X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=fae50d9e45073d08a22f98813773b311637f8fdb;hb=4f8907121d304b0f9b499578578c3381b815db9d;hp=0d6682fb08b25e60872d714acd2801dcdcee1d71;hpb=930a6609bc99bfb0827fc5d0d16666787aaba575;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0d6682f..fae50d9 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -918,6 +918,7 @@ public class AlignFrame
         else
         {
           sg.cs.setConservation(null);
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
         }
 
       }