GlobalGraph.h

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//
// File: GlobalGraph.h
// Authors:
//   Thomas Bigot
//   Laurent Gueguen
// Last modified: vendredi 4 novembre 2016, à 10h 19
//
 
/*
  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_GLOBALGRAPH_H
#define BPP_GRAPH_GLOBALGRAPH_H
 
#include <limits>
#include <map>
#include <set>
#include <string>
 
#include "../Clonable.h"
#include "Graph.h"
 
namespace bpp
{
class GlobalGraph :
  public virtual Graph,
  public virtual Clonable
{
public:
  typedef Graph::NodeId Node;
  typedef Graph::EdgeId Edge;
 
  typedef std::map<Node, std::pair<std::map<Node, Edge>, std::map<Node, Edge> > > nodeStructureType;
 
  typedef std::map<Edge, std::pair<Node, Node> > edgeStructureType;
 
private:
  bool directed_;
 
  std::set<GraphObserver*> observers_;
 
  Node highestNodeID_;
  Edge highestEdgeID_;
 
  nodeStructureType nodeStructure_;
 
  edgeStructureType edgeStructure_;
 
  Node root_;
 
  virtual void topologyHasChanged_() const
  {
    // do nothing: a Graph does not care to be modified
  }
 
  void notify_();
 
  void linkInNodeStructure_(const Node& nodeA, const Node& nodeB, const Edge& edge);
 
  void linkInEdgeStructure_(const Node& nodeA, const Node& nodeB, const Edge& edge);
 
 
  Edge unlinkInNodeStructure_(const Node& nodeA, const Node& nodeB);
 
  void unlinkInEdgeStructure_(const Edge& edge);
 
protected:
  void nodeMustExist_(const Node& node, std::string name = "") const;
 
  void edgeMustExist_(const Edge& edge, std::string name = "") const;
 
private:
  std::vector<Node> getNeighbors_(const Node& node, bool outgoing = true) const;
 
  std::vector<Edge> getEdges_(const Node& node, bool outgoing = true) const;
 
  void isolate_(Node& node);
 
  void fillListOfLeaves_(const Node& startingNode, std::vector<Node>& foundLeaves, const Node& originNode, unsigned int maxRecursions) const;
 
  bool nodesAreMetOnlyOnce_(const Node& node, std::set<Node>& metNodes, const Node& originNode) const;
 
  void nodeToDot_(const Node& node, std::ostream& out, std::set<std::pair<Node, Node> >& alreadyFigured) const;
 
public:
  // /@{
 
 
  GlobalGraph(bool directed = false);
 
  GlobalGraph(const GlobalGraph& gg);
 
  GlobalGraph& operator=(const GlobalGraph& gg);
 
  GlobalGraph* clone() const {return new GlobalGraph(*this); }
 
  ~GlobalGraph() {}
 
protected:
  void setRoot(Graph::NodeId newRoot);
 
public:
  Graph::NodeId getRoot() const;
 
  void makeDirected();
 
  void makeUndirected();
 
  // /@}
 
 
  // /@{
 
  Graph::NodeId createNode();
 
  Graph::NodeId createNodeFromNode(Graph::NodeId origin);
 
  Graph::NodeId createNodeOnEdge(Graph::EdgeId edge);
 
  Graph::NodeId createNodeFromEdge(Graph::NodeId origin);
 
protected:
  Graph::EdgeId link(Graph::NodeId nodeA, Graph::NodeId nodeB);
 
  void link(Graph::NodeId nodeA, Graph::NodeId nodeB, GlobalGraph::Edge edgeID);
 
  void switchNodes(Graph::NodeId nodeA, Graph::NodeId nodeB);
 
 
  std::vector<Graph::EdgeId> unlink(Graph::NodeId nodeA, Graph::NodeId nodeB);
 
public:
  void deleteNode(Graph::NodeId node);
 
  // /@}
 
 
  // /@{
 
  void registerObserver(GraphObserver* observer);
  void unregisterObserver(GraphObserver* observer);
  // /@}
 
 
  // /@{
 
  template<typename T, bool is_const>
  friend class NodesIteratorClass;
 
  template<typename T, bool is_const>
  friend class EdgesIteratorClass;
 
  /*
   * @brief builds iterator on all Nodes of the graph
   *
   */
 
  std::unique_ptr<Graph::NodeIterator> allNodesIterator();
  std::unique_ptr<Graph::NodeIterator> allNodesIterator() const;
 
 
  /*
   * @brief builds iterator on the neighbor nodes of a Node
   *
   */
 
  std::unique_ptr<Graph::NodeIterator> outgoingNeighborNodesIterator(NodeId node);
  std::unique_ptr<Graph::NodeIterator> outgoingNeighborNodesIterator(NodeId node) const;
 
  /*
   * @brief builds iterator on the neighbor nodes of a Node
   *
   */
 
  std::unique_ptr<Graph::NodeIterator> incomingNeighborNodesIterator(NodeId node);
  std::unique_ptr<Graph::NodeIterator> incomingNeighborNodesIterator(NodeId node) const;
 
  size_t getNumberOfNodes() const;
 
  size_t getNumberOfEdges() const;
 
  size_t getDegree(Graph::NodeId node) const;
 
  bool isLeaf(Graph::NodeId node) const;
 
  size_t getNumberOfNeighbors(Graph::NodeId node) const;
 
  size_t getNumberOfOutgoingNeighbors(Graph::NodeId node) const;
 
  size_t getNumberOfIncomingNeighbors(Graph::NodeId node) const;
 
  std::vector<Graph::NodeId> getNeighbors(Graph::NodeId node) const;
 
  std::vector<Graph::NodeId> getOutgoingNeighbors(Graph::NodeId node) const;
 
  std::vector<Graph::NodeId> getIncomingNeighbors(Graph::NodeId node) const;
 
  std::vector<Graph::NodeId> getLeavesFromNode(Graph::NodeId node, unsigned int maxDepth) const;
 
  std::vector<Graph::NodeId> getAllLeaves() const;
  std::set<NodeId> getSetOfAllLeaves() const;
 
  std::vector<Graph::NodeId> getAllNodes() const;
 
  std::vector<Graph::NodeId> getAllInnerNodes() const;
 
  std::pair<Graph::NodeId, Graph::NodeId> getNodes(Graph::EdgeId edge) const;
 
  Graph::NodeId getTop(Graph::EdgeId edge) const;
 
  Graph::NodeId getBottom(Graph::EdgeId edge) const;
 
 
  // /@}
 
  // /@{
 
  bool isTree() const;
 
  bool isDA() const;
 
  void orientate();
 
  bool isDirected() const;
 
 
  bool containsReciprocalRelations() const;
 
 
  // /@}
 
  /*
   * @brief builds iterator on all Nodes of the graph
   *
   */
 
  std::unique_ptr<EdgeIterator> allEdgesIterator();
  std::unique_ptr<EdgeIterator> allEdgesIterator() const;
 
  /*
   * @brief builds iterator on the outgoing neighbor nodes of a Node
   *
   */
 
  std::unique_ptr<EdgeIterator> outgoingEdgesIterator(NodeId node);
  std::unique_ptr<EdgeIterator> outgoingEdgesIterator(NodeId node) const;
 
  /*
   * @brief builds iterator on the incoming neighbor nodes of a Node
   *
   */
 
  std::unique_ptr<EdgeIterator> incomingEdgesIterator(NodeId node);
  std::unique_ptr<EdgeIterator> incomingEdgesIterator(NodeId node) const;
 
  std::vector<Graph::EdgeId> getEdges(Graph::NodeId node) const;
 
  std::vector<Graph::EdgeId> getOutgoingEdges(Graph::NodeId node) const;
 
  std::vector<Graph::EdgeId> getIncomingEdges(Graph::NodeId node) const;
 
  Graph::EdgeId getEdge(Graph::NodeId nodeA, Graph::NodeId nodeB) const;
 
  Graph::EdgeId getAnyEdge(Graph::NodeId nodeA, Graph::NodeId nodeB) const;
 
  std::vector<Graph::EdgeId> getAllEdges() const;
 
  // /@}
 
 
  // /@{
 
  void notifyDeletedEdges(const std::vector<Graph::EdgeId>& edgesToDelete) const;
 
  void notifyDeletedNodes(const std::vector<Graph::NodeId>& nodesToDelete) const;
 
 
  // /@}
 
  void outputToDot(std::ostream& out, const std::string& name) const;
 
  template<class N, class E, class GraphImpl>
  friend class AssociationGraphImplObserver;
};
 
 
/************************************************/
/************************************************/
/************************************************/
/* ITERATORS */
/************************************************/
 
/************************************************/
/* NODES ITERATORS */
/************************************************/
 
template<class T, bool is_const>
class NodesIteratorClass :
  virtual public Graph::NodeIterator
{
  ~NodesIteratorClass<T, is_const>(){}
};
 
 
template<bool is_const>
class NodesIteratorClass<Graph::ALLGRAPHITER, is_const> :
  virtual public Graph::NodeIterator
{
private:
  typedef typename std::conditional<is_const,
                                    GlobalGraph::nodeStructureType::const_iterator,
                                    GlobalGraph::nodeStructureType::iterator >::type itType;
 
  itType it_,  begin_, end_;
 
public:
  template<bool B = is_const>
  NodesIteratorClass<Graph::ALLGRAPHITER, is_const>(const GlobalGraph& gg, typename std::enable_if<B>::type* = 0) : it_(gg.nodeStructure_.begin()),
    begin_(gg.nodeStructure_.begin()),
    end_(gg.nodeStructure_.end()) {}
 
  template<bool B = is_const>
  NodesIteratorClass<Graph::ALLGRAPHITER, is_const>(GlobalGraph& gg, typename std::enable_if<!B>::type* = 0) : it_(gg.nodeStructure_.begin()),
    begin_(gg.nodeStructure_.begin()),
    end_(gg.nodeStructure_.end()) {}
 
  ~NodesIteratorClass<Graph::ALLGRAPHITER, is_const>(){}
 
  void next() { it_++; }
  bool end() const { return it_ == end_;  }
  void start() { it_ = begin_; }
 
  Graph::NodeId operator*() {return it_->first; }
};
 
 
template<bool is_const>
class NeighborIteratorClass
{
protected:
  typedef typename std::conditional<is_const,
                                    const std::map<GlobalGraph::Node, GlobalGraph::Edge>&,
                                    std::map<GlobalGraph::Node, GlobalGraph::Edge>&>::type mapType;
 
  mapType map_;
 
  typedef typename std::conditional<is_const,
                                    std::map<GlobalGraph::Node, GlobalGraph::Edge>::const_iterator,
                                    std::map<GlobalGraph::Node, GlobalGraph::Edge>::iterator>::type itType;
 
  itType it_, begin_, end_;
 
public:
  virtual ~NeighborIteratorClass<is_const>(){}
 
  template<bool B = is_const>
  NeighborIteratorClass<is_const>(const std::map<GlobalGraph::Node, GlobalGraph::Edge>& map, typename std::enable_if<B>::type* = 0) :
    map_(map),
    it_(map_.begin()),
    begin_(map_.begin()),
    end_(map_.end()) {}
 
  template<bool B = is_const>
  NeighborIteratorClass<is_const>(std::map<GlobalGraph::Node, GlobalGraph::Edge>& map, typename std::enable_if<!B>::type* = 0) :
    map_(map),
    it_(map_.begin()),
    begin_(map_.begin()),
    end_(map_.end()) {}
 
  void next() { it_++; }
  bool end() const { return it_ == end_;  }
  void start() { it_ = begin_; }
};
 
 
template<bool is_const>
class NodesIteratorClass<Graph::OUTGOINGNEIGHBORITER, is_const> :
  virtual public NeighborIteratorClass<is_const>,
  virtual public Graph::NodeIterator
{
public:
  NodesIteratorClass<Graph::OUTGOINGNEIGHBORITER, is_const>(const GlobalGraph& gg, GlobalGraph::NodeId node) : NeighborIteratorClass<is_const>(gg.nodeStructure_.find(node)->second.first) {}
 
  NodesIteratorClass<Graph::OUTGOINGNEIGHBORITER, is_const>(GlobalGraph& gg, GlobalGraph::NodeId node) : NeighborIteratorClass<is_const>(gg.nodeStructure_.find(node)->second.first) {}
 
  ~NodesIteratorClass<Graph::OUTGOINGNEIGHBORITER, is_const>(){}
 
  void next() { NeighborIteratorClass<is_const>::next(); }
  bool end() const { return NeighborIteratorClass<is_const>::end(); }
  void start() { NeighborIteratorClass<is_const>::start(); }
 
  Graph::NodeId operator*() {return NeighborIteratorClass<is_const>::it_->first; }
};
 
 
template<bool is_const>
class NodesIteratorClass<Graph::INCOMINGNEIGHBORITER, is_const> :
  virtual public NeighborIteratorClass<is_const>,
  virtual public Graph::NodeIterator
{
public:
  NodesIteratorClass<Graph::INCOMINGNEIGHBORITER, is_const>(const GlobalGraph& gg, GlobalGraph::NodeId node) : NeighborIteratorClass<is_const>(gg.nodeStructure_.find(node)->second.second) {}
 
  NodesIteratorClass<Graph::INCOMINGNEIGHBORITER, is_const>(GlobalGraph& gg, GlobalGraph::NodeId node) : NeighborIteratorClass<is_const>(gg.nodeStructure_.find(node)->second.second) {}
 
  ~NodesIteratorClass<Graph::INCOMINGNEIGHBORITER, is_const>(){}
 
  void next() { NeighborIteratorClass<is_const>::next(); }
  bool end() const { return NeighborIteratorClass<is_const>::end(); }
  void start() { NeighborIteratorClass<is_const>::start(); }
 
  Graph::NodeId operator*() {return NeighborIteratorClass<is_const>::it_->first; }
};
 
 
/************************************************/
/* EDGES ITERATORS */
/************************************************/
 
template<class T, bool is_const>
class EdgesIteratorClass :
  virtual public Graph::EdgeIterator
{};
 
template<bool is_const>
class EdgesIteratorClass<Graph::ALLGRAPHITER, is_const> :
  virtual public Graph::EdgeIterator
{
private:
  typedef typename std::conditional<is_const,
                                    GlobalGraph::edgeStructureType::const_iterator,
                                    GlobalGraph::edgeStructureType::iterator >::type itType;
 
  itType it_, begin_, end_;
 
public:
  template<bool B = is_const>
  EdgesIteratorClass<Graph::ALLGRAPHITER, is_const>(const GlobalGraph& gg, typename std::enable_if<B>::type* = 0) : it_(gg.edgeStructure_.begin()),
    begin_(gg.edgeStructure_.begin()),
    end_(gg.edgeStructure_.end()) {}
 
  template<bool B = is_const>
  EdgesIteratorClass<Graph::ALLGRAPHITER, is_const>(GlobalGraph& gg, typename std::enable_if<!B>::type* = 0) : it_(gg.edgeStructure_.begin()),
    begin_(gg.edgeStructure_.begin()),
    end_(gg.edgeStructure_.end()) {}
 
  ~EdgesIteratorClass<Graph::ALLGRAPHITER, is_const>(){}
 
  void next() { it_++; }
  bool end() const { return it_ == end_;  }
  void start() { it_ = begin_; }
 
  Graph::EdgeId operator*() {return it_->first; }
};
 
 
template<bool is_const>
class EdgesIteratorClass<Graph::OUTGOINGNEIGHBORITER, is_const> :
  public NeighborIteratorClass<is_const>,
  public Graph::EdgeIterator
{
public:
  EdgesIteratorClass<Graph::OUTGOINGNEIGHBORITER, is_const>(const GlobalGraph& gg, GlobalGraph::NodeId node) : NeighborIteratorClass<is_const>(gg.nodeStructure_.find(node)->second.first) {}
 
  EdgesIteratorClass<Graph::OUTGOINGNEIGHBORITER, is_const>(GlobalGraph& gg, GlobalGraph::NodeId node) : NeighborIteratorClass<is_const>(gg.nodeStructure_.find(node)->second.first) {}
 
  ~EdgesIteratorClass<Graph::OUTGOINGNEIGHBORITER, is_const>(){}
 
  void next() { NeighborIteratorClass<is_const>::next(); }
  bool end() const { return NeighborIteratorClass<is_const>::end(); }
  void start() { NeighborIteratorClass<is_const>::start(); }
 
  Graph::EdgeId operator*() {return NeighborIteratorClass<is_const>::it_->second; }
};
 
template<bool is_const>
class EdgesIteratorClass<Graph::INCOMINGNEIGHBORITER, is_const> :
  public NeighborIteratorClass<is_const>,
  public Graph::EdgeIterator
{
public:
  EdgesIteratorClass<Graph::INCOMINGNEIGHBORITER, is_const>(const GlobalGraph& gg, GlobalGraph::NodeId node) : NeighborIteratorClass<is_const>(gg.nodeStructure_.find(node)->second.second) {}
 
  EdgesIteratorClass<Graph::INCOMINGNEIGHBORITER, is_const>(GlobalGraph& gg, GlobalGraph::NodeId node) : NeighborIteratorClass<is_const>(gg.nodeStructure_.find(node)->second.second) {}
 
  ~EdgesIteratorClass<Graph::INCOMINGNEIGHBORITER, is_const>(){}
 
  void next() { NeighborIteratorClass<is_const>::next(); }
  bool end() const { return NeighborIteratorClass<is_const>::end(); }
  void start() { NeighborIteratorClass<is_const>::start(); }
 
  Graph::EdgeId operator*() {return NeighborIteratorClass<is_const>::it_->second; }
};
}
#endif // BPP_GRAPH_GLOBALGRAPH_H