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

Indexes only substitutions between amino-acids. Groups are distinguished by their direction. More...

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

+ Inheritance diagram for bpp::AAExteriorSubstitutionRegister:
+ Collaboration diagram for bpp::AAExteriorSubstitutionRegister:

Public Member Functions

 AAExteriorSubstitutionRegister (std::shared_ptr< const StateMapInterface > stateMap, std::shared_ptr< const GeneticCode > genCode)
 
 AAExteriorSubstitutionRegister (const AAExteriorSubstitutionRegister &ais)
 
AAExteriorSubstitutionRegister & operator= (const AAExteriorSubstitutionRegister &ais)
 
AAExteriorSubstitutionRegister * clone () const
 
 ~AAExteriorSubstitutionRegister ()
 
std::string getTypeName (size_t type) const
 names of the types are their number. More...
 
size_t getType (size_t i, size_t j) const override
 Get the substitution type far a given pair of model states. More...
 
size_t getNumberOfSubstitutionTypes () const override
 
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

void updateMatrix_ ()
 
void updateTypes_ ()
 

Protected Attributes

size_t size_
 The size of the matrix, i.e. the number of states. More...
 
RowMatrix< size_t > matrix_
 The matrix of the substitution register. More...
 
std::map< size_t, std::map< size_t, std::vector< size_t > > > types_
 The map from substitution types to the map of from states to the vector of target states. More...
 
std::shared_ptr< const StateMapInterface > stateMap_
 
std::string name_
 

Private Attributes

std::map< std::string, size_t > categoryCorrespondance_
 
std::shared_ptr< const GeneticCode > genCode_
 

Detailed Description

Indexes only substitutions between amino-acids. Groups are distinguished by their direction.

Author
Juraj Michalik

Definition at line 644 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

◆ AAExteriorSubstitutionRegister() [1/2]

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

Definition at line 651 of file SubstitutionRegister.h.

References updateMatrix_(), and bpp::GeneralSubstitutionRegister::updateTypes_().

Referenced by clone().

◆ AAExteriorSubstitutionRegister() [2/2]

bpp::AAExteriorSubstitutionRegister::AAExteriorSubstitutionRegister ( const AAExteriorSubstitutionRegister &  ais)
inline

Definition at line 662 of file SubstitutionRegister.h.

◆ ~AAExteriorSubstitutionRegister()

bpp::AAExteriorSubstitutionRegister::~AAExteriorSubstitutionRegister ( )
inline

Definition at line 679 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()

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

Reimplemented from bpp::GeneralSubstitutionRegister.

Definition at line 677 of file SubstitutionRegister.h.

References AAExteriorSubstitutionRegister().

◆ 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::GeneralSubstitutionRegister::getNumberOfSubstitutionTypes ( ) const
inlineoverridevirtualinherited
Returns
The number of substitution types supported by this class.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 456 of file SubstitutionRegister.h.

References bpp::GeneralSubstitutionRegister::types_.

◆ 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::GeneralSubstitutionRegister::getType ( size_t  fromState,
size_t  toState 
) const
inlineoverridevirtualinherited

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.

Definition at line 451 of file SubstitutionRegister.h.

References bpp::GeneralSubstitutionRegister::matrix_.

◆ getTypeName()

std::string bpp::AAExteriorSubstitutionRegister::getTypeName ( size_t  type) const
inlinevirtual

names of the types are their number.

Reimplemented from bpp::GeneralSubstitutionRegister.

Definition at line 681 of file SubstitutionRegister.h.

References categoryCorrespondance_, bpp::TextTools::toString(), and bpp::GeneralSubstitutionRegister::types_.

◆ operator=()

AAExteriorSubstitutionRegister& bpp::AAExteriorSubstitutionRegister::operator= ( const AAExteriorSubstitutionRegister &  ais)
inline

Definition at line 668 of file SubstitutionRegister.h.

References categoryCorrespondance_, genCode_, and bpp::GeneralSubstitutionRegister::operator=().

◆ 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(), bpp::CategorySubstitutionRegister::setAlphabetCategories(), bpp::CategorySubstitutionRegister::setModelCategories(), bpp::AAInteriorSubstitutionRegister::updateMatrix_(), and updateMatrix_().

◆ updateMatrix_()

void bpp::AAExteriorSubstitutionRegister::updateMatrix_ ( )
inlineprotected

Definition at line 695 of file SubstitutionRegister.h.

References bpp::StateMapInterface::alphabet(), categoryCorrespondance_, genCode_, bpp::AlphabetState::getNum(), bpp::StateMapInterface::getNumberOfModelStates(), bpp::Alphabet::getStateAt(), bpp::GeneralSubstitutionRegister::matrix_, and bpp::AbstractSubstitutionRegister::stateMap().

Referenced by AAExteriorSubstitutionRegister().

◆ updateTypes_()

void GeneralSubstitutionRegister::updateTypes_ ( )
protectedinherited

Definition at line 10 of file SubstitutionRegister.cpp.

Referenced by AAExteriorSubstitutionRegister(), bpp::AAInteriorSubstitutionRegister::AAInteriorSubstitutionRegister(), bpp::GeneralSubstitutionRegister::GeneralSubstitutionRegister(), and bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister().

Member Data Documentation

◆ categoryCorrespondance_

std::map<std::string, size_t> bpp::AAExteriorSubstitutionRegister::categoryCorrespondance_
private

Definition at line 647 of file SubstitutionRegister.h.

Referenced by getTypeName(), operator=(), and updateMatrix_().

◆ genCode_

std::shared_ptr<const GeneticCode> bpp::AAExteriorSubstitutionRegister::genCode_
private

Definition at line 648 of file SubstitutionRegister.h.

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

◆ matrix_

RowMatrix<size_t> bpp::GeneralSubstitutionRegister::matrix_
protectedinherited

The matrix of the substitution register.

Definition at line 397 of file SubstitutionRegister.h.

Referenced by bpp::GeneralSubstitutionRegister::GeneralSubstitutionRegister(), bpp::GeneralSubstitutionRegister::getType(), bpp::GeneralSubstitutionRegister::operator=(), bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister(), bpp::AAInteriorSubstitutionRegister::updateMatrix_(), and updateMatrix_().

◆ name_

std::string bpp::AbstractSubstitutionRegister::name_
protectedinherited

Definition at line 108 of file SubstitutionRegister.h.

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

◆ size_

size_t bpp::GeneralSubstitutionRegister::size_
protectedinherited

The size of the matrix, i.e. the number of states.

Definition at line 392 of file SubstitutionRegister.h.

Referenced by bpp::GeneralSubstitutionRegister::GeneralSubstitutionRegister(), and bpp::GeneralSubstitutionRegister::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::map<size_t, std::map<size_t, std::vector<size_t> > > bpp::GeneralSubstitutionRegister::types_
protectedinherited

The map from substitution types to the map of from states to the vector of target states.

This is the reverse information of matrix_

Definition at line 405 of file SubstitutionRegister.h.

Referenced by bpp::GeneralSubstitutionRegister::getNumberOfSubstitutionTypes(), bpp::SelectedSubstitutionRegister::getTypeName(), bpp::AAInteriorSubstitutionRegister::getTypeName(), getTypeName(), bpp::GeneralSubstitutionRegister::getTypeName(), and bpp::GeneralSubstitutionRegister::operator=().

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