Laplace estimate of the substitution count. More...

#include <Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h>

Inheritance diagram for bpp::LaplaceSubstitutionCount:

Collaboration diagram for bpp::LaplaceSubstitutionCount:

Public Member Functions
	LaplaceSubstitutionCount (std::shared_ptr< const SubstitutionModelInterface > model, size_t cutOff)

	LaplaceSubstitutionCount (std::shared_ptr< const StateMapInterface > stateMap, size_t cutOff)

	LaplaceSubstitutionCount (const LaplaceSubstitutionCount &asc)

LaplaceSubstitutionCount &	operator= (const LaplaceSubstitutionCount &asc)

virtual	~LaplaceSubstitutionCount ()

LaplaceSubstitutionCount *	clone () const override

double	getNumberOfSubstitutions (size_t initialState, size_t finalState, double length, size_t type=1) const override
	Get the number of susbstitutions on a branch, given the initial and final states, and the branch length. More...

std::unique_ptr< Matrix< double > >	getAllNumbersOfSubstitutions (double length, size_t type=1) const override
	Get the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length. More...

void	storeAllNumbersOfSubstitutions (double length, size_t type, Eigen::MatrixXd &mat) const override
	Stores the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length. More...

std::vector< double >	getNumberOfSubstitutionsPerType (size_t initialState, size_t finalState, double length) const override
	Get the numbers of susbstitutions on a branch for all types, for an initial and final states, given the branch length. More...

void	setSubstitutionModel (std::shared_ptr< const SubstitutionModelInterface > model) override
	Set the substitution model associated with this count, if relevant. More...

void	setSubstitutionRegister (std::shared_ptr< const SubstitutionRegisterInterface > reg) override

bool	hasSubstitutionRegister () const

std::shared_ptr< const SubstitutionRegisterInterface >	getSubstitutionRegister () const

virtual size_t	getNumberOfSubstitutionTypes () const
	Short cut function, equivalent to getSubstitutionRegister().getNumberOfSubstitutionTypes(). More...

virtual std::shared_ptr< const Alphabet >	getAlphabet () const
	Short cut function, equivalent to getSubstitutionRegister()->getAlphabet(). More...

virtual size_t	getNumberOfStates () const
	Short cut function, equivalent to getSubstitutionRegister()->getAlphabet()->getSize(). More...

Protected Member Functions
void	computeCounts (double length) const

void	substitutionRegisterHasChanged () override

Protected Attributes
std::shared_ptr< const SubstitutionRegisterInterface >	register_

Private Attributes
std::shared_ptr< const SubstitutionModelInterface >	model_

size_t	cutOff_

double	currentLength_

RowMatrix< double >	m_

Detailed Description

Laplace estimate of the substitution count.

This method uses Laplace transforms, as described in Dutheil J, Pupko T, Jean-Marie A, Galtier N. A model-based approach for detecting coevolving positions in a molecule. Mol Biol Evol. 2005 Sep;22(9):1919-28.

See also: UniformizationSubstitutionCount; DecompositionSubstitutionCount

Author: Julien Dutheil

Definition at line 26 of file LaplaceSubstitutionCount.h.

Constructor & Destructor Documentation

◆ LaplaceSubstitutionCount() [1/3]

bpp::LaplaceSubstitutionCount::LaplaceSubstitutionCount	(	std::shared_ptr< const SubstitutionModelInterface >	model,
		size_t	cutOff
	)

inline

Definition at line 36 of file LaplaceSubstitutionCount.h.

Referenced by clone().

◆ LaplaceSubstitutionCount() [2/3]

bpp::LaplaceSubstitutionCount::LaplaceSubstitutionCount	(	std::shared_ptr< const StateMapInterface >	stateMap,
		size_t	cutOff
	)

inline

Definition at line 46 of file LaplaceSubstitutionCount.h.

◆ LaplaceSubstitutionCount() [3/3]

bpp::LaplaceSubstitutionCount::LaplaceSubstitutionCount ( const LaplaceSubstitutionCount & asc )

inline

Definition at line 54 of file LaplaceSubstitutionCount.h.

◆ ~LaplaceSubstitutionCount()

virtual bpp::LaplaceSubstitutionCount::~LaplaceSubstitutionCount ( )

inlinevirtual

Definition at line 72 of file LaplaceSubstitutionCount.h.

Member Function Documentation

◆ clone()

LaplaceSubstitutionCount * bpp::LaplaceSubstitutionCount::clone ( ) const

inlineoverridevirtual

Implements bpp::SubstitutionCountInterface.

Definition at line 74 of file LaplaceSubstitutionCount.h.

References LaplaceSubstitutionCount().

◆ computeCounts()

void LaplaceSubstitutionCount::computeCounts ( double length ) const

protected

Definition at line 14 of file LaplaceSubstitutionCount.cpp.

References bpp::MatrixTools::add(), cutOff_, bpp::NumTools::fact(), bpp::MatrixTools::fill(), RowMatrix< double >::getNumberOfRows(), m_, model_, bpp::MatrixTools::mult(), bpp::pow(), bpp::MatrixTools::pow(), and bpp::MatrixTools::scale().

Referenced by getAllNumbersOfSubstitutions(), getNumberOfSubstitutions(), setSubstitutionModel(), and storeAllNumbersOfSubstitutions().

◆ getAllNumbersOfSubstitutions()

unique_ptr< Matrix< double > > LaplaceSubstitutionCount::getAllNumbersOfSubstitutions	(	double	length,
		size_t	type = `1`
	)		const

overridevirtual

Get the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length.

Parameters

length	The length of the branch.
type	The type of susbstitution to count.

Returns: A matrix with all numbers of substitutions for each initial and final states.

Implements bpp::SubstitutionCountInterface.

Definition at line 79 of file LaplaceSubstitutionCount.cpp.

References computeCounts(), currentLength_, m_, and model_.

◆ getAlphabet()

virtual std::shared_ptr< const Alphabet > bpp::SubstitutionCountInterface::getAlphabet ( ) const

inlinevirtualinherited

Short cut function, equivalent to getSubstitutionRegister()->getAlphabet().

Returns: The alphabet associated to this substitution count.

Definition at line 78 of file SubstitutionCount.h.

References bpp::SubstitutionCountInterface::getSubstitutionRegister().

◆ getNumberOfStates()

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

inlinevirtualinherited

Short cut function, equivalent to getSubstitutionRegister()->getAlphabet()->getSize().

Returns: The number of states in the model/alphabet.

Definition at line 85 of file SubstitutionCount.h.

References bpp::SubstitutionCountInterface::getSubstitutionRegister().

◆ getNumberOfSubstitutions()

double LaplaceSubstitutionCount::getNumberOfSubstitutions	(	size_t	initialState,
		size_t	finalState,
		double	length,
		size_t	type = `1`
	)		const

overridevirtual

Get the number of susbstitutions on a branch, given the initial and final states, and the branch length.

Parameters

initialState	The initial state.
finalState	The final state.
length	The length of the branch.
type	The type of substitution to count.

Returns: The number of substitutions on a branch of specified length and according to initial and final states.

Implements bpp::SubstitutionCountInterface.

Definition at line 61 of file LaplaceSubstitutionCount.cpp.

References computeCounts(), currentLength_, m_, and model_.

Referenced by getNumberOfSubstitutionsPerType().

◆ getNumberOfSubstitutionsPerType()

std::vector< double > bpp::LaplaceSubstitutionCount::getNumberOfSubstitutionsPerType	(	size_t	initialState,
		size_t	finalState,
		double	length
	)		const

inlineoverridevirtual

Get the numbers of susbstitutions on a branch for all types, for an initial and final states, given the branch length.

Parameters

initialState	The initial state.
finalState	The final state.
length	The length of the branch.

Returns: A matrix with all numbers of substitutions for each initial and final states.

Implements bpp::SubstitutionCountInterface.

Definition at line 83 of file LaplaceSubstitutionCount.h.

References getNumberOfSubstitutions().

◆ getNumberOfSubstitutionTypes()

virtual size_t bpp::SubstitutionCountInterface::getNumberOfSubstitutionTypes ( ) const

inlinevirtualinherited

Short cut function, equivalent to getSubstitutionRegister().getNumberOfSubstitutionTypes().

Returns: The number of substitution types supported by this instance.

Definition at line 71 of file SubstitutionCount.h.

References bpp::SubstitutionCountInterface::getSubstitutionRegister().

Referenced by bpp::SubstitutionMappingTools::computeCounts(), bpp::DecompositionSubstitutionCount::getNumberOfSubstitutionsPerType(), bpp::NaiveSubstitutionCount::getNumberOfSubstitutionsPerType(), and bpp::UniformizationSubstitutionCount::getNumberOfSubstitutionsPerType().

◆ getSubstitutionRegister()

std::shared_ptr< const SubstitutionRegisterInterface > bpp::AbstractSubstitutionCount::getSubstitutionRegister ( ) const

inlinevirtualinherited

Returns: The SubstitutionRegister object associated to this instance. The register contains the description of the various substitutions types that are mapped.

Implements bpp::SubstitutionCountInterface.

Definition at line 170 of file SubstitutionCount.h.

References bpp::AbstractSubstitutionCount::register_.

◆ hasSubstitutionRegister()

bool bpp::AbstractSubstitutionCount::hasSubstitutionRegister ( ) const

inlinevirtualinherited

Returns: Tell if a substitution register has been attached to this class.

Implements bpp::SubstitutionCountInterface.

Definition at line 156 of file SubstitutionCount.h.

References bpp::AbstractSubstitutionCount::register_.

◆ operator=()

LaplaceSubstitutionCount & bpp::LaplaceSubstitutionCount::operator= ( const LaplaceSubstitutionCount & asc )

inline

Definition at line 62 of file LaplaceSubstitutionCount.h.

References currentLength_, cutOff_, m_, and model_.

◆ setSubstitutionModel()

void LaplaceSubstitutionCount::setSubstitutionModel ( std::shared_ptr< const SubstitutionModelInterface > model )

overridevirtual

Set the substitution model associated with this count, if relevant.

Parameters

model The substitution model to use with this count.

Implements bpp::SubstitutionCountInterface.

Definition at line 150 of file LaplaceSubstitutionCount.cpp.

References computeCounts(), currentLength_, m_, model_, and RowMatrix< double >::resize().

◆ setSubstitutionRegister()

void bpp::LaplaceSubstitutionCount::setSubstitutionRegister ( std::shared_ptr< const SubstitutionRegisterInterface > reg )

inlineoverridevirtual

Parameters

reg	The new SubstitutionRegister object to be associated to this instance. The register contains the description of the various substitutions types that are mapped.

Implements bpp::SubstitutionCountInterface.

Definition at line 96 of file LaplaceSubstitutionCount.h.

◆ storeAllNumbersOfSubstitutions()

void LaplaceSubstitutionCount::storeAllNumbersOfSubstitutions	(	double	length,
		size_t	type,
		Eigen::MatrixXd &	mat
	)		const

overridevirtual

Stores the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length.

Parameters

length	The length of the branch.
type	The type of susbstitution to count.
mat	The matrix filled with all numbers of substitutions for each initial and final states.

Implements bpp::SubstitutionCountInterface.

Definition at line 110 of file LaplaceSubstitutionCount.cpp.

References computeCounts(), currentLength_, m_, and model_.