Node.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Exceptions.h>
#include <Bpp/Text/TextTools.h>
 
#include "Node.h"
#include "TreeTools.h"
#include "PhyloTree.h"
 
using namespace bpp;
 
// from the STL:
#include <algorithm>
#include <iostream>
 
using namespace std;
 
Node::Node(const Node& node) :
  id_(node.id_), name_(0),
  sons_(), father_(0),
  // , sons_(node.sons_), father_(node.father_),
  distanceToFather_(0), nodeProperties_(), branchProperties_()
{
  name_             = node.hasName() ? new string(*node.name_) : 0;
  distanceToFather_ = node.hasDistanceToFather() ? new double(*node.distanceToFather_) : 0;
  for (map<string, Clonable*>::iterator i = node.nodeProperties_.begin(); i != node.nodeProperties_.end(); i++)
  {
    nodeProperties_[i->first] = i->second->clone();
  }
  for (map<string, Clonable*>::iterator i = node.branchProperties_.begin(); i != node.branchProperties_.end(); i++)
  {
    branchProperties_[i->first] = i->second->clone();
  }
}
 
Node& Node::operator=(const Node& node)
{
  id_               = node.id_;
  if (name_)
    delete name_;
  name_             = node.hasName() ? new string(*node.name_) : 0;
  // father_           = node.father_;
  if (distanceToFather_)
    delete distanceToFather_;
  distanceToFather_ = node.hasDistanceToFather() ? new double(*node.distanceToFather_) : 0;
  // sons_             = node.sons_;
  for (map<string, Clonable*>::iterator i = node.nodeProperties_.begin(); i != node.nodeProperties_.end(); i++)
  {
    Clonable* p = nodeProperties_[i->first];
    if (p)
      delete p;
    nodeProperties_[i->first] = i->second->clone();
  }
  for (map<string, Clonable*>::iterator i = node.branchProperties_.begin(); i != node.branchProperties_.end(); i++)
  {
    Clonable* p = branchProperties_[i->first];
    if (p)
      delete p;
    branchProperties_[i->first] = i->second->clone();
  }
  return *this;
}
 
void Node::addSubTree(const PhyloTree& tree, std::shared_ptr<PhyloNode> phyloNode)
{
  // set Id
  setId(static_cast<int>(tree.getNodeIndex(phyloNode)));
 
  // features of the node
  auto vnames = phyloNode->getPropertyNames();
  for (const auto& name:vnames)
  {
    setNodeProperty(name, *phyloNode->getProperty(name));
  }
 
  if (phyloNode->hasName())
    setName(phyloNode->getName());
 
  // look at sons
  vector<shared_ptr<PhyloNode>> sons = tree.getSons(phyloNode);
  for (auto& son : sons)
  {
    Node* s1 = new Node();
 
    // features of the branch
    const auto phylobranch = tree.getIncomingEdges(son)[0]; // Tree -> one incoming edge
 
    if (phylobranch->hasLength())
      s1->setDistanceToFather(phylobranch->getLength());
 
    auto vnames2 = phylobranch->getPropertyNames();
    for (const auto& name:vnames2)
    {
      s1->setBranchProperty(name, *phylobranch->getProperty(name));
    }
 
    // recursive
    s1->addSubTree(tree, son);
 
    // addSon
    addSon(s1);
  }
}
 
void Node::swap(size_t branch1, size_t branch2)
{
  if (branch1 > branch2)
  {
    size_t tmp = branch1;
    branch1 = branch2;
    branch2 = tmp;
  }
  Node* node1 = getSon(branch1);
  Node* node2 = getSon(branch2);
  removeSon(node1);
  removeSon(node2);
  addSon(branch1, node2);
  addSon(branch2, node1);
}
 
vector<const Node*> Node::getNeighbors() const
{
  vector<const Node*> neighbors;
  if (hasFather())
    neighbors.push_back(father_);
  for (size_t i = 0; i < sons_.size(); i++)
  {
    neighbors.push_back(sons_[i]);
  }
  return neighbors;
}
 
vector<Node*> Node::getNeighbors()
{
  vector<Node*> neighbors;
  if (hasFather())
    neighbors.push_back(father_);
  for (size_t i = 0; i < sons_.size(); i++)
  {
    neighbors.push_back(sons_[i]);
  }
  return neighbors;
}
 
size_t Node::getSonPosition(const Node* son) const
{
  if (!son)
    throw NullPointerException("Node::getSonPosition(). Empty node given as input.");
  for (size_t i = 0; i < sons_.size(); i++)
  {
    if (sons_[i] == son)
      return i;
  }
  throw NodeNotFoundException("Son not found", TextTools::toString(son->getId()));
}
 
bool Node::hasBootstrapValue() const
{
  return hasBranchProperty(TreeTools::BOOTSTRAP);
}
 
double Node::getBootstrapValue() const
{
  if (hasBranchProperty(TreeTools::BOOTSTRAP))
    return dynamic_cast<const Number<double>*>(getBranchProperty(TreeTools::BOOTSTRAP))->getValue();
  else
    throw PropertyNotFoundException("", TreeTools::BOOTSTRAP, this);
}
 
/******************************************************************************/