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/***************************************************************************
* Copyright (C) 2009 by BUI Quang Minh *
* minh.bui@univie.ac.at *
* *
* 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., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#ifndef TINATREE_H
#define TINATREE_H
#include "phylotree.h"
/**
@author BUI Quang Minh <minh.bui@univie.ac.at>
*/
class TinaTree : public PhyloTree
{
public:
TinaTree();
/**
* Constructor with given alignment
* @param alignment
*/
TinaTree(Alignment *alignment);
~TinaTree();
/**
SLOW VERSION: compute the parsimony score of the tree, given the alignment
@return the parsimony score
*/
int computeParsimonyScore();
/**
SLOW VERSION: compute the parsimony score of the tree, given the alignment
@return the parsimony score
@param node the current node
@param dad dad of the node, used to direct the search
@param ptn pattern ID
@param states set of admissible states at the current node (in binary code)
*/
int computeParsimonyScore(int ptn, int &states, PhyloNode *node = NULL, PhyloNode *dad = NULL);
virtual void initializeAllPartialLh();
virtual void initializeAllPartialLh(int &index, int &indexlh, PhyloNode *node = NULL, PhyloNode *dad = NULL);
};
#endif
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