X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FChangeCaseCommand.java;h=7f7142f195125fdd4d8acaa84877531e368c367b;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=7a74e08e4fcdb6fddb9f75ecf168353e2f588e77;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/commands/ChangeCaseCommand.java b/src/jalview/commands/ChangeCaseCommand.java
index 7a74e08..7f7142f1 100644
--- a/src/jalview/commands/ChangeCaseCommand.java
+++ b/src/jalview/commands/ChangeCaseCommand.java
@@ -1,24 +1,29 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
public class ChangeCaseCommand implements CommandI
{
@@ -34,10 +39,10 @@ public class ChangeCaseCommand implements CommandI
SequenceI[] seqs;
- int[][] regions;
+ List regions;
public ChangeCaseCommand(String description, SequenceI[] seqs,
- int[][] regions, int caseChange)
+ List regions, int caseChange)
{
this.description = description;
this.seqs = seqs;
@@ -71,21 +76,21 @@ 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)