Sequence evolution framework based on a mixture of substitution processes. More...

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

Inheritance diagram for bpp::PartitionSequenceEvolution:

Collaboration diagram for bpp::PartitionSequenceEvolution:

Public Member Functions
	PartitionSequenceEvolution (std::shared_ptr< SubstitutionProcessCollection > processColl, std::vector< size_t > &posProc)

	PartitionSequenceEvolution (const PartitionSequenceEvolution &mlc)

PartitionSequenceEvolution &	operator= (const PartitionSequenceEvolution &mlc)

virtual	~PartitionSequenceEvolution ()

PartitionSequenceEvolution *	clone () const

size_t	getNumberOfSites () const

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

size_t	getSubstitutionProcessNumber (size_t i) const

std::map< size_t, std::vector< size_t > > &	mapOfProcessSites ()

const std::map< size_t, std::vector< size_t > > &	mapOfProcessSites () const

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

SubstitutionProcessCollection &	collection ()

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

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...

const StateMapInterface &	stateMap () const

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

virtual size_t	getNumberOfIndependentParameters () const=0

size_t	getNumberOfIndependentParameters () const

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

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

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

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

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

virtual const ParameterList &	getIndependentParameters () const=0

const ParameterList &	getIndependentParameters () const

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

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

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

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

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

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

virtual const ParameterList &	getParameters () const=0

const ParameterList &	getParameters () const override

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

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

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

double	getParameterValue (const std::string &name) const override

virtual void	setAllParametersValues (const ParameterList &parameters)=0

void	setAllParametersValues (const ParameterList &parameters) override

virtual void	setParameterValue (const std::string &name, double value)=0

void	setParameterValue (const std::string &name, double value) override

virtual void	setParametersValues (const ParameterList &parameters)=0

void	setParametersValues (const ParameterList &parameters) override

virtual bool	matchParametersValues (const ParameterList &parameters)=0

bool	matchParametersValues (const ParameterList &parameters) override

virtual void	removeConstraint (const std::string &name)=0

void	removeConstraint (const std::string &name) override

virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0

void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override

virtual size_t	getNumberOfParameters () const=0

size_t	getNumberOfParameters () const override

virtual void	setNamespace (const std::string &prefix)=0

void	setNamespace (const std::string &prefix)

virtual std::string	getNamespace () const=0

std::string	getNamespace () const override

virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const=0

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

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

ParameterList	getAliasedParameters (const ParameterList &pl) const

ParameterList	getFromParameters (const ParameterList &pl) const

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

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

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0

ParameterList &	getParameters_ () override

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

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
std::vector< size_t >	vProc_
	vector of the substitution process numbers along the sequence. More...

size_t	vSize_

std::map< size_t, std::vector< size_t > >	mProcPos_
	On the reverse, for each process number, the vector of the sites where it is used. More...

ParameterList	independentParameters_

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

ParameterList	parameters_

std::string	prefix_

Detailed Description

Sequence evolution framework based on a mixture of substitution processes.

See also: MultiProcessSequenceEvolution

Definition at line 20 of file PartitionSequenceEvolution.h.

Constructor & Destructor Documentation

◆ PartitionSequenceEvolution() [1/2]

PartitionSequenceEvolution::PartitionSequenceEvolution	(	std::shared_ptr< SubstitutionProcessCollection >	processColl,
		std::vector< size_t > &	posProc
	)

Definition at line 14 of file PartitionSequenceEvolution.cpp.

References mProcPos_, bpp::MultiProcessSequenceEvolution::nProc_, bpp::MultiProcessSequenceEvolution::processColl_, vProc_, and vSize_.

Referenced by clone().

◆ PartitionSequenceEvolution() [2/2]

bpp::PartitionSequenceEvolution::PartitionSequenceEvolution ( const PartitionSequenceEvolution & mlc )

inline

Definition at line 51 of file PartitionSequenceEvolution.h.

◆ ~PartitionSequenceEvolution()

virtual bpp::PartitionSequenceEvolution::~PartitionSequenceEvolution ( )

inlinevirtual

Definition at line 68 of file PartitionSequenceEvolution.h.

Member Function Documentation

◆ clone()

PartitionSequenceEvolution* bpp::PartitionSequenceEvolution::clone ( ) const

inlinevirtual

Implements bpp::AbstractParameterAliasable.

Definition at line 70 of file PartitionSequenceEvolution.h.

References PartitionSequenceEvolution().

◆ collection() [1/2]

SubstitutionProcessCollection& bpp::MultiProcessSequenceEvolution::collection ( )

inlineinherited

Definition at line 69 of file MultiProcessSequenceEvolution.h.

◆ collection() [2/2]

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

inlineinherited

The collection.

Definition at line 65 of file MultiProcessSequenceEvolution.h.

◆ fireParameterChanged()

void MultiProcessSequenceEvolution::fireParameterChanged ( const ParameterList & parameters )

virtualinherited

Reimplemented from bpp::AbstractParameterAliasable.

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

Definition at line 30 of file MultiProcessSequenceEvolution.cpp.

References bpp::MultiProcessSequenceEvolution::processColl_.

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

◆ getBranchLengthParameters()

ParameterList MultiProcessSequenceEvolution::getBranchLengthParameters ( bool independent ) const

virtualinherited

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(), bpp::MultiProcessSequenceEvolution::nProc_, and bpp::MultiProcessSequenceEvolution::processColl_.

◆ getCollection() [1/2]

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

inlineinherited

Definition at line 71 of file MultiProcessSequenceEvolution.h.

◆ getCollection() [2/2]

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

inlineinherited

Definition at line 67 of file MultiProcessSequenceEvolution.h.

◆ getNonDerivableParameters()

ParameterList MultiProcessSequenceEvolution::getNonDerivableParameters ( ) const

virtualinherited

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::MixtureSequenceEvolution, and bpp::AutoCorrelationSequenceEvolution.

Definition at line 97 of file MultiProcessSequenceEvolution.cpp.

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

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

◆ getNumberOfSites()

size_t bpp::PartitionSequenceEvolution::getNumberOfSites ( ) const

inline

Definition at line 73 of file PartitionSequenceEvolution.h.

References vSize_.

Referenced by bpp::EvolutionSequenceSimulator::resetSiteSimulators().

◆ getNumberOfSubstitutionProcess()

size_t bpp::MultiProcessSequenceEvolution::getNumberOfSubstitutionProcess ( ) const

inlineinherited

Return the number of process used for computation.

Definition at line 76 of file MultiProcessSequenceEvolution.h.

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

◆ getProcessNumbersPerSite()

const std::vector<size_t>& bpp::PartitionSequenceEvolution::getProcessNumbersPerSite ( ) const

inline

Definition at line 78 of file PartitionSequenceEvolution.h.

References vProc_.

◆ getRateDistributionParameters()

ParameterList MultiProcessSequenceEvolution::getRateDistributionParameters ( bool independent ) const

virtualinherited

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(), bpp::MultiProcessSequenceEvolution::nProc_, and bpp::MultiProcessSequenceEvolution::processColl_.

◆ getRootFrequenciesParameters()

ParameterList MultiProcessSequenceEvolution::getRootFrequenciesParameters ( bool independent ) const

virtualinherited

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(), bpp::MultiProcessSequenceEvolution::nProc_, and bpp::MultiProcessSequenceEvolution::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

virtualinherited

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(), bpp::MultiProcessSequenceEvolution::nProc_, and bpp::MultiProcessSequenceEvolution::processColl_.

◆ getSubstitutionProcess()

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

inlinevirtualinherited

Implements bpp::SequenceEvolution.

Definition at line 87 of file MultiProcessSequenceEvolution.h.

◆ getSubstitutionProcessNumber()

size_t bpp::PartitionSequenceEvolution::getSubstitutionProcessNumber ( size_t i ) const

inline

Definition at line 88 of file PartitionSequenceEvolution.h.

References vProc_, and vSize_.

Referenced by bpp::EvolutionSequenceSimulator::resetSiteSimulators().

◆ getSubstitutionProcessNumbers()

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

inlinevirtualinherited

Implements bpp::SequenceEvolution.

Definition at line 92 of file MultiProcessSequenceEvolution.h.

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

◆ getSubstitutionProcessParameters()

ParameterList MultiProcessSequenceEvolution::getSubstitutionProcessParameters ( bool independent ) const

virtualinherited

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(), bpp::MultiProcessSequenceEvolution::nProc_, and bpp::MultiProcessSequenceEvolution::processColl_.

◆ isCompatibleWith()

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

virtualinherited

test if data fits this model

Implements bpp::SequenceEvolution.

Definition at line 122 of file MultiProcessSequenceEvolution.cpp.

References bpp::MultiProcessSequenceEvolution::nProc_, and bpp::MultiProcessSequenceEvolution::processColl_.

◆ mapOfProcessSites() [1/2]

std::map<size_t, std::vector<size_t> >& bpp::PartitionSequenceEvolution::mapOfProcessSites ( )

inline

Definition at line 95 of file PartitionSequenceEvolution.h.

References mProcPos_.

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

◆ mapOfProcessSites() [2/2]

const std::map<size_t, std::vector<size_t> >& bpp::PartitionSequenceEvolution::mapOfProcessSites ( ) const

inline

Definition at line 100 of file PartitionSequenceEvolution.h.

References mProcPos_.

◆ operator=()

PartitionSequenceEvolution& bpp::PartitionSequenceEvolution::operator= ( const PartitionSequenceEvolution & mlc )

inline

Definition at line 57 of file PartitionSequenceEvolution.h.

References mProcPos_, bpp::MultiProcessSequenceEvolution::operator=(), vProc_, and vSize_.

◆ setParameters()

void MultiProcessSequenceEvolution::setParameters ( const ParameterList & parameters )

inherited

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

inlinevirtualinherited

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

Implements bpp::SequenceEvolution.

Definition at line 82 of file MultiProcessSequenceEvolution.h.

Member Data Documentation

◆ mProcPos_

std::map<size_t, std::vector<size_t> > bpp::PartitionSequenceEvolution::mProcPos_

private

On the reverse, for each process number, the vector of the sites where it is used.

Convenient for process specific site patterns.

Definition at line 38 of file PartitionSequenceEvolution.h.

Referenced by mapOfProcessSites(), operator=(), and PartitionSequenceEvolution().

◆ nProc_

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

protectedinherited

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

Definition at line 37 of file MultiProcessSequenceEvolution.h.

◆ processColl_

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

protectedinherited

Definition at line 31 of file MultiProcessSequenceEvolution.h.

◆ vProc_

std::vector<size_t> bpp::PartitionSequenceEvolution::vProc_

private

vector of the substitution process numbers along the sequence.

Definition at line 27 of file PartitionSequenceEvolution.h.

Referenced by getProcessNumbersPerSite(), getSubstitutionProcessNumber(), operator=(), and PartitionSequenceEvolution().

◆ vSize_

size_t bpp::PartitionSequenceEvolution::vSize_

private

Definition at line 29 of file PartitionSequenceEvolution.h.

Referenced by getNumberOfSites(), getSubstitutionProcessNumber(), operator=(), and PartitionSequenceEvolution().

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

Bpp/Phyl/Likelihood/PartitionSequenceEvolution.h
Bpp/Phyl/Likelihood/PartitionSequenceEvolution.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PartitionSequenceEvolution() [1/2]

◆ PartitionSequenceEvolution() [2/2]

◆ ~PartitionSequenceEvolution()

Member Function Documentation

◆ clone()

◆ collection() [1/2]

◆ collection() [2/2]

◆ fireParameterChanged()

◆ getBranchLengthParameters()

◆ getCollection() [1/2]

◆ getCollection() [2/2]

◆ getNonDerivableParameters()

◆ getNumberOfSites()

◆ getNumberOfSubstitutionProcess()

◆ getProcessNumbersPerSite()

◆ getRateDistributionParameters()

◆ getRootFrequenciesParameters()

◆ getStateMap()

◆ getSubstitutionModelParameters()

◆ getSubstitutionProcess()

◆ getSubstitutionProcessNumber()

◆ getSubstitutionProcessNumbers()

◆ getSubstitutionProcessParameters()

◆ isCompatibleWith()

◆ mapOfProcessSites() [1/2]

◆ mapOfProcessSites() [2/2]

◆ operator=()

◆ setParameters()

◆ stateMap()

◆ substitutionProcess()

Member Data Documentation

◆ mProcPos_

◆ nProc_

◆ processColl_

◆ vProc_

◆ vSize_