PhyloBranch.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_TREE_PHYLOBRANCH_H
#define BPP_PHYL_TREE_PHYLOBRANCH_H
 
#include <Bpp/Clonable.h>
#include <Bpp/Numeric/Number.h>
#include <Bpp/Utils/MapTools.h>
 
#include "PhyloTreeExceptions.h"
 
#include <iostream>
 
namespace bpp
{
class PhyloBranchParam;
 
class PhyloBranch
{
protected:
  bool isLengthDefined_;
  double length_;
  mutable std::map<std::string, Clonable*> properties_;
 
public:
  PhyloBranch() :
    isLengthDefined_(false),
    length_(0),
    properties_()
  {}
 
  PhyloBranch(double length) :
    isLengthDefined_(true),
    length_(length),
    properties_()
  {}
 
  PhyloBranch(const PhyloBranchParam& branch);
 
  PhyloBranch(const PhyloBranch& branch);
 
  PhyloBranch& operator=(const PhyloBranch& branch);
 
  PhyloBranch* clone() const { return new PhyloBranch(*this); }
 
  virtual ~PhyloBranch()
  {
    deleteProperties();
  }
 
  bool hasLength() const
  {
    return isLengthDefined_;
  }
 
 
  void deleteLength()
  {
    isLengthDefined_ = false;
  }
 
  double getLength() const
  {
    if (!isLengthDefined_)
      throw PhyloBranchPException("PhyloBranch::getLength: length is not defined.", this);
 
    return length_;
  }
 
 
  void setLength(double newLength)
  {
    length_ = newLength;
    isLengthDefined_ = true;
  }
 
  void setProperty(const std::string& name, const Clonable& property)
  {
    if (hasProperty(name))
      delete properties_[name];
    properties_[name] = property.clone();
  }
 
  Clonable* getProperty(const std::string& name)
  {
    if (hasProperty(name))
      return properties_[name];
    else
      throw PhyloBranchPropertyNotFoundException("", name, this);
  }
 
  const Clonable* getProperty(const std::string& name) const
  {
    if (hasProperty(name))
      return const_cast<const Clonable*>(properties_[name]);
    else
      throw PhyloBranchPropertyNotFoundException("", name, this);
  }
 
  Clonable* removeProperty(const std::string& name)
  {
    if (hasProperty(name))
    {
      Clonable* removed = properties_[name];
      properties_.erase(name);
      return removed;
    }
    else
      throw PhyloBranchPropertyNotFoundException("", name, this);
  }
 
  void deleteProperty(const std::string& name)
  {
    if (hasProperty(name))
    {
      delete properties_[name];
      properties_.erase(name);
    }
    else
      throw PhyloBranchPropertyNotFoundException("", name, this);
  }
 
  void removeProperties()
  {
    properties_.clear();
  }
 
  void deleteProperties()
  {
    for (std::map<std::string, Clonable*>::iterator i = properties_.begin(); i != properties_.end(); i++)
    {
      delete i->second;
    }
    properties_.clear();
  }
 
  bool hasProperty(const std::string& name) const { return properties_.find(name) != properties_.end(); }
 
  std::vector<std::string> getPropertyNames() const { return MapTools::getKeys(properties_); }
 
  bool hasBootstrapValue() const
  {
    return properties_.find("bootstrap") != properties_.end();
  }
 
  double getBootstrapValue() const
  {
    if (!hasBootstrapValue())
      throw PhyloBranchPropertyNotFoundException("", "bootstrap", this);
 
    return (dynamic_cast<const Number<double>*>(properties_.find("bootstrap")->second))->getValue();
  }
}; // end of class PhyloBranch
} // end of namespace bpp.
#endif // BPP_PHYL_TREE_PHYLOBRANCH_H