X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=e513e594a62614f5e352dfd05bca2d3a64ac4a35;hb=e7ed63f1ea56432246a6ed1553f0fe56d26f56ea;hp=10e2766580e9b93626d49e15f965b50b379d717d;hpb=c59fb56cb143b05c5643a71f5b39996ac1cd2fef;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 10e2766..e513e59 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -481,12 +481,12 @@ public class Alignment implements AlignmentI
 
   public void setGapCharacter(char gc)
   {
-    char old = getGapCharacter();
     gapCharacter = gc;
     for (int i=0; i < sequences.size(); i++)
      {
        Sequence seq = (Sequence)sequences.elementAt(i);
-       seq.sequence = seq.sequence.replace(old, gc);
+       seq.sequence = seq.sequence.replace('.', gc);
+       seq.sequence = seq.sequence.replace('-', gc);
      }
   }