X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fcommands%2FTrimRegionCommand.java;h=b4d92a03880ee6c5c028755cd9c57bb1a3dfa560;hb=a23cc416cd520ac6dec6052591575b264f5d25bc;hp=30f813fea584749d6ade0760cf5874db9fd3c5f0;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java
index 30f813f..b4d92a0 100644
--- a/src/jalview/commands/TrimRegionCommand.java
+++ b/src/jalview/commands/TrimRegionCommand.java
@@ -1,27 +1,32 @@
/*
- * 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 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
{
@@ -37,7 +42,7 @@ public class TrimRegionCommand extends EditCommand
SequenceGroup selectionGroup;
- Vector deletedHiddenColumns;
+ List deletedHiddenColumns;
int columnsDeleted;
@@ -57,8 +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))
{
@@ -70,17 +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);
@@ -158,7 +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]);
}
}