-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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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;
+
+/*
+ * 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
+public class RemoveGapsCommand extends EditCommand
{
- public RemoveGapsCommand(String description,
- SequenceI[] seqs, AlignmentI al)
+ public RemoveGapsCommand(String description, SequenceI[] seqs,
+ AlignmentI al)
{
this.description = description;
int width = 0;
findGaps(seqs, 0, width, al);
}
- public RemoveGapsCommand(String description,
- SequenceI[] seqs,
- int start, int end, AlignmentI al)
+ public RemoveGapsCommand(String description, SequenceI[] seqs, int start,
+ int end, AlignmentI al)
{
this.description = description;
findGaps(seqs, start, end, al);
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);
}
}
- performEdit(0,null);
+ performEdit(0, null);
}
}