X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FChangeCaseCommand.java;h=147676863a9e4bb70c8d993e31a2e6da1829ebdf;hb=483ecb5e4541537778844529cc93204f9124b68d;hp=47b4d9dbab60434d9218c4ba5374fe27a142dd93;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/commands/ChangeCaseCommand.java b/src/jalview/commands/ChangeCaseCommand.java
index 47b4d9d..1476768 100644
--- a/src/jalview/commands/ChangeCaseCommand.java
+++ b/src/jalview/commands/ChangeCaseCommand.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.
  * 
@@ -20,7 +20,12 @@
  */
 package jalview.commands;
 
-import jalview.datamodel.*;
+import java.util.Locale;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
 
 public class ChangeCaseCommand implements CommandI
 {
@@ -36,10 +41,10 @@ public class ChangeCaseCommand implements CommandI
 
   SequenceI[] seqs;
 
-  int[][] regions;
+  List<int[]> regions;
 
   public ChangeCaseCommand(String description, SequenceI[] seqs,
-          int[][] regions, int caseChange)
+          List<int[]> regions, int caseChange)
   {
     this.description = description;
     this.seqs = seqs;
@@ -73,21 +78,21 @@ public class ChangeCaseCommand implements CommandI
     String sequence;
     int start, end;
     char nextChar;
-    for (int r = 0; r < regions.length; r++)
+    for (int[] r : regions)
     {
-      start = regions[r][0];
+      start = r[0];
       for (int s = 0; s < seqs.length; s++)
       {
         sequence = seqs[s].getSequenceAsString();
         StringBuffer newSeq = new StringBuffer();
 
-        if (regions[r][1] > sequence.length())
+        if (r[1] > sequence.length())
         {
           end = sequence.length();
         }
         else
         {
-          end = regions[r][1];
+          end = r[1];
         }
 
         if (start > 0)
@@ -98,13 +103,15 @@ public class ChangeCaseCommand implements CommandI
         if ((caseChange == TO_UPPER && doCommand)
                 || (caseChange == TO_LOWER && !doCommand))
         {
-          newSeq.append(sequence.substring(start, end).toUpperCase());
+          newSeq.append(
+                  sequence.substring(start, end).toUpperCase(Locale.ROOT));
         }
 
         else if ((caseChange == TO_LOWER && doCommand)
                 || (caseChange == TO_UPPER && !doCommand))
         {
-          newSeq.append(sequence.substring(start, end).toLowerCase());
+          newSeq.append(
+                  sequence.substring(start, end).toLowerCase(Locale.ROOT));
         }
 
         else