The SubstitutionsCount interface. More...

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

Inheritance diagram for bpp::SubstitutionCount:

Collaboration diagram for bpp::SubstitutionCount:

Public Member Functions
	SubstitutionCount ()

virtual	~SubstitutionCount ()

virtual SubstitutionCount *	clone () const =0

virtual bool	hasSubstitutionRegister () const =0

virtual const SubstitutionRegister *	getSubstitutionRegister () const =0

virtual SubstitutionRegister *	getSubstitutionRegister ()=0

virtual void	setSubstitutionRegister (SubstitutionRegister *reg)=0

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...

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 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 std::vector< double >	getNumberOfSubstitutionsForEachType (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 (const SubstitutionModel *model)=0
	Set the substitution model associated with this count, if relevent. More...

Detailed Description

The SubstitutionsCount interface.

Provide a method to compute the $n_{x,y}(t)$ function, namely the number of substitutions on a branch of length $t$ , with initial state $x$ and final state $y$ .

The new implementation offers to perform several counts simultaneously, distinguishing between different types of substitutions. Therefore substitution count object takes as input a SubstitutionRegister, which describes all types of substitutions and associate them with an index. All counts can be retrieved in one go as a vector, the type serving as an indice.

Author: Julien Dutheil

See: 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. Epub 2005 Jun 8.

Definition at line 70 of file SubstitutionCount.h.

Constructor & Destructor Documentation

◆ SubstitutionCount()

bpp::SubstitutionCount::SubstitutionCount ( )

inline

Definition at line 74 of file SubstitutionCount.h.

◆ ~SubstitutionCount()

virtual bpp::SubstitutionCount::~SubstitutionCount ( )

inlinevirtual

Definition at line 75 of file SubstitutionCount.h.

Member Function Documentation

◆ clone()

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

pure virtual

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

◆ getAllNumbersOfSubstitutions()

virtual Matrix<double>* bpp::SubstitutionCount::getAllNumbersOfSubstitutions	(	double	length,
		size_t	type
	)		const

pure 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.

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

◆ getAlphabet()

virtual const Alphabet* bpp::SubstitutionCount::getAlphabet ( ) const

inlinevirtual

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 getSubstitutionRegister().

◆ getNumberOfStates()

virtual size_t bpp::SubstitutionCount::getNumberOfStates ( ) const

inlinevirtual

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 getSubstitutionRegister().

◆ getNumberOfSubstitutions()

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

pure 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.

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

◆ getNumberOfSubstitutionsForEachType()

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

pure 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.

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

◆ getNumberOfSubstitutionTypes()

virtual size_t bpp::SubstitutionCount::getNumberOfSubstitutionTypes ( ) const

inlinevirtual

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 getSubstitutionRegister().

Referenced by bpp::NaiveSubstitutionCount::getNumberOfSubstitutionsForEachType(), bpp::UniformizationSubstitutionCount::getNumberOfSubstitutionsForEachType(), bpp::DecompositionSubstitutionCount::getNumberOfSubstitutionsForEachType(), and bpp::ProbabilisticSubstitutionMapping::getNumberOfSubstitutionTypes().

◆ getSubstitutionRegister() [1/2]

virtual const SubstitutionRegister* bpp::SubstitutionCount::getSubstitutionRegister ( ) const

pure virtual

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 getAlphabet(), getNumberOfStates(), and getNumberOfSubstitutionTypes().

◆ getSubstitutionRegister() [2/2]

virtual SubstitutionRegister* bpp::SubstitutionCount::getSubstitutionRegister ( )

pure virtual

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.

◆ hasSubstitutionRegister()

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

pure virtual

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

Implemented in bpp::AbstractSubstitutionCount.

◆ setSubstitutionModel()

virtual void bpp::SubstitutionCount::setSubstitutionModel ( const SubstitutionModel * model )

pure virtual

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

Parameters

model The substitution model to use with this count.

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

◆ setSubstitutionRegister()

virtual void bpp::SubstitutionCount::setSubstitutionRegister ( SubstitutionRegister * reg )

pure 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.

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

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

Bpp/Phyl/Mapping/SubstitutionCount.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ SubstitutionCount()

◆ ~SubstitutionCount()

Member Function Documentation

◆ clone()

◆ getAllNumbersOfSubstitutions()

◆ getAlphabet()

◆ getNumberOfStates()

◆ getNumberOfSubstitutions()

◆ getNumberOfSubstitutionsForEachType()

◆ getNumberOfSubstitutionTypes()

◆ getSubstitutionRegister() [1/2]

◆ getSubstitutionRegister() [2/2]

◆ hasSubstitutionRegister()

◆ setSubstitutionModel()

◆ setSubstitutionRegister()