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 (const SubstitutionModel *model, size_t cutOff)

	LaplaceSubstitutionCount (const LaplaceSubstitutionCount &asc)

LaplaceSubstitutionCount &	operator= (const LaplaceSubstitutionCount &asc)

virtual	~LaplaceSubstitutionCount ()

LaplaceSubstitutionCount *	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...

void	setSubstitutionRegister (SubstitutionRegister *reg) throw (Exception)

bool	hasSubstitutionRegister () const

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...

Protected Member Functions
void	computeCounts (double length) const

void	substitutionRegisterHasChanged ()

Protected Attributes
std::auto_ptr< SubstitutionRegister >	register_

Private Attributes
const SubstitutionModel *	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 61 of file LaplaceSubstitutionCount.h.

Constructor & Destructor Documentation

◆ LaplaceSubstitutionCount() [1/2]

bpp::LaplaceSubstitutionCount::LaplaceSubstitutionCount	(	const SubstitutionModel *	model,
		size_t	cutOff
	)

inline

Definition at line 71 of file LaplaceSubstitutionCount.h.

Referenced by clone().

◆ LaplaceSubstitutionCount() [2/2]

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

inline

Definition at line 79 of file LaplaceSubstitutionCount.h.

◆ ~LaplaceSubstitutionCount()

virtual bpp::LaplaceSubstitutionCount::~LaplaceSubstitutionCount ( )

inlinevirtual

Definition at line 97 of file LaplaceSubstitutionCount.h.

Member Function Documentation

◆ clone()

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

inlinevirtual

Implements bpp::SubstitutionCount.

Definition at line 99 of file LaplaceSubstitutionCount.h.

References LaplaceSubstitutionCount().

◆ computeCounts()

void LaplaceSubstitutionCount::computeCounts ( double length ) const

protected

Definition at line 48 of file LaplaceSubstitutionCount.cpp.

References cutOff_, bpp::SubstitutionModel::getGenerator(), bpp::SubstitutionModel::getPij_t(), m_, and model_.

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

◆ getAllNumbersOfSubstitutions()

Matrix< double > * LaplaceSubstitutionCount::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 110 of file LaplaceSubstitutionCount.cpp.

References computeCounts(), currentLength_, bpp::SubstitutionModel::getAlphabet(), m_, and model_.

◆ 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 LaplaceSubstitutionCount::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 95 of file LaplaceSubstitutionCount.cpp.

References computeCounts(), currentLength_, and m_.

Referenced by getNumberOfSubstitutionsForEachType().

◆ getNumberOfSubstitutionsForEachType()

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

inlinevirtual

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 104 of file LaplaceSubstitutionCount.h.

References getNumberOfSubstitutions().

◆ 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(), 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_.

◆ 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_.

◆ operator=()

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

inline

Definition at line 87 of file LaplaceSubstitutionCount.h.

References currentLength_, cutOff_, m_, model_, and bpp::AbstractSubstitutionCount::operator=().

◆ setSubstitutionModel()

void LaplaceSubstitutionCount::setSubstitutionModel ( const SubstitutionModel * model )

virtual

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

Parameters

model The substitution model to use with this count.

Implements bpp::SubstitutionCount.

Definition at line 138 of file LaplaceSubstitutionCount.cpp.

References computeCounts(), currentLength_, bpp::SubstitutionModel::getAlphabet(), m_, and model_.

◆ setSubstitutionRegister()

void bpp::LaplaceSubstitutionCount::setSubstitutionRegister	(	SubstitutionRegister *	reg	)
throw	(	Exception
	)

inlinevirtual

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::SubstitutionCount.

Definition at line 117 of file LaplaceSubstitutionCount.h.