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, int cutOff)
	LaplaceSubstitutionCount (const LaplaceSubstitutionCount &asc)
LaplaceSubstitutionCount &	operator= (const LaplaceSubstitutionCount &asc)
virtual	~LaplaceSubstitutionCount ()
LaplaceSubstitutionCount *	clone () const
double	getNumberOfSubstitutions (int initialState, int 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.
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.
std::vector< double >	getNumberOfSubstitutionsForEachType (int initialState, int 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.
void	setSubstitutionModel (const SubstitutionModel *model)
	Set the substitution model associated with this count, if relevent.
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().
virtual const Alphabet *	getAlphabet () const
	Short cut function, equivalent to getSubstitutionRegister()->getAlphabet().
virtual size_t	getNumberOfStates () const
	Short cut function, equivalent to getSubstitutionRegister()->getAlphabet()->getSize().
Protected Member Functions
void	computeCounts (double length) const
void	substitutionRegisterHasChanged ()
Protected Attributes
SubstitutionRegister *	register_
Private Attributes
const SubstitutionModel *	model_
int	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

bpp::LaplaceSubstitutionCount::LaplaceSubstitutionCount	(	const SubstitutionModel *	model,
		int	cutOff
	)		`[inline]`

Definition at line 71 of file LaplaceSubstitutionCount.h.

Referenced by clone().

bpp::LaplaceSubstitutionCount::LaplaceSubstitutionCount ( const LaplaceSubstitutionCount & asc ) [inline]

Definition at line 79 of file LaplaceSubstitutionCount.h.

virtual bpp::LaplaceSubstitutionCount::~LaplaceSubstitutionCount ( ) [inline, virtual]

Definition at line 97 of file LaplaceSubstitutionCount.h.

Member Function Documentation

LaplaceSubstitutionCount* bpp::LaplaceSubstitutionCount::clone ( ) const [inline, virtual]

Implements bpp::SubstitutionCount.

Definition at line 99 of file LaplaceSubstitutionCount.h.

References LaplaceSubstitutionCount().

void LaplaceSubstitutionCount::computeCounts ( double length ) const [protected]

Definition at line 48 of file LaplaceSubstitutionCount.cpp.

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

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

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(), bpp::Alphabet::getSize(), m_, and model_.

virtual const Alphabet* bpp::SubstitutionCount::getAlphabet ( ) const [inline, virtual, inherited]

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().

virtual size_t bpp::SubstitutionCount::getNumberOfStates ( ) const [inline, virtual, inherited]

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(), bpp::Alphabet::getSize(), and bpp::SubstitutionCount::getSubstitutionRegister().

double LaplaceSubstitutionCount::getNumberOfSubstitutions	(	int	initialState,
		int	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().

std::vector<double> bpp::LaplaceSubstitutionCount::getNumberOfSubstitutionsForEachType	(	int	initialState,
		int	finalState,
		double	length
	)		const `[inline, 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 104 of file LaplaceSubstitutionCount.h.

References getNumberOfSubstitutions().

virtual size_t bpp::SubstitutionCount::getNumberOfSubstitutionTypes ( ) const [inline, virtual, inherited]

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().

const SubstitutionRegister* bpp::AbstractSubstitutionCount::getSubstitutionRegister ( ) const [inline, virtual, inherited]

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 209 of file SubstitutionCount.h.

References bpp::AbstractSubstitutionCount::register_.

SubstitutionRegister* bpp::AbstractSubstitutionCount::getSubstitutionRegister ( ) [inline, virtual, inherited]

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 211 of file SubstitutionCount.h.

References bpp::AbstractSubstitutionCount::register_.

bool bpp::AbstractSubstitutionCount::hasSubstitutionRegister ( ) const [inline, virtual, inherited]

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

Implements bpp::SubstitutionCount.

Definition at line 194 of file SubstitutionCount.h.

References bpp::AbstractSubstitutionCount::register_.

LaplaceSubstitutionCount& bpp::LaplaceSubstitutionCount::operator= ( const LaplaceSubstitutionCount & asc ) [inline]

Definition at line 87 of file LaplaceSubstitutionCount.h.

References currentLength_, cutOff_, m_, and model_.

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(), bpp::Alphabet::getSize(), m_, model_, and bpp::RowMatrix< Scalar >::resize().

void bpp::LaplaceSubstitutionCount::setSubstitutionRegister ( SubstitutionRegister * reg ) throw (Exception) [inline, virtual]

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.

Reimplemented from bpp::AbstractSubstitutionCount.

Definition at line 117 of file LaplaceSubstitutionCount.h.

void bpp::LaplaceSubstitutionCount::substitutionRegisterHasChanged ( ) [inline, protected, virtual]

Implements bpp::AbstractSubstitutionCount.

Definition at line 123 of file LaplaceSubstitutionCount.h.