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Viewing changes to src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp

  • Committer: Package Import Robot
  • Author(s): Julien Dutheil
  • Date: 2013-02-09 16:00:00 UTC
  • mfrom: (1.1.1)
  • Revision ID: package-import@ubuntu.com-20130209160000-5v65ba68z8032nzj
Tags: 2.0.3-1
* Reorganized model hierarchy
* New pairwise models
* Several bugs fixed

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src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp
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MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const Alphabet* alpha,
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                                                         vector<SubstitutionModel*> vpModel_) :
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  AbstractMixedSubstitutionModel(alpha, "Mixture.")
 
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 AbstractParameterAliasable("Mixture."),
 
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 AbstractMixedSubstitutionModel(alpha, "Mixture.")
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{
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  unsigned int i, nbmod = vpModel_.size();
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      addParameters_(vpModel_[i]->getParameters());
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    }
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  //  lParPmodel_.addParameters(getParameters());
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  for (i = 0; i < nbmod; i++){
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    vpModel_[i]->addRateParameter();
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  //   lParPmodel_.addParameter(vpModel_[i]->getParameter("rate"));
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  }
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  updateMatrices();
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                                                         vector<SubstitutionModel*> vpModel_,
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                                                         Vdouble& vproba,
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                                                         Vdouble& vrate) :
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  AbstractMixedSubstitutionModel(alpha, "Mixture.")
 
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 AbstractParameterAliasable("Mixture."),
 
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 AbstractMixedSubstitutionModel(alpha, "Mixture.")
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{
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  unsigned int i, nbmod = vpModel_.size();
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}
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MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(const MixtureOfSubstitutionModels& msm) :
 
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  AbstractParameterAliasable(msm),
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  AbstractMixedSubstitutionModel(msm)
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{
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}
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  for (i = 0; i < getNumberOfStates(); i++){
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    freq_[i] = 0;
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    for (j = 0; j < modelsContainer_.size(); j++)
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      freq_[i] += vProbas_[i]*modelsContainer_[j]->freq(i);
 
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      freq_[i] += vProbas_[j]*modelsContainer_[j]->freq(i);
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  }
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}
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  matchParametersValues(pl);
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}
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void MixtureOfSubstitutionModels::setVRates(Vdouble& vd)
 
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void MixtureOfSubstitutionModels::setVRates(const Vdouble& vd)
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{
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  AbstractMixedSubstitutionModel::setVRates(vd);
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  unsigned int i, nbmod = modelsContainer_.size();
 
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  double sP=0;
 
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  for (i = 0; i < nbmod - 1; i++)
 
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    sP+=vProbas_[i];
 
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  double y=0;
 
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  for (i = 0; i < nbmod - 1; i++) {
 
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    setParameterValue("relrate" + TextTools::toString(i+1), vProbas_[i]/sP * vRates_[i] / (1- y));
 
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    y+=vProbas_[i]/sP*vRates_[i];
 
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  }
 
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}
 
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Vint MixtureOfSubstitutionModels::getSubmodelNumbers(string& desc) const
 
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{
 
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  unsigned int i;
 
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  for (i=0;i< getNumberOfModels(); i++){
 
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    if (getNModel(i)->getName()==desc)
 
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      break;
 
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  }
 
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  if (i==getNumberOfModels())
 
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    throw Exception("MixtureOfSubstitutionModels::getSubmodelNumbers model description do not match " + desc);
 
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  Vint submodnb;
 
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  submodnb.push_back(i);
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   for (i = 0; i < nbmod - 1; i++)
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     {
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       setParameterValue("relrate" + TextTools::toString(i+1), vProbas_[i] * vRates_[i] / (1- y));
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       y+=vProbas_[i]*vRates_[i];
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     }
 
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  return submodnb;
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}