TreeGraph.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1

#ifndef BPP_GRAPH_TREEGRAPH_H
#define BPP_GRAPH_TREEGRAPH_H

#include <iostream>
#include <ostream>
#include <string>
#include <vector>

#include "../Exceptions.h"
#include "../Numeric/VectorTools.h"
#include "Graph.h"

namespace bpp
{
class TreeGraph :
  public virtual Graph
{
public:
  virtual bool isValid() const = 0;

  virtual Graph::NodeId getFatherOfNode(Graph::NodeId nodeid) const = 0;

  virtual Graph::EdgeId getEdgeToFather(Graph::NodeId node) const = 0;

  virtual bool hasFather(Graph::NodeId node) const = 0;

  virtual bool isLeaf(Graph::NodeId node) const = 0;

  virtual std::vector<Graph::NodeId> getLeavesUnderNode(Graph::NodeId node) const = 0;

  virtual std::vector<Graph::NodeId> getSons(Graph::NodeId node) const = 0;

  virtual std::vector<Graph::EdgeId> getBranches(Graph::NodeId node) const = 0;

  virtual std::unique_ptr<Graph::NodeIterator> sonsIterator(Graph::NodeId node) = 0;

  virtual std::unique_ptr<Graph::NodeIterator> sonsIterator(Graph::NodeId node) const = 0;

  virtual std::unique_ptr<Graph::EdgeIterator> branchesIterator(Graph::NodeId node) = 0;

  virtual std::unique_ptr<Graph::EdgeIterator> branchesIterator(Graph::NodeId node) const = 0;

  virtual size_t getNumberOfSons(Graph::NodeId node) const = 0;

  virtual void setFather(Graph::NodeId node, Graph::NodeId fatherNode) = 0;

  virtual void setFather(Graph::NodeId node, Graph::NodeId fatherNode, Graph::EdgeId edgeId) = 0;

  virtual void addSon(Graph::NodeId node, Graph::NodeId sonNode) = 0;

  virtual void addSon(Graph::NodeId node, Graph::NodeId sonNode, Graph::EdgeId edgeId) = 0;

  std::vector<Graph::NodeId> removeSons(Graph::NodeId node);

  virtual void removeSon(Graph::NodeId node, Graph::NodeId son) = 0;

  virtual void rootAt(Graph::NodeId newRoot) = 0;

  virtual void unRoot(bool joinRootSons) = 0;

  virtual void setOutGroup(Graph::NodeId newOutGroup) = 0;

  virtual std::vector<Graph::NodeId> getSubtreeNodes(Graph::NodeId localRoot) const = 0;

  virtual std::vector<Graph::EdgeId> getSubtreeEdges(Graph::NodeId localRoot) const = 0;

  // ///FROM TREETOOLS & TREETOOLS COMPAT


  virtual std::vector<Graph::NodeId> getNodePathBetweenTwoNodes(Graph::NodeId nodeA, Graph::NodeId nodeB, bool includeAncestor = true) const = 0;

  virtual std::vector<Graph::EdgeId> getEdgePathBetweenTwoNodes(Graph::NodeId nodeA, Graph::NodeId nodeB) const = 0;

  /*
   * @bref Compute the MRCA of the gven nodes
   *
   */

  virtual Graph::NodeId MRCA(const std::vector<Graph::NodeId>& nodes) const = 0;
};
}
#endif // BPP_GRAPH_TREEGRAPH_H