/*
- * 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 2.8.2b1)
+ * Copyright (C) 2014 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;
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;
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))
{
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)
{
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);
}
else
{
deletedHiddenColumns = colSel.compensateForEdit(command.position,
- command.number);
+ command.number);
if (selectionGroup != null)
{
selectionGroup.adjustForRemoveRight(command.position);
}
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);
}
}
colSel.compensateForEdit(0, -command.number);
if (selectionGroup != null)
{
- selectionGroup.adjustForRemoveLeft( -command.number);
+ selectionGroup.adjustForRemoveLeft(-command.number);
}
}
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]);
}
}