DecompositionSubstitutionCount.cpp

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//
// File: DecompositionSubstitutionCount.h
// Created by: Julien Dutheil
// Created on: Thu Mar 17 16:08 2011
//

/*
Copyright or © or Copr. Bio++ Development Team, (November 16, 2004, 2005, 2006)

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". 

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that may mean  that it is complicated to manipulate,  and  that  also
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*/

#include "DecompositionSubstitutionCount.h"

#include "Bpp/Numeric/Matrix/MatrixTools.h"
#include <vector>

using namespace bpp;
using namespace std;

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

DecompositionSubstitutionCount::DecompositionSubstitutionCount(const ReversibleSubstitutionModel* model, SubstitutionRegister* reg, const AlphabetIndex2* weights) :
  AbstractSubstitutionCount(reg),
  AbstractWeightedSubstitutionCount(weights, true),
  model_(model),
  nbStates_(model->getNumberOfStates()),
  jMat_(nbStates_, nbStates_),
  v_(nbStates_, nbStates_),
  vInv_(nbStates_, nbStates_),
  lambda_(nbStates_, nbStates_),
  bMatrices_(reg->getNumberOfSubstitutionTypes()),
  insideProducts_(reg->getNumberOfSubstitutionTypes()),
  counts_(reg->getNumberOfSubstitutionTypes()),
  currentLength_(-1.)
{
  //Check compatiblity between model and substitution register:
  if (model->getAlphabet()->getAlphabetType() != reg->getAlphabet()->getAlphabetType())
    throw Exception("DecompositionSubstitutionCount (constructor): alphabets do not match between register and model.");

  //Initialize all B matrices according to substitution register. This is done once for all,
  //unless the number of states changes:
  initBMatrices_();
  fillBMatrices_();
  computeEigen_();
  computeProducts_();
}       
    
/******************************************************************************/

void DecompositionSubstitutionCount::fillBMatrices_()
{
  vector<int> supportedStates = model_->getAlphabetStates();
  for (size_t j = 0; j < nbStates_; ++j) {
    for (size_t k = 0; k < nbStates_; ++k) {
      size_t i = register_->getType(j, k);
      if (i > 0 && k != j) {
        //jdutheil on 25/07/14: I think this is incorrect, weights should only come at the end.
        //bMatrices_[i - 1](j, k) = model_->Qij(j, k) * (weights_ ? weights_->getIndex(fromState, toState) : 1);
        bMatrices_[i - 1](j, k) = model_->Qij(j, k);
      }
    }
  }
}

void DecompositionSubstitutionCount::computeEigen_()
{
  v_      = model_->getColumnRightEigenVectors();
  vInv_   = model_->getRowLeftEigenVectors();
  lambda_ = model_->getEigenValues();
}

void DecompositionSubstitutionCount::computeProducts_()
{
  for (size_t i = 0; i < register_->getNumberOfSubstitutionTypes(); ++i) {
    //vInv_ %*% bMatrices_[i] %*% v_;
    RowMatrix<double> tmp(nbStates_, nbStates_);
    MatrixTools::mult(vInv_, bMatrices_[i], tmp);
    MatrixTools::mult(tmp, v_, insideProducts_[i]);
  }
}

void DecompositionSubstitutionCount::resetBMatrices_()
{
  size_t nbTypes = register_->getNumberOfSubstitutionTypes();
  bMatrices_.resize(nbTypes);
  insideProducts_.resize(nbTypes);
  counts_.resize(nbTypes);
}

void DecompositionSubstitutionCount::resetStates_()
{
  jMat_.resize(nbStates_, nbStates_);
  v_.resize(nbStates_, nbStates_);
  vInv_.resize(nbStates_, nbStates_);
  lambda_.resize(nbStates_);
}

void DecompositionSubstitutionCount::initBMatrices_()
{
  //Re-initialize all B matrices according to substitution register.
  for (size_t i = 0; i < register_->getNumberOfSubstitutionTypes(); ++i) {
    bMatrices_[i].resize(nbStates_, nbStates_);
    insideProducts_[i].resize(nbStates_, nbStates_);
    counts_[i].resize(nbStates_, nbStates_);
  }
}

void DecompositionSubstitutionCount::jFunction_(const std::vector<double>& lambda, double t, RowMatrix<double>& result) const
{
  vector<double> expLam = VectorTools::exp(lambda * t);
  for (unsigned int i = 0; i < nbStates_; ++i) {
    for (unsigned int j = 0; j < nbStates_; ++j) {
      double dd = lambda[i] - lambda[j];
      if (dd == 0) {
        result(i, j) = t * expLam[i];
      } else {
        result(i, j) = (expLam[i] - expLam[j]) / dd;
      }
    }
  }
}

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

void DecompositionSubstitutionCount::computeCounts_(double length) const
{
  jFunction_(lambda_, length, jMat_);
  for (size_t i = 0; i < register_->getNumberOfSubstitutionTypes(); ++i) {
    RowMatrix<double> tmp1(nbStates_, nbStates_), tmp2(nbStates_, nbStates_);
    MatrixTools::hadamardMult(jMat_, insideProducts_[i], tmp1);
    MatrixTools::mult(v_, tmp1, tmp2);
    MatrixTools::mult(tmp2, vInv_, counts_[i]);
  }
  // Now we must divide by pijt and account for putative weights:
  vector<int> supportedStates = model_->getAlphabetStates();
  RowMatrix<double> P = model_->getPij_t(length);
  for (size_t i = 0; i < register_->getNumberOfSubstitutionTypes(); i++) {
    for (size_t j = 0; j < nbStates_; j++) {
      for (size_t k = 0; k < nbStates_; k++) {
        counts_[i](j, k) /= P(j, k);
        if (isnan(counts_[i](j, k)) || counts_[i](j, k) < 0.) {
          counts_[i](j, k) = 0.;
        //Weights:
        if (weights_)
          counts_[i](j, k) *= weights_->getIndex(supportedStates[j], supportedStates[k]);
        }
      }
    }
  }
}

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

Matrix<double>* DecompositionSubstitutionCount::getAllNumbersOfSubstitutions(double length, size_t type) const
{
  if (length < 0)
    throw Exception("DecompositionSubstitutionCount::getAllNumbersOfSubstitutions. Negative branch length: " + TextTools::toString(length) + ".");
  if (length != currentLength_)
  {
  //if (length < 0.000001) // Limit case!
  //{ 
  //  unsigned int s = model_->getAlphabet()->getSize();
  //  for (unsigned int i = 0; i < s; i++)
  //  {
  //    for (unsigned int j = 0; j < s; j++)
  //    {
  //      m_(i, j) = i == j ? 0. : 1.;
  //    }
  //  }
  //}
  //else
  //{
  // Else we need to recompute M:
    computeCounts_(length);
  //}

    currentLength_ = length;
  }
  return new RowMatrix<double>(counts_[type - 1]);
}

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

double DecompositionSubstitutionCount::getNumberOfSubstitutions(size_t initialState, size_t finalState, double length, size_t type) const
{
  if (length < 0)
    throw Exception("DecompositionSubstitutionCount::getNumbersOfSubstitutions. Negative branch length: " + TextTools::toString(length) + ".");
  if (length != currentLength_)
  {
    computeCounts_(length);
    currentLength_ = length;
  }
  return counts_[type - 1](initialState, finalState);
}

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

std::vector<double> DecompositionSubstitutionCount::getNumberOfSubstitutionsForEachType(size_t initialState, size_t finalState, double length) const
{
  if (length < 0)
    throw Exception("DecompositionSubstitutionCount::getNumbersOfSubstitutions. Negative branch length: " + TextTools::toString(length) + ".");
  if (length != currentLength_)
  {
    computeCounts_(length);
    currentLength_ = length;
  }
  std::vector<double> v(getNumberOfSubstitutionTypes());
  for (size_t t = 0; t < getNumberOfSubstitutionTypes(); ++t) {
    v[t] = counts_[t](initialState, finalState);
  }
  return v;
}
    
/******************************************************************************/

void DecompositionSubstitutionCount::setSubstitutionModel(const SubstitutionModel* model)
{
  const ReversibleSubstitutionModel* rModel = dynamic_cast<const ReversibleSubstitutionModel*>(model);
  if (!rModel)
    throw Exception("DecompositionSubstitutionCount::setSubstitutionModel. Only works with reversible models for now.");

  //Check compatiblity between model and substitution register:
  if (model->getAlphabet()->getAlphabetType() != register_->getAlphabet()->getAlphabetType())
    throw Exception("DecompositionSubstitutionCount::setSubstitutionModel: alphabets do not match between register and model.");
  model_ = rModel;
  unsigned int n = model->getAlphabet()->getSize();
  if (n != nbStates_) {
    nbStates_ = n;
    resetStates_();
    initBMatrices_();
  }
  fillBMatrices_();
  computeEigen_();
  computeProducts_();

  //Recompute counts:
  computeCounts_(currentLength_);
}

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

void DecompositionSubstitutionCount::substitutionRegisterHasChanged() throw (Exception)
{
  //Check compatiblity between model and substitution register:
  if (model_->getAlphabet()->getAlphabetType() != register_->getAlphabet()->getAlphabetType())
    throw Exception("DecompositionSubstitutionCount::substitutionRegisterHasChanged: alphabets do not match between register and model.");

  resetBMatrices_();
  initBMatrices_();
  fillBMatrices_();
  computeProducts_();

  //Recompute counts:
  if (currentLength_ > 0)
   computeCounts_(currentLength_);
}

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

void DecompositionSubstitutionCount::weightsHaveChanged() throw (Exception)
{
  if (weights_->getAlphabet()->getAlphabetType() != register_->getAlphabet()->getAlphabetType())
    throw Exception("DecompositionSubstitutionCount::weightsHaveChanged. Incorrect alphabet type.");

  //jdutheil on 25/07/14: not necessary if weights are only accounted for in the end.
  //fillBMatrices_();
  
  //Recompute counts:
  if (currentLength_ > 0)
    computeCounts_(currentLength_);
}

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