JAL-1687 ignore case when determining if sequence matches consensus

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index e688177..1b2d19a 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.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.
  * 
@@ -56,6 +56,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
+import java.util.List;
 import java.util.Vector;
 
 public class APopupMenu extends java.awt.PopupMenu implements
@@ -113,10 +114,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   Menu editMenu = new Menu(MessageManager.getString("action.edit"));
 
-  MenuItem copy = new MenuItem(
-          MessageManager.getString("label.jalview_copy"));
+  MenuItem copy = new MenuItem(MessageManager.getString("action.copy"));
 
-  MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut"));
+  MenuItem cut = new MenuItem(MessageManager.getString("action.cut"));
 
   MenuItem toUpper = new MenuItem(
           MessageManager.getString("label.to_upper_case"));
@@ -619,10 +619,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
     else if (source == toUpper || source == toLower || source == toggleCase)
     {
       SequenceGroup sg = ap.av.getSelectionGroup();
-      Vector regions = new Vector();
       if (sg != null)
       {
-        int[][] startEnd = ap.av.getVisibleRegionBoundaries(
+        List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
                 sg.getStartRes(), sg.getEndRes() + 1);
 
         String description;
@@ -1023,7 +1022,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       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();
 
@@ -1031,7 +1030,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     else
     // remove PIDColouring
     {
-      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+      sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
     }
 
     refresh();