X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FTrimRegionCommand.java;h=b4d92a03880ee6c5c028755cd9c57bb1a3dfa560;hb=a97a5c93ecd4b0ecd0c55ae2c58c6174c05190f0;hp=4110bd1fcd5ecb1c1c5fe82ceb52cdad531679ec;hpb=fa93bb578999b13c0364a712ae368ca8841012a1;p=jalview.git

diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java
index 4110bd1..b4d92a0 100644
--- a/src/jalview/commands/TrimRegionCommand.java
+++ b/src/jalview/commands/TrimRegionCommand.java
@@ -1,32 +1,37 @@
 /*
- * 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 ($$Version-Rel$$)
+ * 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.
- *
- * 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 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
+public class TrimRegionCommand extends EditCommand
 {
   public static String TRIM_LEFT = "TrimLeft";
+
   public static String TRIM_RIGHT = "TrimRight";
 
   public ColumnSelection colSel = null;
@@ -37,17 +42,13 @@ public class TrimRegionCommand
 
   SequenceGroup selectionGroup;
 
-  Vector deletedHiddenColumns;
+  List<int[]> deletedHiddenColumns;
 
   int columnsDeleted;
 
-  public TrimRegionCommand(String description,
-                           String command,
-                           SequenceI[] seqs,
-                           int column,
-                           AlignmentI al,
-                           ColumnSelection colSel,
-                           SequenceGroup selectedRegion)
+  public TrimRegionCommand(String description, String command,
+          SequenceI[] seqs, int column, AlignmentI al,
+          ColumnSelection colSel, SequenceGroup selectedRegion)
   {
     this.description = description;
     this.selectionGroup = selectedRegion;
@@ -61,9 +62,7 @@ public class TrimRegionCommand
 
       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))
     {
@@ -75,21 +74,19 @@ public class TrimRegionCommand
 
       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;
+    // We need to keep a record of the sequence start
+    // in order to restore the state after a redo
+    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);
+    performEdit(0, null);
   }
 
   void cut(Edit command)
@@ -99,13 +96,13 @@ public class TrimRegionCommand
     {
       if (command.position == 0)
       {
-        //This is a TRIM_LEFT command
+        // This is a TRIM_LEFT command
         column = command.seqs[j].findPosition(command.number);
         command.seqs[j].setStart(column);
       }
       else
       {
-        //This is a TRIM_RIGHT command
+        // This is a TRIM_RIGHT command
         column = command.seqs[j].findPosition(command.position) - 1;
         command.seqs[j].setEnd(column);
       }
@@ -124,7 +121,7 @@ public class TrimRegionCommand
     else
     {
       deletedHiddenColumns = colSel.compensateForEdit(command.position,
-          command.number);
+              command.number);
       if (selectionGroup != null)
       {
         selectionGroup.adjustForRemoveRight(command.position);
@@ -144,8 +141,8 @@ public class TrimRegionCommand
       }
       else
       {
-        column = command.seqs[j]
-            .findPosition(command.number + command.position) - 1;
+        column = command.seqs[j].findPosition(command.number
+                + command.position) - 1;
         command.seqs[j].setEnd(column);
       }
     }
@@ -155,7 +152,7 @@ public class TrimRegionCommand
       colSel.compensateForEdit(0, -command.number);
       if (selectionGroup != null)
       {
-        selectionGroup.adjustForRemoveLeft( -command.number);
+        selectionGroup.adjustForRemoveLeft(-command.number);
       }
     }
 
@@ -164,7 +161,7 @@ public class TrimRegionCommand
       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]);
       }
     }