Set gap chararcter replaces all existing gap chars

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 9b6d729..86f5914 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -12,7 +12,7 @@ public class Alignment implements AlignmentI
   protected Vector      sequences;\r
   protected Vector      groups = new Vector();\r
   public    Hashtable[] cons;\r
-  protected String      gapCharacter = ".";\r
+  protected char      gapCharacter = '.';\r
 \r
   /** Make an alignment from an array of Sequences.\r
   *\r
@@ -443,11 +443,18 @@ public class Alignment implements AlignmentI
     return max;\r
   }\r
 \r
-  public void setGapCharacter(String gc) {\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
+     }\r
   }\r
 \r
-  public String getGapCharacter() {\r
+  public char getGapCharacter() {\r
     return gapCharacter;\r
   }\r
 \r