Uses RemoveGapsCommand

[jalview.git] / src / jalview / gui / AnnotationColourChooser.java

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 0209d76..f499217 100755 (executable)
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -49,7 +49,8 @@ public class AnnotationColourChooser
       for (int g = 0; g < allGroups.size(); g++)\r
       {\r
         sg = (SequenceGroup) allGroups.get(g);\r
-        oldgroupColours.put(sg, sg.cs);\r
+        if(sg.cs!=null)\r
+          oldgroupColours.put(sg, sg.cs);\r
       }\r
     }\r
     this.av = av;\r