X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;fp=src%2Fjalview%2Fgui%2FPopupMenu.java;h=26fc93c4a22b1fc8a1daa7d445e84807d12ecf91;hb=9fff97021c2c637e426f6971d54dcf3fd4191985;hp=0b531113e34d8bcad6124356487e173ba27325c8;hpb=309f2ebc93eb5aab5478279a3c40914f216f01a4;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 0b53111..26fc93c 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -595,11 +595,11 @@ public class PopupMenu extends JPopupMenu
 
             if (sg.cs instanceof ResidueColourScheme)
             {
-                ((ResidueColourScheme) sg.cs).setThreshold(threshold);
+                ((ResidueColourScheme) sg.cs).setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
             }
             else if (sg.cs instanceof ScoreColourScheme)
             {
-                ((ScoreColourScheme) sg.cs).setThreshold(threshold);
+                ((ScoreColourScheme) sg.cs).setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
             }
 
             SliderPanel.showPIDSlider();
@@ -607,7 +607,7 @@ public class PopupMenu extends JPopupMenu
         else // remove PIDColouring
         {
             ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
-            rcs.setThreshold(0);
+            rcs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
             sg.cs = rcs;
         }