/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
/**
* Routines for manipulating the order of a multiple sequence alignment
- * TODO: this class retains some global states concerning sort-order which should be made attributes for the caller's alignment visualization.
+ * TODO: this class retains some global states concerning sort-order which should be made attributes for the caller's alignment visualization.
+ * TODO: refactor to allow a subset of selected sequences to be sorted within the context of a whole alignment.
+ * Sort method template is: SequenceI[] tobesorted, [ input data mapping to each tobesorted element to use ], Alignment context of tobesorted that are to be re-ordered, boolean sortinplace, [special data - ie seuqence to be sorted w.r.t.])
+ * sortinplace implies that the sorted vector resulting from applying the operation to tobesorted should be mapped back to the original positions in alignment.
+ * Otherwise, normal behaviour is to re order alignment so that tobesorted is sorted and grouped together starting from the first tobesorted position in the alignment.
+ * e.g. (a,tb2,b,tb1,c,tb3 becomes a,tb1,tb2,tb3,b,c)
*/
public class AlignmentSorter
{
private static String lastSortByScore;
/**
- * Sort by Percentage Identity
+ * Sort by Percentage Identity w.r.t. s
*
* @param align AlignmentI
* @param s SequenceI
+ * @param tosort sequences from align that are to be sorted.
*/
- public static void sortByPID(AlignmentI align, SequenceI s)
+ public static void sortByPID(AlignmentI align, SequenceI s, SequenceI[] tosort)
{
int nSeq = align.getHeight();