Merge branch 'develop' into features/JAL-845splitPaneMergeDevelop

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 638962c..2ac0856 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -2190,14 +2190,14 @@ public class PopupMenu extends JPopupMenu
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
               .getName());
 
-      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+      sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
 
       SliderPanel.showPIDSlider();
     }
     else
     // remove PIDColouring
     {
-      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+      sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
     }
 
     refresh();
@@ -2572,7 +2572,8 @@ public class PopupMenu extends JPopupMenu
 
     if (sg != null)
     {
-      int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
+      List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
+              sg.getStartRes(),
               sg.getEndRes() + 1);
 
       String description;