ged_data.hpp

Go to the documentation of this file.

/***************************************************************************
 *                                                                          *
 *   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_ENV_GED_DATA_HPP_
#define SRC_ENV_GED_DATA_HPP_

#include "ged_graph.hpp"
#include "result.hpp"
#include "matrix.hpp"
#include "common_types.hpp"
#include "node_map.hpp"
#include "../edit_costs/edit_costs.hpp"
#include "../edit_costs/chem_1.hpp"
#include "../edit_costs/chem_2.hpp"
#include "../edit_costs/cmu.hpp"
#include "../edit_costs/grec_1.hpp"
#include "../edit_costs/grec_2.hpp"
#include "../edit_costs/protein.hpp"
#include "../edit_costs/fingerprint.hpp"
#include "../edit_costs/letter.hpp"
#include "../edit_costs/constant.hpp"

namespace ged {

template<class, class, class> class GEDEnv;

template<class UserNodeLabel, class UserEdgeLabel>
class GEDData {

    template<class, class, class> friend class GEDEnv;

public:

    ~GEDData();

    std::size_t num_graphs() const;

    const GEDGraph & graph(GEDGraph::GraphID graph_id) const;

    bool shuffled_graph_copies_available() const;

    std::size_t num_graphs_without_shuffled_copies() const;

    GEDGraph::GraphID id_shuffled_graph_copy(GEDGraph::GraphID graph_id) const;

    bool is_shuffled_graph_copy(GEDGraph::GraphID graph_id) const;

    std::vector<GEDGraph>::const_iterator begin() const;

    std::vector<GEDGraph>::const_iterator end() const;

    std::size_t num_node_labels() const;

    std::size_t num_edge_labels() const;

    std::size_t max_num_nodes() const;

    std::size_t max_num_edges() const;

    double node_cost(LabelID label1, LabelID label2) const;

    void vectorize_node_label(LabelID node_label, std::vector<double> & vector_representation) const;

    double edge_cost(LabelID label1, LabelID label2) const;

    void vectorize_edge_label(LabelID edge_label, std::vector<double> & vector_representation) const;

    void save_node_map(const std::string & filename, GEDGraph::NodeID g_id, GEDGraph::NodeID h_id, const NodeMap & node_map, bool append = true) const;

    void load_node_map(const std::string & filename, GEDGraph::NodeID g_id, GEDGraph::NodeID h_id, NodeMap & node_map) const;

    void compute_induced_cost(const GEDGraph & g, const GEDGraph & h, NodeMap & node_map) const;

    double swap_cost(const GEDGraph & g, const GEDGraph & h, const NodeMap::Assignment & assignment_1, const NodeMap::Assignment & assignment_2, NodeMap & node_map) const;

    void swap_assignments(const NodeMap::Assignment & assignment_1, const NodeMap::Assignment & assignment_2, double swap_cost, NodeMap & node_map) const;

    bool quasimetric_costs() const;

    bool quasimetric_costs(const GEDGraph & g, const GEDGraph & h) const;

    double max_node_edit_cost() const;

    double max_edge_edit_cost() const;

    double max_edit_cost(const GEDGraph & g, const GEDGraph & h) const;

    double min_edit_cost(const GEDGraph & g, const GEDGraph & h) const;

    double max_node_edit_cost(const GEDGraph & g, const GEDGraph & h) const;

    double min_node_edit_cost(const GEDGraph & g, const GEDGraph & h) const;

    double max_edge_edit_cost(const GEDGraph & g, const GEDGraph & h) const;

    double min_edge_edit_cost(const GEDGraph & g, const GEDGraph & h) const;

    double max_node_del_cost(const GEDGraph & graph) const;

    double min_node_del_cost(const GEDGraph & graph) const;

    double mean_node_del_cost(const GEDGraph & graph) const;

    double max_node_ins_cost(const GEDGraph & graph) const;

    double min_node_ins_cost(const GEDGraph & graph) const;

    double mean_node_ins_cost(const GEDGraph & graph) const;

    double max_node_subs_cost(const GEDGraph & g, const GEDGraph & h) const;

    double min_node_subs_cost(const GEDGraph & g, const GEDGraph & h) const;

    double mean_node_subs_cost(const GEDGraph & g, const GEDGraph & h) const;

    double max_edge_del_cost(const GEDGraph & graph) const;

    double min_edge_del_cost(const GEDGraph & graph) const;

    double mean_edge_del_cost(const GEDGraph & graph) const;

    double max_edge_ins_cost(const GEDGraph & graph) const;

    double min_edge_ins_cost(const GEDGraph & graph) const;

    double mean_edge_ins_cost(const GEDGraph & graph) const;

    double max_edge_subs_cost(const GEDGraph & g, const GEDGraph & h) const;

    double min_edge_subs_cost(const GEDGraph & g, const GEDGraph & h) const;

    double mean_edge_subs_cost(const GEDGraph & g, const GEDGraph & h) const;

private:

    std::vector<GEDGraph> graphs_;

    std::vector<std::string> graph_names_;

    std::vector<std::string> graph_classes_;

    std::size_t num_graphs_without_shuffled_copies_;

    std::vector<std::map<std::string, GEDGraph::NodeID>> strings_to_internal_node_ids_;

    std::vector<std::map<GEDGraph::NodeID, std::string>> internal_node_ids_to_strings_;

    EditCosts<UserNodeLabel, UserEdgeLabel> * edit_costs_;

    DMatrix node_costs_;

    DMatrix edge_costs_;

    std::vector<UserNodeLabel> node_labels_;

    std::vector<UserEdgeLabel> edge_labels_;

    Options::InitType init_type_;

    bool delete_edit_costs_;

    std::size_t max_num_nodes_;

    std::size_t max_num_edges_;

    GEDData();

    void set_edit_costs_(Options::EditCosts edit_costs, const std::vector<double> & edit_cost_constants);

    void set_edit_costs_(EditCosts<UserNodeLabel, UserEdgeLabel> * edit_costs);

    void init_cost_matrices_();

    bool eager_init_() const;

    LabelID node_label_to_id_(const UserNodeLabel & node_label);

    UserNodeLabel id_to_node_label(LabelID label_id) const;

    LabelID edge_label_to_id_(const UserEdgeLabel & edge_label);

    UserEdgeLabel id_to_edge_label(LabelID label_id) const;

    GEDGraph::NodeID string_to_node_id_(GEDGraph::GraphID graph_id, const std::string & string) const;

    std::string node_id_to_string_(GEDGraph::GraphID graph_id, GEDGraph::NodeID node_id) const;

};

}

#include "ged_data.ipp"

#endif /* SRC_ENV_GED_DATA_HPP_ */