Check for all gapped seqs

[jalview.git] / src / jalview / appletgui / PairwiseAlignPanel.java

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index d0b0c98..e58dd76 100755 (executable)
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -49,17 +49,20 @@ public class PairwiseAlignPanel
     double totscore = 0;\r
     int count = ap.av.getSelectionGroup().getSize(false);\r
 \r
-    int acount = 0;\r
     Sequence seq;\r
     for (int i = 1; i < count; i++)\r
     {\r
       for (int j = 0; j < i; j++)\r
       {\r
-        acount++;\r
         AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i),\r
                                    ap.av.getSelectionGroup().getSequenceAt(j),\r
                                    "pep");\r
 \r
+        if (as.s1str.length() == 0 || as.s2str.length() == 0)\r
+        {\r
+          continue;\r
+        }\r
+\r
         as.calcScoreMatrix();\r
         as.traceAlignment();\r
         as.printAlignment(System.out);\r