Interface for Substitution models, defined as a mixture of "simple" substitution models. More...

#include <Bpp/Phyl/Model/MixedSubstitutionModel.h>

Inheritance diagram for bpp::MixedSubstitutionModel:

Collaboration diagram for bpp::MixedSubstitutionModel:

Public Member Functions
	MixedSubstitutionModel ()
virtual	~MixedSubstitutionModel ()
virtual MixedSubstitutionModel *	clone () const =0
virtual const SubstitutionModel *	getNModel (size_t i) const =0
	Returns a specific model from the mixture.
virtual SubstitutionModel *	getNModel (size_t i)=0
virtual double	getNProbability (size_t i) const =0
	Returns the probability of a specific model from the mixture.
virtual const std::vector < double > &	getProbabilities () const =0
virtual void	setNProbability (size_t i, double prob)=0
	Sets the probability of a specific model from the mixture.
virtual size_t	getNumberOfModels () const =0
virtual const std::vector < double > &	getVRates () const =0
	Returns the rates of the submodels.
virtual double	getNRate (size_t i) const =0
	Returns the rate of a specific submodel.
virtual void	setVRates (const Vdouble &vd)=0
	Sets the rates of the submodels to be proportional to a given vector, and normalizes them so that the mean rate of the mixture equals rate_.
virtual void	normalizeVRates ()=0
	Normalizes the rates of the submodels so that the mean rate of the mixture equals rate_.
virtual Vint	getSubmodelNumbers (std::string &desc) const =0
virtual std::string	getName () const =0
	Get the name of the model.
virtual const std::vector< int > &	getAlphabetChars () const =0
virtual int	getAlphabetChar (size_t i) const =0
	Get the char in the alphabet corresponding to a given state in the model.
virtual std::vector< size_t >	getModelStates (int i) const =0
	Get the state in the model corresponding to a particular char in the alphabet.
virtual double	freq (size_t i) const =0
virtual double	Qij (size_t i, size_t j) 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 const Matrix< double > &	getGenerator () const =0
virtual const Matrix< double > &	getExchangeabilityMatrix () const =0
virtual double	Sij (size_t i, size_t j) const =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 void	enableEigenDecomposition (bool yn)=0
	Set if eigenValues and Vectors must be computed.
virtual bool	enableEigenDecomposition ()=0
	Tell if eigenValues and Vectors must be computed.
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 const Alphabet *	getAlphabet () const =0
virtual size_t	getNumberOfStates () const =0
	Get the number of states.
virtual double	getInitValue (size_t i, int state) const =0 throw (IndexOutOfBoundsException, BadIntException)
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.
virtual void	setScale (double scale)=0
	Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.
virtual double	getRate () const =0
	Get the rate.
virtual void	setRate (double rate)=0
	Set the rate of the model (must be positive).
virtual void	addRateParameter ()=0
virtual void	setFreqFromData (const SequenceContainer &data, double pseudoCount=0)=0
	Set equilibrium frequencies equal to the frequencies estimated from the data.
virtual void	setFreq (std::map< int, double > &frequencies)
	Set equilibrium frequencies.
virtual const FrequenciesSet *	getFrequenciesSet () const
	If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.
virtual size_t	getNumberOfIndependentParameters () const =0
virtual void	aliasParameters (const std::string &p1, const std::string &p2)=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 bool	hasParameter (const std::string &name) const =0
virtual const ParameterList &	getParameters () const =0
virtual const Parameter &	getParameter (const std::string &name) const =0
virtual double	getParameterValue (const std::string &name) const =0
virtual void	setAllParametersValues (const ParameterList &parameters)=0
virtual void	setParameterValue (const std::string &name, double value)=0
virtual void	setParametersValues (const ParameterList &parameters)=0
virtual bool	matchParametersValues (const ParameterList &parameters)=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

Detailed Description

Interface for Substitution models, defined as a mixture of "simple" substitution models.

Author:: Laurent Guéguen

Definition at line 59 of file MixedSubstitutionModel.h.

Constructor & Destructor Documentation

bpp::MixedSubstitutionModel::MixedSubstitutionModel ( ) [inline]

Definition at line 63 of file MixedSubstitutionModel.h.

virtual bpp::MixedSubstitutionModel::~MixedSubstitutionModel ( ) [inline, virtual]

Definition at line 65 of file MixedSubstitutionModel.h.

Member Function Documentation

virtual void bpp::SubstitutionModel::addRateParameter ( ) [pure virtual, inherited]

Implemented in bpp::AbstractSubstitutionModel, bpp::G2001, bpp::AbstractBiblioSubstitutionModel, and bpp::TS98.

Referenced by bpp::AbstractBiblioSubstitutionModel::addRateParameter().

virtual MixedSubstitutionModel* bpp::MixedSubstitutionModel::clone ( ) const [pure virtual]

Implements bpp::SubstitutionModel.

Implemented in bpp::MixtureOfSubstitutionModels, bpp::MixtureOfASubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::LLG08_EX3, bpp::LLG08_EHO, bpp::LLG08_UL3, bpp::LG10_EX_EHO, bpp::LGL08_CAT, bpp::LLG08_EX2, bpp::LLG08_UL2, bpp::YNGKP_M1, bpp::YNGKP_M8, bpp::YNGKP_M7, bpp::YNGKP_M2, bpp::YNGKP_M3, and bpp::AbstractBiblioMixedSubstitutionModel.

virtual double bpp::SubstitutionModel::d2Pij_dt2	(	size_t	i,
		size_t	j,
		double	t
	)		const `[pure virtual, inherited]`

Returns:: The second order derivative of the probability of change from state i to state j with respect to time t, at time t.

See also:: getd2Pij_dt2(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::JCnuc, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::d2Pij_dt2(), and bpp::RE08::d2Pij_dt2().

virtual double bpp::SubstitutionModel::dPij_dt	(	size_t	i,
		size_t	j,
		double	t
	)		const `[pure virtual, inherited]`

Returns:: The first order derivative of the probability of change from state i to state j with respect to time t, at time t.

See also:: getdPij_dt(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::JCnuc, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::RE08::d2Pij_dt2(), bpp::AbstractBiblioSubstitutionModel::dPij_dt(), and bpp::RE08::dPij_dt().

virtual void bpp::SubstitutionModel::enableEigenDecomposition ( bool yn ) [pure virtual, inherited]

Set if eigenValues and Vectors must be computed.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition(), bpp::gBGC::gBGC(), and bpp::YpR::YpR().

virtual bool bpp::SubstitutionModel::enableEigenDecomposition ( ) [pure virtual, inherited]

Tell if eigenValues and Vectors must be computed.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

virtual double bpp::SubstitutionModel::freq ( size_t i ) const [pure virtual, inherited]

Returns:: Equilibrium frequency associated to character i.

See also:: getFrequencies(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::TwoTreeLikelihood::computeTreeD2Likelihood(), bpp::TwoTreeLikelihood::computeTreeDLikelihood(), bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::AbstractBiblioSubstitutionModel::freq(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::RE08::getPij_t(), bpp::RE08::Pij_t(), and bpp::RE08::updateMatrices().

virtual const Alphabet* bpp::SubstitutionModel::getAlphabet ( ) const [pure virtual, inherited]

Returns:: Get the alphabet associated to this model.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

virtual int bpp::SubstitutionModel::getAlphabetChar ( size_t i ) const [pure virtual, inherited]

Get the char in the alphabet corresponding to a given state in the model.

In most cases, this method will return i.

Parameters:

i	The index of the state.

Returns:: The corresponding state in the alphabet.

See also:: MarkovModulatedSubstitutionModel; getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetChar(), bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(), and bpp::NonHomogeneousSequenceSimulator::multipleEvolve().

virtual const std::vector<int>& bpp::SubstitutionModel::getAlphabetChars ( ) const [pure virtual, inherited]

Returns:: The supported states of the model, as a vector of int codes.

See also:: Alphabet

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetChars(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

virtual const Matrix<double>& bpp::SubstitutionModel::getColumnRightEigenVectors ( ) const [pure virtual, inherited]

Returns:: A matrix with right eigen vectors. Each column in the matrix stands for an eigen vector.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getColumnRightEigenVectors(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

virtual const Matrix<double>& bpp::SubstitutionModel::getd2Pij_dt2 ( double t ) const [pure virtual, inherited]

Returns:: All second order derivatives of the probability of change from state i to state j with respect to time t, at time t.

See also:: d2Pij_dt2()

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::MarkovModulatedSubstitutionModel, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::WordSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioSubstitutionModel::getd2Pij_dt2(), and bpp::RE08::getd2Pij_dt2().

virtual const Matrix<double>& bpp::SubstitutionModel::getdPij_dt ( double t ) const [pure virtual, inherited]

Returns:: Get all first order derivatives of the probability of change from state i to state j with respect to time t, at time t.

See also:: dPij_dt()

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::MarkovModulatedSubstitutionModel, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::WordSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::RE08::getd2Pij_dt2(), bpp::AbstractBiblioSubstitutionModel::getdPij_dt(), and bpp::RE08::getdPij_dt().

virtual const Vdouble& bpp::SubstitutionModel::getEigenValues ( ) const [pure virtual, inherited]

Returns:: A vector with all real parts of the eigen values of the generator of this model;

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getEigenValues(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

virtual const Matrix<double>& bpp::SubstitutionModel::getExchangeabilityMatrix ( ) const [pure virtual, inherited]

Returns:: The matrix of exchangeability terms. It is recommended that exchangeability matrix be normalized so that the normalized generator be obtained directly by the dot product $S . \pi$ .

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getExchangeabilityMatrix(), bpp::RE08::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

virtual const Vdouble& bpp::SubstitutionModel::getFrequencies ( ) const [pure virtual, inherited]

Returns:: A vector of all equilibrium frequencies.

See also:: freq()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::TwoTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioSubstitutionModel::getFrequencies(), bpp::TwoTreeLikelihood::getRootFrequencies(), bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies(), bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

virtual const FrequenciesSet* bpp::SubstitutionModel::getFrequenciesSet ( ) const [inline, virtual, inherited]

If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.

Reimplemented in bpp::JCprot, bpp::AbstractBiblioSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::DSO78, bpp::JTT92, bpp::LG08, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, and bpp::AbstractCodonFrequenciesSubstitutionModel.

Definition at line 463 of file SubstitutionModel.h.

Referenced by bpp::AbstractBiblioSubstitutionModel::getFrequenciesSet(), and bpp::BppOSubstitutionModelFormat::write().

virtual const Matrix<double>& bpp::SubstitutionModel::getGenerator ( ) const [pure virtual, inherited]

Returns:: The normalized Markov generator matrix, i.e. all normalized rates of changes from state i to state j. The generator is normalized so that (i) $\forall i; \sum_j Q_{i,j} = 0$ , meaning that $ $\forall i; Q_{i,i} = -\sum_{j \neq i}Q_{i,j}$ , and (ii) $\sum_i Q_{i,i} \times \pi_i = -1$ . This means that, under normalization, the mean rate of replacement at equilibrium is 1 and that time are measured in units of expected number of changes per site. Additionnaly, the rate_ attibute provides the possibility to increase or decrease this mean rate.

See Kosiol and Goldman (2005), Molecular Biology And Evolution 22(2) 193-9.

See also:: Qij()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::AbstractBiblioSubstitutionModel::getGenerator(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::RE08::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

virtual const Vdouble& bpp::SubstitutionModel::getIEigenValues ( ) const [pure virtual, inherited]

Returns:: A vector with all imaginary parts of the eigen values of the generator of this model;

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getIEigenValues().

virtual double bpp::SubstitutionModel::getInitValue	(	size_t	i,
		int	state
	)		const throw (IndexOutOfBoundsException, BadIntException) `[pure virtual, inherited]`

This method is used to initialize likelihoods in reccursions. 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.

Parameters:

i	the index of the state in the model.
state	An observed state in the sequence/site.

Returns:: 1 or 0 depending if the two states are compatible.

Exceptions:

IndexOutOfBoundsException	if array position is out of range.
BadIntException	if states are not allowed in the associated alphabet.

See also:: getStates();

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getInitValue().

virtual std::vector<size_t> bpp::SubstitutionModel::getModelStates ( int i ) const [pure virtual, inherited]

Get the state in the model corresponding to a particular char in the alphabet.

Parameters:

i	The alphabet char to check.

Returns:: A vector of indices of model states.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getModelStates(), bpp::MarkovModulatedSubstitutionModel::getModelStates(), and bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates().

virtual std::string bpp::SubstitutionModel::getName ( ) const [pure virtual, inherited]

Get the name of the model.

Returns:: The name of this model.

Referenced by bpp::AbstractCodonFitnessSubstitutionModel::AbstractCodonFitnessSubstitutionModel(), bpp::AbstractSubstitutionModel::fireParameterChanged(), bpp::gBGC::getName(), bpp::MixtureOfSubstitutionModels::getSubmodelNumbers(), bpp::BppOSubstitutionModelFormat::readMixed_(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractBiblioSubstitutionModel::updateMatrices(), and bpp::BppOSubstitutionModelFormat::write().

virtual const SubstitutionModel* bpp::MixedSubstitutionModel::getNModel ( size_t i ) const [pure virtual]

Returns a specific model from the mixture.

Implemented in bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(), bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioMixedSubstitutionModel::getNModel(), and bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood().

virtual SubstitutionModel* bpp::MixedSubstitutionModel::getNModel ( size_t i ) [pure virtual]

Implemented in bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

virtual double bpp::MixedSubstitutionModel::getNProbability ( size_t i ) const [pure virtual]

Returns the probability of a specific model from the mixture.

Implemented in bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

Referenced by bpp::MixedSubstitutionModelSet::computeHyperNodesProbabilities(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(), bpp::MixedSubstitutionModelSet::getHyperNodeProbability(), bpp::AbstractBiblioMixedSubstitutionModel::getNProbability(), and bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood().

virtual double bpp::MixedSubstitutionModel::getNRate ( size_t i ) const [pure virtual]

Returns the rate of a specific submodel.

Implemented in bpp::AbstractBiblioMixedSubstitutionModel, and bpp::AbstractMixedSubstitutionModel.

Referenced by bpp::AbstractBiblioMixedSubstitutionModel::getNRate().

virtual size_t bpp::MixedSubstitutionModel::getNumberOfModels ( ) const [pure virtual]

Implemented in bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

Referenced by bpp::MixedSubstitutionModelSet::complete(), bpp::SubstitutionModelSetTools::createNonHomogeneousModelSet(), bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(), bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioMixedSubstitutionModel::getNumberOfModels(), bpp::BppOSubstitutionModelFormat::readMixed_(), and bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood().

virtual size_t bpp::SubstitutionModel::getNumberOfStates ( ) const [pure virtual, inherited]

Get the number of states.

For most models, this equals the size of the alphabet.

Returns:: The number of different states in the model.

Implemented in bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::YpR, bpp::AbstractBiblioSubstitutionModel, bpp::AbstractWordSubstitutionModel, bpp::BinarySubstitutionModel, bpp::gBGC, bpp::NucleotideSubstitutionModel, and bpp::ProteinSubstitutionModel.

Referenced by bpp::SubstitutionModelSet::addModel(), bpp::OneJumpSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::AbstractBiblioSubstitutionModel::getNumberOfStates(), bpp::BranchLikelihood::initModel(), bpp::RE08::RE08(), bpp::SimpleMutationProcess::SimpleMutationProcess(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

virtual const Matrix<double>& bpp::SubstitutionModel::getPij_t ( double t ) const [pure virtual, inherited]

Returns:: All probabilities of change from state i to state j during time t.

See also:: Pij_t()

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::MarkovModulatedSubstitutionModel, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::WordSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeCounts_(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::OneJumpSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::AbstractBiblioSubstitutionModel::getPij_t(), and bpp::RE08::getPij_t().

virtual const std::vector<double>& bpp::MixedSubstitutionModel::getProbabilities ( ) const [pure virtual]

Implemented in bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

Referenced by bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousMixedTreeLikelihood::fireParameterChanged(), and bpp::AbstractBiblioMixedSubstitutionModel::getProbabilities().

virtual double bpp::SubstitutionModel::getRate ( ) const [pure virtual, inherited]

Get the rate.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::G2001, bpp::AbstractBiblioSubstitutionModel, and bpp::TS98.

Referenced by bpp::AbstractBiblioSubstitutionModel::getRate(), and bpp::MarkovModulatedSubstitutionModel::getRate().

virtual const Matrix<double>& bpp::SubstitutionModel::getRowLeftEigenVectors ( ) const [pure virtual, inherited]

Returns:: A matrix with left eigen vectors. Each row in the matrix stands for an eigen vector.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), and bpp::AbstractBiblioSubstitutionModel::getRowLeftEigenVectors().

virtual double bpp::SubstitutionModel::getScale ( ) const [pure virtual, inherited]

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.

Returns:: Minus the scalar product of diagonal elements and the frequencies vector.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getScale().

virtual Vint bpp::MixedSubstitutionModel::getSubmodelNumbers ( std::string & desc ) const [pure virtual]

Implemented in bpp::MixtureOfSubstitutionModels, bpp::AbstractBiblioMixedSubstitutionModel, and bpp::MixtureOfASubstitutionModel.

Referenced by bpp::PhylogeneticsApplicationTools::completeMixedSubstitutionModelSet(), and bpp::AbstractBiblioMixedSubstitutionModel::getSubmodelNumbers().

virtual const std::vector<double>& bpp::MixedSubstitutionModel::getVRates ( ) const [pure virtual]

Returns the rates of the submodels.

Implemented in bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

Referenced by bpp::AbstractBiblioMixedSubstitutionModel::getVRates().

virtual bool bpp::SubstitutionModel::isDiagonalizable ( ) const [pure virtual, inherited]

Returns:: True if the model is diagonalizable in R.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::isDiagonalizable().

virtual bool bpp::SubstitutionModel::isNonSingular ( ) const [pure virtual, inherited]

Returns:: True is the model is non-singular.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::isNonSingular().

virtual void bpp::MixedSubstitutionModel::normalizeVRates ( ) [pure virtual]

Normalizes the rates of the submodels so that the mean rate of the mixture equals rate_.

Implemented in bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

Referenced by bpp::MixedSubstitutionModelSet::computeHyperNodesProbabilities(), and bpp::AbstractBiblioMixedSubstitutionModel::normalizeVRates().

virtual double bpp::SubstitutionModel::Pij_t	(	size_t	i,
		size_t	j,
		double	t
	)		const `[pure virtual, inherited]`

Returns:: The probability of change from state i to state j during time t.

See also:: getPij_t(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::JCnuc, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::SimpleMutationProcess::evolve(), bpp::OneJumpSubstitutionCount::getNumberOfSubstitutions(), bpp::AbstractBiblioSubstitutionModel::Pij_t(), and bpp::RE08::Pij_t().

virtual double bpp::SubstitutionModel::Qij	(	size_t	i,
		size_t	j
	)		const `[pure virtual, inherited]`

Returns:: The rate in the generator of change from state i to state j.

See also:: getStates();

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::UniformizationSubstitutionCount::fillBMatrices_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::AbstractMutationProcess::getTimeBeforeNextMutationEvent(), bpp::AbstractBiblioSubstitutionModel::Qij(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), bpp::gBGC::updateMatrices(), and bpp::YpR::updateMatrices().

virtual void bpp::SubstitutionModel::setFreq ( std::map< int, double > & frequencies ) [inline, virtual, inherited]

Set equilibrium frequencies.

Parameters:

frequencies The map of the frequencies to use.

Reimplemented in bpp::AbstractSubstitutionModel, bpp::F84, bpp::HKY85, bpp::MixtureOfSubstitutionModels, bpp::T92, bpp::AbstractWordSubstitutionModel, bpp::GTR, bpp::RN95, bpp::TN93, bpp::RN95s, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::MixtureOfASubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::BinarySubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::SSR, bpp::L95, bpp::CodonRateFrequenciesSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, and bpp::AbstractCodonFitnessSubstitutionModel.

Definition at line 455 of file SubstitutionModel.h.

Referenced by bpp::AbstractBiblioSubstitutionModel::setFreq().

virtual void bpp::SubstitutionModel::setFreqFromData	(	const SequenceContainer &	data,
		double	pseudoCount = `0`
	)		`[pure virtual, inherited]`

Set equilibrium frequencies equal to the frequencies estimated from the data.

Parameters:

data	The sequences to use.
pseudoCount	A quantity $\psi$ 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 $\pi_i = \frac{n_i+\psi}{\sum_j (f_j+\psi)}$

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::setFreqFromData(), and bpp::MarkovModulatedSubstitutionModel::setFreqFromData().

virtual void bpp::MixedSubstitutionModel::setNProbability	(	size_t	i,
		double	prob
	)		`[pure virtual]`

Sets the probability of a specific model from the mixture.

Implemented in bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

Referenced by bpp::MixedSubstitutionModelSet::computeHyperNodesProbabilities(), and bpp::AbstractBiblioMixedSubstitutionModel::setNProbability().

virtual void bpp::SubstitutionModel::setRate ( double rate ) [pure virtual, inherited]

Set the rate of the model (must be positive).

Parameters:

rate	must be positive.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::G2001, bpp::AbstractBiblioSubstitutionModel, and bpp::TS98.

Referenced by bpp::AbstractBiblioSubstitutionModel::setRate(), and bpp::MarkovModulatedSubstitutionModel::setRate().

virtual void bpp::SubstitutionModel::setScale ( double scale ) [pure virtual, inherited]

Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.

When the generator is normalized, scale=1. Otherwise each element is multiplied such that the correct scale is set.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::setScale(), and bpp::MarkovModulatedSubstitutionModel::setScale().

virtual void bpp::MixedSubstitutionModel::setVRates ( const Vdouble & vd ) [pure virtual]

Sets the rates of the submodels to be proportional to a given vector, and normalizes them so that the mean rate of the mixture equals rate_.

Parameters:

vd	a vector of positive values such that the rates of the respective submodels are in the same proportions (ie this vector does not need to be normalized).

Implemented in bpp::MixtureOfSubstitutionModels, bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

Referenced by bpp::AbstractBiblioMixedSubstitutionModel::setVRates().

virtual double bpp::SubstitutionModel::Sij	(	size_t	i,
		size_t	j
	)		const `[pure virtual, inherited]`

Returns:: The exchangeability between state i and state j.

By definition Sij(i,j) = Sij(j,i).

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::Sij().

The documentation for this class was generated from the following file:

Bpp/Phyl/Model/MixedSubstitutionModel.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation