Evolution of a sequence performed by a unique SubstitutionProcess all along the sequence. More...

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

Inheritance diagram for bpp::OneProcessSequenceEvolution:

Collaboration diagram for bpp::OneProcessSequenceEvolution:

Public Member Functions
	OneProcessSequenceEvolution (std::shared_ptr< SubstitutionProcessInterface > process, size_t nProc=0)

	OneProcessSequenceEvolution (const OneProcessSequenceEvolution &evol)

OneProcessSequenceEvolution &	operator= (const OneProcessSequenceEvolution &evol)

OneProcessSequenceEvolution *	clone () const override

bool	isCompatibleWith (const AlignmentDataInterface &data) const override

const size_t	getSubstitutionProcessNumber () const

const SubstitutionProcessInterface &	substitutionProcess () const

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

SubstitutionProcessInterface &	substitutionProcess ()

std::shared_ptr< SubstitutionProcessInterface >	getSubstitutionProcess ()

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

const SubstitutionProcessInterface &	substitutionProcess (size_t number) const override

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

std::shared_ptr< const ParametrizablePhyloTree >	tree () const
	Get the tree (topology and branch lengths). More...

void	fireParameterChanged (const ParameterList &pl) override

ParameterList	getBranchLengthParameters (bool independent) const override
	Get several categories of parameters. More...

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

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

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

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

const ParameterList &	getParameters () const override

const ParameterList &	getIndependentParameters () const override

ParameterList	getNonDerivableParameters () const override
	get (Non)Derivable INDEPENDENT parameters More...

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 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 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

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 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

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< SubstitutionProcessInterface >	subsProc_

size_t	nProc_
	the substitution process number. More...

std::vector< size_t >	vProc_
	not nice, for inheritance compatibility. More...

Private Attributes
ParameterList	independentParameters_

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

ParameterList	parameters_

std::string	prefix_

Detailed Description

Evolution of a sequence performed by a unique SubstitutionProcess all along the sequence.

Definition at line 26 of file OneProcessSequenceEvolution.h.

Constructor & Destructor Documentation

◆ OneProcessSequenceEvolution() [1/2]

OneProcessSequenceEvolution::OneProcessSequenceEvolution	(	std::shared_ptr< SubstitutionProcessInterface >	process,
		size_t	nProc = `0`
	)

Definition at line 10 of file OneProcessSequenceEvolution.cpp.

References bpp::AbstractParameterAliasable::includeParameters_().

Referenced by clone().

◆ OneProcessSequenceEvolution() [2/2]

OneProcessSequenceEvolution::OneProcessSequenceEvolution ( const OneProcessSequenceEvolution & evol )

Definition at line 22 of file OneProcessSequenceEvolution.cpp.

Member Function Documentation

◆ clone()

OneProcessSequenceEvolution* bpp::OneProcessSequenceEvolution::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractParameterAliasable.

Definition at line 50 of file OneProcessSequenceEvolution.h.

References OneProcessSequenceEvolution().

◆ fireParameterChanged()

void bpp::OneProcessSequenceEvolution::fireParameterChanged ( const ParameterList & pl )

inlineoverridevirtual

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 110 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ getBranchLengthParameters()

ParameterList bpp::OneProcessSequenceEvolution::getBranchLengthParameters ( bool independent ) const

inlineoverridevirtual

Get several categories of parameters.

Implements bpp::SequenceEvolution.

Definition at line 121 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ getIndependentParameters()

const ParameterList& bpp::OneProcessSequenceEvolution::getIndependentParameters ( ) const

inlineoverridevirtual

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 154 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ getNonDerivableParameters()

ParameterList bpp::OneProcessSequenceEvolution::getNonDerivableParameters ( ) const

inlineoverridevirtual

get (Non)Derivable INDEPENDENT parameters

Implements bpp::SequenceEvolution.

Definition at line 163 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ getParameters()

const ParameterList& bpp::OneProcessSequenceEvolution::getParameters ( ) const

inlineoverridevirtual

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 149 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ getRateDistributionParameters()

ParameterList bpp::OneProcessSequenceEvolution::getRateDistributionParameters ( bool independent ) const

inlineoverridevirtual

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

Returns: A ParameterList.

Implements bpp::SequenceEvolution.

Definition at line 131 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ getRootFrequenciesParameters()

ParameterList bpp::OneProcessSequenceEvolution::getRootFrequenciesParameters ( bool independent ) const

inlineoverridevirtual

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

Returns: A ParameterList.

Implements bpp::SequenceEvolution.

Definition at line 126 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ 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 bpp::OneProcessSequenceEvolution::getSubstitutionModelParameters ( bool independent ) const

inlineoverridevirtual

Get the parameters associated to substitution model(s).

Returns: A ParameterList.

Implements bpp::SequenceEvolution.

Definition at line 136 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ getSubstitutionProcess() [1/3]

std::shared_ptr<SubstitutionProcessInterface> bpp::OneProcessSequenceEvolution::getSubstitutionProcess ( )

inline

Definition at line 80 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ getSubstitutionProcess() [2/3]

std::shared_ptr<const SubstitutionProcessInterface> bpp::OneProcessSequenceEvolution::getSubstitutionProcess ( ) const

inline

Definition at line 70 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ getSubstitutionProcess() [3/3]

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

inlineoverridevirtual

Implements bpp::SequenceEvolution.

Definition at line 95 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ getSubstitutionProcessNumber()

const size_t bpp::OneProcessSequenceEvolution::getSubstitutionProcessNumber ( ) const

inline

Definition at line 60 of file OneProcessSequenceEvolution.h.

References nProc_.

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

◆ getSubstitutionProcessNumbers()

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

inlineoverridevirtual

Implements bpp::SequenceEvolution.

Definition at line 85 of file OneProcessSequenceEvolution.h.

References vProc_.

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

◆ getSubstitutionProcessParameters()

ParameterList bpp::OneProcessSequenceEvolution::getSubstitutionProcessParameters ( bool independent ) const

inlineoverridevirtual

Get the parameters associated to substitution processes(s).

Returns: A ParameterList.

Implements bpp::SequenceEvolution.

Definition at line 141 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ isCompatibleWith()

bool bpp::OneProcessSequenceEvolution::isCompatibleWith ( const AlignmentDataInterface & data ) const

inlineoverridevirtual

Implements bpp::SequenceEvolution.

Definition at line 55 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ operator=()

OneProcessSequenceEvolution & OneProcessSequenceEvolution::operator= ( const OneProcessSequenceEvolution & evol )

Definition at line 29 of file OneProcessSequenceEvolution.cpp.

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

◆ 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() [1/3]

SubstitutionProcessInterface& bpp::OneProcessSequenceEvolution::substitutionProcess ( )

inline

Definition at line 75 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ substitutionProcess() [2/3]

const SubstitutionProcessInterface& bpp::OneProcessSequenceEvolution::substitutionProcess ( ) const

inline

Definition at line 65 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ substitutionProcess() [3/3]

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

inlineoverridevirtual

Implements bpp::SequenceEvolution.

Definition at line 90 of file OneProcessSequenceEvolution.h.

References subsProc_.

◆ tree()

std::shared_ptr<const ParametrizablePhyloTree> bpp::OneProcessSequenceEvolution::tree ( ) const

inline

Get the tree (topology and branch lengths).

Returns: The tree of this OneProcessSequenceEvolution object.

Definition at line 105 of file OneProcessSequenceEvolution.h.

References subsProc_.

Member Data Documentation

◆ nProc_

size_t bpp::OneProcessSequenceEvolution::nProc_

protected

the substitution process number.

Definition at line 36 of file OneProcessSequenceEvolution.h.

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

◆ subsProc_

std::shared_ptr<SubstitutionProcessInterface> bpp::OneProcessSequenceEvolution::subsProc_

protected

Definition at line 31 of file OneProcessSequenceEvolution.h.

Referenced by fireParameterChanged(), getBranchLengthParameters(), getIndependentParameters(), getNonDerivableParameters(), getParameters(), getRateDistributionParameters(), getRootFrequenciesParameters(), getSubstitutionModelParameters(), getSubstitutionProcess(), getSubstitutionProcessParameters(), isCompatibleWith(), operator=(), substitutionProcess(), and tree().

◆ vProc_

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

protected

not nice, for inheritance compatibility.

Definition at line 41 of file OneProcessSequenceEvolution.h.

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

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

Bpp/Phyl/Likelihood/OneProcessSequenceEvolution.h
Bpp/Phyl/Likelihood/OneProcessSequenceEvolution.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ OneProcessSequenceEvolution() [1/2]

◆ OneProcessSequenceEvolution() [2/2]

Member Function Documentation

◆ clone()

◆ fireParameterChanged()

◆ getBranchLengthParameters()

◆ getIndependentParameters()

◆ getNonDerivableParameters()

◆ getParameters()

◆ getRateDistributionParameters()

◆ getRootFrequenciesParameters()

◆ getStateMap()

◆ getSubstitutionModelParameters()

◆ getSubstitutionProcess() [1/3]

◆ getSubstitutionProcess() [2/3]

◆ getSubstitutionProcess() [3/3]

◆ getSubstitutionProcessNumber()

◆ getSubstitutionProcessNumbers()

◆ getSubstitutionProcessParameters()

◆ isCompatibleWith()

◆ operator=()

◆ stateMap()

◆ substitutionProcess() [1/3]

◆ substitutionProcess() [2/3]

◆ substitutionProcess() [3/3]

◆ tree()

Member Data Documentation

◆ nProc_

◆ subsProc_

◆ vProc_