X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=7b394a34ac88648251c938856eaecdab2fc18109;hb=b08ae4419c138647b696f440e09a75a39e63383e;hp=f2d0b697cb8e050835c5ff8d862d53b94377bf25;hpb=d738892eea8d903b5b52bdfaf75415f3b2812c96;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f2d0b69..7b394a3 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -217,11 +217,18 @@ public class AlignFrame
 
           type = st.nextToken();
 
+          if (fr.getColour(type) == null)
+          {
+            // Probably the old style groups file
+            UserColourScheme ucs = new UserColourScheme(type);
+            fr.setColour(type, ucs.findColour("A"));
+          }
+
+
           sf = new SequenceFeature(type, desc, "", start, end);
 
           seq.addSequenceFeature(sf);
 
-          System.out.println(sf.getType()+" "+sf.getBegin());
 
          // sg = new SequenceGroup(text, ucs, true, true, false, start, end);
          // sg.addSequence(seq, false);