Test version to switch branches

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

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index a84c449..fc862fe 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -104,6 +104,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     double totscore = 0D;
     int count = seqs.length;
     boolean first = true;
+    //AlignSeq as = new AlignSeq(seqs[1], seqStrings[1], seqs[0], seqStrings[0], type, gapOpenCost, gapExtendCost);
 
     for (int i = 1; i < count; i++)
     {
@@ -113,6 +114,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
       {
         AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
                 seqStrings[j], type, gapOpenCost, gapExtendCost);
+//     as.seqInit(seqs[i], seqStrings[i], seqs[j], seqStrings[j], type);
 
         if (as.s1str.length() == 0 || as.s2str.length() == 0)
         {