MixtureOfSubstitutionModels.cpp

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//
// File: MixtureOfSubstitutionModels.cpp
// Created by: Laurent Gueguen
// Date: mardi 14 septembre 2010, à 20h 43
//
/*
   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,
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 */

#include "MixtureOfSubstitutionModels.h"

#include <Bpp/Numeric/NumConstants.h>
#include <Bpp/Text/TextTools.h>

#include <string>

using namespace bpp;
using namespace std;

MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(
  const Alphabet* alpha,
  vector<SubstitutionModel*> vpModel) :
  AbstractParameterAliasable("Mixture."),
  AbstractMixedSubstitutionModel(alpha, vpModel[0]->getStateMap().clone(), "Mixture.")
{
  size_t i, nbmod = vpModel.size();

  for (i = 0; i < nbmod; i++)
  {
    if (!vpModel[i])
      throw Exception("Empty model number " + TextTools::toString(i) + " in MixtureOfSubstitutionModels constructor");
    for (size_t j = i + 1; j < nbmod; j++)
    {
      if (vpModel[i] == vpModel[j])
        throw Exception("Same model at positions " + TextTools::toString(i) + " and " +
                        TextTools::toString(j) + " in MixtureOfSubstitutionModels constructor");
    }
  }

  // Initialization of modelsContainer_.

  for (i = 0; i < nbmod; i++)
  {
    modelsContainer_.push_back(vpModel[i]);
    vProbas_.push_back(1.0 / static_cast<double>(nbmod));
    vRates_.push_back(1.0);
  }

  // Initialization of parameters_.

  // relative rates and probas
  for (i = 0; i < nbmod - 1; i++)
  {
    addParameter_(new Parameter("Mixture.relproba" + TextTools::toString(i + 1), 1.0 / static_cast<double>(nbmod - i), &Parameter::PROP_CONSTRAINT_EX));
    addParameter_(new Parameter("Mixture.relrate" + TextTools::toString(i + 1), 1.0 / static_cast<double>(nbmod - i), &Parameter::PROP_CONSTRAINT_EX));
  }

  // models parameters

  for (i = 0; i < nbmod; i++)
  {
    modelsContainer_[i]->setNamespace("Mixture." + TextTools::toString(i + 1) + "_" + vpModel[i]->getNamespace());
    addParameters_(vpModel[i]->getParameters());
  }

  for (i = 0; i < nbmod; i++)
  {
    vpModel[i]->addRateParameter();
  }

  updateMatrices();
}

MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(
    const Alphabet* alpha,
    vector<SubstitutionModel*> vpModel,
    Vdouble& vproba,
    Vdouble& vrate) :
  AbstractParameterAliasable("Mixture."),
  AbstractMixedSubstitutionModel(alpha, vpModel[0]->getStateMap().clone(), "Mixture.")
{
  size_t i, nbmod = vpModel.size();

  for (i = 0; i < nbmod; i++)
  {
    if (!vpModel[i])
      throw Exception("Empty model number " + TextTools::toString(i) + " in MixtureOfSubstitutionModels constructor");
    for (size_t j = i + 1; j < nbmod; j++)
    {
      if (vpModel[i] == vpModel[j])
        throw Exception("Same model at positions " + TextTools::toString(i) + " and " +
                        TextTools::toString(j) + " in MixtureOfSubstitutionModels constructor");
    }
  }

  double x = 0;
  double y = 0;

  for (i = 0; i < nbmod; i++)
  {
    if (vrate[i] <= 0)
      throw Exception("Non positive rate: " + TextTools::toString(vrate[i]) + " in MixtureOfSubstitutionModels constructor.");
    if (vproba[i] <= 0)
      throw Exception("Non positive probability: " + TextTools::toString(vproba[i]) + " in MixtureOfSubstitutionModels constructor.");
    x += vproba[i];
    y += vproba[i] * vrate[i];
  }

  if (fabs(1. - x) > NumConstants::SMALL())
    throw Exception("Probabilities must equal 1 (sum = " + TextTools::toString(x) + ").");
  if (fabs(1. - y) > NumConstants::SMALL())
    throw Exception("Expectation on rates must equal 1 (E =" + TextTools::toString(y) + ").");


  // Initialization of modelsContainer_.

  for (i = 0; i < nbmod; i++)
  {
    modelsContainer_.push_back(vpModel[i]);
  }

  // rates & probas

  for (i = 0; i < nbmod; i++)
  {
    vProbas_.push_back(1.0 / static_cast<double>(nbmod));
    vRates_.push_back(1.0);
  }

  // Initialization of parameters_.


  // relative rates and probas
  x = 0; y = 0;

  for (i = 0; i < nbmod - 1; i++)
  {
    addParameter_(new Parameter("Mixture.relproba" + TextTools::toString(i + 1), vproba[i] / (1 - x), &Parameter::PROP_CONSTRAINT_EX));
    x += vproba[i];
    addParameter_(new Parameter("Mixture.relrate" + TextTools::toString(i + 1), vproba[i] * vrate[i] / (1 - y), &Parameter::PROP_CONSTRAINT_EX));
    y += vproba[i] * vrate[i];
  }

  // models parameters

  for (i = 0; i < nbmod; i++)
  {
    modelsContainer_[i]->setNamespace("Mixture." + TextTools::toString(i + 1) + "_" + vpModel[i]->getNamespace());
    addParameters_(vpModel[i]->getParameters());
  }

  for (i = 0; i < nbmod; i++)
  {
    vpModel[i]->addRateParameter();
  }

  updateMatrices();
}

MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const MixtureOfSubstitutionModels& msm) :
  AbstractParameterAliasable(msm),
  AbstractMixedSubstitutionModel(msm)
{}

MixtureOfSubstitutionModels& MixtureOfSubstitutionModels::operator=(const MixtureOfSubstitutionModels& msm)
{
  AbstractMixedSubstitutionModel::operator=(msm);

  return *this;
}


MixtureOfSubstitutionModels::~MixtureOfSubstitutionModels()
{}


void MixtureOfSubstitutionModels::updateMatrices()
{
  size_t i, j, nbmod = modelsContainer_.size();

  double x, y;
  x = 1.0;

  for (i = 0; i < nbmod - 1; i++)
  {
    y = getParameterValue("relproba" + TextTools::toString(i + 1));
    vProbas_[i] = x * y;
    x *= 1 - y;
  }
  vProbas_[nbmod - 1] = x;

  x = 1.0;
  bool approx = false; // used when some categories are avoided
  double s = 0;
  for (i = 0; i < nbmod - 1; i++)
  {
    y = getParameterValue("relrate" + TextTools::toString(i + 1));
    if (vProbas_[i] < NumConstants::SMALL())
    {
      vRates_[i] = NumConstants::SMALL();
      approx = true;
    }
    else
    {
      vRates_[i] = x * y / vProbas_[i];
      s += x * y;
    }
    x *= 1 - y;
  }

  if (vProbas_[nbmod - 1] < NumConstants::SMALL())
  {
    vRates_[nbmod - 1] = NumConstants::SMALL();
    approx = true;
  }
  else
  {
    vRates_[nbmod - 1] = x / vProbas_[nbmod - 1];
    s += x;
  }

  if (approx)
    for (i = 0; i < nbmod; i++)
    {
      vRates_[i] /= s;
    }

  // / models

  for (i = 0; i < nbmod; i++)
  {
    modelsContainer_[i]->setRate(vRates_[i]);
    modelsContainer_[i]->matchParametersValues(getParameters());
  }

  // / freq_

  for (i = 0; i < getNumberOfStates(); i++)
  {
    freq_[i] = 0;
    for (j = 0; j < modelsContainer_.size(); j++)
    {
      freq_[i] += vProbas_[j] * modelsContainer_[j]->freq(i);
    }
  }
}

void MixtureOfSubstitutionModels::setFreq(std::map<int, double>& m)
{
  ParameterList pl;
  for (unsigned int n = 0; n < modelsContainer_.size(); n++)
  {
    modelsContainer_[n]->setFreq(m);
    pl.addParameters(modelsContainer_[n]->getParameters());
  }
  matchParametersValues(pl);
}

void MixtureOfSubstitutionModels::setVRates(const Vdouble& vd)
{
  AbstractMixedSubstitutionModel::setVRates(vd);

  size_t i, nbmod = modelsContainer_.size();
  double sP = 0;
  for (i = 0; i < nbmod - 1; i++)
  {
    sP += vProbas_[i];
  }

  double y = 0;
  for (i = 0; i < nbmod - 1; i++)
  {
    setParameterValue("relrate" + TextTools::toString(i + 1), vProbas_[i] / sP * vRates_[i] / (1 - y));
    y += vProbas_[i] / sP * vRates_[i];
  }
}

Vint MixtureOfSubstitutionModels::getSubmodelNumbers(string& desc) const
{
  size_t i;
  for (i = 0; i < getNumberOfModels(); i++)
  {
    if (getNModel(i)->getName() == desc)
      break;
  }
  if (i == getNumberOfModels())
    throw Exception("MixtureOfSubstitutionModels::getSubmodelNumbers model description do not match " + desc);

  Vint submodnb;
  submodnb.push_back(static_cast<int>(i));

  return submodnb;
}