PhyloTreeTools.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_TREE_PHYLOTREETOOLS_H
#define BPP_PHYL_TREE_PHYLOTREETOOLS_H
 
#include <Bpp/Exceptions.h>
#include <Bpp/Numeric/VectorTools.h>
 
#include "PhyloBranch.h"
#include "PhyloNode.h"
#include "PhyloTree.h"
#include "PhyloTreeExceptions.h"
#include "TreeTemplate.h"
 
// From SeqLib:
#include <Bpp/Seq/Container/VectorSiteContainer.h>
#include <Bpp/Seq/DistanceMatrix.h>
 
#include <memory>
 
namespace bpp
{
class PhyloTreeTools
{
public:
  PhyloTreeTools() {}
  virtual ~PhyloTreeTools() {}
 
public:
  static std::shared_ptr<PhyloTree> buildFromTreeTemplate(const TreeTemplate<Node>& treetemp);
 
  static double getHeight(const PhyloTree& tree, const std::shared_ptr<PhyloNode> node);
 
  static void initBranchLengthsGrafen(PhyloTree& tree);
 
  static void computeBranchLengthsGrafen(PhyloTree& tree, double power = 1, bool init = true);
 
private:
  static size_t initBranchLengthsGrafen(PhyloTree& tree, std::shared_ptr<PhyloNode> node);
 
  static void computeBranchLengthsGrafen(PhyloTree& tree, std::shared_ptr<PhyloNode> node, double power, double total, double& height, double& heightRaised);
 
public:
  static double convertToClockTree(PhyloTree& tree, std::shared_ptr<PhyloNode> node);
 
  static double convertToClockTree2(PhyloTree& tree, std::shared_ptr<PhyloNode> node);
 
 
  static void constrainedMidPointRooting(PhyloTree& tree);
 
  static const std::string BOOTSTRAP;
 
private:
  struct Moments_
  {
    double N;
    double sum, squaredSum;
    Moments_() : N(0),
      sum(0),
      squaredSum(0) {}
  };
 
  static Moments_ statFromNode_(const PhyloTree& tree, const std::shared_ptr<PhyloNode> root);
  static double bestRootPosition_(const PhyloTree& tree, const std::shared_ptr<PhyloNode> node1, const std::shared_ptr<PhyloNode> node2, double length);
 
 
};
} // end of namespace bpp.
#endif // BPP_PHYL_TREE_PHYLOTREETOOLS_H