Interface allowing for using distances between states in substitution counts. More...

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

Inheritance diagram for bpp::SubstitutionDistance:

Collaboration diagram for bpp::SubstitutionDistance:

Public Member Functions
virtual void	setDistances (std::shared_ptr< const AlphabetIndex2 > index)=0

virtual bool	hasDistances () const =0

virtual std::shared_ptr< const AlphabetIndex2 >	getDistances () const =0

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...

Detailed Description

Interface allowing for using distances between states in substitution counts.

These distances are used for integration of substitution distances before the mapping process (see WeightedSubstitutionCount for weight on the final counts, after the mapping process).

Definition at line 27 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().

◆ 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()

virtual std::shared_ptr<const AlphabetIndex2> bpp::SubstitutionDistance::getDistances ( ) const

pure virtual

Implemented in bpp::AbstractSubstitutionDistance.

◆ 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()

virtual bool bpp::SubstitutionDistance::hasDistances ( ) const

pure virtual

Implemented in bpp::AbstractSubstitutionDistance.

◆ 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.

◆ setDistances()

virtual void bpp::SubstitutionDistance::setDistances ( std::shared_ptr< const AlphabetIndex2 > index )

pure virtual

Implemented in bpp::AbstractSubstitutionDistance.

◆ 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.

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

Bpp/Phyl/Mapping/SubstitutionDistance.h

Public Member Functions

Detailed Description

Member Function Documentation

◆ clone()

◆ getAllNumbersOfSubstitutions()

◆ getAlphabet()

◆ getDistances()

◆ getNumberOfStates()

◆ getNumberOfSubstitutions()

◆ getNumberOfSubstitutionsPerType()

◆ getNumberOfSubstitutionTypes()

◆ getSubstitutionRegister()

◆ hasDistances()

◆ hasSubstitutionRegister()

◆ setDistances()

◆ setSubstitutionModel()

◆ setSubstitutionRegister()

◆ storeAllNumbersOfSubstitutions()