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 bccbf8c..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.
  * 
@@ -2548,15 +2548,7 @@ public class PopupMenu extends JPopupMenu
     }
 
     int gsize = sg.getSize();
-    SequenceI[] hseqs;
-
-    hseqs = new SequenceI[gsize];
-
-    int index = 0;
-    for (int i = 0; i < gsize; i++)
-    {
-      hseqs[index++] = sg.getSequenceAt(i);
-    }
+    SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]);
 
     ap.av.hideSequence(hseqs);
     // refresh(); TODO: ? needed ?
@@ -2580,7 +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;