JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java
index 4925d82..32b9847 100644 (file)
--- a/src/jalview/commands/TrimRegionCommand.java
+++ b/src/jalview/commands/TrimRegionCommand.java
@@ -1,26 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * 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 <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 java.util.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.ShiftList;
 
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.util.List;
 
 public class TrimRegionCommand extends EditCommand
 {
@@ -36,7 +42,7 @@ public class TrimRegionCommand extends EditCommand
 
   SequenceGroup selectionGroup;
 
-  Vector deletedHiddenColumns;
+  List<int[]> deletedHiddenColumns;
 
   int columnsDeleted;
 
@@ -56,8 +62,7 @@ public class TrimRegionCommand extends EditCommand
 
       columnsDeleted = column;
 
-      edits = new Edit[]
-      { new Edit(CUT, seqs, 0, column, al) };
+      setEdit(new Edit(Action.CUT, seqs, 0, column, al));
     }
     else if (command.equalsIgnoreCase(TRIM_RIGHT))
     {
@@ -69,17 +74,16 @@ public class TrimRegionCommand extends EditCommand
 
       columnsDeleted = width - 1;
 
-      edits = new Edit[]
-      { new Edit(CUT, seqs, column + 1, width, al) };
+      setEdit(new Edit(Action.CUT, seqs, column + 1, width, al));
     }
 
     // We need to keep a record of the sequence start
     // in order to restore the state after a redo
-    int i, isize = edits[0].seqs.length;
+    int i, isize = getEdit(0).seqs.length;
     start = new int[isize];
     for (i = 0; i < isize; i++)
     {
-      start[i] = edits[0].seqs[i].getStart();
+      start[i] = getEdit(0).seqs[i].getStart();
     }
 
     performEdit(0, null);
@@ -157,7 +161,7 @@ public class TrimRegionCommand extends EditCommand
       int[] region;
       for (int i = 0; i < deletedHiddenColumns.size(); i++)
       {
-        region = (int[]) deletedHiddenColumns.elementAt(i);
+        region = deletedHiddenColumns.get(i);
         colSel.hideColumns(region[0], region[1]);
       }
     }