- /*\r
+/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
\r
import jalview.datamodel.*;\r
\r
-public class ChangeCaseCommand implements CommandI\r
+public class ChangeCaseCommand\r
+ implements CommandI\r
{\r
String description;\r
public static int TO_LOWER = 0;\r
public static int TO_UPPER = 1;\r
public static int TOGGLE_CASE = 2;\r
int caseChange = -1;\r
- SequenceI [] seqs;\r
- int [][] regions;\r
+ SequenceI[] seqs;\r
+ int[][] regions;\r
public ChangeCaseCommand(String description,\r
SequenceI[] seqs,\r
- int [][] regions,\r
+ int[][] regions,\r
int caseChange)\r
{\r
this.description = description;\r
start = regions[r][0];\r
for (int s = 0; s < seqs.length; s++)\r
{\r
- sequence = seqs[s].getSequence();\r
+ sequence = seqs[s].getSequenceAsString();\r
StringBuffer newSeq = new StringBuffer();\r
\r
if (regions[r][1] > sequence.length())\r
+ {\r
end = sequence.length();\r
+ }\r
else\r
+ {\r
end = regions[r][1];\r
+ }\r
\r
if (start > 0)\r
{\r
\r
if ( (caseChange == TO_UPPER && doCommand)\r
|| (caseChange == TO_LOWER && !doCommand))\r
+ {\r
newSeq.append(sequence.substring(start, end).toUpperCase());\r
+ }\r
\r
else if ( (caseChange == TO_LOWER && doCommand)\r
|| (caseChange == TO_UPPER && !doCommand))\r
+ {\r
newSeq.append(sequence.substring(start, end).toLowerCase());\r
+ }\r
\r
else //TOGGLE CASE\r
{\r
}\r
\r
if (end < sequence.length())\r
+ {\r
newSeq.append(sequence.substring(end));\r
+ }\r
\r
seqs[s].setSequence(newSeq.toString());\r
}\r