From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 1 Dec 2004 17:04:57 +0000 (+0000)
Subject: Set gap chararcter replaces all existing gap chars
X-Git-Tag: Release_2_0~892
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e711706016105309d208b06bbfe34ee07c9ebc02;p=jalview.git

Set gap chararcter replaces all existing gap chars
---

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