bpp::PartitionProcessPhyloLikelihood Class Reference

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

Inheritance diagram for bpp::PartitionProcessPhyloLikelihood:

Collaboration diagram for bpp::PartitionProcessPhyloLikelihood:

Public Member Functions
	PartitionProcessPhyloLikelihood (Context &context, std::shared_ptr< PartitionSequenceEvolution > processSeqEvol, size_t nSeqEvol=0)
	PartitionProcessPhyloLikelihood (Context &context, std::shared_ptr< const AlignmentDataInterface > data, std::shared_ptr< PartitionSequenceEvolution > processSeqEvol, size_t nSeqEvol=0, size_t nData=0)
	PartitionProcessPhyloLikelihood (std::shared_ptr< const AlignmentDataInterface > data, std::shared_ptr< PartitionSequenceEvolution > processSeqEvol, std::shared_ptr< CollectionNodes > collNodes, size_t nSeqEvol=0, size_t nData=0)
virtual	~PartitionProcessPhyloLikelihood ()
void	setData (std::shared_ptr< const AlignmentDataInterface > data, size_t nData=0) override
	Set the dataset for which the likelihood must be evaluated. More...
std::shared_ptr< const SingleProcessPhyloLikelihood >	getPhyloLikelihoodForASite (size_t siteIndex) const
std::shared_ptr< LikelihoodCalculationSingleProcess >	getLikelihoodCalculationForASite (size_t siteIndex) const
const SequenceEvolution &	sequenceEvolution () const override
	The Sequence Evolution. More...
std::shared_ptr< const SequenceEvolution >	getSequenceEvolution () const override
const size_t	getSequenceEvolutionNumber () const override
size_t	getNData () const
	Get the number of dataset concerned. More...
size_t	getNumberOfStates () const
	Get the number the states. 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...
virtual bool	isInitialized () const override
	Sets the computeLikelihoods_ to true. More...
const Context &	context () const override
Context &	context () override
ValueRef< DataLik >	getLikelihoodNode () const override
virtual void	enableSecondOrderDerivatives (bool yn)=0
virtual bool	enableSecondOrderDerivatives () const=0
virtual void	enableSecondOrderDerivatives (bool yn) override
bool	enableSecondOrderDerivatives () const override
virtual double	getSecondOrderDerivative (const std::string &variable) const=0
virtual double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const=0
double	getSecondOrderDerivative (const std::string &variable) const override
double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const override
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 void	enableFirstOrderDerivatives (bool yn) override
	Tell if derivatives must be computed: for Function inheritance. More...
bool	enableFirstOrderDerivatives () const override
virtual double	getFirstOrderDerivative (const std::string &variable) const=0
double	getFirstOrderDerivative (const std::string &variable) const override
virtual double	df (const std::string &variable, const ParameterList &parameters)
virtual void	setParameters (const ParameterList &parameters)=0
void	setParameters (const ParameterList &parameters) override
virtual double	getValue () const=0
double	getValue () const override
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
void	setNData (size_t nData)
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
std::shared_ptr< PhyloLikelihoodContainer >	getPhyloContainer () override
std::shared_ptr< const PhyloLikelihoodContainer >	getPhyloContainer () const override
const std::vector< size_t > &	getNumbersOfPhyloLikelihoods () const override
virtual bool	addPhyloLikelihood (size_t nPhyl, const std::string &suff="") override
	adds a PhyloLikelihood already stored in the PhyloLikelihoodContainer, iff it is an AbstractPhyloLikelihood. More...
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
const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const
the Likelihood interface
std::shared_ptr< const Alphabet >	getAlphabet () const override
	Get the alphabet associated to the dataset. More...
The data functions
virtual size_t	getNData () const =0
	Get the number of dataset concerned. More...
virtual size_t	getNumberOfStates () const =0
	Get the number the states. More...
The likelihood functions.
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 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 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
	PartitionProcessPhyloLikelihood (const PartitionProcessPhyloLikelihood &lik)
PartitionProcessPhyloLikelihood &	operator= (const PartitionProcessPhyloLikelihood &lik)
PartitionProcessPhyloLikelihood *	clone () const override
virtual ParameterList &	getParameters_ ()=0
void	setNumberOfSites (size_t nbSites)
Node_DF &	accessVariableNode (const std::string &name) const
ParameterList &	getParameters_ () override
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

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

Protected Attributes
std::shared_ptr< SequenceEvolution >	seqEvol_
	the Sequence Evolution More...
size_t	nSeqEvol_
	the Sequence Evolution number More...
size_t	nbStates_
size_t	nData_
	Number of the concerned data. More...
size_t	nbSites_
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_
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_

Private Attributes
std::shared_ptr< PartitionSequenceEvolution >	mSeqEvol_
	to avoid the dynamic casts More...
std::vector< ProcPos >	vProcPos_
std::map< size_t, std::shared_ptr< AlignmentDataInterface > >	mData_
std::shared_ptr< AlignedLikelihoodCalculation >	likCal_
ParameterList	parameters_
std::string	prefix_

The Likelihood interface.
std::shared_ptr< const AlignmentDataInterface >	getData () const override
	Get the dataset for which the likelihood must be evaluated. More...
const std::vector< ProcPos > &	getProcessSiteRelations () const
LikelihoodCalculation &	likelihoodCalculation () const override
std::shared_ptr< LikelihoodCalculation >	getLikelihoodCalculation () const override
AlignedLikelihoodCalculation &	alignedLikelihoodCalculation () const override
std::shared_ptr< AlignedLikelihoodCalculation >	getAlignedLikelihoodCalculation () const override
size_t	getNumberOfSites () const override
	Get the number of sites in the dataset. More...
std::shared_ptr< PartitionSequenceEvolution >	getPartitionSequenceEvolution () const
void	makeLikCal_ ()

Detailed Description

Definition at line 33 of file PartitionProcessPhyloLikelihood.h.

Constructor & Destructor Documentation

PartitionProcessPhyloLikelihood() [1/4]

PartitionProcessPhyloLikelihood::PartitionProcessPhyloLikelihood	(	Context &	context,
		std::shared_ptr< PartitionSequenceEvolution >	processSeqEvol,
		size_t	nSeqEvol = 0
	)

Definition at line 16 of file PartitionProcessPhyloLikelihood.cpp.

References bpp::AbstractPhyloLikelihoodSet::addPhyloLikelihood(), bpp::AbstractPhyloLikelihood::context(), bpp::AbstractPhyloLikelihoodSet::getPhyloContainer(), bpp::AbstractPhyloLikelihoodSet::pPhyloCont_, and vProcPos_.

Referenced by clone().

PartitionProcessPhyloLikelihood() [2/4]

PartitionProcessPhyloLikelihood::PartitionProcessPhyloLikelihood	(	Context &	context,
		std::shared_ptr< const AlignmentDataInterface >	data,
		std::shared_ptr< PartitionSequenceEvolution >	processSeqEvol,
		size_t	nSeqEvol = 0,
		size_t	nData = 0
	)

Definition at line 68 of file PartitionProcessPhyloLikelihood.cpp.

References bpp::AbstractPhyloLikelihoodSet::addPhyloLikelihood(), bpp::AbstractPhyloLikelihood::context(), bpp::AbstractPhyloLikelihoodSet::getPhyloContainer(), bpp::AbstractPhyloLikelihoodSet::pPhyloCont_, setData(), and vProcPos_.

PartitionProcessPhyloLikelihood() [3/4]

PartitionProcessPhyloLikelihood::PartitionProcessPhyloLikelihood	(	std::shared_ptr< const AlignmentDataInterface >	data,
		std::shared_ptr< PartitionSequenceEvolution >	processSeqEvol,
		std::shared_ptr< CollectionNodes >	collNodes,
		size_t	nSeqEvol = 0,
		size_t	nData = 0
	)

Definition at line 126 of file PartitionProcessPhyloLikelihood.cpp.

References bpp::AbstractPhyloLikelihoodSet::addPhyloLikelihood(), bpp::AbstractPhyloLikelihood::context(), bpp::AbstractPhyloLikelihoodSet::getPhyloContainer(), setData(), and vProcPos_.

PartitionProcessPhyloLikelihood() [4/4]

bpp::PartitionProcessPhyloLikelihood::PartitionProcessPhyloLikelihood ( const PartitionProcessPhyloLikelihood &  lik )

inlineprotected

Definition at line 80 of file PartitionProcessPhyloLikelihood.h.

~PartitionProcessPhyloLikelihood()

virtual bpp::PartitionProcessPhyloLikelihood::~PartitionProcessPhyloLikelihood ( )

inlinevirtual

Definition at line 107 of file PartitionProcessPhyloLikelihood.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 AbstractPhyloLikelihoodSet::addPhyloLikelihood ( size_t  nPhyl, const std::string &  suff = ""  )

overridevirtualinherited

adds a PhyloLikelihood already stored in the PhyloLikelihoodContainer, iff it is an AbstractPhyloLikelihood.

Parameters

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

Returns

if the PhyloLikelihood has been added.

Implements bpp::PhyloLikelihoodSetInterface.

Reimplemented in bpp::AbstractAlignedPhyloLikelihoodSet.

Definition at line 45 of file PhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihood::context_, bpp::ConfiguredParameter::create(), bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::AbstractParametrizable::hasParameter(), bpp::AbstractPhyloLikelihoodSet::nPhylo_, bpp::Parameter::setName(), bpp::AbstractParametrizable::shareParameter_(), bpp::AbstractParametrizable::shareParameters_(), bpp::TextTools::toString(), and bpp::AbstractPhyloLikelihoodSet::vLikCal_.

Referenced by bpp::AbstractPhyloLikelihoodSet::AbstractPhyloLikelihoodSet(), bpp::AbstractAlignedPhyloLikelihoodSet::addPhyloLikelihood(), PartitionProcessPhyloLikelihood(), and bpp::PhyloLikelihoodFormula::readFormula().

alignedLikelihoodCalculation()

AlignedLikelihoodCalculation& bpp::PartitionProcessPhyloLikelihood::alignedLikelihoodCalculation ( ) const

inlineoverridevirtual

Returns

The LikelihoodCalculation.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 163 of file PartitionProcessPhyloLikelihood.h.

References likCal_.

clone()

PartitionProcessPhyloLikelihood* bpp::PartitionProcessPhyloLikelihood::clone ( ) const

inlineoverrideprotectedvirtual

Implements bpp::AbstractParametrizable.

Definition at line 104 of file PartitionProcessPhyloLikelihood.h.

References PartitionProcessPhyloLikelihood().

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(), makeLikCal_(), bpp::MixtureProcessPhyloLikelihood::MixtureProcessPhyloLikelihood(), bpp::OneProcessSequencePhyloLikelihood::OneProcessSequencePhyloLikelihood(), and 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()

std::shared_ptr<AlignedLikelihoodCalculation> bpp::PartitionProcessPhyloLikelihood::getAlignedLikelihoodCalculation ( ) const

inlineoverridevirtual

Returns

A shared pointer toward the LikelihoodCalculation.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 168 of file PartitionProcessPhyloLikelihood.h.

References likCal_.

getAlphabet()

std::shared_ptr<const Alphabet> bpp::AbstractSequencePhyloLikelihood::getAlphabet ( ) const

inlineoverridevirtualinherited

Get the alphabet associated to the dataset.

Returns

the alphabet associated to the dataset.

Implements bpp::SingleDataPhyloLikelihoodInterface.

Definition at line 116 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::seqEvol_.

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_.

getData()

std::shared_ptr<const AlignmentDataInterface> bpp::PartitionProcessPhyloLikelihood::getData ( ) const

inlineoverridevirtual

Get the dataset for which the likelihood must be evaluated.

Returns

A pointer toward the site container where the sequences are stored.

Implements bpp::SingleDataPhyloLikelihoodInterface.

Definition at line 143 of file PartitionProcessPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihoodSet::getNumbersOfPhyloLikelihoods(), and bpp::AbstractPhyloLikelihoodSet::getPhyloContainer().

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()

std::shared_ptr<LikelihoodCalculation> bpp::PartitionProcessPhyloLikelihood::getLikelihoodCalculation ( ) const

inlineoverridevirtual

Returns

A shared pointer toward the LikelihoodCalculation.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 158 of file PartitionProcessPhyloLikelihood.h.

References likCal_.

getLikelihoodCalculationForASite()

std::shared_ptr<LikelihoodCalculationSingleProcess> bpp::PartitionProcessPhyloLikelihood::getLikelihoodCalculationForASite ( size_t  siteIndex ) const

inline

Definition at line 133 of file PartitionProcessPhyloLikelihood.h.

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

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 bpp::AbstractAlignedPhyloLikelihoodSet::getLikelihoodForASiteForAPhyloLikelihood().

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 bpp::AbstractAlignedPhyloLikelihoodSet::getLogLikelihoodForASiteForAPhyloLikelihood(), and bpp::PhylogeneticsApplicationTools::printAnalysisInformation().

getNData() [1/2]

size_t bpp::AbstractSingleDataPhyloLikelihood::getNData ( ) const

inlinevirtualinherited

Get the number of dataset concerned.

Implements bpp::SingleDataPhyloLikelihoodInterface.

Definition at line 126 of file SingleDataPhyloLikelihood.h.

References bpp::AbstractSingleDataPhyloLikelihood::nData_.

getNData() [2/2]

virtual size_t bpp::SingleDataPhyloLikelihoodInterface::getNData ( ) const

pure virtualinherited

Get the number of dataset concerned.

Implemented in bpp::AbstractSingleDataPhyloLikelihood.

Referenced by bpp::PhylogeneticsApplicationTools::printParameters().

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()

size_t bpp::PartitionProcessPhyloLikelihood::getNumberOfSites ( ) const

inlineoverridevirtual

Get the number of sites in the dataset.

Returns

the number of sites in the dataset.

Reimplemented from bpp::AbstractAlignedPhyloLikelihood.

Definition at line 173 of file PartitionProcessPhyloLikelihood.h.

References mSeqEvol_.

Referenced by makeLikCal_().

getNumberOfStates() [1/2]

size_t bpp::AbstractSingleDataPhyloLikelihood::getNumberOfStates ( ) const

inlinevirtualinherited

Get the number the states.

Implements bpp::SingleDataPhyloLikelihoodInterface.

Definition at line 136 of file SingleDataPhyloLikelihood.h.

References bpp::AbstractSingleDataPhyloLikelihood::nbStates_.

getNumberOfStates() [2/2]

virtual size_t bpp::SingleDataPhyloLikelihoodInterface::getNumberOfStates ( ) const

pure virtualinherited

Get the number the states.

Implemented in bpp::AbstractSingleDataPhyloLikelihood.

getNumbersOfPhyloLikelihoods()

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 getData().

getPartitionSequenceEvolution()

std::shared_ptr<PartitionSequenceEvolution> bpp::PartitionProcessPhyloLikelihood::getPartitionSequenceEvolution ( ) const

inline

Definition at line 178 of file PartitionProcessPhyloLikelihood.h.

References mSeqEvol_.

getPhyloContainer() [1/2]

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() [2/2]

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

getPhyloLikelihood() [1/2]

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(), getLikelihoodCalculationForASite(), bpp::AbstractPhyloLikelihoodSet::getNonDerivableParameters(), getPhyloLikelihoodForASite(), bpp::AbstractPhyloLikelihoodSet::getRateDistributionParameters(), bpp::AbstractPhyloLikelihoodSet::getRootFrequenciesParameters(), bpp::AbstractPhyloLikelihoodSet::getSubstitutionModelParameters(), bpp::AbstractPhyloLikelihoodSet::isInitialized(), bpp::PhyloLikelihoodFormula::makeLikelihoodsFromOperator(), and bpp::PhyloLikelihoodFormula::readFormula().

getPhyloLikelihood() [2/2]

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_.

getPhyloLikelihoodForASite()

std::shared_ptr<const SingleProcessPhyloLikelihood> bpp::PartitionProcessPhyloLikelihood::getPhyloLikelihoodForASite ( size_t  siteIndex ) const

inline

Definition at line 123 of file PartitionProcessPhyloLikelihood.h.

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

getProcessSiteRelations()

const std::vector<ProcPos>& bpp::PartitionProcessPhyloLikelihood::getProcessSiteRelations ( ) const

inline

Definition at line 148 of file PartitionProcessPhyloLikelihood.h.

References vProcPos_.

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().

getSequenceEvolution()

std::shared_ptr<const SequenceEvolution> bpp::AbstractSequencePhyloLikelihood::getSequenceEvolution ( ) const

inlineoverridevirtualinherited

Implements bpp::SequencePhyloLikelihoodInterface.

Definition at line 102 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::seqEvol_.

getSequenceEvolutionNumber()

const size_t bpp::AbstractSequencePhyloLikelihood::getSequenceEvolutionNumber ( ) const

inlineoverridevirtualinherited

Implements bpp::SequencePhyloLikelihoodInterface.

Definition at line 107 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::nSeqEvol_.

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()

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().

isInitialized() [1/3]

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() [2/3]

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

inlineoverridevirtualinherited

Sets the computeLikelihoods_ to true.

Implements bpp::PhyloLikelihoodInterface.

Reimplemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, and bpp::MultiProcessSequencePhyloLikelihood.

Definition at line 81 of file AbstractPhyloLikelihood.h.

isInitialized() [3/3]

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()

LikelihoodCalculation& bpp::PartitionProcessPhyloLikelihood::likelihoodCalculation ( ) const

inlineoverridevirtual

Returns

The LikelihoodCalculation.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 153 of file PartitionProcessPhyloLikelihood.h.

References likCal_.

makeLikCal_()

void PartitionProcessPhyloLikelihood::makeLikCal_ ( )

private

Definition at line 204 of file PartitionProcessPhyloLikelihood.cpp.

References bpp::AbstractPhyloLikelihood::context(), bpp::NumericConstant< T >::create(), bpp::SumOfLogarithms< F >::create(), getNumberOfSites(), likCal_, bpp::AbstractPhyloLikelihoodSet::nPhylo_, bpp::AbstractPhyloLikelihoodSet::vLikCal_, and vProcPos_.

Referenced by setData().

operator=()

PartitionProcessPhyloLikelihood& bpp::PartitionProcessPhyloLikelihood::operator= ( const PartitionProcessPhyloLikelihood &  lik )

inlineprotected

Definition at line 93 of file PartitionProcessPhyloLikelihood.h.

References likCal_, mData_, mSeqEvol_, bpp::AbstractPhyloLikelihoodSet::operator=(), bpp::AbstractSequencePhyloLikelihood::operator=(), and vProcPos_.

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().

sequenceEvolution()

const SequenceEvolution& bpp::AbstractSequencePhyloLikelihood::sequenceEvolution ( ) const

inlineoverridevirtualinherited

The Sequence Evolution.

Implements bpp::SequencePhyloLikelihoodInterface.

Definition at line 97 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::seqEvol_.

setData()

void PartitionProcessPhyloLikelihood::setData ( std::shared_ptr< const AlignmentDataInterface >  data, size_t  nData = 0  )

overridevirtual

Set the dataset for which the likelihood must be evaluated.

Parameters

data	The data set to use.
nData	the number of the data (optional, default = 0)

Reimplemented from bpp::AbstractSingleDataPhyloLikelihood.

Definition at line 180 of file PartitionProcessPhyloLikelihood.cpp.

References bpp::AbstractPhyloLikelihoodSet::getPhyloContainer(), bpp::SiteContainerTools::getSelectedSites(), makeLikCal_(), mData_, mSeqEvol_, and bpp::AbstractSingleDataPhyloLikelihood::setData().

Referenced by PartitionProcessPhyloLikelihood().

setNData()

void bpp::AbstractSingleDataPhyloLikelihood::setNData ( size_t  nData )

inlineinherited

Definition at line 131 of file SingleDataPhyloLikelihood.h.

References bpp::AbstractSingleDataPhyloLikelihood::nData_.

setNumberOfSites()

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

inlineprotectedinherited

Definition at line 173 of file AlignedPhyloLikelihood.h.

References bpp::AbstractAlignedPhyloLikelihood::nbSites_.

Referenced by bpp::AbstractAlignedPhyloLikelihoodSet::AbstractAlignedPhyloLikelihoodSet(), bpp::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().

likCal_

std::shared_ptr<AlignedLikelihoodCalculation> bpp::PartitionProcessPhyloLikelihood::likCal_

mutableprivate

AlignedLikelihoodCalculation to store DF nodes

Definition at line 57 of file PartitionProcessPhyloLikelihood.h.

Referenced by alignedLikelihoodCalculation(), getAlignedLikelihoodCalculation(), getLikelihoodCalculation(), likelihoodCalculation(), makeLikCal_(), and operator=().

mData_

std::map<size_t, std::shared_ptr<AlignmentDataInterface> > bpp::PartitionProcessPhyloLikelihood::mData_

private

map nbe of phylolikelihood : created AlignmentDataInterface<std::string>

Definition at line 52 of file PartitionProcessPhyloLikelihood.h.

Referenced by operator=(), and setData().

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=().

mSeqEvol_

std::shared_ptr<PartitionSequenceEvolution> bpp::PartitionProcessPhyloLikelihood::mSeqEvol_

private

to avoid the dynamic casts

Definition at line 41 of file PartitionProcessPhyloLikelihood.h.

Referenced by getNumberOfSites(), getPartitionSequenceEvolution(), operator=(), and setData().

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().

nbStates_

size_t bpp::AbstractSingleDataPhyloLikelihood::nbStates_

protectedinherited

Definition at line 87 of file SingleDataPhyloLikelihood.h.

Referenced by bpp::AbstractSingleDataPhyloLikelihood::getNumberOfStates(), bpp::OneProcessSequencePhyloLikelihood::getPosteriorStateFrequencies(), bpp::AbstractSingleDataPhyloLikelihood::operator=(), and bpp::AbstractSingleDataPhyloLikelihood::setData().

nData_

size_t bpp::AbstractSingleDataPhyloLikelihood::nData_

protectedinherited

Number of the concerned data.

Definition at line 92 of file SingleDataPhyloLikelihood.h.

Referenced by bpp::AbstractSingleDataPhyloLikelihood::getNData(), bpp::AbstractSingleDataPhyloLikelihood::operator=(), bpp::AbstractSingleDataPhyloLikelihood::setData(), and bpp::AbstractSingleDataPhyloLikelihood::setNData().

nPhylo_

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

protectedinherited

vector of AbstractPhyloLikelihood numbers

Definition at line 79 of file PhyloLikelihoodSet.h.

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

nSeqEvol_

size_t bpp::AbstractSequencePhyloLikelihood::nSeqEvol_

protectedinherited

the Sequence Evolution number

Definition at line 62 of file SequencePhyloLikelihood.h.

Referenced by bpp::AbstractSequencePhyloLikelihood::getSequenceEvolutionNumber(), and bpp::AbstractSequencePhyloLikelihood::operator=().

pPhyloCont_

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

protectedinherited

pointer to a PhyloLikelihoodContainer

Definition at line 74 of file PhyloLikelihoodSet.h.

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

seqEvol_

std::shared_ptr<SequenceEvolution> bpp::AbstractSequencePhyloLikelihood::seqEvol_

protectedinherited

the Sequence Evolution

Definition at line 57 of file SequencePhyloLikelihood.h.

Referenced by bpp::AbstractParametrizableSequencePhyloLikelihood::fireParameterChanged(), bpp::AbstractSequencePhyloLikelihood::getAlphabet(), bpp::AbstractParametrizableSequencePhyloLikelihood::getBranchLengthParameters(), bpp::AbstractParametrizableSequencePhyloLikelihood::getDerivableParameters(), bpp::AbstractParametrizableSequencePhyloLikelihood::getNonDerivableParameters(), bpp::AbstractParametrizableSequencePhyloLikelihood::getRateDistributionParameters(), bpp::AbstractParametrizableSequencePhyloLikelihood::getRootFrequenciesParameters(), bpp::AbstractSequencePhyloLikelihood::getSequenceEvolution(), bpp::AbstractParametrizableSequencePhyloLikelihood::getSubstitutionModelParameters(), bpp::AbstractParametrizableSequencePhyloLikelihood::getSubstitutionProcessParameters(), bpp::AbstractSequencePhyloLikelihood::operator=(), bpp::AbstractSequencePhyloLikelihood::sequenceEvolution(), and bpp::AbstractParametrizableSequencePhyloLikelihood::setNamespace().

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(), makeLikCal_(), and bpp::AbstractPhyloLikelihoodSet::operator=().

vProcPos_

std::vector<ProcPos> bpp::PartitionProcessPhyloLikelihood::vProcPos_

private

vector of couples <number of process, site> specific to this partition process.

Definition at line 47 of file PartitionProcessPhyloLikelihood.h.

Referenced by getLikelihoodCalculationForASite(), getPhyloLikelihoodForASite(), getProcessSiteRelations(), makeLikCal_(), operator=(), and PartitionProcessPhyloLikelihood().

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

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