bpp::CategorySubstitutionRegister Class Reference

The CategorySubstitutionRegisters. More...

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

Inheritance diagram for bpp::CategorySubstitutionRegister:

Collaboration diagram for bpp::CategorySubstitutionRegister:

Public Member Functions
	CategorySubstitutionRegister (std::shared_ptr< const StateMapInterface > stateMap, bool within=false)
	Build a new substitution register with categories. This class is meant to be inherited. More...
virtual size_t	getCategory (size_t state) const
virtual size_t	getCategoryFrom (size_t type) const
virtual size_t	getCategoryTo (size_t type) const
virtual std::string	getCategoryName (size_t category) const
virtual bool	allowWithin () const
bool	isStationary () const
void	setStationarity (bool stat)
size_t	getNumberOfCategories () const
size_t	getNumberOfSubstitutionTypes () const
virtual 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...
virtual SubstitutionRegisterInterface *	clone () const =0

Protected Member Functions
template<class T >
void	setAlphabetCategories (const std::map< int, T > &categories)
template<class T >
void	setModelCategories (const std::map< size_t, T > &categories)

Protected Attributes
bool	within_
size_t	nbCategories_
std::map< size_t, size_t >	categories_
std::vector< std::string >	categoryNames_
std::vector< std::vector< size_t > >	index_
std::vector< std::vector< size_t > >	revIndex_
bool	stationarity_
std::shared_ptr< const StateMapInterface >	stateMap_
std::string	name_

Detailed Description

The CategorySubstitutionRegisters.

Author

Julien Dutheil

Gather states into defined categories, and count the changes between categories.

Optionally allows for within categories substitutions.

Definition at line 25 of file CategorySubstitutionRegister.h.

Constructor & Destructor Documentation

CategorySubstitutionRegister()

bpp::CategorySubstitutionRegister::CategorySubstitutionRegister ( std::shared_ptr< const StateMapInterface >  stateMap, bool  within = false  )

inline

Build a new substitution register with categories. This class is meant to be inherited.

Parameters

stateMap	The stateMap defining the states.
within	Specifies if within categories substitutions should be counted as well.

Definition at line 45 of file CategorySubstitutionRegister.h.

Member Function Documentation

allowWithin()

virtual bool bpp::CategorySubstitutionRegister::allowWithin ( ) const

inlinevirtual

Definition at line 177 of file CategorySubstitutionRegister.h.

References within_.

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()

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

pure virtualinherited

Implements bpp::Clonable.

Implemented in bpp::GeneralSubstitutionRegister, bpp::VectorOfSubstitutionRegisters, bpp::CompleteSubstitutionRegister, bpp::TotalSubstitutionRegister, bpp::KrKcSubstitutionRegister, bpp::DnDsSubstitutionRegister, bpp::SWSubstitutionRegister, bpp::TsTvSubstitutionRegister, bpp::AAExteriorSubstitutionRegister, bpp::AAInteriorSubstitutionRegister, bpp::SelectedSubstitutionRegister, bpp::GCPositionSubstitutionRegister, bpp::GCSynonymousSubstitutionRegister, bpp::GCSubstitutionRegister, and bpp::ComprehensiveSubstitutionRegister.

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_.

getCategory()

virtual size_t bpp::CategorySubstitutionRegister::getCategory ( size_t  state ) const

inlinevirtual

Definition at line 137 of file CategorySubstitutionRegister.h.

References categories_.

getCategoryFrom()

virtual size_t bpp::CategorySubstitutionRegister::getCategoryFrom ( size_t  type ) const

inlinevirtual

Definition at line 142 of file CategorySubstitutionRegister.h.

References nbCategories_, revIndex_, and within_.

Referenced by getTypeName().

getCategoryName()

virtual std::string bpp::CategorySubstitutionRegister::getCategoryName ( size_t  category ) const

inlinevirtual

Definition at line 172 of file CategorySubstitutionRegister.h.

References categoryNames_.

Referenced by getTypeName().

getCategoryTo()

virtual size_t bpp::CategorySubstitutionRegister::getCategoryTo ( size_t  type ) const

inlinevirtual

Definition at line 157 of file CategorySubstitutionRegister.h.

References nbCategories_, revIndex_, and within_.

Referenced by getTypeName().

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_.

getNumberOfCategories()

size_t bpp::CategorySubstitutionRegister::getNumberOfCategories ( ) const

inline

Definition at line 189 of file CategorySubstitutionRegister.h.

References nbCategories_.

getNumberOfSubstitutionTypes()

size_t bpp::CategorySubstitutionRegister::getNumberOfSubstitutionTypes ( ) const

inlinevirtual

Returns

The number of substitution types supported by this class.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 191 of file CategorySubstitutionRegister.h.

References nbCategories_, and within_.

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()

virtual size_t bpp::CategorySubstitutionRegister::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.

Reimplemented in bpp::GCPositionSubstitutionRegister, and bpp::GCSynonymousSubstitutionRegister.

Definition at line 193 of file CategorySubstitutionRegister.h.

References categories_, and index_.

getTypeName()

std::string bpp::CategorySubstitutionRegister::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.

Reimplemented in bpp::GCPositionSubstitutionRegister, and bpp::GCSynonymousSubstitutionRegister.

Definition at line 203 of file CategorySubstitutionRegister.h.

References getCategoryFrom(), getCategoryName(), and getCategoryTo().

isStationary()

bool bpp::CategorySubstitutionRegister::isStationary ( ) const

inline

Definition at line 179 of file CategorySubstitutionRegister.h.

References stationarity_.

setAlphabetCategories()

template<class T >

void bpp::CategorySubstitutionRegister::setAlphabetCategories ( const std::map< int, T > &  categories )

inlineprotected

Definition at line 58 of file CategorySubstitutionRegister.h.

References bpp::StateMapInterface::getModelStates(), and bpp::AbstractSubstitutionRegister::stateMap().

setModelCategories()

template<class T >

void bpp::CategorySubstitutionRegister::setModelCategories ( const std::map< size_t, T > &  categories )

inlineprotected

Definition at line 75 of file CategorySubstitutionRegister.h.

References categories_, categoryNames_, count(), bpp::StateMapInterface::getNumberOfModelStates(), bpp::StateMapInterface::getStateDescription(), index_, nbCategories_, revIndex_, bpp::AbstractSubstitutionRegister::stateMap(), and within_.

setStationarity()

void bpp::CategorySubstitutionRegister::setStationarity ( bool  stat )

inline

Definition at line 184 of file CategorySubstitutionRegister.h.

References stationarity_.

Referenced by bpp::PhylogeneticsApplicationTools::getSubstitutionRegister().

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(), bpp::KrKcSubstitutionRegister::getType(), bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister(), setAlphabetCategories(), setModelCategories(), bpp::AAInteriorSubstitutionRegister::updateMatrix_(), and bpp::AAExteriorSubstitutionRegister::updateMatrix_().

Member Data Documentation

categories_

std::map<size_t, size_t> bpp::CategorySubstitutionRegister::categories_

mutableprotected

Definition at line 31 of file CategorySubstitutionRegister.h.

Referenced by getCategory(), getType(), bpp::GCSynonymousSubstitutionRegister::getType(), bpp::GCPositionSubstitutionRegister::getType(), and setModelCategories().

categoryNames_

std::vector<std::string> bpp::CategorySubstitutionRegister::categoryNames_

protected

Definition at line 32 of file CategorySubstitutionRegister.h.

Referenced by getCategoryName(), and setModelCategories().

index_

std::vector< std::vector<size_t> > bpp::CategorySubstitutionRegister::index_

protected

Definition at line 33 of file CategorySubstitutionRegister.h.

Referenced by getType(), bpp::GCSynonymousSubstitutionRegister::getType(), bpp::GCPositionSubstitutionRegister::getType(), and setModelCategories().

name_

std::string bpp::AbstractSubstitutionRegister::name_

protectedinherited

Definition at line 108 of file SubstitutionRegister.h.

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

nbCategories_

size_t bpp::CategorySubstitutionRegister::nbCategories_

protected

Definition at line 30 of file CategorySubstitutionRegister.h.

Referenced by getCategoryFrom(), getCategoryTo(), getNumberOfCategories(), getNumberOfSubstitutionTypes(), and setModelCategories().

revIndex_

std::vector< std::vector<size_t> > bpp::CategorySubstitutionRegister::revIndex_

protected

Definition at line 34 of file CategorySubstitutionRegister.h.

Referenced by getCategoryFrom(), getCategoryTo(), and setModelCategories().

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().

stationarity_

bool bpp::CategorySubstitutionRegister::stationarity_

protected

Definition at line 36 of file CategorySubstitutionRegister.h.

Referenced by isStationary(), and setStationarity().

within_

bool bpp::CategorySubstitutionRegister::within_

protected

Definition at line 29 of file CategorySubstitutionRegister.h.

Referenced by allowWithin(), getCategoryFrom(), getCategoryTo(), getNumberOfSubstitutionTypes(), and setModelCategories().

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

• Bpp/Phyl/Mapping/CategorySubstitutionRegister.h