From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 28 Apr 2005 15:27:57 +0000 (+0000)
Subject: set gap char modified
X-Git-Tag: Release_2_0~367
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e7ed63f1ea56432246a6ed1553f0fe56d26f56ea;p=jalview.git

set gap char modified
---

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);
      }
   }