X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FChangeCaseCommand.java;h=f0ea2f69b205805e090fe8059ece4673ddc36425;hb=2ec8c12977f14c382fcf7887937d2a58b144b092;hp=47b4d9dbab60434d9218c4ba5374fe27a142dd93;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/commands/ChangeCaseCommand.java b/src/jalview/commands/ChangeCaseCommand.java
index 47b4d9d..f0ea2f6 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.
  * 
@@ -20,26 +20,29 @@
  */
 package jalview.commands;
 
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
 
 public class ChangeCaseCommand implements CommandI
 {
   String description;
 
-  public static int TO_LOWER = 0;
+  public final static int TO_LOWER = 0;
 
-  public static int TO_UPPER = 1;
+  public final static int TO_UPPER = 1;
 
-  public static int TOGGLE_CASE = 2;
+  public final static int TOGGLE_CASE = 2;
 
-  int caseChange = -1;
+  private int caseChange;
 
-  SequenceI[] seqs;
+  private SequenceI[] seqs;
 
-  int[][] regions;
+  private List<int[]> regions;
 
   public ChangeCaseCommand(String description, SequenceI[] seqs,
-          int[][] regions, int caseChange)
+          List<int[]> regions, int caseChange)
   {
     this.description = description;
     this.seqs = seqs;
@@ -48,21 +51,25 @@ public class ChangeCaseCommand implements CommandI
     doCommand(null);
   }
 
+  @Override
   public String getDescription()
   {
     return description;
   }
 
+  @Override
   public int getSize()
   {
     return 1;
   }
 
+  @Override
   public void doCommand(AlignmentI[] views)
   {
     changeCase(true);
   }
 
+  @Override
   public void undoCommand(AlignmentI[] views)
   {
     changeCase(false);
@@ -73,21 +80,21 @@ 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)