DAGraphImpl.h

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//
// File: DAGraphImpl.h
// Authors:
//   Laurent Guéguen
// 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
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  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_DAGRAPHIMPL_H
#define BPP_GRAPH_DAGRAPHIMPL_H
 
#include <iostream>
#include <ostream>
#include <string>
#include <vector>
 
#include "../Exceptions.h"
#include "../Numeric/VectorTools.h"
#include "DAGraph.h"
#include "GlobalGraph.h"
 
namespace bpp
{
template<class GraphImpl>
class DAGraphImpl :
  public virtual DAGraph,
  public GraphImpl
{
protected:
  mutable bool isValid_;
 
  mutable bool isRooted_;
 
  // unvalidate the DAG
  virtual void topologyHasChanged_() const;
 
  // will throw an exception if the DA is not valid
  void mustBeValid_() const;
 
  // will throw an exception if the DA is not rooted, ie as more
  // than one node with no father.
 
  void mustBeRooted_() const;
 
  // test the validity of the DAG
  bool validate_() const;
 
  void propagateDirection_(Graph::NodeId node);
 
  void orientGraphFrom_(std::set<Graph::NodeId>& metNodes, Graph::NodeId localRoot);
 
public:
  DAGraphImpl(bool b = true);
 
  bool isValid() const;
 
  bool isRooted() const;
 
  bool isLeaf(Graph::NodeId node) const;
 
  bool hasFather(Graph::NodeId node) const;
 
  std::vector<Graph::NodeId> getFathers(Graph::NodeId nodeid) const;
 
  size_t getNumberOfFathers(Graph::NodeId node) const;
 
  void addFather(Graph::NodeId node, Graph::NodeId father);
 
  void addFather(Graph::NodeId node, Graph::NodeId father, Graph::EdgeId edgeId);
 
  void removeFather(Graph::NodeId node, Graph::NodeId father);
 
  std::vector<Graph::NodeId> removeFathers(Graph::NodeId node);
 
  std::vector<Graph::NodeId> getLeavesUnderNode(Graph::NodeId node) const;
 
  std::vector<Graph::NodeId> getSons(Graph::NodeId node) const;
 
  size_t getNumberOfSons(Graph::NodeId node) const;
 
  void addSon(Graph::NodeId node, Graph::NodeId sonNode);
 
  void addSon(Graph::NodeId node, Graph::NodeId sonNode, Graph::EdgeId edge);
 
  std::vector<Graph::NodeId> removeSons(Graph::NodeId node);
 
  void removeSon(Graph::NodeId node, Graph::NodeId son);
 
  void rootAt(Graph::NodeId newRoot);
 
  std::vector<Graph::NodeId> getBelowNodes(Graph::NodeId localRoot) const;
 
  std::vector<Graph::EdgeId> getBelowEdges(Graph::NodeId localRoot) const;
 
  // recursive function for getSubtreeNodes
  void fillSubtreeMetNodes_(std::vector<Graph::NodeId>& metNodes, Graph::NodeId localRoot) const;
 
  // recursive function for getSubtreeEdges
  void fillSubtreeMetEdges_(std::vector<Graph::EdgeId>& metEdges, Graph::NodeId localRoot) const;
 
  // recursive function for getLeavesUnderNode
  void fillListOfLeaves_(Graph::NodeId startingNode, std::vector<Graph::NodeId>& foundLeaves) const;
};
 
 
/******************/
 
typedef DAGraphImpl<GlobalGraph> DAGlobalGraph;
 
/*****************/
 
 
template<class GraphImpl>
DAGraphImpl<GraphImpl>::DAGraphImpl(bool b) :
  GraphImpl(true),
  isValid_(false),
  isRooted_(false)
{}
 
 
template<class GraphImpl>
bool DAGraphImpl<GraphImpl>::isValid() const
{
  return isValid_ || validate_();
}
 
 
template<class GraphImpl>
bool DAGraphImpl<GraphImpl>::isRooted() const
{
  if (isRooted_)
    return true;
 
  std::unique_ptr<Graph::NodeIterator> allIt = allNodesIterator();
  bool seen = false;
 
  for ( ; !allIt->end(); allIt->next())
  {
    if (getNumberOfFathers(**allIt) == 0)
    {
      if (seen)
        return false;
      seen = true;
    }
  }
 
  isRooted_ = seen;
  return true;
}
 
template<class GraphImpl>
bool DAGraphImpl<GraphImpl>::isLeaf(Graph::NodeId node) const
{
  return GraphImpl::isLeaf(node);
}
 
template<class GraphImpl>
bool DAGraphImpl<GraphImpl>::hasFather(Graph::NodeId node) const
{
  return GraphImpl::getNumberOfIncomingNeighbors(node) >= 1;
}
 
template<class GraphImpl>
std::vector<Graph::NodeId> DAGraphImpl<GraphImpl>::getFathers(Graph::NodeId node) const
{
  return getIncomingNeighbors(node);
}
 
template<class GraphImpl>
size_t DAGraphImpl<GraphImpl>::getNumberOfFathers(Graph::NodeId node) const
{
  return GraphImpl::getNumberOfIncomingNeighbors(node);
}
 
template<class GraphImpl>
void DAGraphImpl<GraphImpl>::addFather(Graph::NodeId node, Graph::NodeId fatherNode)
{
  GraphImpl::link(fatherNode, node);
  topologyHasChanged_();
  isRooted_ = false;
}
 
template<class GraphImpl>
void DAGraphImpl<GraphImpl>::addFather(Graph::NodeId node, Graph::NodeId fatherNode, Graph::EdgeId edge)
{
  GraphImpl::link(fatherNode, node, edge);
  topologyHasChanged_();
  isRooted_ = false;
}
 
template<class GraphImpl>
std::vector<Graph::NodeId> DAGraphImpl<GraphImpl>::removeFathers(Graph::NodeId node)
{
  std::vector<Graph::NodeId> fathers = getFathers(node);
  for (std::vector<Graph::NodeId>::iterator currFather = fathers.begin(); currFather != fathers.end(); currFather++)
  {
    removeFather(node, *currFather);
  }
  return fathers;
}
 
template<class GraphImpl>
void DAGraphImpl<GraphImpl>::removeFather(Graph::NodeId node, Graph::NodeId father)
{
  if (getNumberOfIncomingNeighbors(node) == 1)
    isRooted_ = false;
 
  GraphImpl::unlink(father, node);
}
 
template<class GraphImpl>
std::vector<Graph::NodeId> DAGraphImpl<GraphImpl>::getLeavesUnderNode(Graph::NodeId node) const
{
  std::vector<Graph::NodeId> foundLeaves;
  fillListOfLeaves_(node, foundLeaves);
 
  return foundLeaves;
}
 
template<class GraphImpl>
void DAGraphImpl<GraphImpl>::fillListOfLeaves_(Graph::NodeId startingNode, std::vector<Graph::NodeId>& foundLeaves) const
{
  const std::vector<Graph::NodeId> sons = getSons(startingNode);
  if (sons.size() > 1)
  {
    for (std::vector<Graph::NodeId>::const_iterator currNeighbor = sons.begin(); currNeighbor != sons.end(); currNeighbor++)
    {
      fillListOfLeaves_(*currNeighbor, foundLeaves);
    }
  }
  else
  {
    foundLeaves.push_back(startingNode);
  }
}
 
template<class GraphImpl>
void DAGraphImpl<GraphImpl>::mustBeRooted_() const
{
  if (!isRooted())
    throw Exception("DAGraphImpl<GraphImpl>: The DAG must be rooted.");
}
 
template<class GraphImpl>
void DAGraphImpl<GraphImpl>::mustBeValid_() const
{
  if (!isValid())
    throw Exception("DAGraphImpl<GraphImpl>: The DAG is not valid.");
}
 
 
template<class GraphImpl>
bool DAGraphImpl<GraphImpl>::validate_() const
{
  isValid_ = GraphImpl::isDA();
  return isValid_;
}
 
template<class GraphImpl>
void DAGraphImpl<GraphImpl>::topologyHasChanged_() const
{
  isValid_ = false;
}
 
 
template<class GraphImpl>
std::vector<Graph::NodeId> DAGraphImpl<GraphImpl>::getSons(Graph::NodeId node) const
{
  return GraphImpl::getOutgoingNeighbors(node);
}
 
template<class GraphImpl>
size_t DAGraphImpl<GraphImpl>::getNumberOfSons(Graph::NodeId node) const
{
  return GraphImpl::getNumberOfOutgoingNeighbors(node);
}
 
template<class GraphImpl>
void DAGraphImpl<GraphImpl>::addSon(Graph::NodeId node, Graph::NodeId sonNode)
{
  GraphImpl::link(node, sonNode);
  topologyHasChanged_();
}
 
template<class GraphImpl>
void DAGraphImpl<GraphImpl>::addSon(Graph::NodeId node, Graph::NodeId sonNode, Graph::EdgeId edge)
{
  GraphImpl::link(node, sonNode, edge);
  topologyHasChanged_();
}
 
 
template<class GraphImpl>
std::vector<Graph::NodeId> DAGraphImpl<GraphImpl>::removeSons(Graph::NodeId node)
{
  std::vector<Graph::NodeId> sons = getSons(node);
  for (std::vector<Graph::NodeId>::iterator currSon = sons.begin(); currSon != sons.end(); currSon++)
  {
    removeSon(node, *currSon);
  }
  return sons;
}
 
 
template<class GraphImpl>
void DAGraphImpl<GraphImpl>::removeSon(Graph::NodeId node, Graph::NodeId son)
{
  GraphImpl::unlink(node, son);
}
 
 
template<class GraphImpl>
void DAGraphImpl<GraphImpl>::rootAt(Graph::NodeId newRoot)
{
  GraphImpl::setRoot(newRoot);
 
  // change edge direction between the new node and the former fathers
  if (isRooted() && isValid())
    propagateDirection_(newRoot);
  else
  {
    GraphImpl::orientate();
    isRooted_ = true;
  }
}
 
 
template<class GraphImpl>
void DAGraphImpl<GraphImpl>::propagateDirection_(Graph::NodeId node)
{
  std::vector<Graph::NodeId> vFat = getFathers(node);
  for (auto fat:vFat)
  {
    propagateDirection_(fat);
  }
 
  for (auto fat:vFat)
  {
    GraphImpl::switchNodes(fat, node);
  }
}
 
 
template<class GraphImpl>
std::vector<Graph::NodeId> DAGraphImpl<GraphImpl>::getBelowNodes(Graph::NodeId localRoot) const
{
  mustBeValid_();
  std::vector<Graph::EdgeId> metNodes;
  fillSubtreeMetNodes_(metNodes, localRoot);
  return metNodes;
}
 
template<class GraphImpl>
std::vector<Graph::EdgeId> DAGraphImpl<GraphImpl>::getBelowEdges(Graph::NodeId localRoot) const
{
  mustBeValid_();
  std::vector<Graph::EdgeId> metEdges;
  fillSubtreeMetEdges_(metEdges, localRoot);
  return metEdges;
}
 
 
template<class GraphImpl>
void DAGraphImpl<GraphImpl>::fillSubtreeMetNodes_(std::vector<Graph::NodeId>& metNodes, Graph::NodeId localRoot) const
{
  metNodes.push_back(localRoot);
  std::vector<Graph::NodeId> sons = GraphImpl::getOutgoingNeighbors(localRoot);
  for (std::vector<Graph::NodeId>::iterator currSon = sons.begin(); currSon != sons.end(); currSon++)
  {
    fillSubtreeMetNodes_(metNodes, *currSon);
  }
}
 
template<class GraphImpl>
void DAGraphImpl<GraphImpl>::fillSubtreeMetEdges_(std::vector<Graph::EdgeId>& metEdges, Graph::NodeId localRoot) const
{
  std::vector<Graph::EdgeId> edgesToSons = GraphImpl::getOutgoingEdges(localRoot);
  for (std::vector<Graph::EdgeId>::iterator currEdgeToSon = edgesToSons.begin(); currEdgeToSon != edgesToSons.end(); currEdgeToSon++)
  {
    metEdges.push_back(*currEdgeToSon);
    fillSubtreeMetEdges_(metEdges, GraphImpl::getBottom(*currEdgeToSon));
  }
}
}
#endif // BPP_GRAPH_DAGRAPHIMPL_H