IgnoreGapsConsensus

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 858770a..0cfa537 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -387,11 +387,11 @@ public class APopupMenu
           getGroup().getName());\r
       if (sg.cs instanceof ResidueColourScheme)\r
       {\r
-        ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
+        ( (ResidueColourScheme) sg.cs).setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
       }\r
       else if (sg.cs instanceof ScoreColourScheme)\r
       {\r
-        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
+        ( (ScoreColourScheme) sg.cs).setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
       }\r
 \r
       SliderPanel.showPIDSlider();\r
@@ -400,7 +400,7 @@ public class APopupMenu
     else // remove PIDColouring\r
     {\r
       ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
-      rcs.setThreshold(0);\r
+      rcs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
       sg.cs = rcs;\r
     }\r
 \r