protein.hpp

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/***************************************************************************
*                                                                          *
*   Copyright (C) 2018 by David B. Blumenthal                              *
*                                                                          *
*   This file is part of GEDLIB.                                           *
*                                                                          *
*   GEDLIB is free software: you can redistribute it and/or modify it      *
*   under the terms of the GNU Lesser General Public License as published  *
*   by the Free Software Foundation, either version 3 of the License, or   *
*   (at your option) any later version.                                    *
*                                                                          *
*   GEDLIB 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 Lesser General Public License for more details.                    *
*                                                                          *
*   You should have received a copy of the GNU Lesser General Public       *
*   License along with GEDLIB. If not, see <http://www.gnu.org/licenses/>. *
*                                                                          *
***************************************************************************/

#ifndef SRC_EDIT_COSTS_PROTEIN_HPP_
#define SRC_EDIT_COSTS_PROTEIN_HPP_

#include "edit_costs.hpp"
#include "../util/lsape_solver.hpp"

namespace ged {

template<class UserNodeLabel, class UserEdgeLabel>
class Protein : public EditCosts<UserNodeLabel, UserEdgeLabel> {
public:

    virtual ~Protein();

    Protein(double node_ins_del_cost = 11, double edge_ins_del_cost = 1, double alpha = 0.75);

    virtual double node_ins_cost_fun(const UserNodeLabel & node_label) const final;

    virtual double node_del_cost_fun(const UserNodeLabel & node_label) const final;

    virtual double node_rel_cost_fun(const UserNodeLabel & node_label_1, const UserNodeLabel & node_label_2) const final;

    virtual double edge_ins_cost_fun(const UserEdgeLabel & edge_label) const final;

    virtual double edge_del_cost_fun(const UserEdgeLabel & edge_label) const final;

    virtual double edge_rel_cost_fun(const UserEdgeLabel & edge_label_1, const UserEdgeLabel & edge_label_2) const final;

private:

    double levenshtein_distance_(const std::string & string_1, const std::string & string_2) const;

    double node_ins_del_cost_;

    double edge_ins_del_cost_;

    double alpha_;
};

}

#include "protein.ipp"

#endif /* SRC_EDIT_COSTS_PROTEIN_HPP_ */