AbstractHomogeneousTreeLikelihood.cpp

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//
// File: AbstractHomogeneousTreeLikelihood.cpp
// Created by: Julien Dutheil
// Created on: Thr Dec 23 12:03 2004
//

/*
   Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)

   This software is a computer program whose purpose is to provide classes
   for phylogenetic data analysis.

   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
   professionals having in-depth computer knowledge. Users are therefore
   encouraged to load and test the software's suitability as regards their
   requirements in conditions enabling the security of their systems and/or
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   same conditions as regards security.

   The fact that you are presently reading this means that you have had
   knowledge of the CeCILL license and that you accept its terms.
 */

#include "AbstractHomogeneousTreeLikelihood.h"
#include "../PatternTools.h"

#include <Bpp/Text/TextTools.h>
#include <Bpp/App/ApplicationTools.h>

// From bpp-seq:
#include <Bpp/Seq/SiteTools.h>
#include <Bpp/Seq/Container/SequenceContainerTools.h>

using namespace bpp;

// From the STL:
#include <iostream>

using namespace std;

/******************************************************************************/

AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(
  const Tree& tree,
  SubstitutionModel* model,
  DiscreteDistribution* rDist,
  bool checkRooted,
  bool verbose)
throw (Exception) :
  AbstractDiscreteRatesAcrossSitesTreeLikelihood(rDist, verbose),
  model_(0),
  brLenParameters_(),
  pxy_(),
  dpxy_(),
  d2pxy_(),
  rootFreqs_(),
  nodes_(),
  nbSites_(),
  nbDistinctSites_(),
  nbClasses_(),
  nbStates_(),
  nbNodes_(),
  verbose_(),
  minimumBrLen_(),
  maximumBrLen_(),
  brLenConstraint_()
{
  init_(tree, model, rDist, checkRooted, verbose);
}

/******************************************************************************/

AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(
  const AbstractHomogeneousTreeLikelihood& lik) :
  AbstractDiscreteRatesAcrossSitesTreeLikelihood(lik),
  model_(lik.model_),
  brLenParameters_(lik.brLenParameters_),
  pxy_(lik.pxy_),
  dpxy_(lik.dpxy_),
  d2pxy_(lik.d2pxy_),
  rootFreqs_(lik.rootFreqs_),
  nodes_(),
  nbSites_(lik.nbSites_),
  nbDistinctSites_(lik.nbDistinctSites_),
  nbClasses_(lik.nbClasses_),
  nbStates_(lik.nbStates_),
  nbNodes_(lik.nbNodes_),
  verbose_(lik.verbose_),
  minimumBrLen_(lik.minimumBrLen_),
  maximumBrLen_(lik.maximumBrLen_),
  brLenConstraint_(lik.brLenConstraint_->clone())
{
  nodes_ = tree_->getNodes();
  nodes_.pop_back(); // Remove the root node (the last added!).
}

/******************************************************************************/

AbstractHomogeneousTreeLikelihood& AbstractHomogeneousTreeLikelihood::operator=(
  const AbstractHomogeneousTreeLikelihood& lik)
{
  AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=(lik);
  model_           = lik.model_;
  brLenParameters_ = lik.brLenParameters_;
  pxy_             = lik.pxy_;
  dpxy_            = lik.dpxy_;
  d2pxy_           = lik.d2pxy_;
  rootFreqs_       = lik.rootFreqs_;
  nodes_ = tree_->getNodes();
  nodes_.pop_back(); // Remove the root node (the last added!).
  nbSites_         = lik.nbSites_;
  nbDistinctSites_ = lik.nbDistinctSites_;
  nbClasses_       = lik.nbClasses_;
  nbStates_        = lik.nbStates_;
  nbNodes_         = lik.nbNodes_;
  verbose_         = lik.verbose_;
  minimumBrLen_    = lik.minimumBrLen_;
  maximumBrLen_    = lik.maximumBrLen_;
  if (brLenConstraint_.get()) brLenConstraint_.release();
  brLenConstraint_.reset(lik.brLenConstraint_->clone());
  return *this;
}

/******************************************************************************/

void AbstractHomogeneousTreeLikelihood::init_(
  const Tree& tree,
  SubstitutionModel* model,
  DiscreteDistribution* rDist,
  bool checkRooted,
  bool verbose) throw (Exception)
{
  TreeTools::checkIds(tree, true);
  tree_ = new TreeTemplate<Node>(tree);
  if (checkRooted && tree_->isRooted())
  {
    if (verbose)
      ApplicationTools::displayWarning("Tree has been unrooted.");
    tree_->unroot();
  }
  nodes_ = tree_->getNodes();
  nodes_.pop_back(); // Remove the root node (the last added!).
  nbNodes_ = nodes_.size();
  nbClasses_ = rateDistribution_->getNumberOfCategories();
  setSubstitutionModel(model);

  verbose_ = verbose;

  minimumBrLen_ = 0.000001;
  maximumBrLen_ = 10000;
  brLenConstraint_.reset(new IntervalConstraint(minimumBrLen_, maximumBrLen_, true, true));
}

/******************************************************************************/

void AbstractHomogeneousTreeLikelihood::setSubstitutionModel(SubstitutionModel* model) throw (Exception)
{
  // Check:
  if (data_)
  {
    if (model->getAlphabet()->getAlphabetType() != data_->getAlphabet()->getAlphabetType())
      throw Exception("AbstractHomogeneousTreeLikelihood::setSubstitutionModel(). Model alphabet do not match existing data.");
  }

  model_ = model;

  if (data_)
  {
    if (model->getNumberOfStates() != model_->getNumberOfStates())
      setData(*data_);  // Have to reinitialize the whole data structure.
  }

  nbStates_ = model->getNumberOfStates();

  // Allocate transition probabilities arrays:
  for (unsigned int l = 0; l < nbNodes_; l++)
  {
    // For each son node,i
    Node* son = nodes_[l];

    VVVdouble* pxy__son = &pxy_[son->getId()];
    pxy__son->resize(nbClasses_);
    for (unsigned int c = 0; c < nbClasses_; c++)
    {
      VVdouble* pxy__son_c = &(*pxy__son)[c];
      pxy__son_c->resize(nbStates_);
      for (unsigned int x = 0; x < nbStates_; x++)
      {
        (*pxy__son_c)[x].resize(nbStates_);
      }
    }

    VVVdouble* dpxy__son = &dpxy_[son->getId()];
    dpxy__son->resize(nbClasses_);
    for (unsigned int c = 0; c < nbClasses_; c++)
    {
      VVdouble* dpxy__son_c = &(*dpxy__son)[c];
      dpxy__son_c->resize(nbStates_);
      for (unsigned int x = 0; x < nbStates_; x++)
      {
        (*dpxy__son_c)[x].resize(nbStates_);
      }
    }

    VVVdouble* d2pxy__son = &d2pxy_[son->getId()];
    d2pxy__son->resize(nbClasses_);
    for (unsigned int c = 0; c < nbClasses_; c++)
    {
      VVdouble* d2pxy__son_c = &(*d2pxy__son)[c];
      d2pxy__son_c->resize(nbStates_);
      for (unsigned int x = 0; x < nbStates_; x++)
      {
        (*d2pxy__son_c)[x].resize(nbStates_);
      }
    }
  }
}

/******************************************************************************/

void AbstractHomogeneousTreeLikelihood::initialize() throw (Exception)
{
  if (initialized_)
    throw Exception("AbstractHomogeneousTreeLikelihood::initialize(). Object is already initialized.");
  if (!data_)
    throw Exception("AbstractHomogeneousTreeLikelihood::initialize(). Data are no set.");
  initParameters();
  initialized_ = true;
  fireParameterChanged(getParameters());
}

/******************************************************************************/

ParameterList AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters() const
{
  if (!initialized_)
    throw Exception("AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters(). Object is not initialized.");
  return brLenParameters_.getCommonParametersWith(getParameters());
}

/******************************************************************************/

ParameterList AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters() const
{
  if (!initialized_)
    throw Exception("AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(). Object is not initialized.");
  return model_->getParameters().getCommonParametersWith(getParameters());
}

/******************************************************************************/

void AbstractHomogeneousTreeLikelihood::initParameters()
{
  // Reset parameters:
  resetParameters_();

  // Branch lengths:
  initBranchLengthsParameters();
  addParameters_(brLenParameters_);

  // Substitution model:
  addParameters_(model_->getIndependentParameters());

  // Rate distribution:
  addParameters_(rateDistribution_->getIndependentParameters());
}

/******************************************************************************/

void AbstractHomogeneousTreeLikelihood::applyParameters() throw (Exception)
{
  if (!initialized_)
    throw Exception("AbstractHomogeneousTreeLikelihood::applyParameters(). Object not initialized.");
  // Apply branch lengths:
  // brLenParameters_.matchParametersValues(parameters_); Not necessary!
  for (unsigned int i = 0; i < nbNodes_; i++)
  {
    const Parameter* brLen = &getParameter(string("BrLen") + TextTools::toString(i));
    if (brLen)
      nodes_[i]->setDistanceToFather(brLen->getValue());
  }
  // Apply substitution model parameters:
  model_->matchParametersValues(getParameters());
  rootFreqs_ = model_->getFrequencies();
  // Apply rate distribution parameters:
  rateDistribution_->matchParametersValues(getParameters());
}

/******************************************************************************/

void AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters()
{
  brLenParameters_.reset();
  for (unsigned int i = 0; i < nbNodes_; i++)
  {
    double d = minimumBrLen_;
    if (!nodes_[i]->hasDistanceToFather())
    {
      ApplicationTools::displayWarning("Missing branch length " + TextTools::toString(i) + ". Value is set to " + TextTools::toString(minimumBrLen_));
      nodes_[i]->setDistanceToFather(minimumBrLen_);
    }
    else
    {
      d = nodes_[i]->getDistanceToFather();
      if (d < minimumBrLen_)
      {
        ApplicationTools::displayWarning("Branch length " + TextTools::toString(i) + " is too small: " + TextTools::toString(d) + ". Value is set to " + TextTools::toString(minimumBrLen_));
        nodes_[i]->setDistanceToFather(minimumBrLen_);
        d = minimumBrLen_;
      }
      if (d > maximumBrLen_)
      {
        ApplicationTools::displayWarning("Branch length " + TextTools::toString(i) + " is too big: " + TextTools::toString(d) + ". Value is set to " + TextTools::toString(maximumBrLen_));
        nodes_[i]->setDistanceToFather(maximumBrLen_);
        d = maximumBrLen_;
      }
    }
    brLenParameters_.addParameter(Parameter("BrLen" + TextTools::toString(i), d, brLenConstraint_->clone(), true)); // Attach constraint to avoid clonage problems!
  }
}

/*******************************************************************************/

void AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities()
{
  for (unsigned int l = 0; l < nbNodes_; l++)
  {
    // For each node,
    Node* node = nodes_[l];
    computeTransitionProbabilitiesForNode(node);
  }
  rootFreqs_ = model_->getFrequencies();
}

/*******************************************************************************/

void AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(const Node* node)
{
  double l = node->getDistanceToFather();

  // Computes all pxy and pyx once for all:
  VVVdouble* pxy__node = &pxy_[node->getId()];
  for (unsigned int c = 0; c < nbClasses_; c++)
  {
    VVdouble* pxy__node_c = &(*pxy__node)[c];
    RowMatrix<double> Q = model_->getPij_t(l * rateDistribution_->getCategory(c));

    for (unsigned int x = 0; x < nbStates_; x++)
    {
      Vdouble* pxy__node_c_x = &(*pxy__node_c)[x];
      for (unsigned int y = 0; y < nbStates_; y++)
      {
        (*pxy__node_c_x)[y] = Q(x, y);
      }
    }
  }
  
  if (computeFirstOrderDerivatives_)
  {
    // Computes all dpxy/dt once for all:
    VVVdouble* dpxy__node = &dpxy_[node->getId()];
    for (unsigned int c = 0; c < nbClasses_; c++)
    {
      VVdouble* dpxy__node_c = &(*dpxy__node)[c];
      double rc = rateDistribution_->getCategory(c);
      RowMatrix<double> dQ = model_->getdPij_dt(l * rc);
      for (unsigned int x = 0; x < nbStates_; x++)
      {
        Vdouble* dpxy__node_c_x = &(*dpxy__node_c)[x];
        for (unsigned int y = 0; y < nbStates_; y++)
        {
          (*dpxy__node_c_x)[y] = rc * dQ(x, y);
        }
      }
    }
  }

  if (computeSecondOrderDerivatives_)
  {
    // Computes all d2pxy/dt2 once for all:
    VVVdouble* d2pxy__node = &d2pxy_[node->getId()];
    for (unsigned int c = 0; c < nbClasses_; c++)
    {
      VVdouble* d2pxy__node_c = &(*d2pxy__node)[c];
      double rc =  rateDistribution_->getCategory(c);
      RowMatrix<double> d2Q = model_->getd2Pij_dt2(l * rc);
      for (unsigned int x = 0; x < nbStates_; x++)
      {
        Vdouble* d2pxy__node_c_x = &(*d2pxy__node_c)[x];
        for (unsigned int y = 0; y < nbStates_; y++)
        {
          (*d2pxy__node_c_x)[y] = rc * rc * d2Q(x, y);
        }
      }
    }
  }
}

/*******************************************************************************/