X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=ba3c9ac04001fc31a55d8b7947b1228436f56f6e;hb=c1e82b5f51e05f64318bfc8eae4e85b58d1922b5;hp=f52a1d8a6bd48175fd0870998c190d3965400943;hpb=7c05496d1da22f21ce5ae1a199afb9b16c8777ea;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index f52a1d8..ba3c9ac 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -54,7 +54,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         sequences = new Vector();
 
         SequenceI [] seqs;
-        String []  seqStrings = av.getSelectionAsString();
+        String []  seqStrings = av.getViewAsString(true);
 
         if(av.getSelectionGroup()==null)
         {
@@ -70,20 +70,25 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         double totscore = 0;
         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(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];
@@ -91,7 +96,8 @@ 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);