bpp-seq  2.2.0
Public Member Functions | List of all members
bpp::AlphabetIndex2 Class Referenceabstract

Two dimensionnal alphabet index interface. More...

#include <Bpp/Seq/AlphabetIndex/AlphabetIndex2.h>

+ Inheritance diagram for bpp::AlphabetIndex2:
+ Collaboration diagram for bpp::AlphabetIndex2:

Public Member Functions

 AlphabetIndex2 ()
 
virtual ~AlphabetIndex2 ()
 
virtual AlphabetIndex2 * clone () const =0
 
virtual double getIndex (int state1, int state2) const =0
 Get the index associated to a pair of states. More...
 
virtual double getIndex (const std::string &state1, const std::string &state2) const =0
 Get the index associated to a pair of states. More...
 
virtual const Alphabet * getAlphabet () const =0
 Get the alphabet associated to this index. More...
 
virtual Matrix< double > * getIndexMatrix () const =0
 
virtual bool isSymmetric () const =0
 

Detailed Description

Two dimensionnal alphabet index interface.

Derivatives of this interface implement distances between two states.

Definition at line 57 of file AlphabetIndex2.h.

Constructor & Destructor Documentation

◆ AlphabetIndex2()

bpp::AlphabetIndex2::AlphabetIndex2 ( )
inline

Definition at line 60 of file AlphabetIndex2.h.

◆ ~AlphabetIndex2()

virtual bpp::AlphabetIndex2::~AlphabetIndex2 ( )
inlinevirtual

Definition at line 61 of file AlphabetIndex2.h.

Member Function Documentation

◆ clone()

virtual AlphabetIndex2* bpp::AlphabetIndex2::clone ( ) const
pure virtual

Implemented in bpp::GranthamAAChemicalDistance, bpp::SimpleIndexDistance, bpp::DefaultNucleotideScore, bpp::BLOSUM50, bpp::MiyataAAChemicalDistance, bpp::AAIndex2Entry, and bpp::SimpleScore.

◆ getAlphabet()

virtual const Alphabet* bpp::AlphabetIndex2::getAlphabet ( ) const
pure virtual

Get the alphabet associated to this index.

Returns
Alphabet The alphabet associated to this index.

Implemented in bpp::GranthamAAChemicalDistance, bpp::MiyataAAChemicalDistance, bpp::SimpleIndexDistance, bpp::DefaultNucleotideScore, bpp::SimpleScore, bpp::BLOSUM50, and bpp::AAIndex2Entry.

◆ getIndex() [1/2]

virtual double bpp::AlphabetIndex2::getIndex ( int  state1,
int  state2 
) const
pure virtual

Get the index associated to a pair of states.

Parameters
state1First state to consider, as a int value.
state2Second state to consider, as a int value.
Returns
The index associated to the pair of states.

Implemented in bpp::GranthamAAChemicalDistance, bpp::MiyataAAChemicalDistance, bpp::DefaultNucleotideScore, bpp::SimpleScore, bpp::AAIndex2Entry, bpp::BLOSUM50, and bpp::SimpleIndexDistance.

◆ getIndex() [2/2]

virtual double bpp::AlphabetIndex2::getIndex ( const std::string &  state1,
const std::string &  state2 
) const
pure virtual

Get the index associated to a pair of states.

Parameters
state1First state to consider, as a string value.
state2Second state to consider, as a string value.
Returns
The index associated to the pair of states.

Implemented in bpp::GranthamAAChemicalDistance, bpp::MiyataAAChemicalDistance, bpp::AAIndex2Entry, bpp::DefaultNucleotideScore, bpp::SimpleScore, bpp::BLOSUM50, and bpp::SimpleIndexDistance.

◆ getIndexMatrix()

virtual Matrix<double>* bpp::AlphabetIndex2::getIndexMatrix ( ) const
pure virtual
Returns
A matrix object with all indices.

Implemented in bpp::GranthamAAChemicalDistance, bpp::AAIndex2Entry, bpp::MiyataAAChemicalDistance, bpp::SimpleIndexDistance, bpp::DefaultNucleotideScore, bpp::SimpleScore, and bpp::BLOSUM50.

◆ isSymmetric()

virtual bool bpp::AlphabetIndex2::isSymmetric ( ) const
pure virtual
Returns
True if the index is symatric (that is, index(i,j) == index(j, i)).

Implemented in bpp::GranthamAAChemicalDistance, bpp::SimpleIndexDistance, bpp::AAIndex2Entry, bpp::MiyataAAChemicalDistance, bpp::DefaultNucleotideScore, bpp::SimpleScore, and bpp::BLOSUM50.

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