/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
* Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*/
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
public class RemoveGapsCommand extends EditCommand
{
int j, jSize;
- edits = new Edit[0];
+ clearEdits();
boolean delete = true;
char[] sequence;
{
delete = true;
- if (!jalview.util.Comparison.isGap(sequence[j]))
+ if (!Comparison.isGap(sequence[j]))
{
if (delete)
{
if (!delete && startCol > -1)
{
- this.appendEdit(DELETE_GAP, new SequenceI[]
+ this.appendEdit(Action.DELETE_GAP, new SequenceI[]
{ seqs[s] }, start + startCol - deletedCols, endCol - startCol,
al, false, null);
}
if (delete && startCol > -1)
{
- this.appendEdit(DELETE_GAP, new SequenceI[]
+ this.appendEdit(Action.DELETE_GAP, new SequenceI[]
{ seqs[s] }, start + startCol - deletedCols, jSize - startCol, al,
false, null);
}