Analytical (weighted) substitution count using the uniformization method. More...

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

Inheritance diagram for bpp::UniformizationSubstitutionCount:

Collaboration diagram for bpp::UniformizationSubstitutionCount:

Public Member Functions
	UniformizationSubstitutionCount (const SubstitutionModel model, SubstitutionRegister reg, const AlphabetIndex2 *weights=0)

	UniformizationSubstitutionCount (const UniformizationSubstitutionCount &usc)

UniformizationSubstitutionCount &	operator= (const UniformizationSubstitutionCount &usc)

virtual	~UniformizationSubstitutionCount ()

UniformizationSubstitutionCount *	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 associated with this count, if relevent. 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	substitutionRegisterHasChanged () throw (Exception)

void	weightsHaveChanged () throw (Exception)

Protected Attributes
std::auto_ptr< SubstitutionRegister >	register_

const AlphabetIndex2 *	weights_

bool	ownWeights_

Private Member Functions
void	resetBMatrices_ ()

void	initBMatrices_ ()

void	fillBMatrices_ ()

Private Attributes
const SubstitutionModel *	model_

size_t	nbStates_

std::vector< RowMatrix< double > >	bMatrices_

std::vector< RowMatrix< double > >	power_

std::vector< std::vector< RowMatrix< double > > >	s_

double	miu_

std::vector< RowMatrix< double > >	counts_

double	currentLength_

Detailed Description

Analytical (weighted) substitution count using the uniformization method.

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

Author: Julien Dutheil

Definition at line 57 of file UniformizationSubstitutionCount.h.

Constructor & Destructor Documentation

◆ UniformizationSubstitutionCount() [1/2]

UniformizationSubstitutionCount::UniformizationSubstitutionCount	(	const SubstitutionModel *	model,
		SubstitutionRegister *	reg,
		const AlphabetIndex2 *	weights = `0`
	)

Definition at line 51 of file UniformizationSubstitutionCount.cpp.

References fillBMatrices_(), bpp::SubstitutionRegister::getAlphabet(), bpp::SubstitutionModel::getAlphabet(), initBMatrices_(), miu_, model_, nbStates_, and bpp::SubstitutionModel::Qij().

Referenced by clone().

◆ UniformizationSubstitutionCount() [2/2]

bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount ( const UniformizationSubstitutionCount & usc )

inline

Definition at line 74 of file UniformizationSubstitutionCount.h.

◆ ~UniformizationSubstitutionCount()

virtual bpp::UniformizationSubstitutionCount::~UniformizationSubstitutionCount ( )

inlinevirtual

Definition at line 102 of file UniformizationSubstitutionCount.h.

Member Function Documentation

◆ clone()

UniformizationSubstitutionCount* bpp::UniformizationSubstitutionCount::clone ( ) const

inlinevirtual

Implements bpp::SubstitutionCount.

Definition at line 104 of file UniformizationSubstitutionCount.h.

References UniformizationSubstitutionCount().

◆ computeCounts_()

void UniformizationSubstitutionCount::computeCounts_ ( double length ) const

protected

◆ fillBMatrices_()

void UniformizationSubstitutionCount::fillBMatrices_ ( )

private

Definition at line 103 of file UniformizationSubstitutionCount.cpp.

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

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

◆ getAllNumbersOfSubstitutions()

Matrix< double > * UniformizationSubstitutionCount::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 178 of file UniformizationSubstitutionCount.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 UniformizationSubstitutionCount::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 192 of file UniformizationSubstitutionCount.cpp.

References computeCounts_(), counts_, and currentLength_.

◆ getNumberOfSubstitutionsForEachType()

std::vector< double > UniformizationSubstitutionCount::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 206 of file UniformizationSubstitutionCount.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(), getNumberOfSubstitutionsForEachType(), bpp::DecompositionSubstitutionCount::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_.