bpp::TsTvSubstitutionRegister Class Reference

Distinguishes transitions from transversions. More...

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

Inheritance diagram for bpp::TsTvSubstitutionRegister:

Collaboration diagram for bpp::TsTvSubstitutionRegister:

Public Member Functions
	TsTvSubstitutionRegister (const NucleotideSubstitutionModel *model)
TsTvSubstitutionRegister *	clone () const
size_t	getNumberOfSubstitutionTypes () const
size_t	getType (size_t fromState, size_t toState) const
	Get the substitution type far a given pair of model states. More...
std::string	getTypeName (size_t type) const
	Get the name of a given substitution type. More...
const SubstitutionModel *	getSubstitutionModel () const
const Alphabet *	getAlphabet () const

Protected Attributes
const SubstitutionModel *	model_

Detailed Description

Distinguishes transitions from transversions.

This register has two substitution types, mapped as:

• 0 not a substitution
• 1 a transition
• 2 a transversion

Definition at line 806 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

TsTvSubstitutionRegister()

bpp::TsTvSubstitutionRegister::TsTvSubstitutionRegister ( const NucleotideSubstitutionModel *  model )

inline

Definition at line 810 of file SubstitutionRegister.h.

Referenced by clone().

Member Function Documentation

clone()

TsTvSubstitutionRegister* bpp::TsTvSubstitutionRegister::clone ( ) const

inlinevirtual

Implements bpp::SubstitutionRegister.

Definition at line 814 of file SubstitutionRegister.h.

References TsTvSubstitutionRegister().

getAlphabet()

const Alphabet* bpp::AbstractSubstitutionRegister::getAlphabet ( ) const

inlinevirtualinherited

Returns

The alphabet associated to this instance.

Implements bpp::SubstitutionRegister.

Definition at line 147 of file SubstitutionRegister.h.

References bpp::SubstitutionModel::getAlphabet(), and bpp::AbstractSubstitutionRegister::model_.

getNumberOfSubstitutionTypes()

size_t bpp::TsTvSubstitutionRegister::getNumberOfSubstitutionTypes ( ) const

inlinevirtual

Returns

The number of substitution types supported by this class.

Implements bpp::SubstitutionRegister.

Definition at line 817 of file SubstitutionRegister.h.

getSubstitutionModel()

const SubstitutionModel* bpp::AbstractSubstitutionRegister::getSubstitutionModel ( ) const

inlinevirtualinherited

Returns

The substitution model associated to this instance.

Implements bpp::SubstitutionRegister.

Definition at line 145 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::model_.

getType()

size_t bpp::TsTvSubstitutionRegister::getType ( size_t  fromState, size_t  toState  ) const

inlinevirtual

Get the substitution type far a given pair of model 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.

Implements bpp::SubstitutionRegister.

Definition at line 819 of file SubstitutionRegister.h.

References bpp::SubstitutionModel::getAlphabetStateAsInt(), and bpp::AbstractSubstitutionRegister::model_.

getTypeName()

std::string bpp::TsTvSubstitutionRegister::getTypeName ( size_t  type ) const

inlinevirtual

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.

Implements bpp::SubstitutionRegister.

Definition at line 833 of file SubstitutionRegister.h.

Member Data Documentation

model_

const SubstitutionModel* bpp::AbstractSubstitutionRegister::model_

protectedinherited

Definition at line 125 of file SubstitutionRegister.h.

Referenced by bpp::AbstractSubstitutionRegister::getAlphabet(), bpp::CategorySubstitutionRegister::getCategory(), bpp::AbstractSubstitutionRegister::getSubstitutionModel(), bpp::CategorySubstitutionRegister::getType(), getType(), bpp::DnDsSubstitutionRegister::getType(), bpp::GCSynonymousSubstitutionRegister::getType(), bpp::AbstractSubstitutionRegister::operator=(), bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister(), and bpp::CategorySubstitutionRegister::setCategories().

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

• Bpp/Phyl/Mapping/SubstitutionRegister.h