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 (const ReversibleSubstitutionModel model, SubstitutionRegister reg, const AlphabetIndex2 *weights=0)

	DecompositionSubstitutionCount (const DecompositionSubstitutionCount &dsc)

DecompositionSubstitutionCount &	operator= (const DecompositionSubstitutionCount &dsc)

virtual	~DecompositionSubstitutionCount ()

DecompositionSubstitutionCount *	clone () const

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

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

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

void	setSubstitutionModel (const SubstitutionModel *model)
	Set the substitution model. More...

bool	hasSubstitutionRegister () const

void	setSubstitutionRegister (SubstitutionRegister *reg)
	attribution of a SubstitutionRegister More...

const SubstitutionRegister *	getSubstitutionRegister () const

SubstitutionRegister *	getSubstitutionRegister ()

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

virtual 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 (const AlphabetIndex2 *weights, bool ownWeights)

bool	hasWeights () const

const AlphabetIndex2 *	getWeights () const

Protected Member Functions
void	computeCounts_ (double length) const

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

void	substitutionRegisterHasChanged () throw (Exception)

void	weightsHaveChanged () throw (Exception)

Protected Attributes
std::auto_ptr< SubstitutionRegister >	register_

const AlphabetIndex2 *	weights_

bool	ownWeights_

Private Member Functions
void	resetStates_ ()

void	resetBMatrices_ ()

void	initBMatrices_ ()

void	fillBMatrices_ ()

void	computeEigen_ ()

void	computeProducts_ ()

Private Attributes
const ReversibleSubstitutionModel *	model_

size_t	nbStates_

RowMatrix< double >	jMat_

RowMatrix< double >	v_

RowMatrix< double >	vInv_

std::vector< double >	lambda_

std::vector< RowMatrix< double > >	bMatrices_

std::vector< RowMatrix< double > >	insideProducts_

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. Only reversible models are supported for now.

Author: Julien Dutheil

Definition at line 58 of file DecompositionSubstitutionCount.h.

Constructor & Destructor Documentation

◆ DecompositionSubstitutionCount() [1/2]

DecompositionSubstitutionCount::DecompositionSubstitutionCount	(	const ReversibleSubstitutionModel *	model,
		SubstitutionRegister *	reg,
		const AlphabetIndex2 *	weights = `0`
	)

Definition at line 50 of file DecompositionSubstitutionCount.cpp.

References computeEigen_(), computeProducts_(), fillBMatrices_(), bpp::SubstitutionRegister::getAlphabet(), bpp::SubstitutionModel::getAlphabet(), and initBMatrices_().

Referenced by clone().

◆ DecompositionSubstitutionCount() [2/2]

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

inline

Definition at line 74 of file DecompositionSubstitutionCount.h.

◆ ~DecompositionSubstitutionCount()

virtual bpp::DecompositionSubstitutionCount::~DecompositionSubstitutionCount ( )

inlinevirtual

Definition at line 106 of file DecompositionSubstitutionCount.h.

Member Function Documentation

◆ clone()

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

inlinevirtual

Implements bpp::SubstitutionCount.

Definition at line 108 of file DecompositionSubstitutionCount.h.

References DecompositionSubstitutionCount().

◆ computeCounts_()

void DecompositionSubstitutionCount::computeCounts_ ( double length ) const

protected

◆ computeEigen_()

void DecompositionSubstitutionCount::computeEigen_ ( )

private

Definition at line 93 of file DecompositionSubstitutionCount.cpp.

References bpp::SubstitutionModel::getColumnRightEigenVectors(), bpp::SubstitutionModel::getEigenValues(), bpp::SubstitutionModel::getRowLeftEigenVectors(), lambda_, model_, v_, and vInv_.

Referenced by DecompositionSubstitutionCount(), and setSubstitutionModel().

◆ computeProducts_()

void DecompositionSubstitutionCount::computeProducts_ ( )

private

Definition at line 100 of file DecompositionSubstitutionCount.cpp.

References bMatrices_, insideProducts_, nbStates_, bpp::AbstractSubstitutionCount::register_, v_, and vInv_.

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

◆ fillBMatrices_()

void DecompositionSubstitutionCount::fillBMatrices_ ( )

private

Definition at line 78 of file DecompositionSubstitutionCount.cpp.

References bMatrices_, bpp::SubstitutionModel::getAlphabetStates(), model_, nbStates_, bpp::SubstitutionModel::Qij(), and bpp::AbstractSubstitutionCount::register_.

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

◆ getAllNumbersOfSubstitutions()

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

virtual

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::SubstitutionCount.

Definition at line 182 of file DecompositionSubstitutionCount.cpp.

References computeCounts_(), counts_, and currentLength_.

◆ getAlphabet()

virtual const Alphabet* bpp::SubstitutionCount::getAlphabet ( ) const

inlinevirtualinherited

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

Returns: The alphabet associated to this substitution count.

Definition at line 112 of file SubstitutionCount.h.

References bpp::SubstitutionRegister::getAlphabet(), and bpp::SubstitutionCount::getSubstitutionRegister().

◆ getNumberOfStates()

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

inlinevirtualinherited

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

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

Definition at line 119 of file SubstitutionCount.h.

References bpp::SubstitutionRegister::getAlphabet(), and bpp::SubstitutionCount::getSubstitutionRegister().

◆ getNumberOfSubstitutions()

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

virtual

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::SubstitutionCount.

Definition at line 212 of file DecompositionSubstitutionCount.cpp.

References computeCounts_(), counts_, and currentLength_.

◆ getNumberOfSubstitutionsForEachType()

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

virtual

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::SubstitutionCount.

Definition at line 226 of file DecompositionSubstitutionCount.cpp.

References computeCounts_(), counts_, currentLength_, and bpp::SubstitutionCount::getNumberOfSubstitutionTypes().

◆ getNumberOfSubstitutionTypes()

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

inlinevirtualinherited

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

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

Definition at line 105 of file SubstitutionCount.h.

References bpp::SubstitutionRegister::getNumberOfSubstitutionTypes(), and bpp::SubstitutionCount::getSubstitutionRegister().

Referenced by bpp::NaiveSubstitutionCount::getNumberOfSubstitutionsForEachType(), bpp::UniformizationSubstitutionCount::getNumberOfSubstitutionsForEachType(), getNumberOfSubstitutionsForEachType(), and bpp::ProbabilisticSubstitutionMapping::getNumberOfSubstitutionTypes().

◆ getSubstitutionRegister() [1/2]

const SubstitutionRegister* 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::SubstitutionCount.

Definition at line 206 of file SubstitutionCount.h.

References bpp::AbstractSubstitutionCount::register_.

◆ getSubstitutionRegister() [2/2]

SubstitutionRegister* bpp::AbstractSubstitutionCount::getSubstitutionRegister ( )

inlinevirtualinherited

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

Implements bpp::SubstitutionCount.

Definition at line 208 of file SubstitutionCount.h.

References bpp::AbstractSubstitutionCount::register_.

◆ getWeights()

const AlphabetIndex2* bpp::AbstractWeightedSubstitutionCount::getWeights ( ) const

inlinevirtualinherited

Implements bpp::WeightedSubstitutionCount.

Definition at line 106 of file WeightedSubstitutionCount.h.

References bpp::AbstractWeightedSubstitutionCount::weights_.

◆ hasSubstitutionRegister()

bool bpp::AbstractSubstitutionCount::hasSubstitutionRegister ( ) const

inlinevirtualinherited

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

Implements bpp::SubstitutionCount.

Definition at line 192 of file SubstitutionCount.h.

References bpp::AbstractSubstitutionCount::register_.

◆ hasWeights()

bool bpp::AbstractWeightedSubstitutionCount::hasWeights ( ) const

inlinevirtualinherited

Implements bpp::WeightedSubstitutionCount.

Definition at line 105 of file WeightedSubstitutionCount.h.

References bpp::AbstractWeightedSubstitutionCount::weights_.

◆ initBMatrices_()

void DecompositionSubstitutionCount::initBMatrices_ ( )

private

Definition at line 126 of file DecompositionSubstitutionCount.cpp.

References bMatrices_, counts_, insideProducts_, nbStates_, and bpp::AbstractSubstitutionCount::register_.

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

◆ jFunction_()

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

protected

Definition at line 136 of file DecompositionSubstitutionCount.cpp.

References nbStates_.

Referenced by computeCounts_().

◆ operator=()

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

inline

Definition at line 89 of file DecompositionSubstitutionCount.h.

References bMatrices_, counts_, currentLength_, insideProducts_, jMat_, lambda_, model_, nbStates_, bpp::AbstractWeightedSubstitutionCount::operator=(), bpp::AbstractSubstitutionCount::operator=(), v_, and vInv_.

◆ resetBMatrices_()

void DecompositionSubstitutionCount::resetBMatrices_ ( )

private

Definition at line 110 of file DecompositionSubstitutionCount.cpp.

References bMatrices_, counts_, insideProducts_, and bpp::AbstractSubstitutionCount::register_.

Referenced by substitutionRegisterHasChanged().

◆ resetStates_()

void DecompositionSubstitutionCount::resetStates_ ( )

private

Definition at line 118 of file DecompositionSubstitutionCount.cpp.

References jMat_, lambda_, nbStates_, v_, and vInv_.

Referenced by setSubstitutionModel().

◆ setSubstitutionModel()

void DecompositionSubstitutionCount::setSubstitutionModel ( const SubstitutionModel * model )

virtual

Set the substitution model.

Parameters

model A pointer toward the substitution model to use. Only reversible models are currently supported. Setting a non-reversible model will throw an exception.

Implements bpp::SubstitutionCount.

Definition at line 244 of file DecompositionSubstitutionCount.cpp.

References computeCounts_(), computeEigen_(), computeProducts_(), currentLength_, fillBMatrices_(), bpp::SubstitutionModel::getAlphabet(), initBMatrices_(), model_, nbStates_, bpp::AbstractSubstitutionCount::register_, and resetStates_().