Partial implementation of multiple processes of sequences. More...

#include <Bpp/Phyl/Likelihood/MultiProcessSequenceEvolution.h>

Inheritance diagram for bpp::MultiProcessSequenceEvolution:

Collaboration diagram for bpp::MultiProcessSequenceEvolution:

Public Member Functions
	MultiProcessSequenceEvolution (std::shared_ptr< SubstitutionProcessCollection > processColl, std::vector< size_t > nProc, const std::string &prefix="")

	MultiProcessSequenceEvolution (const MultiProcessSequenceEvolution &lik)

MultiProcessSequenceEvolution &	operator= (const MultiProcessSequenceEvolution &lik)

const SubstitutionProcessCollection &	collection () const
	The collection. More...

std::shared_ptr< const SubstitutionProcessCollection >	getCollection () const

SubstitutionProcessCollection &	collection ()

std::shared_ptr< SubstitutionProcessCollection >	getCollection ()

size_t	getNumberOfSubstitutionProcess () const
	Return the number of process used for computation. More...

const SubstitutionProcessInterface &	substitutionProcess (size_t number) const
	Return the SubstitutionProcess of a given index position (in nProc_ vector). More...

std::shared_ptr< const SubstitutionProcessInterface >	getSubstitutionProcess (size_t number) const

const std::vector< size_t > &	getSubstitutionProcessNumbers () const

ParameterList	getSubstitutionProcessParameters (bool independent) const
	Get the parameters associated to substitution processes(s). More...

ParameterList	getSubstitutionModelParameters (bool independent) const
	Get the parameters associated to substitution model(s). More...

ParameterList	getRateDistributionParameters (bool independent) const
	Get the parameters associated to the rate distribution(s). More...

ParameterList	getRootFrequenciesParameters (bool independent) const
	Get the parameters associated to the root frequencies(s). More...

ParameterList	getBranchLengthParameters (bool independent) const
	Get the branch lengths parameters. More...

virtual ParameterList	getNonDerivableParameters () const
	All non derivable parameters. More...

virtual void	fireParameterChanged (const ParameterList &parameters)

void	setParameters (const ParameterList &parameters)

virtual bool	isCompatibleWith (const AlignmentDataInterface &data) const
	test if data fits this model More...

virtual SequenceEvolution *	clone () const override=0

const StateMapInterface &	stateMap () const

std::shared_ptr< const StateMapInterface >	getStateMap () const

virtual size_t	getNumberOfIndependentParameters () const=0

virtual void	aliasParameters (const std::string &p1, const std::string &p2)=0

virtual void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0

virtual void	unaliasParameters (const std::string &p1, const std::string &p2)=0

virtual const ParameterList &	getIndependentParameters () const=0

virtual std::vector< std::string >	getAlias (const std::string &name) const=0

virtual std::map< std::string, std::string >	getAliases () const=0

virtual bool	hasParameter (const std::string &name) const=0

virtual const ParameterList &	getParameters () const=0

virtual const Parameter &	parameter (const std::string &name) const=0

virtual double	getParameterValue (const std::string &name) const=0

virtual void	setAllParametersValues (const ParameterList &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	setNamespace (const std::string &prefix)

bool	hasIndependentParameter (const std::string &name) const

const ParameterList &	getIndependentParameters () const

size_t	getNumberOfIndependentParameters () const

void	aliasParameters (const std::string &p1, const std::string &p2)

void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)

void	unaliasParameters (const std::string &p1, const std::string &p2)

ParameterList	getAliasedParameters (const ParameterList &pl) const

ParameterList	getFromParameters (const ParameterList &pl) const

virtual std::vector< std::string >	getAlias (const std::string &name) const

virtual std::map< std::string, std::string >	getAliases () const

std::string	getFrom (const std::string &name) const

bool	hasParameter (const std::string &name) const override

const ParameterList &	getParameters () const override

const Parameter &	parameter (const std::string &name) const override

const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const

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

std::string	getNamespace () const override

std::string	getParameterNameWithoutNamespace (const std::string &name) const override

virtual Clonable *	clone () const=0

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0

const std::shared_ptr< Parameter > &	getParameter (size_t i) const

std::shared_ptr< Parameter > &	getParameter (size_t i)

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)

void	shareParameters_ (const ParameterList &parameters)

void	includeParameters_ (const ParameterList &parameters)

void	deleteParameter_ (size_t index)

void	deleteParameter_ (std::string &name)

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

ParameterList &	getParameters_ () override

Protected Attributes
std::shared_ptr< SubstitutionProcessCollection >	processColl_

std::vector< size_t >	nProc_
	the vector of the substitution process numbers, as they are used in this order. More...

Private Attributes
ParameterList	independentParameters_

std::map< std::string, std::shared_ptr< AliasParameterListener > >	aliasListenersRegister_

ParameterList	parameters_

std::string	prefix_

Detailed Description

Partial implementation of multiple processes of sequences.

Definition at line 26 of file MultiProcessSequenceEvolution.h.

Constructor & Destructor Documentation

◆ MultiProcessSequenceEvolution() [1/2]

MultiProcessSequenceEvolution::MultiProcessSequenceEvolution	(	std::shared_ptr< SubstitutionProcessCollection >	processColl,
		std::vector< size_t >	nProc,
		const std::string &	prefix = `""`
	)

Definition at line 12 of file MultiProcessSequenceEvolution.cpp.

References bpp::AbstractParameterAliasable::includeParameters_(), nProc_, and processColl_.

◆ MultiProcessSequenceEvolution() [2/2]

bpp::MultiProcessSequenceEvolution::MultiProcessSequenceEvolution ( const MultiProcessSequenceEvolution & lik )

inline

Definition at line 45 of file MultiProcessSequenceEvolution.h.

Member Function Documentation

◆ clone()

virtual SequenceEvolution * bpp::SequenceEvolution::clone ( ) const

overridepure virtualinherited

Implements bpp::ParameterAliasable.

Implemented in bpp::AutoCorrelationSequenceEvolution, bpp::HmmSequenceEvolution, bpp::PartitionSequenceEvolution, bpp::MixtureSequenceEvolution, and bpp::OneProcessSequenceEvolution.

◆ collection() [1/2]

SubstitutionProcessCollection & bpp::MultiProcessSequenceEvolution::collection ( )

inline

Definition at line 69 of file MultiProcessSequenceEvolution.h.

References processColl_.

◆ collection() [2/2]

const SubstitutionProcessCollection & bpp::MultiProcessSequenceEvolution::collection ( ) const

inline

The collection.

Definition at line 65 of file MultiProcessSequenceEvolution.h.

References processColl_.

◆ fireParameterChanged()

void MultiProcessSequenceEvolution::fireParameterChanged ( const ParameterList & parameters )

virtual

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::AutoCorrelationSequenceEvolution, bpp::HmmSequenceEvolution, and bpp::MixtureSequenceEvolution.

Definition at line 30 of file MultiProcessSequenceEvolution.cpp.

References processColl_.

Referenced by bpp::AutoCorrelationSequenceEvolution::fireParameterChanged(), bpp::HmmSequenceEvolution::fireParameterChanged(), and bpp::MixtureSequenceEvolution::fireParameterChanged().

◆ getBranchLengthParameters()

ParameterList MultiProcessSequenceEvolution::getBranchLengthParameters ( bool independent ) const

virtual

Get the branch lengths parameters.

Returns: A ParameterList with all branch lengths.

Implements bpp::SequenceEvolution.

Definition at line 85 of file MultiProcessSequenceEvolution.cpp.

References bpp::ParameterList::includeParameters(), nProc_, and processColl_.

◆ getCollection() [1/2]

std::shared_ptr< SubstitutionProcessCollection > bpp::MultiProcessSequenceEvolution::getCollection ( )

inline

Definition at line 71 of file MultiProcessSequenceEvolution.h.

References processColl_.

◆ getCollection() [2/2]

std::shared_ptr< const SubstitutionProcessCollection > bpp::MultiProcessSequenceEvolution::getCollection ( ) const

inline

Definition at line 67 of file MultiProcessSequenceEvolution.h.

References processColl_.

◆ getNonDerivableParameters()

ParameterList MultiProcessSequenceEvolution::getNonDerivableParameters ( ) const

virtual

All non derivable parameters.

Usually, this contains all substitution model parameters and rate distribution, and alias.

Returns: A ParameterList.

Implements bpp::SequenceEvolution.

Reimplemented in bpp::AutoCorrelationSequenceEvolution, and bpp::MixtureSequenceEvolution.

Definition at line 97 of file MultiProcessSequenceEvolution.cpp.

References bpp::AbstractParameterAliasable::getAliasedParameters(), bpp::ParameterList::includeParameters(), nProc_, and processColl_.

Referenced by bpp::AutoCorrelationSequenceEvolution::getNonDerivableParameters(), and bpp::MixtureSequenceEvolution::getNonDerivableParameters().

◆ getNumberOfSubstitutionProcess()

size_t bpp::MultiProcessSequenceEvolution::getNumberOfSubstitutionProcess ( ) const

inline

Return the number of process used for computation.

Definition at line 76 of file MultiProcessSequenceEvolution.h.

References nProc_.

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

◆ getRateDistributionParameters()

ParameterList MultiProcessSequenceEvolution::getRateDistributionParameters ( bool independent ) const

virtual

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

Returns: A ParameterList.

Implements bpp::SequenceEvolution.

Definition at line 61 of file MultiProcessSequenceEvolution.cpp.

References bpp::ParameterList::includeParameters(), nProc_, and processColl_.

◆ getRootFrequenciesParameters()

ParameterList MultiProcessSequenceEvolution::getRootFrequenciesParameters ( bool independent ) const

virtual

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

Returns: A ParameterList.

Implements bpp::SequenceEvolution.

Definition at line 73 of file MultiProcessSequenceEvolution.cpp.

References bpp::ParameterList::includeParameters(), nProc_, and processColl_.

◆ getStateMap()

std::shared_ptr< const StateMapInterface > bpp::SequenceEvolution::getStateMap ( ) const

inlineinherited

Definition at line 53 of file SequenceEvolution.h.

References bpp::SubstitutionProcessInterface::getStateMap(), bpp::SequenceEvolution::getSubstitutionProcessNumbers(), and bpp::SequenceEvolution::substitutionProcess().

◆ getSubstitutionModelParameters()

ParameterList MultiProcessSequenceEvolution::getSubstitutionModelParameters ( bool independent ) const

virtual

Get the parameters associated to substitution model(s).

Returns: A ParameterList.

Implements bpp::SequenceEvolution.

Definition at line 49 of file MultiProcessSequenceEvolution.cpp.

References bpp::ParameterList::includeParameters(), nProc_, and processColl_.

◆ getSubstitutionProcess()

std::shared_ptr< const SubstitutionProcessInterface > bpp::MultiProcessSequenceEvolution::getSubstitutionProcess ( size_t number ) const

inlinevirtual

Implements bpp::SequenceEvolution.

Definition at line 87 of file MultiProcessSequenceEvolution.h.

References processColl_.

◆ getSubstitutionProcessNumbers()

const std::vector< size_t > & bpp::MultiProcessSequenceEvolution::getSubstitutionProcessNumbers ( ) const

inlinevirtual

Implements bpp::SequenceEvolution.

Definition at line 92 of file MultiProcessSequenceEvolution.h.

References nProc_.

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

◆ getSubstitutionProcessParameters()

ParameterList MultiProcessSequenceEvolution::getSubstitutionProcessParameters ( bool independent ) const

virtual

Get the parameters associated to substitution processes(s).

Returns: A ParameterList.

Implements bpp::SequenceEvolution.

Definition at line 37 of file MultiProcessSequenceEvolution.cpp.

References bpp::ParameterList::includeParameters(), nProc_, and processColl_.

◆ isCompatibleWith()

bool MultiProcessSequenceEvolution::isCompatibleWith ( const AlignmentDataInterface & data ) const

virtual

test if data fits this model

Implements bpp::SequenceEvolution.

Definition at line 122 of file MultiProcessSequenceEvolution.cpp.

References nProc_, and processColl_.

◆ operator=()

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

inline

Definition at line 51 of file MultiProcessSequenceEvolution.h.

References nProc_, bpp::AbstractParameterAliasable::operator=(), and processColl_.

Referenced by bpp::AutoCorrelationSequenceEvolution::operator=(), bpp::HmmSequenceEvolution::operator=(), bpp::MixtureSequenceEvolution::operator=(), and bpp::PartitionSequenceEvolution::operator=().

◆ setParameters()

void MultiProcessSequenceEvolution::setParameters ( const ParameterList & parameters )

Definition at line 114 of file MultiProcessSequenceEvolution.cpp.

References bpp::AbstractParameterAliasable::setParametersValues().

◆ stateMap()

const StateMapInterface & bpp::SequenceEvolution::stateMap ( ) const

inlineinherited

Definition at line 48 of file SequenceEvolution.h.

References bpp::SequenceEvolution::getSubstitutionProcessNumbers(), bpp::SubstitutionProcessInterface::stateMap(), and bpp::SequenceEvolution::substitutionProcess().

◆ substitutionProcess()

const SubstitutionProcessInterface & bpp::MultiProcessSequenceEvolution::substitutionProcess ( size_t number ) const

inlinevirtual

Return the SubstitutionProcess of a given index position (in nProc_ vector).

Implements bpp::SequenceEvolution.

Definition at line 82 of file MultiProcessSequenceEvolution.h.

References processColl_.

Member Data Documentation

◆ nProc_

std::vector<size_t> bpp::MultiProcessSequenceEvolution::nProc_

protected

the vector of the substitution process numbers, as they are used in this order.

Definition at line 37 of file MultiProcessSequenceEvolution.h.

Referenced by getBranchLengthParameters(), getNonDerivableParameters(), getNumberOfSubstitutionProcess(), getRateDistributionParameters(), getRootFrequenciesParameters(), getSubstitutionModelParameters(), getSubstitutionProcessNumbers(), getSubstitutionProcessParameters(), isCompatibleWith(), MultiProcessSequenceEvolution(), operator=(), and bpp::PartitionSequenceEvolution::PartitionSequenceEvolution().

◆ processColl_

std::shared_ptr<SubstitutionProcessCollection> bpp::MultiProcessSequenceEvolution::processColl_

protected

Definition at line 31 of file MultiProcessSequenceEvolution.h.

Referenced by bpp::AutoCorrelationSequenceEvolution::AutoCorrelationSequenceEvolution(), collection(), fireParameterChanged(), getBranchLengthParameters(), getCollection(), getNonDerivableParameters(), getRateDistributionParameters(), getRootFrequenciesParameters(), getSubstitutionModelParameters(), getSubstitutionProcess(), getSubstitutionProcessParameters(), bpp::HmmSequenceEvolution::HmmSequenceEvolution(), isCompatibleWith(), MultiProcessSequenceEvolution(), operator=(), bpp::PartitionSequenceEvolution::PartitionSequenceEvolution(), and substitutionProcess().

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

Bpp/Phyl/Likelihood/MultiProcessSequenceEvolution.h
Bpp/Phyl/Likelihood/MultiProcessSequenceEvolution.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MultiProcessSequenceEvolution() [1/2]

◆ MultiProcessSequenceEvolution() [2/2]

Member Function Documentation

◆ clone()

◆ collection() [1/2]

◆ collection() [2/2]

◆ fireParameterChanged()

◆ getBranchLengthParameters()

◆ getCollection() [1/2]

◆ getCollection() [2/2]

◆ getNonDerivableParameters()

◆ getNumberOfSubstitutionProcess()

◆ getRateDistributionParameters()

◆ getRootFrequenciesParameters()

◆ getStateMap()

◆ getSubstitutionModelParameters()

◆ getSubstitutionProcess()

◆ getSubstitutionProcessNumbers()

◆ getSubstitutionProcessParameters()

◆ isCompatibleWith()

◆ operator=()

◆ setParameters()

◆ stateMap()

◆ substitutionProcess()

Member Data Documentation

◆ nProc_

◆ processColl_