Analytical substitution count using the eigen decomposition method. More...

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

Inheritance diagram for bpp::DecompositionSubstitutionCount:

Collaboration diagram for bpp::DecompositionSubstitutionCount:

Public Member Functions
	DecompositionSubstitutionCount (std::shared_ptr< const SubstitutionModelInterface > model, std::shared_ptr< const SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > weights=nullptr, std::shared_ptr< const AlphabetIndex2 > distances=nullptr)

	DecompositionSubstitutionCount (std::shared_ptr< const SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > weights=nullptr, std::shared_ptr< const AlphabetIndex2 > distances=nullptr)

	DecompositionSubstitutionCount (const DecompositionSubstitutionCount &dsc)

DecompositionSubstitutionCount &	operator= (const DecompositionSubstitutionCount &dsc)

virtual	~DecompositionSubstitutionCount ()

DecompositionSubstitutionCount *	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. More...

bool	hasSubstitutionRegister () const

void	setSubstitutionRegister (std::shared_ptr< const SubstitutionRegisterInterface > reg)
	attribution of a SubstitutionRegister More...

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...

void	setWeights (std::shared_ptr< const AlphabetIndex2 > weights)

bool	hasWeights () const

std::shared_ptr< const AlphabetIndex2 >	getWeights () const

void	setDistances (std::shared_ptr< const AlphabetIndex2 > distances)

bool	hasDistances () const

std::shared_ptr< const AlphabetIndex2 >	getDistances () const

Protected Member Functions
void	initCounts_ ()

void	computeCounts_ (double length) const

void	substitutionRegisterHasChanged () override

void	weightsHaveChanged () override

void	distancesHaveChanged () override

void	initStates_ ()

void	initBMatrices_ ()

void	computeProducts_ ()

void	computeExpectations (RowMatrix< double > &mapping, double length) const

void	computeExpectations (std::vector< RowMatrix< double >> &mappings, double length) const

void	jFunction_ (const std::vector< double > &lambda, double t, RowMatrix< double > &result) const
	Compute the integral part of the computation. More...

void	jFunction_ (const std::vector< double > &lambda, const std::vector< double > &ilambda, double t, RowMatrix< double > &result, RowMatrix< double > &iresult) const
	Compute the integral part of the computation, in complex numbers. More...

Protected Attributes
std::shared_ptr< const SubstitutionRegisterInterface >	register_

std::shared_ptr< const AlphabetIndex2 >	weights_

std::shared_ptr< const AlphabetIndex2 >	distances_

std::shared_ptr< const SubstitutionModelInterface >	model_

size_t	nbStates_

size_t	nbTypes_

RowMatrix< double >	jMat_

RowMatrix< double >	jIMat_

ColMatrix< double >	rightEigenVectors_
	Real and imaginary eigenvectors, for non-reversible computation. More...

ColMatrix< double >	rightIEigenVectors_

RowMatrix< double >	leftEigenVectors_

RowMatrix< double >	leftIEigenVectors_

std::vector< RowMatrix< double > >	bMatrices_
	computation matrices More...

std::vector< RowMatrix< double > >	insideProducts_

std::vector< RowMatrix< double > >	insideIProducts_

Private Member Functions
void	fillBMatrices_ ()

void	setDistanceBMatrices_ ()

Private Attributes
std::vector< RowMatrix< double > >	counts_

double	currentLength_

Detailed Description

Analytical substitution count using the eigen decomposition method.

The codes is adapted from the original R code by Paula Tataru and Asger Hobolth.

Author: Julien Dutheil

Definition at line 24 of file DecompositionSubstitutionCount.h.

Constructor & Destructor Documentation

◆ DecompositionSubstitutionCount() [1/3]

DecompositionSubstitutionCount::DecompositionSubstitutionCount	(	std::shared_ptr< const SubstitutionModelInterface >	model,
		std::shared_ptr< const SubstitutionRegisterInterface >	reg,
		std::shared_ptr< const AlphabetIndex2 >	weights = `nullptr`,
		std::shared_ptr< const AlphabetIndex2 >	distances = `nullptr`
	)

Definition at line 16 of file DecompositionSubstitutionCount.cpp.

References bpp::DecompositionMethods::computeProducts_(), fillBMatrices_(), bpp::DecompositionMethods::initBMatrices_(), and initCounts_().

Referenced by clone().

◆ DecompositionSubstitutionCount() [2/3]

DecompositionSubstitutionCount::DecompositionSubstitutionCount	(	std::shared_ptr< const SubstitutionRegisterInterface >	reg,
		std::shared_ptr< const AlphabetIndex2 >	weights = `nullptr`,
		std::shared_ptr< const AlphabetIndex2 >	distances = `nullptr`
	)

Definition at line 39 of file DecompositionSubstitutionCount.cpp.

References initCounts_().

◆ DecompositionSubstitutionCount() [3/3]

bpp::DecompositionSubstitutionCount::DecompositionSubstitutionCount ( const DecompositionSubstitutionCount & dsc )

inline

Definition at line 46 of file DecompositionSubstitutionCount.h.

◆ ~DecompositionSubstitutionCount()

virtual bpp::DecompositionSubstitutionCount::~DecompositionSubstitutionCount ( )

inlinevirtual

Definition at line 66 of file DecompositionSubstitutionCount.h.

Member Function Documentation

◆ clone()

DecompositionSubstitutionCount* bpp::DecompositionSubstitutionCount::clone ( ) const

inlineoverridevirtual

Implements bpp::SubstitutionCountInterface.

Definition at line 68 of file DecompositionSubstitutionCount.h.

References DecompositionSubstitutionCount().

◆ computeCounts_()

void DecompositionSubstitutionCount::computeCounts_ ( double length ) const

protected

Definition at line 109 of file DecompositionSubstitutionCount.cpp.

References bpp::DecompositionMethods::computeExpectations(), counts_, bpp::DecompositionMethods::model_, bpp::DecompositionMethods::nbStates_, bpp::DecompositionMethods::nbTypes_, and bpp::AbstractWeightedSubstitutionCount::weights_.

Referenced by distancesHaveChanged(), getAllNumbersOfSubstitutions(), getNumberOfSubstitutions(), getNumberOfSubstitutionsPerType(), setSubstitutionModel(), storeAllNumbersOfSubstitutions(), substitutionRegisterHasChanged(), and weightsHaveChanged().

◆ computeExpectations() [1/2]

void DecompositionMethods::computeExpectations	(	RowMatrix< double > &	mapping,
		double	length
	)		const

protectedinherited

Definition at line 166 of file DecompositionMethods.cpp.

Referenced by computeCounts_(), and bpp::DecompositionReward::computeRewards_().

◆ computeExpectations() [2/2]

void DecompositionMethods::computeExpectations	(	std::vector< RowMatrix< double >> &	mappings,
		double	length
	)		const

protectedinherited

Definition at line 196 of file DecompositionMethods.cpp.

◆ computeProducts_()

void DecompositionMethods::computeProducts_ ( )

protectedinherited

Definition at line 91 of file DecompositionMethods.cpp.

References bpp::DecompositionMethods::bMatrices_, bpp::DecompositionMethods::insideIProducts_, bpp::DecompositionMethods::insideProducts_, bpp::DecompositionMethods::leftEigenVectors_, bpp::DecompositionMethods::leftIEigenVectors_, bpp::DecompositionMethods::model_, bpp::MatrixTools::mult(), bpp::DecompositionMethods::nbStates_, bpp::DecompositionMethods::nbTypes_, bpp::DecompositionMethods::rightEigenVectors_, and bpp::DecompositionMethods::rightIEigenVectors_.

Referenced by bpp::DecompositionReward::alphabetIndexHasChanged(), bpp::DecompositionReward::DecompositionReward(), DecompositionSubstitutionCount(), distancesHaveChanged(), bpp::DecompositionReward::setSubstitutionModel(), setSubstitutionModel(), and substitutionRegisterHasChanged().

◆ distancesHaveChanged()

void DecompositionSubstitutionCount::distancesHaveChanged ( )

overrideprotectedvirtual

Implements bpp::AbstractSubstitutionDistance.

Definition at line 278 of file DecompositionSubstitutionCount.cpp.

References computeCounts_(), bpp::DecompositionMethods::computeProducts_(), currentLength_, bpp::AbstractSubstitutionDistance::distances_, bpp::DecompositionMethods::model_, bpp::AbstractSubstitutionCount::register_, and setDistanceBMatrices_().

◆ fillBMatrices_()

void DecompositionSubstitutionCount::fillBMatrices_ ( )

private

Definition at line 66 of file DecompositionSubstitutionCount.cpp.

References bpp::DecompositionMethods::bMatrices_, bpp::AbstractSubstitutionDistance::distances_, bpp::DecompositionMethods::model_, bpp::DecompositionMethods::nbStates_, bpp::AbstractSubstitutionCount::register_, and setDistanceBMatrices_().

Referenced by DecompositionSubstitutionCount(), setSubstitutionModel(), and substitutionRegisterHasChanged().

◆ getAllNumbersOfSubstitutions()

unique_ptr< Matrix< double > > DecompositionSubstitutionCount::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 134 of file DecompositionSubstitutionCount.cpp.

References computeCounts_(), counts_, currentLength_, bpp::DecompositionMethods::model_, and bpp::TextTools::toString().

◆ 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().

◆ getDistances()

std::shared_ptr<const AlphabetIndex2> bpp::AbstractSubstitutionDistance::getDistances ( ) const

inlinevirtualinherited

Implements bpp::SubstitutionDistance.

Definition at line 67 of file SubstitutionDistance.h.

References bpp::AbstractSubstitutionDistance::distances_.

◆ 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 DecompositionSubstitutionCount::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 179 of file DecompositionSubstitutionCount.cpp.

References computeCounts_(), counts_, currentLength_, bpp::DecompositionMethods::model_, and bpp::TextTools::toString().

◆ getNumberOfSubstitutionsPerType()

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

overridevirtual

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 196 of file DecompositionSubstitutionCount.cpp.

References computeCounts_(), counts_, currentLength_, bpp::SubstitutionCountInterface::getNumberOfSubstitutionTypes(), bpp::DecompositionMethods::model_, and bpp::TextTools::toString().

◆ 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(), 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_.

◆ getWeights()

std::shared_ptr<const AlphabetIndex2> bpp::AbstractWeightedSubstitutionCount::getWeights ( ) const

inlinevirtualinherited

Implements bpp::WeightedSubstitutionCount.

Definition at line 66 of file WeightedSubstitutionCount.h.

References bpp::AbstractWeightedSubstitutionCount::weights_.

◆ hasDistances()

bool bpp::AbstractSubstitutionDistance::hasDistances ( ) const

inlinevirtualinherited

Implements bpp::SubstitutionDistance.

Definition at line 66 of file SubstitutionDistance.h.

References bpp::AbstractSubstitutionDistance::distances_.

◆ 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_.

◆ hasWeights()

bool bpp::AbstractWeightedSubstitutionCount::hasWeights ( ) const

inlinevirtualinherited

Implements bpp::WeightedSubstitutionCount.

Definition at line 65 of file WeightedSubstitutionCount.h.

References bpp::AbstractWeightedSubstitutionCount::weights_.

◆ initBMatrices_()

void DecompositionMethods::initBMatrices_ ( )

protectedinherited

Definition at line 306 of file DecompositionMethods.cpp.

References bpp::DecompositionMethods::bMatrices_, bpp::DecompositionMethods::insideProducts_, bpp::DecompositionMethods::nbStates_, and bpp::DecompositionMethods::nbTypes_.

Referenced by bpp::DecompositionMethods::DecompositionMethods(), bpp::DecompositionReward::DecompositionReward(), DecompositionSubstitutionCount(), bpp::DecompositionMethods::initStates_(), bpp::DecompositionMethods::setSubstitutionModel(), and substitutionRegisterHasChanged().

◆ initCounts_()

void DecompositionSubstitutionCount::initCounts_ ( )

protected

Definition at line 54 of file DecompositionSubstitutionCount.cpp.

References counts_, bpp::DecompositionMethods::nbStates_, and bpp::AbstractSubstitutionCount::register_.

Referenced by DecompositionSubstitutionCount(), setSubstitutionModel(), and substitutionRegisterHasChanged().

◆ initStates_()

void DecompositionMethods::initStates_ ( )

protectedinherited

Definition at line 233 of file DecompositionMethods.cpp.

References bpp::DecompositionMethods::initBMatrices_(), bpp::DecompositionMethods::jMat_, bpp::DecompositionMethods::nbStates_, and RowMatrix< double >::resize().

Referenced by substitutionRegisterHasChanged().

◆ jFunction_() [1/2]

void DecompositionMethods::jFunction_	(	const std::vector< double > &	lambda,
		const std::vector< double > &	ilambda,
		double	t,
		RowMatrix< double > &	result,
		RowMatrix< double > &	iresult
	)		const

protectedinherited

Compute the integral part of the computation, in complex numbers.

Definition at line 135 of file DecompositionMethods.cpp.

References bpp::abs(), bpp::VectorTools::cos(), bpp::VectorTools::exp(), bpp::DecompositionMethods::nbStates_, bpp::VectorTools::sin(), and bpp::NumConstants::TINY().

◆ jFunction_() [2/2]

void DecompositionMethods::jFunction_	(	const std::vector< double > &	lambda,
		double	t,
		RowMatrix< double > &	result
	)		const

protectedinherited

Compute the integral part of the computation.

Definition at line 117 of file DecompositionMethods.cpp.

References bpp::abs(), bpp::VectorTools::exp(), bpp::DecompositionMethods::nbStates_, and bpp::NumConstants::TINY().

Referenced by bpp::DecompositionMethods::computeExpectations().

◆ operator=()

DecompositionSubstitutionCount& bpp::DecompositionSubstitutionCount::operator= ( const DecompositionSubstitutionCount & dsc )

inline

Definition at line 55 of file DecompositionSubstitutionCount.h.

References counts_, currentLength_, bpp::AbstractSubstitutionDistance::operator=(), bpp::AbstractWeightedSubstitutionCount::operator=(), and bpp::DecompositionMethods::operator=().

◆ setDistanceBMatrices_()

void DecompositionSubstitutionCount::setDistanceBMatrices_ ( )

private

Definition at line 88 of file DecompositionSubstitutionCount.cpp.

References bpp::DecompositionMethods::bMatrices_, bpp::AbstractSubstitutionDistance::distances_, bpp::DecompositionMethods::model_, bpp::DecompositionMethods::nbStates_, and bpp::AbstractSubstitutionCount::register_.

Referenced by distancesHaveChanged(), and fillBMatrices_().

◆ setDistances()

void AbstractSubstitutionDistance::setDistances ( std::shared_ptr< const AlphabetIndex2 > distances )

virtualinherited

Implements bpp::SubstitutionDistance.

Definition at line 9 of file SubstitutionDistance.cpp.

References bpp::AbstractSubstitutionDistance::distances_, and bpp::AbstractSubstitutionDistance::distancesHaveChanged().

◆ setSubstitutionModel()

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

overridevirtual

Set the substitution model.

Parameters

model A pointer toward the substitution model to use.

Implements bpp::SubstitutionCountInterface.

Definition at line 219 of file DecompositionSubstitutionCount.cpp.

References computeCounts_(), bpp::DecompositionMethods::computeProducts_(), currentLength_, fillBMatrices_(), initCounts_(), bpp::AbstractSubstitutionCount::register_, and bpp::DecompositionMethods::setSubstitutionModel().

◆ setSubstitutionRegister()

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

inlinevirtualinherited

attribution of a SubstitutionRegister

Parameters

reg	pointer to a SubstitutionRegister

Implements bpp::SubstitutionCountInterface.

Definition at line 164 of file SubstitutionCount.h.

References bpp::AbstractSubstitutionCount::register_, and bpp::AbstractSubstitutionCount::substitutionRegisterHasChanged().

◆ setWeights()

void AbstractWeightedSubstitutionCount::setWeights ( std::shared_ptr< const AlphabetIndex2 > weights )

virtualinherited

Implements bpp::WeightedSubstitutionCount.

Definition at line 9 of file WeightedSubstitutionCount.cpp.

References bpp::AbstractWeightedSubstitutionCount::weights_, and bpp::AbstractWeightedSubstitutionCount::weightsHaveChanged().

◆ storeAllNumbersOfSubstitutions()

void DecompositionSubstitutionCount::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 152 of file DecompositionSubstitutionCount.cpp.

References computeCounts_(), counts_, currentLength_, bpp::DecompositionMethods::model_, bpp::DecompositionMethods::nbStates_, and bpp::TextTools::toString().