* 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 License
+ * 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 License for more details.
+ * PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General License
+ * You should have received a copy of the GNU General Public License
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
*/
AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
+ /**
+ * Set the hidden columns collection on the alignment
+ *
+ * @param cols
+ */
public void setHiddenColumns(HiddenColumns cols);
+ /**
+ * Set the first sequence as representative and hide its insertions. Typically
+ * used when loading JPred files.
+ */
+ public void setupJPredAlignment();
+
}