X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=db1f9c9e84c326e0dc94f13f5a6f84c86c3178eb;hb=06eca7433e037f1d8ae07172528bc751dc9a0320;hp=0bdcb55f4915cfd2f897950f624ea662c3df35f3;hpb=08620e4438a99912019631c0b1c9deb341b76ae0;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0bdcb55..db1f9c9 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -808,14 +808,14 @@ public class AlignFrame
 
       if (cs instanceof ResidueColourScheme)
       {
-        ( (ResidueColourScheme) cs).setThreshold(threshold);
+        ( (ResidueColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());
       }
 
       viewport.setGlobalColourScheme(cs);
     }
     else if (cs instanceof ResidueColourScheme)
     {
-      ( (ResidueColourScheme) cs).setThreshold(0);
+      ( (ResidueColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());
     }
 
     if (viewport.getConservationSelected())
@@ -885,7 +885,7 @@ public class AlignFrame
         {
           if (sg.cs instanceof ResidueColourScheme)
           {
-            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
+            ( (ResidueColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());
           }
 
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
@@ -914,6 +914,8 @@ public class AlignFrame
       }
     }
 
+    updateCSConsensus();
+
     if (alignPanel.getOverviewPanel() != null)
     {
       alignPanel.getOverviewPanel().updateOverviewImage();
@@ -922,6 +924,12 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  public void updateCSConsensus()
+  {
+    //Colour schemes must have their consensus updated
+
+  }
+
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
     if (viewport.getAbovePIDThreshold())