bpp-phyl  2.4.0
bpp::SubstitutionRegister Class Referenceabstract

The SubstitutionRegister interface. More...

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

+ Inheritance diagram for bpp::SubstitutionRegister:
+ Collaboration diagram for bpp::SubstitutionRegister:

Public Member Functions

 SubstitutionRegister ()
 
virtual ~SubstitutionRegister ()
 
virtual SubstitutionRegisterclone () const =0
 
virtual const AlphabetgetAlphabet () const =0
 
virtual const SubstitutionModelgetSubstitutionModel () const =0
 
virtual size_t getNumberOfSubstitutionTypes () const =0
 
virtual const std::string & getName () const =0
 Get the name of the register. More...
 
virtual size_t getType (size_t fromState, size_t toState) const =0
 Get the substitution type far a given pair of model states. More...
 
virtual std::string getTypeName (size_t type) const =0
 Get the name of a given substitution type. More...
 

Detailed Description

The SubstitutionRegister interface.

Substitution registers are simple classes that define categories of substitutions, and assign an index to them. Substitution registers are defined according to a given substitution model.

Author
Julien Dutheil

Definition at line 74 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

bpp::SubstitutionRegister::SubstitutionRegister ( )
inline

Definition at line 78 of file SubstitutionRegister.h.

virtual bpp::SubstitutionRegister::~SubstitutionRegister ( )
inlinevirtual

Member Function Documentation

virtual const std::string& bpp::SubstitutionRegister::getName ( ) const
pure virtual

Get the name of the register.

Returns
A string describing the register.

Implemented in bpp::AbstractSubstitutionRegister.

Referenced by ~SubstitutionRegister().

virtual const SubstitutionModel* bpp::SubstitutionRegister::getSubstitutionModel ( ) const
pure virtual
Returns
The substitution model associated to this instance.

Implemented in bpp::AbstractSubstitutionRegister.

Referenced by bpp::VectorOfSubstitionRegisters::addRegister(), and ~SubstitutionRegister().

virtual size_t bpp::SubstitutionRegister::getType ( size_t  fromState,
size_t  toState 
) const
pure virtual

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