X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=248a54c4ba013bb37b28942ab6bd2b654341e975;hb=0fc704a18faa7d11b6d02876bb6c1e8bc19f343c;hp=31efd8497f96b8da4ccfafbfeef31689b7930367;hpb=9c5d69ef1e102b1eac18ec13c362522f40c9000d;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 31efd84..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.
@@ -50,40 +51,61 @@ 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];
 
                 textarea.append(as.getOutput());
-                sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));
-                sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));
+                seq = new Sequence(as.getS1().getName(),
+                                   as.getAStr1(),
+                                   as.getS1().getStart(),
+                                   as.getS1().getEnd()
+                );
+                sequences.add(seq);
+
+                seq = new Sequence(as.getS2().getName(),
+                                   as.getAStr2(),
+                                   as.getS2().getStart(),
+                                   as.getS2().getEnd() );
+                sequences.add(seq);
             }
         }
 
@@ -96,7 +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");
@@ -128,8 +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);
     }
 }