X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;fp=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=46945b6369bb01155f3887690b764351d5328d5e;hb=6a3f4318037072a77588afb951a5a53835d5da99;hp=ff8f7df33959c561cc8eefe9cdd119a15e87edab;hpb=1379350f04bc63ca05bd428afb86717c4764755d;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index ff8f7df..46945b6 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1478,6 +1478,7 @@ public class AlignViewport implements SelectionSource, VamsasSource
     ColourSchemeI cs = globalColourScheme;
     if (cs != null)
     {
+      cs.alignmentChanged(alignment);
       if (cs instanceof ClustalxColourScheme)
       {
         ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),