+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
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
+ * 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.*;
-public class RemoveGapColCommand
- extends EditCommand
+public class RemoveGapColCommand extends EditCommand
{
int columnsDeleted;
- public RemoveGapColCommand(String description,
- SequenceI[] seqs,
- int start, int end, AlignmentI al)
+
+ public RemoveGapColCommand(String description, SequenceI[] seqs,
+ int start, int end, AlignmentI al)
{
this.description = description;
if (!delete && startCol > -1)
{
- this.appendEdit(DELETE_GAP, seqs,
- startCol - columnsDeleted,
- endCol - startCol,
- al,
- false,null);
+ this.appendEdit(DELETE_GAP, seqs, startCol - columnsDeleted, endCol
+ - startCol, al, false, null);
columnsDeleted += (endCol - startCol);
startCol = -1;
if (delete && startCol > -1)
{
- //This is for empty columns at the
- //end of the alignment
+ // This is for empty columns at the
+ // end of the alignment
- this.appendEdit(DELETE_GAP, seqs,
- startCol - columnsDeleted,
- end - startCol + 1,
- al,
- false,null);
+ this.appendEdit(DELETE_GAP, seqs, startCol - columnsDeleted, end
+ - startCol + 1, al, false, null);
columnsDeleted += (end - startCol + 1);
}
- performEdit(0,null);
+ performEdit(0, null);
}
public int getSize()
{
- //We're interested in the number of columns deleted,
- //Not the number of sequence edits.
+ // We're interested in the number of columns deleted,
+ // Not the number of sequence edits.
return columnsDeleted;
}