AssociationTreeGraphImplObserver.h

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//
// File: AssociationTreeGraphImplObserver.h
// Authors:
//   Thomas Bigot
// Last modified: vendredi 4 novembre 2016, à 10h 21
//
 
/*
  Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
  
  This software is a computer program whose purpose is to provide utilitary
  classes. This file belongs to the Bio++ Project.
  
  This software is governed by the CeCILL license under French law and
  abiding by the rules of distribution of free software. You can use,
  modify and/ or redistribute the software under the terms of the CeCILL
  license as circulated by CEA, CNRS and INRIA at the following URL
  "http://www.cecill.info".
  
  As a counterpart to the access to the source code and rights to copy,
  modify and redistribute granted by the license, users are provided only
  with a limited warranty and the software's author, the holder of the
  economic rights, and the successive licensors have only limited
  liability.
  
  In this respect, the user's attention is drawn to the risks associated
  with loading, using, modifying and/or developing or reproducing the
  software by the user in light of its specific status of free software,
  that may mean that it is complicated to manipulate, and that also
  therefore means that it is reserved for developers and experienced
  professionals having in-depth computer knowledge. Users are therefore
  encouraged to load and test the software's suitability as regards their
  requirements in conditions enabling the security of their systems and/or
  data to be ensured and, more generally, to use and operate it in the
  same conditions as regards security.
  
  The fact that you are presently reading this means that you have had
  knowledge of the CeCILL license and that you accept its terms.
*/
 
#ifndef BPP_GRAPH_ASSOCIATIONTREEGRAPHIMPLOBSERVER_H
#define BPP_GRAPH_ASSOCIATIONTREEGRAPHIMPLOBSERVER_H
 
#include <iostream>
#include <map>
#include <memory>
#include <ostream>
#include <vector>
 
#include "AssociationGraphImplObserver.h"
#include "AssociationTreeGraphObserver.h"
#include "TreeGraphImpl.h"
 
namespace bpp
{
template<class N, class E, class TreeGraphImpl>
class AssociationTreeGraphImplObserver :
  public AssociationTreeGraphObserver<N, E>,
  public AssociationGraphImplObserver<N, E, TreeGraphImpl>
{
public:
  typedef typename AssociationGraphObserver<N, E>::NodeIndex NodeIndex;
  typedef typename AssociationGraphObserver<N, E>::EdgeIndex EdgeIndex;
 
  typedef typename Graph::NodeId NodeGraphid;
 
  typedef typename Graph::EdgeId EdgeGraphid;
 
public:
  AssociationTreeGraphImplObserver(bool rooted = false) :
    AssociationGraphImplObserver<N, E, TreeGraphImpl>(rooted)
  {}
 
  AssociationTreeGraphImplObserver(std::shared_ptr<TreeGraphImpl> subjectTreeGraph) :
    AssociationGraphImplObserver<N, E, TreeGraphImpl>(subjectTreeGraph)
  {}
 
  AssociationTreeGraphImplObserver(bpp::AssociationTreeGraphImplObserver<N, E, TreeGraphImpl> const& treeGraphObserver) :
    AssociationGraphImplObserver<N, E, TreeGraphImpl>(treeGraphObserver)
  {}
 
  template<class N2, class E2>
  AssociationTreeGraphImplObserver(bpp::AssociationTreeGraphImplObserver<N2, E2, TreeGraphImpl> const& treeGraphObserver) :
    AssociationGraphImplObserver<N, E, TreeGraphImpl>::AssociationGraphImplObserver(treeGraphObserver)
  {}
 
 
  AssociationTreeGraphImplObserver<N, E, TreeGraphImpl>& operator=(bpp::AssociationTreeGraphImplObserver<N, E, TreeGraphImpl> const& treeGraphObserver)
  {
    AssociationGraphImplObserver<N, E, TreeGraphImpl>::operator=(treeGraphObserver);
    return *this;
  }
 
 
  ~AssociationTreeGraphImplObserver()
  {}
 
 
  AssociationTreeGraphImplObserver<N, E, TreeGraphImpl>* clone() const { return new AssociationTreeGraphImplObserver<N, E, TreeGraphImpl>(*this); }
 
 
  bool isValid() const
  {
    return this->getGraph()->isValid();
  }
 
  std::shared_ptr<E>  getEdgeToFather(const std::shared_ptr<N>  nodeObject) const
  {
    return this->getEdgeFromGraphid(this->getGraph()->getEdgeToFather(this->getNodeGraphid(nodeObject)));
  }
 
  std::shared_ptr<E>  getEdgeToFather(const NodeIndex index) const
  {
    return this->getEdgeFromGraphid(this->getGraph()->getEdgeToFather(this->getNodeGraphid(this->getNode(index))));
  }
 
 
  void rootAt(const std::shared_ptr<N> root)
  {
    this->getGraph()->rootAt(this->getNodeGraphid(root));
  }
 
  /*
   * @brief check if rooted, ie directed
   *
   */
  bool isRooted() const
  {
    return this->getGraph()->isRooted();
  }
 
  std::shared_ptr<N>  getFatherOfNode(const std::shared_ptr<N>  nodeObject) const
  {
    return this->getNodeFromGraphid(this->getGraph()->getFatherOfNode(this->getNodeGraphid(nodeObject)));
  }
 
  bool hasFather(const std::shared_ptr<N>  nodeObject) const
  {
    return this->getGraph()->hasFather(this->getNodeGraphid(nodeObject));
  }
 
  bool hasFather(const NodeIndex index) const
  {
    return this->getGraph()->hasFather(this->getNodeGraphid(this->getNode(index)));
  }
 
  std::vector<std::shared_ptr<N> > getSons(const std::shared_ptr<N>  node) const
  {
    return this->getNodesFromGraphid(this->getGraph()->getSons(this->getNodeGraphid(node)));
  }
 
  std::vector<NodeIndex> getSons(const NodeIndex node) const
  {
    return this->getNodeIndexes(this->getNodesFromGraphid(this->getGraph()->getSons(this->getNodeGraphid(this->getNode(node)))));
  }
 
  std::vector<std::shared_ptr<E> > getBranches(const std::shared_ptr<N>  node) const
  {
    return this->getEdgesFromGraphid(this->getGraph()->getBranches(this->getNodeGraphid(node)));
  }
 
  std::vector<EdgeIndex> getBranches(const NodeIndex node) const
  {
    return this->getEdgeIndexes(this->getEdgesFromGraphid(this->getGraph()->getBranches(this->getNodeGraphid(this->getNode(node)))));
  }
 
  std::shared_ptr<N> getSon(const std::shared_ptr<E>  edge) const
  {
    return this->getNodeFromGraphid(this->getGraph()->getBottom(this->getEdgeGraphid(edge)));
  }
 
  NodeIndex getSon(const EdgeIndex edge) const
  {
    return this->getNodeIndex(this->getNodeFromGraphid(this->getGraph()->getBottom(this->getEdgeGraphid(this->getEdge(edge)))));
  }
 
  std::shared_ptr<N> getFatherOfEdge(const std::shared_ptr<E>  edge) const
  {
    return this->getNodeFromGraphid(this->getGraph()->getTop(this->getEdgeGraphid(edge)));
  }
 
  NodeIndex getFatherOfEdge(const EdgeIndex edge) const
  {
    return this->getNodeIndex(this->getNodeFromGraphid(this->getGraph()->getTop(this->getEdgeGraphid(this->getEdge(edge)))));
  }
 
 
  size_t getNumberOfSons(const std::shared_ptr<N>  node) const
  {
    return this->getGraph()->getNumberOfSons(this->getNodeGraphid(node));
  }
 
  std::vector<std::shared_ptr<N> > getLeavesUnderNode(std::shared_ptr<N>  node) const
  {
    return this->getNodesFromGraphid(this->getGraph()->getLeavesUnderNode(this->getNodeGraphid(node)));
  }
 
  std::vector<NodeIndex> getLeavesUnderNode(NodeIndex node) const
  {
    return this->getNodeIndexes(getLeavesUnderNode(this->getNode(node)));
  }
 
  std::vector<std::shared_ptr<N> > removeSons(const std::shared_ptr<N>  node)
  {
    return this->getNodesFromGraphid(this->getGraph()->removeSons(this->getNodeGraphid(node)));
  }
 
  void removeSon(const std::shared_ptr<N> node, const std::shared_ptr<N> son)
  {
    this->getGraph()->removeSon(this->getNodeGraphid(node), this->getNodeGraphid(son));
  }
 
  void setFather(const std::shared_ptr<N>  nodeObject, const std::shared_ptr<N> fatherNodeObject, const std::shared_ptr<E> edgeObject = 0)
  {
    if (edgeObject)
      this->getGraph()->setFather(this->getNodeGraphid(nodeObject), this->getNodeGraphid(fatherNodeObject), this->getEdgeGraphid(edgeObject));
    else
      this->getGraph()->setFather(this->getNodeGraphid(nodeObject), this->getNodeGraphid(fatherNodeObject));
  }
 
 
  void addSon(const std::shared_ptr<N>  nodeObject, const std::shared_ptr<N> sonNodeObject, const std::shared_ptr<E> edgeObject = 0)
  {
    if (edgeObject)
      this->getGraph()->addSon(this->getNodeGraphid(nodeObject), this->getNodeGraphid(sonNodeObject), this->getEdgeGraphid(edgeObject));
    else
      this->getGraph()->addSon(this->getNodeGraphid(nodeObject), this->getNodeGraphid(sonNodeObject));
  }
 
  /*
   * @brief builds iterator on the sons of a Node
   *
   */
  std::unique_ptr<typename AssociationTreeGraphObserver<N, E>::NodeIterator> sonsIterator(std::shared_ptr<N> node)
  {
    return this->outgoingNeighborNodesIterator(node);
  }
 
  std::unique_ptr<typename AssociationTreeGraphObserver<N, E>::NodeIterator> sonsIterator(std::shared_ptr<N> node) const
  {
    return this->outgoingNeighborNodesIterator(node);
  }
 
  /*
   * @brief builds iterator on the branches to sons of a Node
   *
   */
  std::unique_ptr<typename AssociationTreeGraphObserver<N, E>::EdgeIterator> branchesIterator(std::shared_ptr<N> node)
  {
    return this->outgoingEdgesIterator(node);
  }
 
  std::unique_ptr<typename AssociationTreeGraphObserver<N, E>::EdgeIterator> branchesIterator(std::shared_ptr<N> node) const
  {
    return this->outgoingEdgesIterator(node);
  }
 
  std::vector<std::shared_ptr<N> > getNodePathBetweenTwoNodes(const std::shared_ptr<N>  nodeA, const std::shared_ptr<N>  nodeB, bool includeAncestor = true) const
  {
    return this->getNodesFromGraphid(this->getGraph()->getNodePathBetweenTwoNodes(this->getNodeGraphid(nodeA), this->getNodeGraphid(nodeB), includeAncestor));
  }
 
  std::vector<std::shared_ptr<E> > getEdgePathBetweenTwoNodes(const std::shared_ptr<N>  nodeA, const std::shared_ptr<N>  nodeB) const
  {
    return this->getEdgesFromGraphid(this->getGraph()->getEdgePathBetweenTwoNodes(this->getNodeGraphid(nodeA), this->getNodeGraphid(nodeB)));
  }
 
  std::vector<NodeIndex> getNodePathBetweenTwoNodes(const NodeIndex nodeA, const NodeIndex nodeB, bool includeAncestor = true) const
  {
    return getNodeIndexes(getNodePathBetweenTwoNodes(this->getNode(nodeA), this->getNode(nodeB), includeAncestor));
  }
 
  std::vector<EdgeIndex> getEdgePathBetweenTwoNodes(const NodeIndex nodeA, const NodeIndex nodeB, bool includeAncestor = true) const
  {
    return this->getEdgeIndexes(getEdgePathBetweenTwoNodes(this->getNode(nodeA), this->getNode(nodeB), includeAncestor));
  }
 
  std::vector<std::shared_ptr<N> > getSubtreeNodes(const std::shared_ptr<N> localRoot) const
  {
    return this->getNodesFromGraphid(this->getGraph()->getSubtreeNodes(this->getNodeGraphid(localRoot)));
  }
 
  std::vector<std::shared_ptr<E> > getSubtreeEdges(const std::shared_ptr<N> localRoot) const
  {
    return AssociationGraphImplObserver<N, E, TreeGraphImpl>::getEdgesFromGraphid(this->getGraph()->getSubtreeEdges(this->getNodeGraphid(localRoot)));
  }
 
  std::vector<NodeIndex> getSubtreeNodes(const NodeIndex localRoot) const
  {
    return getNodeIndexes(getSubtreeNodes(this->getNode(localRoot)));
  }
 
  std::vector<EdgeIndex> getSubtreeEdges(const NodeIndex localRoot) const
  {
    return this->getEdgeIndexes(getSubtreeEdges(this->getNode(localRoot)));
  }
 
  std::shared_ptr<N>  MRCA(const std::vector<std::shared_ptr<N> >  vNodeObject) const
  {
    std::vector<Graph::NodeId> vNid(vNodeObject.size());
 
    std::transform(vNodeObject.begin(), vNodeObject.end(), vNid.begin(), [this](const std::shared_ptr<N>& nodeObject){return this->getNodeGraphid(nodeObject);});
 
    return this->getNodeFromGraphid(this->getGraph()->MRCA(vNid));
  }
};
 
/********************/
 
template<class N, class E>
using AssociationTreeGlobalGraphObserver =  AssociationTreeGraphImplObserver<N, E, TreeGlobalGraph>;
}
#endif // BPP_GRAPH_ASSOCIATIONTREEGRAPHIMPLOBSERVER_H