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Viewing changes to src/Bpp/Phyl/Model/YNGKP_M8.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/YNGKP_M8.cpp
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/******************************************************************************/
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YNGKP_M8::YNGKP_M8(const GeneticCode* gc, FrequenciesSet* codonFreqs, unsigned int nbclass) :
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  AbstractMixedSubstitutionModel(gc->getSourceAlphabet(), "YNGKP_M8."), pmixmodel_(0),
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  synfrom_(-1), synto_(-1),
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  mapParNamesFromPmodel_(), lParPmodel_()
 
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YNGKP_M8::YNGKP_M8(const GeneticCode* gc, FrequenciesSet* codonFreqs, unsigned int nclass) :
 
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  AbstractBiblioMixedSubstitutionModel("YNGKP_M8."),
 
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  pmixmodel_(0),
 
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  synfrom_(-1), synto_(-1)
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{
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  if (nbclass<=0)
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    throw Exception("Bad number of classes for model YNGKP_M8: " + TextTools::toString(nbclass));
 
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  if (nclass<=0)
 
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    throw Exception("Bad number of classes for model YNGKP_M8: " + TextTools::toString(nclass));
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  // build the submodel
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  BetaDiscreteDistribution* pbdd=new BetaDiscreteDistribution(nbclass,2,2);
 
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  BetaDiscreteDistribution* pbdd=new BetaDiscreteDistribution(nclass,2,2);
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  vector<double> val; val.push_back(2);
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  vector<double> prob; prob.push_back(1);
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  updateMatrices();
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}
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YNGKP_M8::YNGKP_M8(const YNGKP_M8& mod2) : AbstractMixedSubstitutionModel(mod2),
 
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YNGKP_M8::YNGKP_M8(const YNGKP_M8& mod2) : AbstractBiblioMixedSubstitutionModel(mod2),
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                                           pmixmodel_(new MixtureOfASubstitutionModel(*mod2.pmixmodel_)),
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                                           synfrom_(mod2.synfrom_), synto_(mod2.synto_),
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                                           mapParNamesFromPmodel_(mod2.mapParNamesFromPmodel_),
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                                           lParPmodel_(mod2.lParPmodel_)
 
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                                           synfrom_(mod2.synfrom_), synto_(mod2.synto_)
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{
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}
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YNGKP_M8& YNGKP_M8::operator=(const YNGKP_M8& mod2)
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{
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  AbstractMixedSubstitutionModel::operator=(mod2);
 
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  AbstractBiblioMixedSubstitutionModel::operator=(mod2);
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  if (pmixmodel_)
 
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    delete pmixmodel_;
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  pmixmodel_=new MixtureOfASubstitutionModel(*mod2.pmixmodel_);
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  mapParNamesFromPmodel_=mod2.mapParNamesFromPmodel_;
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  lParPmodel_=mod2.lParPmodel_;
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  synfrom_=mod2.synfrom_;
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  synto_=mod2.synto_;
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void YNGKP_M8::updateMatrices()
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{
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  map<string,string>::iterator it;
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  for (it=mapParNamesFromPmodel_.begin();it!=mapParNamesFromPmodel_.end();it++)
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    lParPmodel_.setParameterValue(it->first,getParameter(it->second).getValue());
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  pmixmodel_->matchParametersValues(lParPmodel_);
 
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  AbstractBiblioSubstitutionModel::updateMatrices();
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  // homogeneization of the synonymous substittion rates
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  pmixmodel_->setVRates(vd);
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}
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void YNGKP_M8::setFreq(std::map<int,double>& m)
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{
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  pmixmodel_->setFreq(m);
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  map<string,string>::iterator it;
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  ParameterList pl;
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  for (it=mapParNamesFromPmodel_.begin();it!=mapParNamesFromPmodel_.end();it++)
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    pl.addParameter(Parameter(getNamespace()+it->second,pmixmodel_->getParameterValue(it->first)));
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  matchParametersValues(pl);
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}