/*
 * BindingModel.hpp
 *
 *  Created on: Oct 5, 2016
 *      Author: heber
 */


#ifndef POTENTIALS_BINDINGMODEL_HPP_
#define POTENTIALS_BINDINGMODEL_HPP_

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <vector>

#include "Fragmentation/Homology/FragmentNode.hpp"
#include "Fragmentation/Homology/HomologyGraph.hpp"

/** This class extends HomologyGraph by an additional vector of FragmentNode's
 * because their ordering is important (which is lost upon insertion into
 * HomologyGraph::nodes_t)
 *
 * The sequence is important because it determines how the sequence of pair-wise
 * distance arguments needs to be, see FunctionApproximation
 */
struct BindingModel
{
  typedef std::vector<FragmentNode> vector_nodes_t;

  /** Default cstor for class BindingModel.
   *
   */
  BindingModel() {}

  /** Cstor for class BindingModel.
   *
   * \param _nodes, vector of nodes, converted to map and passed on
   * \param _edges map of edges, passed on to HomologyGraph
   */
  BindingModel(const vector_nodes_t &_nodes, const HomologyGraph::edges_t &_edges);

  /** Const getter for the internal homology graph.
   *
   * \return const ref to graph
   */
  const HomologyGraph& getGraph() const { return graph; }

  /** Const getter to the sequence of nodes.
   *
   * \return const ref to vector of FragmentNodes
   */
  const vector_nodes_t& getNodes() const { return nodes; }

private:
  //!> the homology graph of this binding model
  const HomologyGraph graph;

  //!> vector of nodes
  const vector_nodes_t nodes;
};

#endif /* POTENTIALS_BINDINGMODEL_HPP_ */