From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 3 Dec 2004 16:23:43 +0000 (+0000)
Subject: default gap char is -. Getting ready for group select mode
X-Git-Tag: Release_2_0~875
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a021dd7b53a19b1805821385fa7beb1fc08df3f1;p=jalview.git

default gap char is -. Getting ready for group select mode
---

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 86f5914..abc7cf6 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 char      gapCharacter = '.';
+  protected char      gapCharacter = '-';
 
   /** Make an alignment from an array of Sequences.
   *
@@ -24,17 +24,6 @@ public class Alignment implements AlignmentI
     for (int i=0; i < seqs.length; i++)
       sequences.addElement(seqs[i]);
 
-    SequenceGroup all = new SequenceGroup();
-    all.setName("Group 1");
-    groups.addElement(all);
-
-    int i = 0;
-
-    while (i < seqs.length) {
-      addToGroup(all,seqs[i]);
-      i++;
-    }
-
     getWidth();
   }