/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 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.
- *
+ *
* 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
if (viewonly)
{
- int[] viscontigs = alview.getVisibleContigs();
- int spos = 0;
- int i = 0;
- if (viscontigs != null)
- {
- // Construct the delMap - mapping from the positions within the input to
- // Jnet to the contigs in the original sequence
-
- delMap = new int[seq.getEnd() - seq.getStart() + 1];
- int gapMap[] = seq.gapMap();
- for (int contig = 0; contig < viscontigs.length; contig += 2)
- {
-
- while (spos < gapMap.length && gapMap[spos] < viscontigs[contig])
- {
- spos++;
- }
- while (spos < gapMap.length
- && gapMap[spos] <= viscontigs[contig + 1])
- {
- delMap[i++] = spos++;
- }
- }
- int tmap[] = new int[i];
- System.arraycopy(delMap, 0, tmap, 0, i);
- delMap = tmap;
- }
+ delMap = alview.getVisibleContigMapFor(seq.gapMap());
}
if (msa && msf.length > 1)
{