X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;fp=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=ca32ee759b06087939e9eac5ef8ea61a8957b6b9;hb=0356abc2cb7040672bc8fde68cafb77a2d623b5d;hp=1366ada6cc7acd4188e867b289fb0e6aa827d015;hpb=b53d11f22f9c5db694835ba27490e7c19671872d;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 1366ada..ca32ee7 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -662,7 +662,7 @@ public abstract class AlignmentViewport
          * retain any colour thresholds per group while
          * changing choice of colour scheme (JAL-2386)
          */
-        sg.setColourScheme(cs);
+        sg.setColourScheme(cs.getInstance(sg, hiddenRepSequences));
         if (cs != null)
         {
           sg.getGroupColourScheme().alignmentChanged(sg,