IgnoreGapsConsensus

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 0b53111..26fc93c 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -595,11 +595,11 @@ public class PopupMenu extends JPopupMenu
 \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
@@ -607,7 +607,7 @@ public class PopupMenu extends JPopupMenu
         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