X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FChangeCaseCommand.java;h=d34552dfa850920fefe29eb48a12b13d2e9c3d48;hb=7157dfd20efd2e1db47db1ac12e879eb51c67b92;hp=49faa50ec476d2202514cdbcbe0ad97c766edb2a;hpb=0c40653e5033e68c8d87955ea9f96879c8114b62;p=jalview.git

diff --git a/src/jalview/commands/ChangeCaseCommand.java b/src/jalview/commands/ChangeCaseCommand.java
index 49faa50..d34552d 100644
--- a/src/jalview/commands/ChangeCaseCommand.java
+++ b/src/jalview/commands/ChangeCaseCommand.java
@@ -1,6 +1,6 @@
-  /*
+/*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -20,18 +20,19 @@ package jalview.commands;
 
 import jalview.datamodel.*;
 
-public class ChangeCaseCommand implements CommandI
+public class ChangeCaseCommand
+    implements CommandI
 {
   String description;
   public static int TO_LOWER = 0;
   public static int TO_UPPER = 1;
   public static int TOGGLE_CASE = 2;
   int caseChange = -1;
-  SequenceI [] seqs;
-  int [][] regions;
+  SequenceI[] seqs;
+  int[][] regions;
   public ChangeCaseCommand(String description,
                            SequenceI[] seqs,
-                           int [][] regions,
+                           int[][] regions,
                            int caseChange)
   {
     this.description = description;
@@ -71,13 +72,17 @@ public class ChangeCaseCommand implements CommandI
       start = regions[r][0];
       for (int s = 0; s < seqs.length; s++)
       {
-        sequence = seqs[s].getSequence();
+        sequence = seqs[s].getSequenceAsString();
         StringBuffer newSeq = new StringBuffer();
 
         if (regions[r][1] > sequence.length())
+        {
           end = sequence.length();
+        }
         else
+        {
           end = regions[r][1];
+        }
 
         if (start > 0)
         {
@@ -86,11 +91,15 @@ public class ChangeCaseCommand implements CommandI
 
         if ( (caseChange == TO_UPPER && doCommand)
             || (caseChange == TO_LOWER && !doCommand))
+        {
           newSeq.append(sequence.substring(start, end).toUpperCase());
+        }
 
         else if ( (caseChange == TO_LOWER && doCommand)
                  || (caseChange == TO_UPPER && !doCommand))
+        {
           newSeq.append(sequence.substring(start, end).toLowerCase());
+        }
 
         else //TOGGLE CASE
         {
@@ -112,7 +121,9 @@ public class ChangeCaseCommand implements CommandI
         }
 
         if (end < sequence.length())
+        {
           newSeq.append(sequence.substring(end));
+        }
 
         seqs[s].setSequence(newSeq.toString());
       }