aa33715685
git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1335 331e1502-861f-0410-8da2-ba01fb791d7f
61 lines
3 KiB
C++
61 lines
3 KiB
C++
/***************************************************************************
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* Copyright (C) 2005 by Waldo Cancino *
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* wcancino@icmc.usp.br *
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* *
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* This program is free software; you can redistribute it and/or modify *
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* it under the terms of the GNU General Public License as published by *
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* the Free Software Foundation; either version 2 of the License, or *
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* (at your option) any later version. *
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* *
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* This program is distributed in the hope that it will be useful, *
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* but WITHOUT ANY WARRANTY; without even the implied warranty of *
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
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* GNU General Public License for more details. *
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* *
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* You should have received a copy of the GNU General Public License *
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* along with this program; if not, write to the *
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* Free Software Foundation, Inc., *
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* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
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***************************************************************************/
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#ifndef PARSIMONYCALCULATOR_H
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#define PARSIMONYCALCULATOR_H
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#include <phylotreeIND.h>
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/**
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@author Waldo Cancino
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*/
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class ParsimonyCalculator
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{
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private:
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phylotreeIND *tree_ptr; // point to a tree;
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unsigned char *set_memory_allocate;
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unsigned char *char_memory_allocate;
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unsigned char *set_internal_memory_allocate; // sequences for sets in an internal node
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unsigned char *set_taxon_memory_allocate; // sequences for sets in an taxon nodes
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unsigned char *char_internal_memory_allocate; // assignment chars for internal nodes
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unsigned char *char_taxon_memory_allocate; // assignment chars for taxon nodes
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bool invalid_set_taxons;
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long int parsimony;
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node_map<unsigned char*> set_internal; // internal set for fitch phase I
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node_map<unsigned char*> char_internal; // internal characters for fitch phase II
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Sequences *SeqData; // maintain the current pattern
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int set_intersection( unsigned char *a, unsigned char *b, unsigned char *result);
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void set_union( unsigned char *a, unsigned char *b, unsigned char *result);
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int set_parsimony( unsigned char *a, unsigned char *b, unsigned char *result);
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int node_parsimony( node a, node b, unsigned char *result);
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void fitch_post_order(node n, node *antecessor);
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void seq_assignment(node n, node ancestor);
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void fitch_pre_order(node n, node *antecessor);
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void init_set_char_taxon(node n);
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void init_sets_chars();
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public:
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void set_tree(phylotreeIND &t);
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long int fitch();
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void save_informative(char *fn);
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ParsimonyCalculator(phylotreeIND &t);
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~ParsimonyCalculator();
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};
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#endif
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