bpp-phyl  2.2.0
Public Member Functions | Protected Attributes | Private Attributes | List of all members
bpp::CompleteSubstitutionRegister Class Reference

Completion of a given substitution register to consider all substitutions. The new substitutions are considered in an additional type. More...

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

+ Inheritance diagram for bpp::CompleteSubstitutionRegister:
+ Collaboration diagram for bpp::CompleteSubstitutionRegister:

Public Member Functions

 CompleteSubstitutionRegister (const SubstitutionRegister &reg)
 
CompleteSubstitutionRegister * clone () const
 
 CompleteSubstitutionRegister (const CompleteSubstitutionRegister &csr)
 
CompleteSubstitutionRegister & operator= (const CompleteSubstitutionRegister &csr)
 
 ~CompleteSubstitutionRegister ()
 
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_
 

Private Attributes

const SubstitutionRegister * preg_
 
bool isRegComplete_
 

Detailed Description

Completion of a given substitution register to consider all substitutions. The new substitutions are considered in an additional type.

Definition at line 359 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

◆ CompleteSubstitutionRegister() [1/2]

bpp::CompleteSubstitutionRegister::CompleteSubstitutionRegister ( const SubstitutionRegister &  reg)
inline

Definition at line 368 of file SubstitutionRegister.h.

References bpp::SubstitutionRegister::getAlphabet(), bpp::SubstitutionRegister::getType(), and isRegComplete_.

Referenced by clone().

◆ CompleteSubstitutionRegister() [2/2]

bpp::CompleteSubstitutionRegister::CompleteSubstitutionRegister ( const CompleteSubstitutionRegister &  csr)
inline

Definition at line 389 of file SubstitutionRegister.h.

◆ ~CompleteSubstitutionRegister()

bpp::CompleteSubstitutionRegister::~CompleteSubstitutionRegister ( )
inline

Definition at line 403 of file SubstitutionRegister.h.

References preg_.

Member Function Documentation

◆ clone()

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

Implements bpp::SubstitutionRegister.

Definition at line 387 of file SubstitutionRegister.h.

References CompleteSubstitutionRegister().

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

Implements bpp::SubstitutionRegister.

Definition at line 411 of file SubstitutionRegister.h.

References bpp::SubstitutionRegister::getNumberOfSubstitutionTypes(), isRegComplete_, and preg_.

Referenced by getType(), and getTypeName().

◆ 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::CompleteSubstitutionRegister::getType ( size_t  fromState,
size_t  toState 
) const
inlinevirtual

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::SubstitutionRegister.

Definition at line 416 of file SubstitutionRegister.h.

References getNumberOfSubstitutionTypes(), bpp::SubstitutionRegister::getType(), and preg_.

◆ getTypeName()

std::string bpp::CompleteSubstitutionRegister::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
typeIndex 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 425 of file SubstitutionRegister.h.

References getNumberOfSubstitutionTypes(), bpp::SubstitutionRegister::getTypeName(), and preg_.

◆ operator=()

CompleteSubstitutionRegister& bpp::CompleteSubstitutionRegister::operator= ( const CompleteSubstitutionRegister &  csr)
inline

Definition at line 395 of file SubstitutionRegister.h.

References bpp::SubstitutionRegister::clone(), isRegComplete_, bpp::AbstractSubstitutionRegister::operator=(), and preg_.

Member Data Documentation

◆ isRegComplete_

bool bpp::CompleteSubstitutionRegister::isRegComplete_
private

Definition at line 365 of file SubstitutionRegister.h.

Referenced by CompleteSubstitutionRegister(), getNumberOfSubstitutionTypes(), and operator=().

◆ 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(), bpp::TsTvSubstitutionRegister::getType(), bpp::DnDsSubstitutionRegister::getType(), bpp::GCSynonymousSubstitutionRegister::getType(), bpp::AbstractSubstitutionRegister::operator=(), bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister(), and bpp::CategorySubstitutionRegister::setCategories().

◆ preg_

const SubstitutionRegister* bpp::CompleteSubstitutionRegister::preg_
private

Definition at line 363 of file SubstitutionRegister.h.

Referenced by getNumberOfSubstitutionTypes(), getType(), getTypeName(), operator=(), and ~CompleteSubstitutionRegister().

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