X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fcommands%2FChangeCaseCommand.java;h=b68b47c30bfe63e398c8923060499523bc006a3e;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=7ba4027a01118594ddeea1391b497bad882de248;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/commands/ChangeCaseCommand.java b/src/jalview/commands/ChangeCaseCommand.java
index 7ba4027..b68b47c 100644
--- a/src/jalview/commands/ChangeCaseCommand.java
+++ b/src/jalview/commands/ChangeCaseCommand.java
@@ -1,23 +1,29 @@
/*
- * 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 2.9)
+ * Copyright (C) 2015 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 .
+ * You should have received a copy of the GNU General Public License
+ * 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
{
@@ -33,10 +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;
@@ -70,21 +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)