bpp-phyl3
3.0.0
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Interface for reversible codon models. More...
#include <Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h>
Public Member Functions | |
CodonReversibleSubstitutionModelInterface () | |
virtual | ~CodonReversibleSubstitutionModelInterface () |
virtual CodonReversibleSubstitutionModelInterface * | clone () const override=0 |
virtual std::shared_ptr< const GeneticCode > | getGeneticCode () const =0 |
virtual double | getCodonsMulRate (size_t, size_t) const =0 |
Returns the multiplicative rate specific to two codons specified by their number. The respective generator rate is this rate multiplied by the rate defined by the model defined on nucleotides. More... | |
virtual const CodonFrequencySetInterface & | codonFrequencySet () const =0 |
virtual bool | hasCodonFrequencySet () const =0 |
virtual void | setFreq (std::map< int, double > &frequencies)=0 |
virtual void | setFreq (std::map< int, double > &frequencies)=0 |
Set equilibrium frequencies. More... | |
virtual size_t | getNumberOfIndependentParameters () const=0 |
virtual void | aliasParameters (const std::string &p1, const std::string &p2)=0 |
virtual void | aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0 |
virtual void | unaliasParameters (const std::string &p1, const std::string &p2)=0 |
virtual const ParameterList & | getIndependentParameters () const=0 |
virtual std::vector< std::string > | getAlias (const std::string &name) const=0 |
virtual std::map< std::string, std::string > | getAliases () const=0 |
virtual bool | hasParameter (const std::string &name) const=0 |
virtual const ParameterList & | getParameters () const=0 |
virtual const Parameter & | parameter (const std::string &name) const=0 |
virtual double | getParameterValue (const std::string &name) const=0 |
virtual void | setAllParametersValues (const ParameterList ¶meters)=0 |
virtual void | setParameterValue (const std::string &name, double value)=0 |
virtual void | setParametersValues (const ParameterList ¶meters)=0 |
virtual bool | matchParametersValues (const ParameterList ¶meters)=0 |
virtual void | removeConstraint (const std::string &name)=0 |
virtual void | setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0 |
virtual size_t | getNumberOfParameters () const=0 |
virtual void | setNamespace (const std::string &prefix)=0 |
virtual std::string | getNamespace () const=0 |
virtual std::string | getParameterNameWithoutNamespace (const std::string &name) const=0 |
virtual double | Qij (size_t i, size_t j) const =0 |
A method for computing all necessary matrices. More... | |
virtual const Matrix< double > & | generator () const =0 |
virtual const Matrix< double > & | exchangeabilityMatrix () const =0 |
virtual double | Sij (size_t i, size_t j) const =0 |
virtual void | enableEigenDecomposition (bool yn)=0 |
Set if eigenValues and Vectors must be computed. More... | |
virtual bool | enableEigenDecomposition ()=0 |
Tell if eigenValues and Vectors must be computed. More... | |
virtual const Vdouble & | getEigenValues () const =0 |
virtual const Vdouble & | getIEigenValues () const =0 |
virtual bool | isDiagonalizable () const =0 |
virtual bool | isNonSingular () const =0 |
virtual const Matrix< double > & | getRowLeftEigenVectors () const =0 |
virtual const Matrix< double > & | getColumnRightEigenVectors () const =0 |
virtual void | setScalable (bool scalable)=0 |
sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example. More... | |
virtual bool | isScalable () const =0 |
returns if model is scalable More... | |
virtual double | getScale () const =0 |
Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale. More... | |
virtual void | setScale (double scale)=0 |
Multiplies the current generator by the given scale. More... | |
virtual void | normalize ()=0 |
Normalize the generator. More... | |
virtual void | setDiagonal ()=0 |
set the diagonal of the generator such that sum on each line equals 0. More... | |
virtual double | freq (size_t i) const =0 |
virtual double | Pij_t (size_t i, size_t j, double t) const =0 |
virtual double | dPij_dt (size_t i, size_t j, double t) const =0 |
virtual double | d2Pij_dt2 (size_t i, size_t j, double t) const =0 |
virtual const Vdouble & | getFrequencies () const =0 |
virtual bool | computeFrequencies () const =0 |
virtual void | computeFrequencies (bool yn)=0 |
virtual const Matrix< double > & | getPij_t (double t) const =0 |
virtual const Matrix< double > & | getdPij_dt (double t) const =0 |
virtual const Matrix< double > & | getd2Pij_dt2 (double t) const =0 |
virtual const Eigen::VectorXd & | Lik_t (const Eigen::VectorXd &values, double t) const =0 |
virtual const Eigen::VectorXd & | dLik_dt (const Eigen::VectorXd &values, double t) const =0 |
virtual const Eigen::VectorXd & | d2Lik_dt2 (const Eigen::VectorXd &values, double t) const =0 |
virtual void | setFreqFromData (const SequenceDataInterface &data, double pseudoCount=0)=0 |
Set equilibrium frequencies equal to the frequencies estimated from the data. More... | |
virtual std::string | getName () const =0 |
Get the name of the model. More... | |
virtual const std::vector< int > & | getAlphabetStates () const =0 |
virtual const StateMapInterface & | stateMap () const =0 |
virtual std::shared_ptr< const StateMapInterface > | getStateMap () const =0 |
virtual std::vector< size_t > | getModelStates (int code) const =0 |
Get the state in the model corresponding to a particular state in the alphabet. More... | |
virtual std::vector< size_t > | getModelStates (const std::string &code) const =0 |
Get the state in the model corresponding to a particular state in the alphabet. More... | |
virtual int | getAlphabetStateAsInt (size_t index) const =0 |
virtual std::string | getAlphabetStateAsChar (size_t index) const =0 |
virtual const Alphabet & | alphabet () const =0 |
virtual std::shared_ptr< const Alphabet > | getAlphabet () const =0 |
virtual const FrequencySetInterface & | frequencySet () const =0 |
virtual size_t | getNumberOfStates () const =0 |
Get the number of states. More... | |
virtual double | getInitValue (size_t i, int state) const =0 |
virtual double | getRate () const =0 |
Get the rate. More... | |
virtual void | setRate (double rate)=0 |
Set the rate of the model (must be positive). More... | |
virtual void | addRateParameter ()=0 |
Protected Member Functions | |
virtual ParameterList & | getParameters_ ()=0 |
virtual Vdouble & | getFrequencies_ ()=0 |
Interface for reversible codon models.
Definition at line 66 of file CodonSubstitutionModel.h.
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inline |
Definition at line 71 of file CodonSubstitutionModel.h.
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inlinevirtual |
Definition at line 72 of file CodonSubstitutionModel.h.
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pure virtualinherited |
Implemented in bpp::TS98, bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::MultinomialFromTransitionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::FromMixtureSubstitutionModel, bpp::AbstractTransitionModel, bpp::AbstractFromSubstitutionModelTransitionModel, and bpp::AbstractBiblioTransitionModel.
Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::AbstractFromSubstitutionModelTransitionModel::addRateParameter(), bpp::FromMixtureSubstitutionModel::addRateParameter(), bpp::InMixedSubstitutionModel::addRateParameter(), bpp::MultinomialFromTransitionModel::addRateParameter(), bpp::TransitionFromTransitionModel::addRateParameter(), and bpp::BppOSubstitutionModelFormat::updateParameters_().
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pure virtualinherited |
Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractWrappedModel, and bpp::AbstractTransitionModel.
Referenced by bpp::SubstitutionModelSet::addModel(), bpp::AbstractWrappedModel::alphabet(), bpp::NonHomogeneousSubstitutionProcess::createHomogeneousSubstitutionProcess(), bpp::NonHomogeneousSubstitutionProcess::createNonHomogeneousSubstitutionProcess(), and bpp::SENCA::setFreq().
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overridepure virtual |
Implements bpp::CodonSubstitutionModelInterface.
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pure virtualinherited |
Implemented in bpp::RE08Codon, bpp::YN98, bpp::SENCA, bpp::MG94, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, bpp::AbstractCodonFitnessSubstitutionModel, bpp::AbstractCodonDistanceSubstitutionModel, bpp::AbstractCodonCpGSubstitutionModel, bpp::AbstractCodonClusterAASubstitutionModel, bpp::AbstractCodonBGCSubstitutionModel, bpp::AbstractCodonAARateSubstitutionModel, and bpp::AbstractCodonAAFitnessSubstitutionModel.
Referenced by bpp::CodonSameAARateSubstitutionModel::CodonSameAARateSubstitutionModel().
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pure virtualinherited |
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractFromSubstitutionModelTransitionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedTransitionModel::computeFrequencies(), bpp::InMixedSubstitutionModel::computeFrequencies(), bpp::RELAX::RELAX(), bpp::SENCA::SENCA(), bpp::YNGP_M1::YNGP_M1(), bpp::YNGP_M10::YNGP_M10(), bpp::YNGP_M2::YNGP_M2(), bpp::YNGP_M3::YNGP_M3(), bpp::YNGP_M7::YNGP_M7(), bpp::YNGP_M8::YNGP_M8(), and bpp::YNGP_M9::YNGP_M9().
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pure virtualinherited |
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractFromSubstitutionModelTransitionModel, and bpp::AbstractSubstitutionModel.
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pure virtualinherited |
Implements bpp::BranchModelInterface.
Implemented in bpp::AbstractLkTransitionModel.
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pure virtualinherited |
Implemented in bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedTransitionModel::d2Pij_dt2(), bpp::InMixedSubstitutionModel::d2Pij_dt2(), and bpp::OneChangeRegisterTransitionModel::d2Pij_dt2().
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pure virtualinherited |
Implements bpp::BranchModelInterface.
Implemented in bpp::AbstractLkTransitionModel.
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pure virtualinherited |
Implemented in bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.
Referenced by bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::AbstractTotallyWrappedTransitionModel::dPij_dt(), and bpp::InMixedSubstitutionModel::dPij_dt().
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pure virtualinherited |
Tell if eigenValues and Vectors must be computed.
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel().
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pure virtualinherited |
Set if eigenValues and Vectors must be computed.
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::enableEigenDecomposition(), and bpp::InMixedSubstitutionModel::enableEigenDecomposition().
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pure virtualinherited |
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::Coala::Coala(), bpp::AbstractTotallyWrappedSubstitutionModel::exchangeabilityMatrix(), and bpp::InMixedSubstitutionModel::exchangeabilityMatrix().
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pure virtualinherited |
Implemented in bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, and bpp::AbstractTransitionModel.
Referenced by bpp::AbstractTotallyWrappedTransitionModel::freq(), bpp::InMixedSubstitutionModel::freq(), bpp::OneChangeRegisterTransitionModel::freq(), and bpp::OneChangeTransitionModel::freq().
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pure virtualinherited |
Exception | if no FrequenceSet is associated to this model. |
Implemented in bpp::RegisterRatesSubstitutionModel, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::D1WalkSubstitutionModel, bpp::YN98, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::AbstractWrappedTransitionModel, bpp::AbstractWrappedModel, bpp::AbstractTransitionModel, and bpp::AbstractBiblioMixedTransitionModel.
Referenced by bpp::RE08Codon::codonFrequencySet(), bpp::AbstractWrappedModel::frequencySet(), bpp::AbstractWrappedTransitionModel::frequencySet(), bpp::OneChangeRegisterTransitionModel::frequencySet(), bpp::OneChangeTransitionModel::frequencySet(), and bpp::BppOSubstitutionModelFormat::write().
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pure virtualinherited |
See Kosiol and Goldman (2005), Molecular Biology And Evolution 22(2) 193-9.
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::dPij_dt(), bpp::AbstractTotallyWrappedSubstitutionModel::generator(), bpp::InMixedSubstitutionModel::generator(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::getdPij_dt(), bpp::OneChangeRegisterTransitionModel::getPij_t(), bpp::OneChangeRegisterTransitionModel::Pij_t(), bpp::OneChangeRegisterTransitionModel::updateMatrices_(), and bpp::RegisterRatesSubstitutionModel::updateMatrices_().
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pure virtualinherited |
Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractWrappedModel, and bpp::AbstractTransitionModel.
Referenced by bpp::NonHomogeneousSubstitutionProcess::addModel(), bpp::YpR::checkModel(), bpp::NonHomogeneousSubstitutionProcess::createHomogeneousSubstitutionProcess(), bpp::NonHomogeneousSubstitutionProcess::createNonHomogeneousSubstitutionProcess(), bpp::AbstractWrappedModel::getAlphabet(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::SENCA::setFreq(), bpp::NonHomogeneousSubstitutionProcess::setModel(), and bpp::BppOSubstitutionModelFormat::writeMixed_().
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pure virtualinherited |
index | The model state. |
Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractTransitionModel, and bpp::AbstractWrappedModel.
Referenced by bpp::AbstractWrappedModel::getAlphabetStateAsChar(), and bpp::SubstitutionModelSet::getAlphabetStateAsChar().
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pure virtualinherited |
index | The model state. |
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::AbstractTransitionModel, bpp::RegisterRatesSubstitutionModel, and bpp::AbstractWrappedModel.
Referenced by bpp::AbstractWrappedModel::getAlphabetStateAsInt(), bpp::SubstitutionModelSet::getAlphabetStateAsInt(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns().
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pure virtualinherited |
Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractWrappedModel, and bpp::AbstractTransitionModel.
Referenced by bpp::SubstitutionModelSet::getAlphabetStates(), and bpp::AbstractWrappedModel::getAlphabetStates().
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pure virtualinherited |
Returns the multiplicative rate specific to two codons specified by their number. The respective generator rate is this rate multiplied by the rate defined by the model defined on nucleotides.
Implemented in bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, bpp::RE08Codon, bpp::YN98, bpp::SENCA, bpp::MG94, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::AbstractKroneckerCodonSubstitutionModel, bpp::AbstractDFPSubstitutionModel, bpp::AbstractCodonFitnessSubstitutionModel, bpp::AbstractCodonDistanceSubstitutionModel, bpp::AbstractCodonCpGSubstitutionModel, bpp::AbstractCodonClusterAASubstitutionModel, bpp::AbstractCodonBGCSubstitutionModel, bpp::AbstractCodonAARateSubstitutionModel, bpp::AbstractCodonAAFitnessSubstitutionModel, and bpp::CodonDistanceSubstitutionModel.
Referenced by bpp::AbstractCodonSubstitutionModel::completeMatrices_(), and bpp::RE08Codon::getCodonsMulRate().
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pure virtualinherited |
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getColumnRightEigenVectors(), and bpp::InMixedSubstitutionModel::getColumnRightEigenVectors().
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pure virtualinherited |
Implemented in bpp::AbstractTransitionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.
Referenced by bpp::AbstractLkTransitionModel::d2Lik_dt2(), bpp::AbstractTotallyWrappedTransitionModel::getd2Pij_dt2(), bpp::InMixedSubstitutionModel::getd2Pij_dt2(), and bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2().
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pure virtualinherited |
Implemented in bpp::AbstractTransitionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.
Referenced by bpp::AbstractLkTransitionModel::dLik_dt(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::AbstractTotallyWrappedTransitionModel::getdPij_dt(), bpp::InMixedSubstitutionModel::getdPij_dt(), and bpp::OneChangeRegisterTransitionModel::getdPij_dt().
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pure virtualinherited |
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getEigenValues(), and bpp::InMixedSubstitutionModel::getEigenValues().
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pure virtualinherited |
Implemented in bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, and bpp::AbstractTransitionModel.
Referenced by bpp::EquilibriumFrequenciesFromModel::compute(), bpp::AbstractTotallyWrappedTransitionModel::getFrequencies(), bpp::InMixedSubstitutionModel::getFrequencies(), bpp::OneChangeRegisterTransitionModel::getFrequencies(), and bpp::OneChangeTransitionModel::getFrequencies().
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protectedpure virtualinherited |
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, and bpp::AbstractFromSubstitutionModelTransitionModel.
Referenced by bpp::AbstractTotallyWrappedTransitionModel::getFrequencies_(), and bpp::InMixedSubstitutionModel::getFrequencies_().
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pure virtualinherited |
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pure virtualinherited |
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getIEigenValues(), and bpp::InMixedSubstitutionModel::getIEigenValues().
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pure virtualinherited |
This method is used to initialize likelihoods in recursions. It typically sends 1 if i = state, 0 otherwise, where i is one of the possible states of the alphabet allowed in the model and state is the observed state in the considered sequence/site.
i | the index of the state in the model. |
state | An observed state in the sequence/site. |
IndexOutOfBoundsException | if array position is out of range. |
BadIntException | if states are not allowed in the associated alphabet. |
Implemented in bpp::TransitionFromTransitionModel, bpp::RE08, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MultinomialFromTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, and bpp::AbstractTransitionModel.
Referenced by bpp::AbstractTotallyWrappedTransitionModel::getInitValue(), bpp::InMixedSubstitutionModel::getInitValue(), bpp::MultinomialFromTransitionModel::getInitValue(), bpp::OneChangeRegisterTransitionModel::getInitValue(), bpp::OneChangeTransitionModel::getInitValue(), and bpp::TransitionFromTransitionModel::getInitValue().
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pure virtualinherited |
Get the state in the model corresponding to a particular state in the alphabet.
code | The alphabet state to check. |
Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractWrappedModel, and bpp::AbstractTransitionModel.
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pure virtualinherited |
Get the state in the model corresponding to a particular state in the alphabet.
code | The alphabet state to check. |
Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractWrappedModel, and bpp::AbstractTransitionModel.
Referenced by bpp::SubstitutionModelSet::getModelStates(), and bpp::AbstractWrappedModel::getModelStates().
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pure virtualinherited |
Get the name of the model.
Implemented in bpp::WordSubstitutionModel, bpp::TS98, bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::RE08, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LLG08_UL3, bpp::LLG08_UL3::EmbeddedModel, bpp::LLG08_UL2, bpp::LLG08_UL2::EmbeddedModel, bpp::LLG08_EX3, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_EX2, bpp::LLG08_EX2::EmbeddedModel, bpp::LLG08_EHO, bpp::LLG08_EHO::EmbeddedModel, bpp::LGL08_CAT, bpp::LGL08_CAT::EmbeddedModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::Coala, bpp::POMO, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::YpR_Gen, bpp::YpR_Sym, bpp::TN93, bpp::T92, bpp::SSR, bpp::RN95s, bpp::RN95, bpp::L95, bpp::K80, bpp::JCnuc, bpp::GTR, bpp::gBGC, bpp::F81, bpp::MultinomialFromTransitionModel, bpp::MixtureOfTransitionModels, bpp::MixtureOfATransitionModel, bpp::KroneckerWordSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::FromMixtureSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::D1WalkSubstitutionModel, bpp::YNGP_M9, bpp::YNGP_M8, bpp::YNGP_M7, bpp::YNGP_M3, bpp::YNGP_M2, bpp::YNGP_M10, bpp::YNGP_M1, bpp::YN98, bpp::TripletSubstitutionModel, bpp::SENCA, bpp::RELAX, bpp::MG94, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::GY94, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::DFP07, bpp::CodonSameAARateSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::AnonymousSubstitutionModel, bpp::AbstractWrappedModel, bpp::TwoParameterBinarySubstitutionModel, bpp::LG10_EX_EHO, bpp::LG10_EX_EHO::EmbeddedModel, bpp::HKY85, bpp::F84, bpp::CodonDistanceSubstitutionModel, and bpp::BinarySubstitutionModel.
Referenced by bpp::YpR::checkModel(), bpp::TransitionMatrixFromModel::compute(), bpp::AbstractWrappedModel::getName(), bpp::FromMixtureSubstitutionModel::getName(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::BppOSubstitutionModelFormat::initialize_(), bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(), bpp::MixtureOfATransitionModel::model(), bpp::LegacyPhylogeneticsApplicationTools::setSubstitutionModelParametersInitialValuesWithAliases(), bpp::ModelPath::toString(), and bpp::BppOSubstitutionModelFormat::write().
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pure virtualinherited |
Get the number of states.
For most models, this equals the size of the alphabet.
Implemented in bpp::RegisterRatesSubstitutionModel, bpp::RE08Codon, bpp::RE08Protein, bpp::RE08Nucleotide, bpp::YpR, bpp::gBGC, bpp::MarkovModulatedSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::AbstractWrappedModel, bpp::AbstractTransitionModel, bpp::TwoParameterBinarySubstitutionModel, and bpp::BinarySubstitutionModel.
Referenced by bpp::NonHomogeneousSubstitutionProcess::addModel(), bpp::SubstitutionModelSet::addModel(), bpp::AbstractWrappedModel::getNumberOfStates(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), and bpp::NonHomogeneousSubstitutionProcess::setModel().
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pure virtualinherited |
Implemented in bpp::AbstractTransitionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.
Referenced by bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::getdPij_dt(), bpp::AbstractTotallyWrappedTransitionModel::getPij_t(), bpp::InMixedSubstitutionModel::getPij_t(), bpp::OneChangeRegisterTransitionModel::getPij_t(), and bpp::AbstractLkTransitionModel::Lik_t().
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pure virtualinherited |
Get the rate.
Implemented in bpp::TS98, bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MultinomialFromTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::AbstractTotallyWrappedTransitionModel, and bpp::AbstractTransitionModel.
Referenced by bpp::AbstractFromSubstitutionModelTransitionModel::addRateParameter(), bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::dPij_dt(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::getdPij_dt(), bpp::OneChangeRegisterTransitionModel::getPij_t(), bpp::AbstractTotallyWrappedTransitionModel::getRate(), bpp::InMixedSubstitutionModel::getRate(), bpp::MultinomialFromTransitionModel::getRate(), bpp::OneChangeRegisterTransitionModel::getRate(), bpp::OneChangeTransitionModel::getRate(), bpp::RegisterRatesSubstitutionModel::getRate(), and bpp::TransitionFromTransitionModel::getRate().
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pure virtualinherited |
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getRowLeftEigenVectors(), and bpp::InMixedSubstitutionModel::getRowLeftEigenVectors().
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pure virtualinherited |
Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getScale(), and bpp::InMixedSubstitutionModel::getScale().
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pure virtualinherited |
Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractWrappedModel, and bpp::AbstractTransitionModel.
Referenced by bpp::SubstitutionModelSet::getStateMap(), bpp::SubstitutionProcessCollectionMember::getStateMap(), and bpp::AbstractWrappedModel::getStateMap().
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pure virtualinherited |
Implemented in bpp::RE08Codon, bpp::YN98, bpp::SENCA, bpp::MG94, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, bpp::AbstractCodonFitnessSubstitutionModel, bpp::AbstractCodonDistanceSubstitutionModel, bpp::AbstractCodonCpGSubstitutionModel, bpp::AbstractCodonClusterAASubstitutionModel, bpp::AbstractCodonBGCSubstitutionModel, bpp::AbstractCodonAARateSubstitutionModel, and bpp::AbstractCodonAAFitnessSubstitutionModel.
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pure virtualinherited |
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::isDiagonalizable(), and bpp::InMixedSubstitutionModel::isDiagonalizable().
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pure virtualinherited |
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::isNonSingular(), and bpp::InMixedSubstitutionModel::isNonSingular().
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pure virtualinherited |
returns if model is scalable
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::isScalable(), and bpp::InMixedSubstitutionModel::isScalable().
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pure virtualinherited |
This method is used to compute likelihoods in recursions. It computes the probability of a vector given a start state.
values | An vector of states on the site. |
t | the branch length |
Implements bpp::BranchModelInterface.
Implemented in bpp::AbstractLkTransitionModel.
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pure virtualinherited |
Normalize the generator.
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::normalize(), and bpp::InMixedSubstitutionModel::normalize().
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pure virtualinherited |
Implemented in bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.
Referenced by bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::AbstractTotallyWrappedTransitionModel::Pij_t(), bpp::InMixedSubstitutionModel::Pij_t(), and bpp::OneChangeRegisterTransitionModel::Pij_t().
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pure virtualinherited |
A method for computing all necessary matrices.
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::YpR::checkModel(), bpp::DFP07::DFP07(), bpp::AbstractTotallyWrappedSubstitutionModel::Qij(), bpp::InMixedSubstitutionModel::Qij(), bpp::RELAX::RELAX(), bpp::DFP07::updateMatrices_(), bpp::RELAX::updateMatrices_(), bpp::YNGP_M1::updateMatrices_(), bpp::YNGP_M10::updateMatrices_(), bpp::YNGP_M2::updateMatrices_(), bpp::YNGP_M3::updateMatrices_(), bpp::YNGP_M7::updateMatrices_(), bpp::YNGP_M8::updateMatrices_(), bpp::YNGP_M9::updateMatrices_(), bpp::YNGP_M1::YNGP_M1(), bpp::YNGP_M10::YNGP_M10(), bpp::YNGP_M2::YNGP_M2(), bpp::YNGP_M3::YNGP_M3(), bpp::YNGP_M7::YNGP_M7(), bpp::YNGP_M8::YNGP_M8(), and bpp::YNGP_M9::YNGP_M9().
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pure virtualinherited |
set the diagonal of the generator such that sum on each line equals 0.
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::setDiagonal(), and bpp::InMixedSubstitutionModel::setDiagonal().
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pure virtualinherited |
Implemented in bpp::RE08Codon, bpp::YN98, bpp::SENCA, bpp::MG94, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, bpp::AbstractCodonFitnessSubstitutionModel, bpp::AbstractCodonDistanceSubstitutionModel, bpp::AbstractCodonCpGSubstitutionModel, bpp::AbstractCodonClusterAASubstitutionModel, bpp::AbstractCodonBGCSubstitutionModel, bpp::AbstractCodonAARateSubstitutionModel, and bpp::AbstractCodonAAFitnessSubstitutionModel.
Referenced by bpp::CodonSameAARateSubstitutionModel::setFreq().
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pure virtualinherited |
Set equilibrium frequencies.
frequencies | The map of the frequencies to use. |
Implemented in bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::RE08Codon, bpp::RE08, bpp::POMO, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::YN98, bpp::SENCA, bpp::MG94, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractBiblioTransitionModel, bpp::TN93, bpp::T92, bpp::GTR, bpp::F81, bpp::AbstractTransitionModel, bpp::HKY85, bpp::BinarySubstitutionModel, bpp::AbstractWordSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::D1WalkSubstitutionModel, bpp::SSR, bpp::RN95s, bpp::RN95, bpp::L95, bpp::MixtureOfTransitionModels, bpp::MixtureOfATransitionModel, and bpp::F84.
Referenced by bpp::AbstractTotallyWrappedTransitionModel::setFreq(), bpp::InMixedSubstitutionModel::setFreq(), bpp::RE08Codon::setFreq(), bpp::MultinomialFromTransitionModel::setFreq(), bpp::TransitionFromTransitionModel::setFreq(), bpp::OneChangeRegisterTransitionModel::setFreq(), bpp::OneChangeTransitionModel::setFreq(), and bpp::AbstractTotallyWrappedTransitionModel::setFreqFromData().
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pure virtualinherited |
Set equilibrium frequencies equal to the frequencies estimated from the data.
data | The sequences to use. |
pseudoCount | A quantity to add to adjust the observed values in order to prevent issues due to missing states on small data set. The corrected frequencies shall be computed as
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Implemented in bpp::RE08, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::Coala, bpp::K80, bpp::JCnuc, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::AbstractBiblioTransitionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, and bpp::AbstractMixedTransitionModel.
Referenced by bpp::TransitionFromTransitionModel::setFreqFromData(), bpp::OneChangeRegisterTransitionModel::setFreqFromData(), bpp::OneChangeTransitionModel::setFreqFromData(), bpp::MultinomialFromTransitionModel::setFreqFromData(), and bpp::InMixedSubstitutionModel::setFreqFromData().
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pure virtualinherited |
Set the rate of the model (must be positive).
rate | must be positive. |
Implemented in bpp::TS98, bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MultinomialFromTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, and bpp::AbstractMixedTransitionModel.
Referenced by bpp::AbstractBiblioTransitionModel::fireParameterChanged(), bpp::AbstractTotallyWrappedTransitionModel::setRate(), bpp::InMixedSubstitutionModel::setRate(), bpp::MultinomialFromTransitionModel::setRate(), bpp::OneChangeRegisterTransitionModel::setRate(), bpp::OneChangeTransitionModel::setRate(), bpp::RegisterRatesSubstitutionModel::setRate(), and bpp::TransitionFromTransitionModel::setRate().
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pure virtualinherited |
sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example.
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::setScalable(), and bpp::InMixedSubstitutionModel::setScalable().
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pure virtualinherited |
Multiplies the current generator by the given scale.
scale | the scale by which the generator is multiplied. |
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::setScale(), and bpp::InMixedSubstitutionModel::setScale().
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pure virtualinherited |
By definition Sij(i,j) = Sij(j,i).
Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.
Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::Sij(), and bpp::InMixedSubstitutionModel::Sij().
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pure virtualinherited |
Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractWrappedModel, and bpp::AbstractTransitionModel.
Referenced by bpp::SubstitutionModelSet::stateMap(), bpp::SubstitutionProcessCollectionMember::stateMap(), and bpp::AbstractWrappedModel::stateMap().