bpp::AbstractAlignedPhyloLikelihoodSet Class Reference

The AlignedPhyloLikelihoodSet abstract class. More...

#include <Bpp/Phyl/Likelihood/PhyloLikelihoods/AlignedPhyloLikelihoodSet.h>

Inheritance diagram for bpp::AbstractAlignedPhyloLikelihoodSet:

Collaboration diagram for bpp::AbstractAlignedPhyloLikelihoodSet:

Public Member Functions
	AbstractAlignedPhyloLikelihoodSet (Context &context, std::shared_ptr< PhyloLikelihoodContainer > pC, bool inCollection=true, const std::string &prefix="")
	AbstractAlignedPhyloLikelihoodSet (Context &context, std::shared_ptr< PhyloLikelihoodContainer > pC, const std::vector< size_t > &nPhylo, bool inCollection=true, const std::string &prefix="")
virtual	~AbstractAlignedPhyloLikelihoodSet ()
bool	addPhyloLikelihood (size_t nPhyl, const std::string &suff) override
	adds a PhyloLikelihood already stored in the m ap, iff it is an AlignedPhyloLikelihood of the same size More...
std::shared_ptr< const AlignedPhyloLikelihoodInterface >	getAlignedPhyloLikelihood (size_t nPhyl) const override
std::shared_ptr< AlignedPhyloLikelihoodInterface >	getAlignedPhyloLikelihood (size_t nPhyl) override
const AlignedPhyloLikelihoodInterface &	alignedPhyloLikelihood (size_t nPhyl) const override
AlignedPhyloLikelihoodInterface &	alignedPhyloLikelihood (size_t nPhyl) override
DataLik	getLikelihoodForASiteForAPhyloLikelihood (size_t site, size_t nPhyl) const override
	Get the likelihood for a site for an aligned phyloLikelihood. More...
double	getLogLikelihoodForASiteForAPhyloLikelihood (size_t site, size_t nPhyl) const override
	Get the log likelihood for a site for an aligned phyloLikelihood. More...
AlignedPhyloLikelihoodSetInterface *	clone () const override=0
virtual std::shared_ptr< PhyloLikelihoodContainer >	getPhyloContainer ()=0
virtual std::shared_ptr< const PhyloLikelihoodContainer >	getPhyloContainer () const =0
virtual const std::vector< size_t > &	getNumbersOfPhyloLikelihoods () const =0
virtual LikelihoodCalculation &	likelihoodCalculation () const =0
virtual std::shared_ptr< LikelihoodCalculation >	getLikelihoodCalculation () const =0
virtual void	enableSecondOrderDerivatives (bool yn)=0
virtual bool	enableSecondOrderDerivatives () const=0
virtual double	getSecondOrderDerivative (const std::string &variable) const=0
virtual double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const=0
virtual double	d2f (const std::string &variable, const ParameterList &parameters)
virtual double	d2f (const std::string &variable1, const std::string &variable2, const ParameterList &parameters)
virtual void	enableFirstOrderDerivatives (bool yn)=0
virtual bool	enableFirstOrderDerivatives () const=0
virtual double	getFirstOrderDerivative (const std::string &variable) const=0
virtual double	df (const std::string &variable, const ParameterList &parameters)
virtual void	setParameters (const ParameterList &parameters)=0
virtual double	getValue () const=0
virtual double	f (const ParameterList &parameters)
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 &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 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
std::shared_ptr< PhyloLikelihoodContainer >	getPhyloContainer () override
std::shared_ptr< const PhyloLikelihoodContainer >	getPhyloContainer () const override
const std::vector< size_t > &	getNumbersOfPhyloLikelihoods () const override
virtual Clonable *	clone () const=0
const Context &	context () const override
Context &	context () override
ValueRef< DataLik >	getLikelihoodNode () const override
virtual void	enableSecondOrderDerivatives (bool yn) override
bool	enableSecondOrderDerivatives () const override
double	getSecondOrderDerivative (const std::string &variable) const override
double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const override
virtual void	enableFirstOrderDerivatives (bool yn) override
	Tell if derivatives must be computed: for Function inheritance. More...
bool	enableFirstOrderDerivatives () const override
double	getFirstOrderDerivative (const std::string &variable) const override
void	setParameters (const ParameterList &parameters) override
double	getValue () const override
bool	hasParameter (const std::string &name) const override
const ParameterList &	getParameters () const override
const Parameter &	parameter (const std::string &name) const override
double	getParameterValue (const std::string &name) const override
void	setAllParametersValues (const ParameterList &parameters) override
void	setParameterValue (const std::string &name, double value) override
void	setParametersValues (const ParameterList &parameters) override
bool	matchParametersValues (const ParameterList &parameters) override
void	removeConstraint (const std::string &name) override
void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
size_t	getNumberOfParameters () const override
void	setNamespace (const std::string &prefix) override
std::string	getNamespace () const override
std::string	getParameterNameWithoutNamespace (const std::string &name) const override
void	shareParameters (const ParameterList &variableNodes)
	Share Parameters, that are DF_parameters. More...
ValueRef< DataLik >	firstOrderDerivativeNode (const std::string &variable) const
ValueRef< DataLik >	secondOrderDerivativeNode (const std::string &variable1, const std::string &variable2) const
const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const
size_t	getNumberOfSites () const
	Get the number of sites in the dataset. More...
DataLik	getLikelihoodForASite (size_t site) const
	Get the likelihood for a site (on uncompressed data) More...
double	getLogLikelihoodForASite (size_t site) const
	Get the log likelihood for a site, and its derivatives. More...
VDataLik	getLikelihoodPerSite () const
	Get the likelihood for each site. More...
The PhyloLikelihood storage.
virtual bool	hasPhyloLikelihood (size_t nPhyl)=0
virtual std::shared_ptr< const PhyloLikelihoodInterface >	getPhyloLikelihood (size_t nPhyl) const =0
virtual std::shared_ptr< PhyloLikelihoodInterface >	getPhyloLikelihood (size_t nPhyl)=0
The data functions
virtual bool	isInitialized () const =0
virtual const Context &	context () const =0
virtual Context &	context ()=0
The likelihood functions.
virtual ValueRef< DataLik >	getLikelihoodNode () const =0
double	getLogLikelihood () const
	Get the logarithm of the likelihood for the whole dataset. More...
Retrieve some particular independent parameters subsets.
Get the derivates of the LogLikelihood.
virtual ParameterList	getNonDerivableParameters () const =0
virtual ParameterList	getDerivableParameters () const =0
virtual ParameterList	getBranchLengthParameters () const =0
	Get the independent branch lengths parameters. More...
virtual ParameterList	getSubstitutionModelParameters () const =0
	Get the independent parameters associated to substitution model(s). More...
virtual ParameterList	getRateDistributionParameters () const =0
	Get the independent parameters associated to the rate distribution(s). More...
virtual ParameterList	getRootFrequenciesParameters () const =0
	Get the independent parameters associated to the root frequencies(s). More...
The data functions
virtual size_t	getNumberOfSites () const =0
	Get the number of sites in the dataset. More...
The likelihood functions.
virtual AlignedLikelihoodCalculation &	alignedLikelihoodCalculation () const =0
virtual std::shared_ptr< AlignedLikelihoodCalculation >	getAlignedLikelihoodCalculation () const =0
virtual DataLik	getLikelihoodForASite (size_t site) const =0
	Get the likelihood for a site. More...
virtual double	getLogLikelihoodForASite (size_t site) const =0
	Get the log likelihood for a site, and its derivatives. More...
virtual VDataLik	getLikelihoodPerSite () const =0
	Get the likelihood for each site. More...
The PhyloLikelihood storage.
bool	hasPhyloLikelihood (size_t nPhyl) override
std::shared_ptr< const PhyloLikelihoodInterface >	getPhyloLikelihood (size_t nPhyl) const override
std::shared_ptr< PhyloLikelihoodInterface >	getPhyloLikelihood (size_t nPhyl) override
Inherited from PhyloLikelihood
bool	isInitialized () const override
virtual void	fireParameterChanged (const ParameterList &params) override
Retrieve some particular parameters subsets.
ParameterList	getNonDerivableParameters () const override
ParameterList	getDerivableParameters () const override
ParameterList	getBranchLengthParameters () const override
	Get the branch lengths parameters. More...
ParameterList	getSubstitutionModelParameters () const override
	Get the parameters associated to substitution model(s). More...
ParameterList	getRateDistributionParameters () const override
	Get the parameters associated to the rate distribution(s). More...
ParameterList	getRootFrequenciesParameters () const override
	Get the parameters associated to the root frequencies(s). More...

Protected Member Functions
	AbstractAlignedPhyloLikelihoodSet (const AbstractAlignedPhyloLikelihoodSet &soap)
AbstractAlignedPhyloLikelihoodSet &	operator= (const AbstractAlignedPhyloLikelihoodSet &soap)
virtual ParameterList &	getParameters_ ()=0
ParameterList &	getParameters_ () override
Node_DF &	accessVariableNode (const std::string &name) const
const std::shared_ptr< Parameter > &	getParameter (size_t i) const
std::shared_ptr< Parameter > &	getParameter (size_t i)
virtual void	addParameter_ (Parameter *parameter)
virtual void	addParameters_ (const ParameterList &parameters)
virtual void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)
virtual void	shareParameters_ (const ParameterList &parameters)
virtual void	includeParameters_ (const ParameterList &parameters)
virtual void	deleteParameter_ (size_t index)
virtual void	deleteParameter_ (std::string &name)
virtual void	deleteParameters_ (const std::vector< std::string > &names)
void	resetParameters_ ()
Parameter &	getParameter_ (const std::string &name)
Parameter &	getParameter_ (size_t index)
const Parameter &	getParameter_ (size_t index) const
Parameter &	getParameterWithNamespace_ (const std::string &name)
const Parameter &	getParameterWithNamespace_ (const std::string &name) const
void	setNumberOfSites (size_t nbSites)

Static Protected Member Functions
static Node_DF &	accessVariableNode (const Parameter &param)

Protected Attributes
std::shared_ptr< PhyloLikelihoodContainer >	pPhyloCont_
	pointer to a PhyloLikelihoodContainer More...
std::vector< size_t >	nPhylo_
	vector of AbstractPhyloLikelihood numbers More...
std::vector< std::shared_ptr< LikelihoodCalculation > >	vLikCal_
Context &	context_
DataLik	minusLogLik_
	the value More...
std::unordered_map< std::string, ValueRef< DataLik > >	firstOrderDerivativeNodes_
	For Dataflow computing. More...
std::unordered_map< std::pair< std::string, std::string >, ValueRef< DataLik >, StringPairHash >	secondOrderDerivativeNodes_
size_t	nbSites_

Private Attributes
ParameterList	parameters_
std::string	prefix_

Detailed Description

The AlignedPhyloLikelihoodSet abstract class.

This class defines the common methods needed to compute a likelihood from aligned phylogenies.

Definition at line 62 of file AlignedPhyloLikelihoodSet.h.

Constructor & Destructor Documentation

AbstractAlignedPhyloLikelihoodSet() [1/3]

AbstractAlignedPhyloLikelihoodSet::AbstractAlignedPhyloLikelihoodSet	(	Context &	context,
		std::shared_ptr< PhyloLikelihoodContainer >	pC,
		bool	inCollection = true,
		const std::string &	prefix = ""
	)

Definition at line 11 of file AlignedPhyloLikelihoodSet.cpp.

References getAlignedPhyloLikelihood(), bpp::AbstractAlignedPhyloLikelihood::getNumberOfSites(), bpp::AbstractPhyloLikelihoodSet::nPhylo_, bpp::AbstractAlignedPhyloLikelihood::setNumberOfSites(), and bpp::TextTools::toString().

AbstractAlignedPhyloLikelihoodSet() [2/3]

AbstractAlignedPhyloLikelihoodSet::AbstractAlignedPhyloLikelihoodSet	(	Context &	context,
		std::shared_ptr< PhyloLikelihoodContainer >	pC,
		const std::vector< size_t > &	nPhylo,
		bool	inCollection = true,
		const std::string &	prefix = ""
	)

Definition at line 35 of file AlignedPhyloLikelihoodSet.cpp.

References getAlignedPhyloLikelihood(), bpp::AbstractAlignedPhyloLikelihood::getNumberOfSites(), bpp::AbstractAlignedPhyloLikelihood::setNumberOfSites(), and bpp::TextTools::toString().

AbstractAlignedPhyloLikelihoodSet() [3/3]

bpp::AbstractAlignedPhyloLikelihoodSet::AbstractAlignedPhyloLikelihoodSet ( const AbstractAlignedPhyloLikelihoodSet &  soap )

inlineprotected

Definition at line 82 of file AlignedPhyloLikelihoodSet.h.

~AbstractAlignedPhyloLikelihoodSet()

virtual bpp::AbstractAlignedPhyloLikelihoodSet::~AbstractAlignedPhyloLikelihoodSet ( )

inlinevirtual

Definition at line 96 of file AlignedPhyloLikelihoodSet.h.

Member Function Documentation

accessVariableNode() [1/2]

static Node_DF& bpp::AbstractPhyloLikelihood::accessVariableNode ( const Parameter &  param )

inlinestaticprotectedinherited

Definition at line 188 of file AbstractPhyloLikelihood.h.

Referenced by bpp::AbstractPhyloLikelihood::accessVariableNode(), bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::firstOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::firstOrderDerivativeVector(), bpp::SingleProcessPhyloLikelihood::firstOrderDerivativeVector(), bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::secondOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::secondOrderDerivativeVector(), and bpp::SingleProcessPhyloLikelihood::secondOrderDerivativeVector().

accessVariableNode() [2/2]

Node_DF& bpp::AbstractPhyloLikelihood::accessVariableNode ( const std::string &  name ) const

inlineprotectedinherited

Definition at line 193 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::accessVariableNode(), and bpp::SecondOrderDerivable::parameter().

addPhyloLikelihood()

bool AbstractAlignedPhyloLikelihoodSet::addPhyloLikelihood ( size_t  nPhyl, const std::string &  suff  )

overridevirtual

adds a PhyloLikelihood already stored in the m ap, iff it is an AlignedPhyloLikelihood of the same size

Parameters

nPhyl	number of the phylolikelihood
suff	for parameters names if use specific parameters names

Returns

if the PhyloLikelihood has been added.

Reimplemented from bpp::AbstractPhyloLikelihoodSet.

Definition at line 60 of file AlignedPhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihoodSet::addPhyloLikelihood(), getAlignedPhyloLikelihood(), bpp::AbstractAlignedPhyloLikelihood::getNumberOfSites(), and bpp::AbstractAlignedPhyloLikelihood::setNumberOfSites().

alignedLikelihoodCalculation()

virtual AlignedLikelihoodCalculation& bpp::AlignedPhyloLikelihoodInterface::alignedLikelihoodCalculation ( ) const

pure virtualinherited

Returns

The LikelihoodCalculation.

Implemented in bpp::AutoCorrelationProcessPhyloLikelihood, bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, bpp::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

Referenced by bpp::AlignedPhyloLikelihoodMixture::AlignedPhyloLikelihoodMixture(), and bpp::AbstractAlignedPhyloLikelihood::getLikelihoodForASite().

alignedPhyloLikelihood() [1/2]

const AlignedPhyloLikelihoodInterface& bpp::AbstractAlignedPhyloLikelihoodSet::alignedPhyloLikelihood ( size_t  nPhyl ) const

inlineoverridevirtual

Implements bpp::AlignedPhyloLikelihoodSetInterface.

Definition at line 120 of file AlignedPhyloLikelihoodSet.h.

Referenced by bpp::AlignedPhyloLikelihoodMixture::AlignedPhyloLikelihoodMixture(), getLikelihoodForASiteForAPhyloLikelihood(), and getLogLikelihoodForASiteForAPhyloLikelihood().

alignedPhyloLikelihood() [2/2]

AlignedPhyloLikelihoodInterface& bpp::AbstractAlignedPhyloLikelihoodSet::alignedPhyloLikelihood ( size_t  nPhyl )

inlineoverridevirtual

Implements bpp::AlignedPhyloLikelihoodSetInterface.

Definition at line 125 of file AlignedPhyloLikelihoodSet.h.

clone()

AlignedPhyloLikelihoodSetInterface* bpp::AlignedPhyloLikelihoodSetInterface::clone ( ) const

overridepure virtualinherited

Implements bpp::AlignedPhyloLikelihoodInterface.

Implemented in bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, bpp::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

context() [1/4]

virtual const Context& bpp::PhyloLikelihoodInterface::context ( ) const

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihood.

context() [2/4]

const Context& bpp::AbstractPhyloLikelihood::context ( ) const

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodInterface.

Definition at line 73 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::context_.

Referenced by bpp::AlignedPhyloLikelihoodMixture::AlignedPhyloLikelihoodMixture(), bpp::AutoCorrelationProcessPhyloLikelihood::AutoCorrelationProcessPhyloLikelihood(), bpp::HmmProcessPhyloLikelihood::HmmProcessPhyloLikelihood(), bpp::PartitionProcessPhyloLikelihood::makeLikCal_(), bpp::MixtureProcessPhyloLikelihood::MixtureProcessPhyloLikelihood(), bpp::OneProcessSequencePhyloLikelihood::OneProcessSequencePhyloLikelihood(), and bpp::PartitionProcessPhyloLikelihood::PartitionProcessPhyloLikelihood().

context() [3/4]

Context& bpp::AbstractPhyloLikelihood::context ( )

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodInterface.

Definition at line 75 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::context_.

context() [4/4]

virtual Context& bpp::PhyloLikelihoodInterface::context ( )

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihood.

enableFirstOrderDerivatives() [1/2]

bool bpp::AbstractPhyloLikelihood::enableFirstOrderDerivatives ( ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 115 of file AbstractPhyloLikelihood.h.

enableFirstOrderDerivatives() [2/2]

virtual void bpp::AbstractPhyloLikelihood::enableFirstOrderDerivatives ( bool  yn )

inlineoverridevirtualinherited

Tell if derivatives must be computed: for Function inheritance.

Implements bpp::SecondOrderDerivable.

Definition at line 113 of file AbstractPhyloLikelihood.h.

enableSecondOrderDerivatives() [1/2]

bool bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives ( ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 116 of file AbstractPhyloLikelihood.h.

enableSecondOrderDerivatives() [2/2]

virtual void bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives ( bool  yn )

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 114 of file AbstractPhyloLikelihood.h.

fireParameterChanged()

virtual void bpp::AbstractPhyloLikelihoodSet::fireParameterChanged ( const ParameterList &  params )

inlineoverridevirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Reimplemented in bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

Definition at line 208 of file PhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), and bpp::AbstractPhyloLikelihoodSet::nPhylo_.

Referenced by bpp::AlignedPhyloLikelihoodAutoCorrelation::fireParameterChanged(), and bpp::AlignedPhyloLikelihoodHmm::fireParameterChanged().

firstOrderDerivativeNode()

ValueRef<DataLik> bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode ( const std::string &  variable ) const

inlineinherited

Definition at line 139 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::accessVariableNode(), bpp::AbstractPhyloLikelihood::context_, bpp::AbstractPhyloLikelihood::firstOrderDerivativeNodes_, and bpp::AbstractPhyloLikelihood::getLikelihoodNode().

Referenced by bpp::AbstractPhyloLikelihood::getFirstOrderDerivative(), and bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode().

getAlignedLikelihoodCalculation()

virtual std::shared_ptr<AlignedLikelihoodCalculation> bpp::AlignedPhyloLikelihoodInterface::getAlignedLikelihoodCalculation ( ) const

pure virtualinherited

Returns

A shared pointer toward the LikelihoodCalculation.

Implemented in bpp::AutoCorrelationProcessPhyloLikelihood, bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, bpp::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

Referenced by bpp::AbstractAlignedPhyloLikelihood::getLikelihoodPerSite(), and bpp::AbstractAlignedPhyloLikelihood::getLogLikelihoodForASite().

getAlignedPhyloLikelihood() [1/2]

std::shared_ptr<const AlignedPhyloLikelihoodInterface> bpp::AbstractAlignedPhyloLikelihoodSet::getAlignedPhyloLikelihood ( size_t  nPhyl ) const

inlineoverridevirtual

Implements bpp::AlignedPhyloLikelihoodSetInterface.

Definition at line 110 of file AlignedPhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::pPhyloCont_.

Referenced by AbstractAlignedPhyloLikelihoodSet(), and addPhyloLikelihood().

getAlignedPhyloLikelihood() [2/2]

std::shared_ptr<AlignedPhyloLikelihoodInterface> bpp::AbstractAlignedPhyloLikelihoodSet::getAlignedPhyloLikelihood ( size_t  nPhyl )

inlineoverridevirtual

Implements bpp::AlignedPhyloLikelihoodSetInterface.

Definition at line 115 of file AlignedPhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::pPhyloCont_.

getBranchLengthParameters() [1/2]

virtual ParameterList bpp::PhyloLikelihoodInterface::getBranchLengthParameters ( ) const

pure virtualinherited

Get the independent branch lengths parameters.

Returns

A ParameterList with all branch lengths.

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, and bpp::OnABranchPhyloLikelihood.

Referenced by bpp::BppPhylogeneticsApplication::displayParameters().

getBranchLengthParameters() [2/2]

ParameterList AbstractPhyloLikelihoodSet::getBranchLengthParameters ( ) const

overridevirtualinherited

Get the branch lengths parameters.

Returns

A ParameterList with all branch lengths.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 107 of file PhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::ParameterList::includeParameters(), and bpp::AbstractPhyloLikelihoodSet::nPhylo_.

getDerivableParameters() [1/2]

virtual ParameterList bpp::PhyloLikelihoodInterface::getDerivableParameters ( ) const

pure virtualinherited

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, and bpp::OnABranchPhyloLikelihood.

getDerivableParameters() [2/2]

ParameterList AbstractPhyloLikelihoodSet::getDerivableParameters ( ) const

overridevirtualinherited

Implements bpp::PhyloLikelihoodInterface.

Definition at line 95 of file PhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::ParameterList::includeParameters(), and bpp::AbstractPhyloLikelihoodSet::nPhylo_.

getFirstOrderDerivative()

double bpp::AbstractPhyloLikelihood::getFirstOrderDerivative ( const std::string &  variable ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 131 of file AbstractPhyloLikelihood.h.

References bpp::convert(), and bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode().

getLikelihoodCalculation()

virtual std::shared_ptr<LikelihoodCalculation> bpp::PhyloLikelihoodInterface::getLikelihoodCalculation ( ) const

pure virtualinherited

Returns

A shared pointer toward the LikelihoodCalculation.

Implemented in bpp::AutoCorrelationProcessPhyloLikelihood, bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, bpp::PhyloLikelihoodFormula, bpp::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

Referenced by bpp::AbstractPhyloLikelihood::getLikelihoodNode().

getLikelihoodForASite() [1/2]

DataLik bpp::AbstractAlignedPhyloLikelihood::getLikelihoodForASite ( size_t  site ) const

inlinevirtualinherited

Get the likelihood for a site (on uncompressed data)

Parameters

site	The site index to analyse.

Returns

The likelihood for site site.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 143 of file AlignedPhyloLikelihood.h.

References bpp::AlignedPhyloLikelihoodInterface::alignedLikelihoodCalculation(), and bpp::AlignedLikelihoodCalculation::getLikelihoodForASite().

getLikelihoodForASite() [2/2]

virtual DataLik bpp::AlignedPhyloLikelihoodInterface::getLikelihoodForASite ( size_t  site ) const

pure virtualinherited

Get the likelihood for a site.

Parameters

site	The site index to analyse.

Returns

The likelihood for site site.

Implemented in bpp::AbstractAlignedPhyloLikelihood.

Referenced by getLikelihoodForASiteForAPhyloLikelihood().

getLikelihoodForASiteForAPhyloLikelihood()

DataLik bpp::AbstractAlignedPhyloLikelihoodSet::getLikelihoodForASiteForAPhyloLikelihood ( size_t  site, size_t  nPhyl  ) const

inlineoverridevirtual

Get the likelihood for a site for an aligned phyloLikelihood.

Parameters

site	The site index to analyse.
nPhyl	the phyloLikelihood index.

Returns

The likelihood for site site.

Implements bpp::AlignedPhyloLikelihoodSetInterface.

Definition at line 130 of file AlignedPhyloLikelihoodSet.h.

References alignedPhyloLikelihood(), and bpp::AlignedPhyloLikelihoodInterface::getLikelihoodForASite().

getLikelihoodNode() [1/2]

virtual ValueRef<DataLik> bpp::PhyloLikelihoodInterface::getLikelihoodNode ( ) const

pure virtualinherited

Returns

the LikDF node where the Likelihood is computed.

Implemented in bpp::AbstractPhyloLikelihood.

getLikelihoodNode() [2/2]

ValueRef<DataLik> bpp::AbstractPhyloLikelihood::getLikelihoodNode ( ) const

inlineoverridevirtualinherited

Returns

the LikDF node where the Likelihood is computed.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 100 of file AbstractPhyloLikelihood.h.

References bpp::PhyloLikelihoodInterface::getLikelihoodCalculation().

Referenced by bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode(), and bpp::AbstractPhyloLikelihood::getValue().

getLikelihoodPerSite() [1/2]

VDataLik bpp::AbstractAlignedPhyloLikelihood::getLikelihoodPerSite ( ) const

inlinevirtualinherited

Get the likelihood for each site.

Returns

A vector with all site likelihoods.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 167 of file AlignedPhyloLikelihood.h.

References bpp::AlignedPhyloLikelihoodInterface::getAlignedLikelihoodCalculation().

Referenced by bpp::MixtureProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerProcess(), and bpp::OneProcessSequencePhyloLikelihood::getPosteriorRatePerSite().

getLikelihoodPerSite() [2/2]

virtual VDataLik bpp::AlignedPhyloLikelihoodInterface::getLikelihoodPerSite ( ) const

pure virtualinherited

Get the likelihood for each site.

Returns

A vector with all site likelihoods.

Implemented in bpp::AbstractAlignedPhyloLikelihood.

getLogLikelihood()

double bpp::PhyloLikelihoodInterface::getLogLikelihood ( ) const

inlineinherited

Get the logarithm of the likelihood for the whole dataset.

Returns

The logarithm of the likelihood of the dataset.

Definition at line 66 of file PhyloLikelihood.h.

References bpp::SecondOrderDerivable::getValue().

getLogLikelihoodForASite() [1/2]

double bpp::AbstractAlignedPhyloLikelihood::getLogLikelihoodForASite ( size_t  site ) const

inlinevirtualinherited

Get the log likelihood for a site, and its derivatives.

Parameters

site	The site index to analyse.

Returns

The (D)log likelihood for site site.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 154 of file AlignedPhyloLikelihood.h.

References bpp::convert(), and bpp::AlignedPhyloLikelihoodInterface::getAlignedLikelihoodCalculation().

getLogLikelihoodForASite() [2/2]

virtual double bpp::AlignedPhyloLikelihoodInterface::getLogLikelihoodForASite ( size_t  site ) const

pure virtualinherited

Get the log likelihood for a site, and its derivatives.

Parameters

site	The site index to analyse.

Returns

The (D)log likelihood for site site.

Implemented in bpp::AbstractAlignedPhyloLikelihood.

Referenced by getLogLikelihoodForASiteForAPhyloLikelihood(), and bpp::PhylogeneticsApplicationTools::printAnalysisInformation().

getLogLikelihoodForASiteForAPhyloLikelihood()

double bpp::AbstractAlignedPhyloLikelihoodSet::getLogLikelihoodForASiteForAPhyloLikelihood ( size_t  site, size_t  nPhyl  ) const

inlineoverridevirtual

Get the log likelihood for a site for an aligned phyloLikelihood.

Parameters

site	The site index to analyse.
nPhyl	the phyloLikelihood index.

Returns

The log likelihood for site site.

Implements bpp::AlignedPhyloLikelihoodSetInterface.

Definition at line 135 of file AlignedPhyloLikelihoodSet.h.

References alignedPhyloLikelihood(), and bpp::AlignedPhyloLikelihoodInterface::getLogLikelihoodForASite().

getNonDerivableParameters() [1/2]

virtual ParameterList bpp::PhyloLikelihoodInterface::getNonDerivableParameters ( ) const

pure virtualinherited

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, and bpp::OnABranchPhyloLikelihood.

getNonDerivableParameters() [2/2]

ParameterList AbstractPhyloLikelihoodSet::getNonDerivableParameters ( ) const

overridevirtualinherited

Implements bpp::PhyloLikelihoodInterface.

Definition at line 84 of file PhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::ParameterList::includeParameters(), and bpp::AbstractPhyloLikelihoodSet::nPhylo_.

getNumberOfSites() [1/2]

size_t bpp::AbstractAlignedPhyloLikelihood::getNumberOfSites ( ) const

inlinevirtualinherited

Get the number of sites in the dataset.

Returns

the number of sites in the dataset.

Implements bpp::AlignedPhyloLikelihoodInterface.

Reimplemented in bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, and bpp::OnABranchPhyloLikelihood.

Definition at line 135 of file AlignedPhyloLikelihood.h.

References bpp::AbstractAlignedPhyloLikelihood::nbSites_.

Referenced by AbstractAlignedPhyloLikelihoodSet(), addPhyloLikelihood(), bpp::OneProcessSequencePhyloLikelihood::getClassWithMaxPostProbPerSite(), bpp::MultiProcessSequencePhyloLikelihood::getLikelihoodPerSitePerProcess(), bpp::OneProcessSequencePhyloLikelihood::getPosteriorRatePerSite(), and bpp::OneProcessSequencePhyloLikelihood::getPosteriorStateFrequencies().

getNumberOfSites() [2/2]

virtual size_t bpp::AlignedPhyloLikelihoodInterface::getNumberOfSites ( ) const

pure virtualinherited

Get the number of sites in the dataset.

Returns

the number of sites in the dataset.

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OnABranchPhyloLikelihood, and bpp::AbstractAlignedPhyloLikelihood.

Referenced by bpp::HmmPhyloAlphabet::HmmPhyloAlphabet(), and bpp::PhylogeneticsApplicationTools::printAnalysisInformation().

getNumbersOfPhyloLikelihoods() [1/2]

virtual const std::vector<size_t>& bpp::PhyloLikelihoodSetInterface::getNumbersOfPhyloLikelihoods ( ) const

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

Referenced by bpp::HmmPhyloAlphabet::HmmPhyloAlphabet(), and bpp::PhylogeneticsApplicationTools::printAnalysisInformation().

getNumbersOfPhyloLikelihoods() [2/2]

const std::vector<size_t>& bpp::AbstractPhyloLikelihoodSet::getNumbersOfPhyloLikelihoods ( ) const

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 139 of file PhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::nPhylo_.

Referenced by bpp::AbstractPhyloLikelihoodSet::AbstractPhyloLikelihoodSet(), bpp::AlignedPhyloLikelihoodMixture::AlignedPhyloLikelihoodMixture(), and bpp::PartitionProcessPhyloLikelihood::getData().

getPhyloContainer() [1/4]

virtual std::shared_ptr<const PhyloLikelihoodContainer> bpp::PhyloLikelihoodSetInterface::getPhyloContainer ( ) const

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

getPhyloContainer() [2/4]

std::shared_ptr<const PhyloLikelihoodContainer> bpp::AbstractPhyloLikelihoodSet::getPhyloContainer ( ) const

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 134 of file PhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::pPhyloCont_.

getPhyloContainer() [3/4]

std::shared_ptr<PhyloLikelihoodContainer> bpp::AbstractPhyloLikelihoodSet::getPhyloContainer ( )

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 129 of file PhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::pPhyloCont_.

Referenced by bpp::AbstractPhyloLikelihoodSet::AbstractPhyloLikelihoodSet(), bpp::PartitionProcessPhyloLikelihood::getData(), bpp::PartitionProcessPhyloLikelihood::PartitionProcessPhyloLikelihood(), bpp::PhyloLikelihoodFormula::readFormula(), and bpp::PartitionProcessPhyloLikelihood::setData().

getPhyloContainer() [4/4]

virtual std::shared_ptr<PhyloLikelihoodContainer> bpp::PhyloLikelihoodSetInterface::getPhyloContainer ( )

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

getPhyloLikelihood() [1/4]

virtual std::shared_ptr<const PhyloLikelihoodInterface> bpp::PhyloLikelihoodSetInterface::getPhyloLikelihood ( size_t  nPhyl ) const

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

getPhyloLikelihood() [2/4]

std::shared_ptr<const PhyloLikelihoodInterface> bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood ( size_t  nPhyl ) const

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 169 of file PhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::pPhyloCont_.

Referenced by bpp::AbstractPhyloLikelihoodSet::addPhyloLikelihood(), bpp::AbstractPhyloLikelihoodSet::fireParameterChanged(), bpp::AbstractPhyloLikelihoodSet::getBranchLengthParameters(), bpp::AbstractPhyloLikelihoodSet::getDerivableParameters(), bpp::PartitionProcessPhyloLikelihood::getLikelihoodCalculationForASite(), bpp::AbstractPhyloLikelihoodSet::getNonDerivableParameters(), bpp::PartitionProcessPhyloLikelihood::getPhyloLikelihoodForASite(), bpp::AbstractPhyloLikelihoodSet::getRateDistributionParameters(), bpp::AbstractPhyloLikelihoodSet::getRootFrequenciesParameters(), bpp::AbstractPhyloLikelihoodSet::getSubstitutionModelParameters(), bpp::AbstractPhyloLikelihoodSet::isInitialized(), bpp::PhyloLikelihoodFormula::makeLikelihoodsFromOperator(), and bpp::PhyloLikelihoodFormula::readFormula().

getPhyloLikelihood() [3/4]

std::shared_ptr<PhyloLikelihoodInterface> bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood ( size_t  nPhyl )

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 175 of file PhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::pPhyloCont_.

getPhyloLikelihood() [4/4]

virtual std::shared_ptr<PhyloLikelihoodInterface> bpp::PhyloLikelihoodSetInterface::getPhyloLikelihood ( size_t  nPhyl )

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

getRateDistributionParameters() [1/2]

virtual ParameterList bpp::PhyloLikelihoodInterface::getRateDistributionParameters ( ) const

pure virtualinherited

Get the independent parameters associated to the rate distribution(s).

Returns

A ParameterList.

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, and bpp::OnABranchPhyloLikelihood.

getRateDistributionParameters() [2/2]

ParameterList AbstractPhyloLikelihoodSet::getRateDistributionParameters ( ) const

overridevirtualinherited

Get the parameters associated to the rate distribution(s).

Returns

A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 129 of file PhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::ParameterList::includeParameters(), and bpp::AbstractPhyloLikelihoodSet::nPhylo_.

getRootFrequenciesParameters() [1/2]

virtual ParameterList bpp::PhyloLikelihoodInterface::getRootFrequenciesParameters ( ) const

pure virtualinherited

Get the independent parameters associated to the root frequencies(s).

Returns

A ParameterList.

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, and bpp::OnABranchPhyloLikelihood.

getRootFrequenciesParameters() [2/2]

ParameterList AbstractPhyloLikelihoodSet::getRootFrequenciesParameters ( ) const

overridevirtualinherited

Get the parameters associated to the root frequencies(s).

Returns

A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 140 of file PhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::ParameterList::includeParameters(), and bpp::AbstractPhyloLikelihoodSet::nPhylo_.

getSecondOrderDerivative() [1/2]

double bpp::AbstractPhyloLikelihood::getSecondOrderDerivative ( const std::string &  variable ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 155 of file AbstractPhyloLikelihood.h.

getSecondOrderDerivative() [2/2]

double bpp::AbstractPhyloLikelihood::getSecondOrderDerivative ( const std::string &  variable1, const std::string &  variable2  ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 160 of file AbstractPhyloLikelihood.h.

References bpp::convert(), and bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode().

getSubstitutionModelParameters() [1/2]

virtual ParameterList bpp::PhyloLikelihoodInterface::getSubstitutionModelParameters ( ) const

pure virtualinherited

Get the independent parameters associated to substitution model(s).

Returns

A ParameterList.

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, and bpp::OnABranchPhyloLikelihood.

getSubstitutionModelParameters() [2/2]

ParameterList AbstractPhyloLikelihoodSet::getSubstitutionModelParameters ( ) const

overridevirtualinherited

Get the parameters associated to substitution model(s).

Returns

A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 118 of file PhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::ParameterList::includeParameters(), and bpp::AbstractPhyloLikelihoodSet::nPhylo_.

getValue()

double bpp::AbstractPhyloLikelihood::getValue ( ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 124 of file AbstractPhyloLikelihood.h.

References bpp::convert(), bpp::AbstractPhyloLikelihood::getLikelihoodNode(), and bpp::AbstractPhyloLikelihood::minusLogLik_.

hasPhyloLikelihood() [1/2]

bool bpp::AbstractPhyloLikelihoodSet::hasPhyloLikelihood ( size_t  nPhyl )

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 164 of file PhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::nPhylo_.

Referenced by bpp::PhyloLikelihoodFormula::readFormula().

hasPhyloLikelihood() [2/2]

virtual bool bpp::PhyloLikelihoodSetInterface::hasPhyloLikelihood ( size_t  nPhyl )

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

isInitialized() [1/2]

virtual bool bpp::PhyloLikelihoodInterface::isInitialized ( ) const

pure virtualinherited

Returns

'true' is the likelihood function has been initialized.

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::MultiProcessSequencePhyloLikelihood, and bpp::AbstractPhyloLikelihood.

isInitialized() [2/2]

bool bpp::AbstractPhyloLikelihoodSet::isInitialized ( ) const

inlineoverridevirtualinherited

Returns

'true' is the likelihood function has been initialized.

Reimplemented from bpp::AbstractPhyloLikelihood.

Definition at line 197 of file PhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), and bpp::AbstractPhyloLikelihoodSet::nPhylo_.

likelihoodCalculation()

virtual LikelihoodCalculation& bpp::PhyloLikelihoodInterface::likelihoodCalculation ( ) const

pure virtualinherited

Returns

The LikelihoodCalculation.

Implemented in bpp::AutoCorrelationProcessPhyloLikelihood, bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, bpp::PhyloLikelihoodFormula, bpp::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

operator=()

AbstractAlignedPhyloLikelihoodSet& bpp::AbstractAlignedPhyloLikelihoodSet::operator= ( const AbstractAlignedPhyloLikelihoodSet &  soap )

inlineprotected

Definition at line 88 of file AlignedPhyloLikelihoodSet.h.

References bpp::AbstractAlignedPhyloLikelihood::operator=(), and bpp::AbstractPhyloLikelihoodSet::operator=().

Referenced by bpp::AlignedPhyloLikelihoodAutoCorrelation::operator=(), bpp::AlignedPhyloLikelihoodHmm::operator=(), bpp::AlignedPhyloLikelihoodMixture::operator=(), and bpp::AlignedPhyloLikelihoodProduct::operator=().

secondOrderDerivativeNode()

ValueRef<DataLik> bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode ( const std::string &  variable1, const std::string &  variable2  ) const

inlineinherited

Definition at line 168 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::accessVariableNode(), bpp::AbstractPhyloLikelihood::context_, bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode(), and bpp::AbstractPhyloLikelihood::secondOrderDerivativeNodes_.

Referenced by bpp::AbstractPhyloLikelihood::getSecondOrderDerivative().

setNumberOfSites()

void bpp::AbstractAlignedPhyloLikelihood::setNumberOfSites ( size_t  nbSites )

inlineprotectedinherited

Definition at line 173 of file AlignedPhyloLikelihood.h.

References bpp::AbstractAlignedPhyloLikelihood::nbSites_.

Referenced by AbstractAlignedPhyloLikelihoodSet(), addPhyloLikelihood(), and bpp::AbstractSingleDataPhyloLikelihood::setData().

setParameters()

void bpp::AbstractPhyloLikelihood::setParameters ( const ParameterList &  parameters )

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 95 of file AbstractPhyloLikelihood.h.

References bpp::SecondOrderDerivable::setParametersValues().

shareParameters()

void bpp::AbstractPhyloLikelihood::shareParameters ( const ParameterList &  variableNodes )

inlineinherited

Share Parameters, that are DF_parameters.

Definition at line 90 of file AbstractPhyloLikelihood.h.

References bpp::SecondOrderDerivable::getParameters_(), and bpp::ParameterList::shareParameters().

Referenced by bpp::AbstractPhyloLikelihood::AbstractPhyloLikelihood(), and bpp::AbstractPhyloLikelihood::operator=().

Member Data Documentation

context_

Context& bpp::AbstractPhyloLikelihood::context_

protectedinherited

Definition at line 34 of file AbstractPhyloLikelihood.h.

Referenced by bpp::AbstractPhyloLikelihoodSet::addPhyloLikelihood(), bpp::AbstractPhyloLikelihood::context(), bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::firstOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::firstOrderDerivativeVector(), bpp::SingleProcessPhyloLikelihood::firstOrderDerivativeVector(), bpp::PhyloLikelihoodFormula::makeLikelihoodsFromOperator(), bpp::AbstractPhyloLikelihood::operator=(), bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::secondOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::secondOrderDerivativeVector(), and bpp::SingleProcessPhyloLikelihood::secondOrderDerivativeVector().

firstOrderDerivativeNodes_

std::unordered_map<std::string, ValueRef<DataLik> > bpp::AbstractPhyloLikelihood::firstOrderDerivativeNodes_

mutableprotectedinherited

For Dataflow computing.

Definition at line 44 of file AbstractPhyloLikelihood.h.

Referenced by bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode().

minusLogLik_

DataLik bpp::AbstractPhyloLikelihood::minusLogLik_

mutableprotectedinherited

the value

Definition at line 39 of file AbstractPhyloLikelihood.h.

Referenced by bpp::AbstractPhyloLikelihood::getValue(), and bpp::AbstractPhyloLikelihood::operator=().

nbSites_

size_t bpp::AbstractAlignedPhyloLikelihood::nbSites_

protectedinherited

Definition at line 111 of file AlignedPhyloLikelihood.h.

Referenced by bpp::AlignedPhyloLikelihoodMixture::AlignedPhyloLikelihoodMixture(), bpp::AbstractAlignedPhyloLikelihood::getNumberOfSites(), bpp::MixtureProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerProcess(), bpp::AbstractAlignedPhyloLikelihood::operator=(), and bpp::AbstractAlignedPhyloLikelihood::setNumberOfSites().

nPhylo_

std::vector<size_t> bpp::AbstractPhyloLikelihoodSet::nPhylo_

protectedinherited

vector of AbstractPhyloLikelihood numbers

Definition at line 79 of file PhyloLikelihoodSet.h.

Referenced by AbstractAlignedPhyloLikelihoodSet(), bpp::AbstractPhyloLikelihoodSet::addPhyloLikelihood(), bpp::AbstractPhyloLikelihoodSet::fireParameterChanged(), bpp::AbstractPhyloLikelihoodSet::getBranchLengthParameters(), bpp::AbstractPhyloLikelihoodSet::getDerivableParameters(), bpp::AbstractPhyloLikelihoodSet::getNonDerivableParameters(), bpp::AbstractPhyloLikelihoodSet::getNumbersOfPhyloLikelihoods(), bpp::AbstractPhyloLikelihoodSet::getRateDistributionParameters(), bpp::AbstractPhyloLikelihoodSet::getRootFrequenciesParameters(), bpp::AbstractPhyloLikelihoodSet::getSubstitutionModelParameters(), bpp::AbstractPhyloLikelihoodSet::hasPhyloLikelihood(), bpp::AbstractPhyloLikelihoodSet::isInitialized(), bpp::PartitionProcessPhyloLikelihood::makeLikCal_(), and bpp::AbstractPhyloLikelihoodSet::operator=().

pPhyloCont_

std::shared_ptr<PhyloLikelihoodContainer> bpp::AbstractPhyloLikelihoodSet::pPhyloCont_

protectedinherited

pointer to a PhyloLikelihoodContainer

Definition at line 74 of file PhyloLikelihoodSet.h.

Referenced by getAlignedPhyloLikelihood(), bpp::AbstractPhyloLikelihoodSet::getPhyloContainer(), bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::AbstractPhyloLikelihoodSet::operator=(), and bpp::PartitionProcessPhyloLikelihood::PartitionProcessPhyloLikelihood().

secondOrderDerivativeNodes_

std::unordered_map<std::pair<std::string, std::string>, ValueRef<DataLik>, StringPairHash> bpp::AbstractPhyloLikelihood::secondOrderDerivativeNodes_

mutableprotectedinherited

Definition at line 48 of file AbstractPhyloLikelihood.h.

Referenced by bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode().

vLikCal_

std::vector<std::shared_ptr<LikelihoodCalculation> > bpp::AbstractPhyloLikelihoodSet::vLikCal_

mutableprotectedinherited

vector of pointers towards LikelihoodCalculation, used for the global likelihood.

Definition at line 85 of file PhyloLikelihoodSet.h.

Referenced by bpp::AbstractPhyloLikelihoodSet::addPhyloLikelihood(), bpp::PartitionProcessPhyloLikelihood::makeLikCal_(), and bpp::AbstractPhyloLikelihoodSet::operator=().

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

• Bpp/Phyl/Likelihood/PhyloLikelihoods/AlignedPhyloLikelihoodSet.h
• Bpp/Phyl/Likelihood/PhyloLikelihoods/AlignedPhyloLikelihoodSet.cpp