/*
- * 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;
-/*
- * 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 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.
- *
- * 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
- */
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
public class RemoveGapsCommand extends EditCommand
{
int j, jSize;
- edits = new Edit[0];
+ clearEdits();
boolean delete = true;
char[] sequence;
if (!delete && startCol > -1)
{
- this.appendEdit(DELETE_GAP, new SequenceI[]
- { seqs[s] }, start + startCol - deletedCols, endCol - startCol,
- al, false, null);
+ this.appendEdit(
+ Action.DELETE_GAP, new SequenceI[]
+ { seqs[s] }, start + startCol - deletedCols,
+ endCol - startCol, al, false, null);
deletedCols += (endCol - startCol);
startCol = -1;
}
if (delete && startCol > -1)
{
- this.appendEdit(DELETE_GAP, new SequenceI[]
- { seqs[s] }, start + startCol - deletedCols, jSize - startCol, al,
- false, null);
+ this.appendEdit(
+ Action.DELETE_GAP, new SequenceI[]
+ { seqs[s] }, start + startCol - deletedCols,
+ jSize - startCol, al, false, null);
}
}