X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;fp=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=8af0af0b249b8211084ffda4ceb2aa1931123e30;hb=8e1be43e250107a4d86898bd554cf03098fa5957;hp=012edb6ea8a09836b499ff019e80a15b36ce34b7;hpb=8b55eedb9d76a8c65b80f756c4412bf029906bf7;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 012edb6..8af0af0 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -109,7 +109,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (seqGroup != null)
     {
-      oldColourScheme = seqGroup.cs;
+      oldColourScheme = seqGroup.getColourScheme();
     }
     else
     {
@@ -521,7 +521,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (seqGroup != null)
     {
-      seqGroup.cs = ucs;
+      seqGroup.setColourScheme(ucs);
       ap.paintAlignment(true);
     }
     else if (ap != null)
@@ -585,10 +585,10 @@ public class UserDefinedColours extends GUserDefinedColours implements
       ucs.setLowerCaseColours(newColours);
     }
 
-    if (ap != null)
-    {
-      ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
-    }
+    // if (ap != null)
+    // {
+    // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+    // }
 
     return ucs;
   }
@@ -820,7 +820,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     {
       if (seqGroup != null)
       {
-        seqGroup.cs = oldColourScheme;
+        seqGroup.setColourScheme(oldColourScheme);
       }
       else
       {