i < count; i++)
         {
             for (int j = 0; j < i; j++)
             {
-                acount++;
 
-                AlignSeq as = new AlignSeq((SequenceI) selsubset.elementAt(i),
-                        (SequenceI) selsubset.elementAt(j), "pep");
+                AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
+                        seqs[j], seqStrings[j], "pep");
+
+                if(as.s1str.length()==0 || as.s2str.length()==0)
+                {
+                  continue;
+                }
+
                 as.calcScoreMatrix();
                 as.traceAlignment();
+
+
                 as.printAlignment(System.out);
                 scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
                 totscore = totscore + scores[i][j];
@@ -85,14 +96,15 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
                 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.add(seq);
 
                 seq = new Sequence(as.getS2().getName(),
                                    as.getAStr2(),
-                                   as.getS2().getStart(), as.getS2().getEnd()
-                    );
+                                   as.getS2().getStart(),
+                                   as.getS2().getEnd() );
                 sequences.add(seq);
             }
         }
@@ -106,7 +118,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
             {
                 jalview.util.Format.print(System.out, "%s \n",
                     ("" + i) + " " +
-                    ((SequenceI) selsubset.elementAt(i)).getName());
+                    seqs[i].getName());
             }
 
             System.out.println("\n");
@@ -138,8 +150,11 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
             seq[i] = (Sequence) sequences.elementAt(i);
         }
 
-        AlignFrame af = new AlignFrame(new Alignment(seq));
+        AlignFrame af = new AlignFrame(new Alignment(seq),
+                                           AlignFrame.DEFAULT_WIDTH,
+                                           AlignFrame.DEFAULT_HEIGHT);
+
         Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
-            AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
+            AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
     }
 }