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/*
* Copyright (C) 2009-2012 Simon A. Berger
*
* This file is part of papara.
*
* papara 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.
*
* papara 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 papara. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __raxml_interface_h
#define __raxml_interface_h
#include "ivymike/tree_parser.h"
#include <string>
#include <vector>
#include <map>
#include <stdint.h>
#include <boost/array.hpp>
#include <boost/numeric/ublas/fwd.hpp>
#include <iosfwd>
void optimize_branch_lengths( ivy_mike::tree_parser_ms::lnode *tree, const std::map<std::string, const std::vector<uint8_t> * const> &name_to_seq );
ivy_mike::tree_parser_ms::lnode *optimize_branch_lengths2( ivy_mike::tree_parser_ms::lnode *tree, const std::map<std::string, const std::vector<uint8_t> * const> &name_to_seq, ivy_mike::tree_parser_ms::ln_pool &pool );
std::vector<boost::numeric::ublas::matrix<double> > read_binary_anc_probs( std::istream &pis );
//ivy_mike::tree_parser_ms::lnode *generate_marginal_ancestral_state_pvecs( ivy_mike::tree_parser_ms::ln_pool &pool, const std::string &tree_name, const std::string &ali_name, std::vector<boost::array<std::vector<double>, 4> > *pvecs );
ivy_mike::tree_parser_ms::lnode *generate_marginal_ancestral_state_pvecs( ivy_mike::tree_parser_ms::ln_pool &pool, const std::string &tree_name, const std::string &ali_name, std::vector<boost::numeric::ublas::matrix<double> > *pvecs );
#endif