NNITopologySearch.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LEGACY_TREE_NNITOPOLOGYSEARCH_H
#define BPP_PHYL_LEGACY_TREE_NNITOPOLOGYSEARCH_H
 
 
#include "../../Tree/NNISearchable.h"
#include "../../Tree/TopologySearch.h"
 
namespace bpp
{
class NNITopologySearch :
  public virtual TopologySearch
{
public:
  const static std::string FAST;
  const static std::string BETTER;
  const static std::string PHYML;
 
private:
  std::shared_ptr<NNISearchable> searchableTree_;
  std::string algorithm_;
  unsigned int verbose_;
  std::vector<std::shared_ptr<TopologyListener>> topoListeners_;
 
public:
  NNITopologySearch(
      std::shared_ptr<NNISearchable> tree,
      const std::string& algorithm = FAST,
      unsigned int verbose = 2) :
    searchableTree_(tree), algorithm_(algorithm), verbose_(verbose), topoListeners_()
  {}
 
  NNITopologySearch(const NNITopologySearch& ts) :
    searchableTree_(ts.searchableTree_),
    algorithm_(ts.algorithm_),
    verbose_(ts.verbose_),
    topoListeners_(ts.topoListeners_)
  {
    // Hard-copy all listeners:
    for (unsigned int i = 0; i < topoListeners_.size(); i++)
    {
      topoListeners_[i].reset(ts.topoListeners_[i]->clone());
    }
  }
 
  NNITopologySearch& operator=(const NNITopologySearch& ts)
  {
    searchableTree_ = ts.searchableTree_;
    algorithm_      = ts.algorithm_;
    verbose_        = ts.verbose_;
    topoListeners_  = ts.topoListeners_;
    // Hard-copy all listeners:
    for (unsigned int i = 0; i < topoListeners_.size(); i++)
    {
      topoListeners_[i].reset(ts.topoListeners_[i]->clone());
    }
    return *this;
  }
 
 
  virtual ~NNITopologySearch()
  {}
 
public:
  void search();
 
  void addTopologyListener(std::shared_ptr<TopologyListener> listener)
  {
    if (listener)
      topoListeners_.push_back(listener);
  }
 
public:
  const Tree& topology() const { return searchableTree_->topology(); }
 
  std::shared_ptr<NNISearchable> getSearchableObject() { return searchableTree_; }
 
  std::shared_ptr<const NNISearchable> getSearchableObject() const { return searchableTree_; }
 
protected:
  void searchFast();
  void searchBetter();
  void searchPhyML();
 
  void notifyAllPerformed(const TopologyChangeEvent& event);
  void notifyAllTested(const TopologyChangeEvent& event);
  void notifyAllSuccessful(const TopologyChangeEvent& event);
};
} // end of namespace bpp.
#endif // BPP_PHYL_LEGACY_TREE_NNITOPOLOGYSEARCH_H