Partial implementation of the SubstitutionDistance interface. More...

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

Inheritance diagram for bpp::AbstractSubstitutionDistance:

Collaboration diagram for bpp::AbstractSubstitutionDistance:

Public Member Functions
	AbstractSubstitutionDistance (std::shared_ptr< const AlphabetIndex2 > distances)

	AbstractSubstitutionDistance (const AbstractSubstitutionDistance &index)

AbstractSubstitutionDistance &	operator= (const AbstractSubstitutionDistance &index)

virtual	~AbstractSubstitutionDistance ()

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

bool	hasDistances () const

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

virtual SubstitutionCountInterface *	clone () const =0

virtual bool	hasSubstitutionRegister () const =0

virtual std::shared_ptr< const SubstitutionRegisterInterface >	getSubstitutionRegister () const =0

virtual void	setSubstitutionRegister (std::shared_ptr< const SubstitutionRegisterInterface > reg)=0

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...

virtual double	getNumberOfSubstitutions (size_t initialState, size_t finalState, double length, size_t type) const =0
	Get the number of susbstitutions on a branch, given the initial and final states, and the branch length. More...

virtual std::unique_ptr< Matrix< double > >	getAllNumbersOfSubstitutions (double length, size_t type) const =0
	Get the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length. More...

virtual void	storeAllNumbersOfSubstitutions (double length, size_t type, Eigen::MatrixXd &mat) const =0
	Stores the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length. More...

virtual std::vector< double >	getNumberOfSubstitutionsPerType (size_t initialState, size_t finalState, double length) const =0
	Get the numbers of susbstitutions on a branch for all types, for an initial and final states, given the branch length. More...

virtual void	setSubstitutionModel (std::shared_ptr< const SubstitutionModelInterface > model)=0
	Set the substitution model associated with this count, if relevant. More...

Protected Member Functions
virtual void	distancesHaveChanged ()=0

Protected Attributes
std::shared_ptr< const AlphabetIndex2 >	distances_

Detailed Description

Partial implementation of the SubstitutionDistance interface.

Definition at line 39 of file SubstitutionDistance.h.

Constructor & Destructor Documentation

◆ AbstractSubstitutionDistance() [1/2]

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

inline

Definition at line 46 of file SubstitutionDistance.h.

◆ AbstractSubstitutionDistance() [2/2]

bpp::AbstractSubstitutionDistance::AbstractSubstitutionDistance ( const AbstractSubstitutionDistance & index )

inline

Definition at line 50 of file SubstitutionDistance.h.

◆ ~AbstractSubstitutionDistance()

virtual bpp::AbstractSubstitutionDistance::~AbstractSubstitutionDistance ( )

inlinevirtual

Definition at line 61 of file SubstitutionDistance.h.

Member Function Documentation

◆ clone()

virtual SubstitutionCountInterface* bpp::SubstitutionCountInterface::clone ( ) const

pure virtualinherited

Implements bpp::Clonable.

Implemented in bpp::UniformizationSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::LabelSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::DecompositionSubstitutionCount.

Referenced by bpp::SubstitutionMappingTools::computeCounts().

◆ distancesHaveChanged()

virtual void bpp::AbstractSubstitutionDistance::distancesHaveChanged ( )

protectedpure virtual

Implemented in bpp::UniformizationSubstitutionCount, and bpp::DecompositionSubstitutionCount.

Referenced by setDistances().

◆ getAllNumbersOfSubstitutions()

virtual std::unique_ptr< Matrix<double> > bpp::SubstitutionCountInterface::getAllNumbersOfSubstitutions	(	double	length,
		size_t	type
	)		const

pure virtualinherited

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.

Implemented in bpp::UniformizationSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::LabelSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::DecompositionSubstitutionCount.

◆ 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

inlinevirtual

Implements bpp::SubstitutionDistance.

Definition at line 67 of file SubstitutionDistance.h.

References 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()

virtual double bpp::SubstitutionCountInterface::getNumberOfSubstitutions	(	size_t	initialState,
		size_t	finalState,
		double	length,
		size_t	type
	)		const

pure virtualinherited

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.

Implemented in bpp::UniformizationSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::LabelSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::DecompositionSubstitutionCount.

◆ getNumberOfSubstitutionsPerType()

virtual std::vector<double> bpp::SubstitutionCountInterface::getNumberOfSubstitutionsPerType	(	size_t	initialState,
		size_t	finalState,
		double	length
	)		const

pure virtualinherited

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.

Implemented in bpp::UniformizationSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::LabelSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::DecompositionSubstitutionCount.

◆ 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(), bpp::DecompositionSubstitutionCount::getNumberOfSubstitutionsPerType(), bpp::NaiveSubstitutionCount::getNumberOfSubstitutionsPerType(), and bpp::UniformizationSubstitutionCount::getNumberOfSubstitutionsPerType().

◆ getSubstitutionRegister()

virtual std::shared_ptr<const SubstitutionRegisterInterface> bpp::SubstitutionCountInterface::getSubstitutionRegister ( ) const

pure virtualinherited

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

Implemented in bpp::AbstractSubstitutionCount.

Referenced by bpp::SubstitutionCountInterface::getAlphabet(), bpp::SubstitutionCountInterface::getNumberOfStates(), and bpp::SubstitutionCountInterface::getNumberOfSubstitutionTypes().

◆ hasDistances()

bool bpp::AbstractSubstitutionDistance::hasDistances ( ) const

inlinevirtual

Implements bpp::SubstitutionDistance.

Definition at line 66 of file SubstitutionDistance.h.

References distances_.

◆ hasSubstitutionRegister()

virtual bool bpp::SubstitutionCountInterface::hasSubstitutionRegister ( ) const

pure virtualinherited

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

Implemented in bpp::AbstractSubstitutionCount.

◆ operator=()

AbstractSubstitutionDistance& bpp::AbstractSubstitutionDistance::operator= ( const AbstractSubstitutionDistance & index )

inline

Definition at line 54 of file SubstitutionDistance.h.

References distances_.

Referenced by bpp::DecompositionSubstitutionCount::operator=(), and bpp::UniformizationSubstitutionCount::operator=().

◆ setDistances()

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

virtual

Implements bpp::SubstitutionDistance.

Definition at line 9 of file SubstitutionDistance.cpp.

References distances_, and distancesHaveChanged().

◆ setSubstitutionModel()

virtual void bpp::SubstitutionCountInterface::setSubstitutionModel ( std::shared_ptr< const SubstitutionModelInterface > model )

pure virtualinherited

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

Parameters

model The substitution model to use with this count.

Implemented in bpp::UniformizationSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::LabelSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::DecompositionSubstitutionCount.

◆ setSubstitutionRegister()

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

pure virtualinherited

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.

Implemented in bpp::OneJumpSubstitutionCount, bpp::LabelSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::AbstractSubstitutionCount.

◆ storeAllNumbersOfSubstitutions()

virtual void bpp::SubstitutionCountInterface::storeAllNumbersOfSubstitutions	(	double	length,
		size_t	type,
		Eigen::MatrixXd &	mat
	)		const

pure virtualinherited

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.

Implemented in bpp::UniformizationSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::LabelSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::LaplaceSubstitutionCount, and bpp::DecompositionSubstitutionCount.

Member Data Documentation

◆ distances_

std::shared_ptr<const AlphabetIndex2> bpp::AbstractSubstitutionDistance::distances_

protected

Definition at line 43 of file SubstitutionDistance.h.

Referenced by bpp::DecompositionSubstitutionCount::distancesHaveChanged(), bpp::UniformizationSubstitutionCount::distancesHaveChanged(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::UniformizationSubstitutionCount::fillBMatrices_(), getDistances(), hasDistances(), operator=(), bpp::DecompositionSubstitutionCount::setDistanceBMatrices_(), bpp::UniformizationSubstitutionCount::setDistanceBMatrices_(), and setDistances().

The documentation for this class was generated from the following files:

Bpp/Phyl/Mapping/SubstitutionDistance.h
Bpp/Phyl/Mapping/SubstitutionDistance.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AbstractSubstitutionDistance() [1/2]

◆ AbstractSubstitutionDistance() [2/2]

◆ ~AbstractSubstitutionDistance()

Member Function Documentation

◆ clone()

◆ distancesHaveChanged()

◆ getAllNumbersOfSubstitutions()

◆ getAlphabet()

◆ getDistances()

◆ getNumberOfStates()

◆ getNumberOfSubstitutions()

◆ getNumberOfSubstitutionsPerType()

◆ getNumberOfSubstitutionTypes()

◆ getSubstitutionRegister()

◆ hasDistances()

◆ hasSubstitutionRegister()

◆ operator=()

◆ setDistances()

◆ setSubstitutionModel()

◆ setSubstitutionRegister()

◆ storeAllNumbersOfSubstitutions()

Member Data Documentation

◆ distances_