bpp::SubstitutionRegister Class Reference

The SubstitutionRegister interface. More...

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

Inheritance diagram for bpp::SubstitutionRegister:

Collaboration diagram for bpp::SubstitutionRegister:

List of all members.

Public Member Functions
	SubstitutionRegister ()
virtual	~SubstitutionRegister ()
virtual SubstitutionRegister *	clone () const =0
virtual const Alphabet *	getAlphabet () const =0
virtual size_t	getNumberOfSubstitutionTypes () const =0
virtual size_t	getType (int fromState, int toState) const =0
	Get the substitution type far a given pair of states.
virtual std::string	getTypeName (size_t type) const =0
	Get the name of a given substitution type.

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Detailed Description

The SubstitutionRegister interface.

Substitution registers are simple classes that define categories of substitutions, and assign them an index.

Author:

Julien Dutheil

Definition at line 63 of file SubstitutionRegister.h.

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Constructor & Destructor Documentation

bpp::SubstitutionRegister::SubstitutionRegister

(

)

[inline]

Definition at line 67 of file SubstitutionRegister.h.

virtual bpp::SubstitutionRegister::~SubstitutionRegister

(

)

[inline, virtual]

Definition at line 68 of file SubstitutionRegister.h.

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Member Function Documentation

virtual SubstitutionRegister* bpp::SubstitutionRegister::clone

(

)

const [pure virtual]

Implements bpp::Clonable.

Implemented in bpp::GCSynonymousSubstitutionRegister, bpp::DnDsSubstitutionRegister, bpp::TsTvSubstitutionRegister, bpp::GCSubstitutionRegister, bpp::ComprehensiveSubstitutionRegister, and bpp::TotalSubstitutionRegister.

Referenced by bpp::AbstractSubstitutionCount::operator=().

virtual const Alphabet* bpp::SubstitutionRegister::getAlphabet

(

)

const [pure virtual]

Returns:

The alphabet associated to this instance.

Implemented in bpp::AbstractSubstitutionRegister.

Referenced by bpp::DecompositionSubstitutionCount::DecompositionSubstitutionCount(), bpp::NaiveSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::SubstitutionCount::getAlphabet(), bpp::SubstitutionCount::getNumberOfStates(), bpp::LabelSubstitutionCount::LabelSubstitutionCount(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::DecompositionSubstitutionCount::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::substitutionRegisterHasChanged(), bpp::DecompositionSubstitutionCount::substitutionRegisterHasChanged(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), bpp::UniformizationSubstitutionCount::weightsHaveChanged(), and bpp::DecompositionSubstitutionCount::weightsHaveChanged().

virtual size_t bpp::SubstitutionRegister::getNumberOfSubstitutionTypes

(

)

const [pure virtual]

Returns:

The number of substitution types supported by this class.

Implemented in bpp::GCSynonymousSubstitutionRegister, bpp::DnDsSubstitutionRegister, bpp::TsTvSubstitutionRegister, bpp::TotalSubstitutionRegister, and bpp::CategorySubstitutionRegister.

Referenced by bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeProducts_(), bpp::MutationPath::getEventCounts(), bpp::SubstitutionCount::getNumberOfSubstitutionTypes(), bpp::SiteSimulationResult::getSubstitutionVector(), bpp::UniformizationSubstitutionCount::initBMatrices_(), bpp::DecompositionSubstitutionCount::initBMatrices_(), bpp::UniformizationSubstitutionCount::resetBMatrices_(), and bpp::DecompositionSubstitutionCount::resetBMatrices_().

virtual size_t bpp::SubstitutionRegister::getType	(	int	fromState,
		int	toState
	)		const [pure virtual]

Get the substitution type far a given pair of states.

Parameters:

fromState	Initial state (should be a state supported by the specified alphabet).
toState	Final state (should be a state supported by the specified alphabet).

Returns:

The index of the corresponding substitution type, ranging from 0 to 'getNumberOfSubstitutionTypes' + 1, as non-substitution (that is when fromState == toState) will always return 0.

Implemented in bpp::GCSynonymousSubstitutionRegister, bpp::DnDsSubstitutionRegister, bpp::TsTvSubstitutionRegister, bpp::TotalSubstitutionRegister, and bpp::CategorySubstitutionRegister.

Referenced by bpp::UniformizationSubstitutionCount::fillBMatrices_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::NaiveSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::MutationPath::getEventCounts(), and bpp::NaiveSubstitutionCount::getNumberOfSubstitutions().

virtual std::string bpp::SubstitutionRegister::getTypeName

(

size_t

type

)

const [pure virtual]

Get the name of a given substitution type.

This method is only used for user-friendlyness purposes, not computational goal. I can therefore be left unimplemented in some cases.

Parameters:

type	Index of the substitution (should be an size_t contained in the register).

Returns:

A string describing the substitution type.

Implemented in bpp::GCSynonymousSubstitutionRegister, bpp::DnDsSubstitutionRegister, bpp::TsTvSubstitutionRegister, bpp::TotalSubstitutionRegister, and bpp::CategorySubstitutionRegister.

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

• Bpp/Phyl/Mapping/SubstitutionRegister.h