bpp::AlphabetIndex2 Class Reference

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 std::shared_ptr< const Alphabet >	getAlphabet () const =0
	Get the alphabet associated to this index. More...
virtual const Alphabet &	alphabet () const =0
	Get the alphabet associated to this index. More...
virtual const 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 25 of file AlphabetIndex2.h.

Constructor & Destructor Documentation

AlphabetIndex2()

bpp::AlphabetIndex2::AlphabetIndex2 ( )

inline

Definition at line 28 of file AlphabetIndex2.h.

~AlphabetIndex2()

virtual bpp::AlphabetIndex2::~AlphabetIndex2 ( )

inlinevirtual

Definition at line 29 of file AlphabetIndex2.h.

Member Function Documentation

alphabet()

virtual const Alphabet& bpp::AlphabetIndex2::alphabet ( ) const

pure virtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implemented in bpp::SimpleScore, bpp::SimpleIndexDistance, bpp::DefaultNucleotideScore, bpp::CodonFromProteicAlphabetIndex2, bpp::ProteicAlphabetIndex2, and bpp::UserAlphabetIndex2.

clone()

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

pure virtual

Implements bpp::Clonable.

Implemented in bpp::ProteicAlphabetIndex2, bpp::SimpleScore, bpp::SimpleIndexDistance, bpp::MiyataAAChemicalDistance, bpp::GranthamAAChemicalDistance, bpp::DefaultNucleotideScore, bpp::CodonFromProteicAlphabetIndex2, bpp::BLOSUM50, bpp::AAIndex2Entry, and bpp::UserAlphabetIndex2.

getAlphabet()

virtual std::shared_ptr<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::SimpleScore, bpp::SimpleIndexDistance, bpp::DefaultNucleotideScore, bpp::CodonFromProteicAlphabetIndex2, bpp::ProteicAlphabetIndex2, and bpp::UserAlphabetIndex2.

Referenced by bpp::SiteContainerTools::alignNW().

getIndex() [1/2]

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

state1	First state to consider, as a string value.
state2	Second state to consider, as a string value.

Returns

The index associated to the pair of states.

Implemented in bpp::SimpleScore, bpp::SimpleIndexDistance, bpp::MiyataAAChemicalDistance, bpp::GranthamAAChemicalDistance, bpp::DefaultNucleotideScore, bpp::CodonFromProteicAlphabetIndex2, bpp::BLOSUM50, bpp::AAIndex2Entry, and bpp::UserAlphabetIndex2.

getIndex() [2/2]

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

pure virtual

Get the index associated to a pair of states.

Parameters

state1	First state to consider, as a int value in the Alphabet
state2	Second state to consider, as a int value in the Alphabet

Returns

The index associated to the pair of states.

Implemented in bpp::SimpleScore, bpp::SimpleIndexDistance, bpp::MiyataAAChemicalDistance, bpp::GranthamAAChemicalDistance, bpp::DefaultNucleotideScore, bpp::CodonFromProteicAlphabetIndex2, bpp::BLOSUM50, bpp::AAIndex2Entry, and bpp::UserAlphabetIndex2.

Referenced by bpp::SiteContainerTools::alignNW().

getIndexMatrix()

virtual const Matrix<double>& bpp::AlphabetIndex2::getIndexMatrix ( ) const

pure virtual

Returns

A matrix object with all indices.

Implemented in bpp::SimpleScore, bpp::SimpleIndexDistance, bpp::MiyataAAChemicalDistance, bpp::GranthamAAChemicalDistance, bpp::DefaultNucleotideScore, bpp::CodonFromProteicAlphabetIndex2, bpp::BLOSUM50, bpp::AAIndex2Entry, and bpp::UserAlphabetIndex2.

isSymmetric()

virtual bool bpp::AlphabetIndex2::isSymmetric ( ) const

pure virtual

Returns

True if the index is symetric (that is, index(i,j) == index(j, i)).

Implemented in bpp::SimpleScore, bpp::SimpleIndexDistance, bpp::MiyataAAChemicalDistance, bpp::GranthamAAChemicalDistance, bpp::DefaultNucleotideScore, bpp::CodonFromProteicAlphabetIndex2, bpp::BLOSUM50, bpp::AAIndex2Entry, and bpp::UserAlphabetIndex2.

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

• Bpp/Seq/AlphabetIndex/AlphabetIndex2.h