1 /***************************************************************************
2  *   Copyright (C) 2009 by BUI Quang Minh   *
3  *   minh.bui@univie.ac.at   *
4  *                                                                         *
5  *   This program is free software; you can redistribute it and/or modify  *
6  *   it under the terms of the GNU General Public License as published by  *
7  *   the Free Software Foundation; either version 2 of the License, or     *
8  *   (at your option) any later version.                                   *
9  *                                                                         *
10  *   This program is distributed in the hope that it will be useful,       *
11  *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
12  *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
13  *   GNU General Public License for more details.                          *
14  *                                                                         *
15  *   You should have received a copy of the GNU General Public License     *
16  *   along with this program; if not, write to the                         *
17  *   Free Software Foundation, Inc.,                                       *
18  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
19  ***************************************************************************/
20 #ifndef TINATREE_H
21 #define TINATREE_H
22 
23 #include "phylotree.h"
24 
25 /**
26 	@author BUI Quang Minh <minh.bui@univie.ac.at>
27 */
28 class TinaTree : public PhyloTree
29 {
30 public:
31     TinaTree();
32     /**
33      * Constructor with given alignment
34      * @param alignment
35      */
36     TinaTree(Alignment *alignment);
37 
38     ~TinaTree();
39     /**
40             SLOW VERSION: compute the parsimony score of the tree, given the alignment
41             @return the parsimony score
42      */
43     int computeParsimonyScore();
44 
45     /**
46             SLOW VERSION: compute the parsimony score of the tree, given the alignment
47             @return the parsimony score
48             @param node the current node
49             @param dad dad of the node, used to direct the search
50             @param ptn pattern ID
51             @param states set of admissible states at the current node (in binary code)
52      */
53     int computeParsimonyScore(int ptn, int &states, PhyloNode *node = NULL, PhyloNode *dad = NULL);
54 
55 	virtual void initializeAllPartialLh();
56 
57 	virtual void initializeAllPartialLh(int &index, int &indexlh, PhyloNode *node = NULL, PhyloNode *dad = NULL);
58 
59 };
60 
61 #endif
62