bpp-phyl3  3.0.0
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
bpp::ComprehensiveSubstitutionRegister Class Reference

Distinguishes all types of substitutions. More...

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

+ Inheritance diagram for bpp::ComprehensiveSubstitutionRegister:
+ Collaboration diagram for bpp::ComprehensiveSubstitutionRegister:

Public Member Functions

 ComprehensiveSubstitutionRegister (std::shared_ptr< const StateMapInterface > stateMap, bool within=false)
 
ComprehensiveSubstitutionRegister * clone () const
 
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...
 

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

Distinguishes all types of substitutions.

This register has all n * (n-1) substitution type, where n is the size of the alphabet, mapped as:

  • 0 not a substitution
  • x in [1, n(n-1)] a substitution

Definition at line 217 of file CategorySubstitutionRegister.h.

Constructor & Destructor Documentation

◆ ComprehensiveSubstitutionRegister()

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

Definition at line 221 of file CategorySubstitutionRegister.h.

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

Referenced by clone().

Member Function Documentation

◆ allowWithin()

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

Definition at line 177 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::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()

ComprehensiveSubstitutionRegister* bpp::ComprehensiveSubstitutionRegister::clone ( ) const
inlinevirtual

Implements bpp::SubstitutionRegisterInterface.

Definition at line 232 of file CategorySubstitutionRegister.h.

References 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
inlinevirtualinherited

Definition at line 137 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::categories_.

◆ getCategoryFrom()

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

Definition at line 142 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::nbCategories_, bpp::CategorySubstitutionRegister::revIndex_, and bpp::CategorySubstitutionRegister::within_.

Referenced by bpp::CategorySubstitutionRegister::getTypeName().

◆ getCategoryName()

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

Definition at line 172 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::categoryNames_.

Referenced by bpp::CategorySubstitutionRegister::getTypeName().

◆ getCategoryTo()

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

Definition at line 157 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::nbCategories_, bpp::CategorySubstitutionRegister::revIndex_, and bpp::CategorySubstitutionRegister::within_.

Referenced by bpp::CategorySubstitutionRegister::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
inlineinherited

Definition at line 189 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::nbCategories_.

◆ getNumberOfSubstitutionTypes()

size_t bpp::CategorySubstitutionRegister::getNumberOfSubstitutionTypes ( ) const
inlinevirtualinherited
Returns
The number of substitution types supported by this class.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 191 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::nbCategories_, and bpp::CategorySubstitutionRegister::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
inlinevirtualinherited

Get the substitution type far a given pair of model states.

Parameters
fromStateInitial state (should be a state supported by the specified alphabet).
toStateFinal 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 bpp::CategorySubstitutionRegister::categories_, and bpp::CategorySubstitutionRegister::index_.

◆ getTypeName()

std::string bpp::CategorySubstitutionRegister::getTypeName ( size_t  type) const
inlinevirtualinherited

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
typeIndex 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 bpp::CategorySubstitutionRegister::getCategoryFrom(), bpp::CategorySubstitutionRegister::getCategoryName(), and bpp::CategorySubstitutionRegister::getCategoryTo().

◆ isStationary()

bool bpp::CategorySubstitutionRegister::isStationary ( ) const
inlineinherited

Definition at line 179 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::stationarity_.

◆ setAlphabetCategories()

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

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)
inlineprotectedinherited

Definition at line 75 of file CategorySubstitutionRegister.h.

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

◆ setStationarity()

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

Definition at line 184 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::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(), ComprehensiveSubstitutionRegister(), bpp::GCSynonymousSubstitutionRegister::getType(), bpp::GCPositionSubstitutionRegister::getType(), bpp::TsTvSubstitutionRegister::getType(), bpp::SWSubstitutionRegister::getType(), bpp::DnDsSubstitutionRegister::getType(), bpp::KrKcSubstitutionRegister::getType(), bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister(), bpp::CategorySubstitutionRegister::setAlphabetCategories(), bpp::CategorySubstitutionRegister::setModelCategories(), bpp::AAInteriorSubstitutionRegister::updateMatrix_(), and bpp::AAExteriorSubstitutionRegister::updateMatrix_().

Member Data Documentation

◆ categories_

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

Definition at line 31 of file CategorySubstitutionRegister.h.

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

◆ categoryNames_

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

Definition at line 32 of file CategorySubstitutionRegister.h.

Referenced by bpp::CategorySubstitutionRegister::getCategoryName(), and bpp::CategorySubstitutionRegister::setModelCategories().

◆ index_

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

Definition at line 33 of file CategorySubstitutionRegister.h.

Referenced by bpp::CategorySubstitutionRegister::getType(), bpp::GCSynonymousSubstitutionRegister::getType(), bpp::GCPositionSubstitutionRegister::getType(), and bpp::CategorySubstitutionRegister::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_
protectedinherited

Definition at line 30 of file CategorySubstitutionRegister.h.

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

◆ revIndex_

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

Definition at line 34 of file CategorySubstitutionRegister.h.

Referenced by bpp::CategorySubstitutionRegister::getCategoryFrom(), bpp::CategorySubstitutionRegister::getCategoryTo(), and bpp::CategorySubstitutionRegister::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_
protectedinherited

Definition at line 36 of file CategorySubstitutionRegister.h.

Referenced by bpp::CategorySubstitutionRegister::isStationary(), and bpp::CategorySubstitutionRegister::setStationarity().

◆ within_

bool bpp::CategorySubstitutionRegister::within_
protectedinherited

Definition at line 29 of file CategorySubstitutionRegister.h.

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

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