bpp::KrKcSubstitutionRegister Class Reference

Count conservative and radical amino-acid substitutions. More...

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

Inheritance diagram for bpp::KrKcSubstitutionRegister:

Collaboration diagram for bpp::KrKcSubstitutionRegister:

Public Member Functions
	KrKcSubstitutionRegister (std::shared_ptr< const StateMapInterface > stateMap)
	KrKcSubstitutionRegister (std::shared_ptr< const StateMapInterface > stateMap, std::shared_ptr< const GeneticCode > genCode)
	KrKcSubstitutionRegister (const KrKcSubstitutionRegister &kreg)
KrKcSubstitutionRegister &	operator= (const KrKcSubstitutionRegister &kreg)
void	init ()
KrKcSubstitutionRegister *	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 StateMapInterface &	stateMap () const override
std::shared_ptr< const StateMapInterface >	getStateMap () const override
const Alphabet &	alphabet () const override
std::shared_ptr< const Alphabet >	getAlphabet () const override
const std::string &	getName () const override
	Get the name of the register. More...

Protected Attributes
std::shared_ptr< const StateMapInterface >	stateMap_
std::string	name_

Private Attributes
std::vector< std::vector< bool > >	types_
std::shared_ptr< const GeneticCode >	genCode_

Detailed Description

Count conservative and radical amino-acid substitutions.

Categories are defined as in Sainudiin et al (2005).

• 1 a conservative (C) substitution
• 2 a radical (R) substitution

Author

Jonathan Romiguier, Emeric Figuet, Julien Dutheil

Definition at line 1074 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

KrKcSubstitutionRegister() [1/3]

bpp::KrKcSubstitutionRegister::KrKcSubstitutionRegister ( std::shared_ptr< const StateMapInterface >  stateMap )

inline

Definition at line 1084 of file SubstitutionRegister.h.

References init().

Referenced by clone().

KrKcSubstitutionRegister() [2/3]

bpp::KrKcSubstitutionRegister::KrKcSubstitutionRegister ( std::shared_ptr< const StateMapInterface >  stateMap, std::shared_ptr< const GeneticCode >  genCode  )

inline

Definition at line 1092 of file SubstitutionRegister.h.

References init().

KrKcSubstitutionRegister() [3/3]

bpp::KrKcSubstitutionRegister::KrKcSubstitutionRegister ( const KrKcSubstitutionRegister &  kreg )

inline

Definition at line 1102 of file SubstitutionRegister.h.

Member Function Documentation

alphabet()

const Alphabet& bpp::AbstractSubstitutionRegister::alphabet ( ) const

inlineoverridevirtualinherited

Returns

The alphabet associated to this instance.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 133 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::stateMap_.

clone()

KrKcSubstitutionRegister* bpp::KrKcSubstitutionRegister::clone ( ) const

inlinevirtual

Implements bpp::SubstitutionRegisterInterface.

Definition at line 1219 of file SubstitutionRegister.h.

References KrKcSubstitutionRegister().

getAlphabet()

std::shared_ptr<const Alphabet> bpp::AbstractSubstitutionRegister::getAlphabet ( ) const

inlineoverridevirtualinherited

Returns

A shared_ptr toward the alphabet associated to this instance.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 135 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::stateMap_.

getName()

const std::string& bpp::AbstractSubstitutionRegister::getName ( ) const

inlineoverridevirtualinherited

Get the name of the register.

Returns

A string describing the register.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 137 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::name_.

getNumberOfSubstitutionTypes()

size_t bpp::KrKcSubstitutionRegister::getNumberOfSubstitutionTypes ( ) const

inlinevirtual

Returns

The number of substitution types supported by this class.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 1222 of file SubstitutionRegister.h.

getStateMap()

std::shared_ptr<const StateMapInterface> bpp::AbstractSubstitutionRegister::getStateMap ( ) const

inlineoverridevirtualinherited

Returns

A shared_ptr toward the state map associated to this instance.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 131 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::stateMap_.

getType()

size_t bpp::KrKcSubstitutionRegister::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::SubstitutionRegisterInterface.

Definition at line 1224 of file SubstitutionRegister.h.

References genCode_, bpp::StateMapInterface::getAlphabetStateAsInt(), bpp::AbstractSubstitutionRegister::stateMap(), and types_.

getTypeName()

std::string bpp::KrKcSubstitutionRegister::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::SubstitutionRegisterInterface.

Definition at line 1261 of file SubstitutionRegister.h.

init()

void bpp::KrKcSubstitutionRegister::init ( )

inline

Definition at line 1117 of file SubstitutionRegister.h.

References types_.

Referenced by KrKcSubstitutionRegister().

operator=()

KrKcSubstitutionRegister& bpp::KrKcSubstitutionRegister::operator= ( const KrKcSubstitutionRegister &  kreg )

inline

Definition at line 1108 of file SubstitutionRegister.h.

References genCode_, bpp::AbstractSubstitutionRegister::operator=(), and types_.

stateMap()

const StateMapInterface& bpp::AbstractSubstitutionRegister::stateMap ( ) const

inlineoverridevirtualinherited

Returns

The state map associated to this instance.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 129 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::stateMap_.

Referenced by bpp::VectorOfSubstitutionRegisters::addRegister(), bpp::ComprehensiveSubstitutionRegister::ComprehensiveSubstitutionRegister(), bpp::GCSynonymousSubstitutionRegister::getType(), bpp::GCPositionSubstitutionRegister::getType(), bpp::TsTvSubstitutionRegister::getType(), bpp::SWSubstitutionRegister::getType(), bpp::DnDsSubstitutionRegister::getType(), getType(), bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister(), bpp::CategorySubstitutionRegister::setAlphabetCategories(), bpp::CategorySubstitutionRegister::setModelCategories(), bpp::AAInteriorSubstitutionRegister::updateMatrix_(), and bpp::AAExteriorSubstitutionRegister::updateMatrix_().

Member Data Documentation

genCode_

std::shared_ptr<const GeneticCode> bpp::KrKcSubstitutionRegister::genCode_

private

Definition at line 1081 of file SubstitutionRegister.h.

Referenced by getType(), and operator=().

name_

std::string bpp::AbstractSubstitutionRegister::name_

protectedinherited

Definition at line 108 of file SubstitutionRegister.h.

Referenced by bpp::AbstractSubstitutionRegister::getName(), and bpp::AbstractSubstitutionRegister::operator=().

stateMap_

std::shared_ptr<const StateMapInterface> bpp::AbstractSubstitutionRegister::stateMap_

protectedinherited

Definition at line 107 of file SubstitutionRegister.h.

Referenced by bpp::AbstractSubstitutionRegister::alphabet(), bpp::AbstractSubstitutionRegister::getAlphabet(), bpp::AbstractSubstitutionRegister::getStateMap(), bpp::AbstractSubstitutionRegister::operator=(), and bpp::AbstractSubstitutionRegister::stateMap().

types_

std::vector< std::vector<bool> > bpp::KrKcSubstitutionRegister::types_

private

Definition at line 1078 of file SubstitutionRegister.h.

Referenced by getType(), init(), and operator=().

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

• Bpp/Phyl/Mapping/SubstitutionRegister.h