set gap char modified

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