JAL-1894 update year/version in copyright

[jalview.git] / src / jalview / commands / ChangeCaseCommand.java

diff --git a/src/jalview/commands/ChangeCaseCommand.java b/src/jalview/commands/ChangeCaseCommand.java
index 976be92..6a1287a 100644 (file)
--- a/src/jalview/commands/ChangeCaseCommand.java
+++ b/src/jalview/commands/ChangeCaseCommand.java
@@ -1,39 +1,48 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * 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
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * 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.
- *
- * 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 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.commands;
 
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
 
-public class ChangeCaseCommand
-    implements CommandI
+import java.util.List;
+
+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;
-  public ChangeCaseCommand(String description,
-                           SequenceI[] seqs,
-                           int[][] regions,
-                           int caseChange)
+
+  List<int[]> regions;
+
+  public ChangeCaseCommand(String description, SequenceI[] seqs,
+          List<int[]> regions, int caseChange)
   {
     this.description = description;
     this.seqs = seqs;
@@ -67,21 +76,21 @@ public class ChangeCaseCommand
     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)
@@ -89,19 +98,20 @@ public class ChangeCaseCommand
           newSeq.append(sequence.substring(0, start));
         }
 
-        if ( (caseChange == TO_UPPER && doCommand)
-            || (caseChange == TO_LOWER && !doCommand))
+        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))
+        else if ((caseChange == TO_LOWER && doCommand)
+                || (caseChange == TO_UPPER && !doCommand))
         {
           newSeq.append(sequence.substring(start, end).toLowerCase());
         }
 
-        else //TOGGLE CASE
+        else
+        // TOGGLE CASE
         {
           for (int c = start; c < end; c++)
           {