X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=0f565614511a17a8a022af614d73acbe31a488ec;hb=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=03807c503b7fd74a626206eaa4a164d711e998c2;hpb=f1f528a731ee18c62c4f1944ea3eda41960f16f9;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 03807c5..0f56561 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,