Naive substitution count. More...

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

Inheritance diagram for bpp::NaiveSubstitutionCount:

Collaboration diagram for bpp::NaiveSubstitutionCount:

Public Member Functions
	NaiveSubstitutionCount (const SubstitutionModel model, SubstitutionRegister reg, bool allowSelf=false, const AlphabetIndex2 *weights=0)
	Build a new simple substitution count. More...

virtual	~NaiveSubstitutionCount ()

NaiveSubstitutionCount *	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...

bool	hasSubstitutionRegister () const

void	setSubstitutionRegister (SubstitutionRegister *reg)
	attribution of a SubstitutionRegister More...

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...

void	setWeights (const AlphabetIndex2 *weights, bool ownWeights)

bool	hasWeights () const

const AlphabetIndex2 *	getWeights () const

Protected Attributes
std::auto_ptr< SubstitutionRegister >	register_

const AlphabetIndex2 *	weights_

bool	ownWeights_

Private Member Functions
void	substitutionRegisterHasChanged ()

void	weightsHaveChanged ()

Private Attributes
bool	allowSelf_

std::vector< int >	supportedChars_

Detailed Description

Naive substitution count.

This substitution count is defined as follow:

0 if ,
1 if $i \neq j$ .

Reference (for instance): Tufféry P, Darlu P. Exploring a phylogenetic approach for the detection of correlated substitutions in proteins. Mol Biol Evol. 2000 Nov;17(11):1753-9

Author: Julien Dutheil

Definition at line 64 of file NaiveSubstitutionCount.h.

Constructor & Destructor Documentation

◆ NaiveSubstitutionCount()

bpp::NaiveSubstitutionCount::NaiveSubstitutionCount	(	const SubstitutionModel *	model,
		SubstitutionRegister *	reg,
		bool	allowSelf = `false`,
		const AlphabetIndex2 *	weights = `0`
	)

inline

Build a new simple substitution count.

Parameters

model	The substitution model for which this substitution count is parametrized. The model is not used in the calculation, only for specifying the modeled states.
reg	A pointer toward a substitution register object which discribes the type of substitutions to map.
allowSelf	Tells if "self" mutations, from X to X should be counted together with the ones of type X to Y where X and Y are in the same category, if relevent. The default is "no", to be consistent with other types of substitution counts which account for multiple substitutions, in which case it does not make sense to count "X to X".
weights	the weights of the counts

Definition at line 83 of file NaiveSubstitutionCount.h.

Referenced by clone().

◆ ~NaiveSubstitutionCount()

virtual bpp::NaiveSubstitutionCount::~NaiveSubstitutionCount ( )

inlinevirtual

Definition at line 89 of file NaiveSubstitutionCount.h.

Member Function Documentation

◆ clone()

NaiveSubstitutionCount* bpp::NaiveSubstitutionCount::clone ( ) const

inlinevirtual

Implements bpp::SubstitutionCount.

Definition at line 91 of file NaiveSubstitutionCount.h.

References NaiveSubstitutionCount().

◆ getAllNumbersOfSubstitutions()

Matrix< double > * NaiveSubstitutionCount::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 44 of file NaiveSubstitutionCount.cpp.

References bpp::AbstractSubstitutionCount::register_, supportedChars_, and bpp::AbstractWeightedSubstitutionCount::weights_.

◆ 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 bpp::NaiveSubstitutionCount::getNumberOfSubstitutions	(	size_t	initialState,
		size_t	finalState,
		double	length,
		size_t	type = `1`
	)		const

inlinevirtual

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 94 of file NaiveSubstitutionCount.h.

References allowSelf_, bpp::AbstractSubstitutionCount::register_, supportedChars_, and bpp::AbstractWeightedSubstitutionCount::weights_.

Referenced by getNumberOfSubstitutionsForEachType().

◆ getNumberOfSubstitutionsForEachType()

std::vector<double> bpp::NaiveSubstitutionCount::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 107 of file NaiveSubstitutionCount.h.

References getNumberOfSubstitutions(), and bpp::SubstitutionCount::getNumberOfSubstitutionTypes().

◆ 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 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_.