/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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
{
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;
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)
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