bpp::ProteicAlphabetIndex2 Class Reference

Virtual AlphabetIndex2 for proteic alphabet. More...

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

Inheritance diagram for bpp::ProteicAlphabetIndex2:

Collaboration diagram for bpp::ProteicAlphabetIndex2:

Public Member Functions
	ProteicAlphabetIndex2 ()
virtual	~ProteicAlphabetIndex2 ()
virtual ProteicAlphabetIndex2 *	clone () const override=0
	ProteicAlphabetIndex2 (const ProteicAlphabetIndex2 &pt)
ProteicAlphabetIndex2 &	operator= (const ProteicAlphabetIndex2 &pt)
std::shared_ptr< const Alphabet >	getAlphabet () const override
	Get the alphabet associated to this index. More...
const Alphabet &	alphabet () const override
	Get the alphabet associated to this index. More...
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 Matrix< double > &	getIndexMatrix () const =0
virtual bool	isSymmetric () const =0

Private Attributes
std::shared_ptr< const ProteicAlphabet >	alpha_

Detailed Description

Virtual AlphabetIndex2 for proteic alphabet.

Definition at line 80 of file AlphabetIndex2.h.

Constructor & Destructor Documentation

ProteicAlphabetIndex2() [1/2]

bpp::ProteicAlphabetIndex2::ProteicAlphabetIndex2 ( )

inline

Definition at line 87 of file AlphabetIndex2.h.

~ProteicAlphabetIndex2()

virtual bpp::ProteicAlphabetIndex2::~ProteicAlphabetIndex2 ( )

inlinevirtual

Definition at line 88 of file AlphabetIndex2.h.

ProteicAlphabetIndex2() [2/2]

bpp::ProteicAlphabetIndex2::ProteicAlphabetIndex2 ( const ProteicAlphabetIndex2 &  pt )

inline

Definition at line 92 of file AlphabetIndex2.h.

Member Function Documentation

alphabet()

const Alphabet& bpp::ProteicAlphabetIndex2::alphabet ( ) const

inlineoverridevirtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex2.

Definition at line 104 of file AlphabetIndex2.h.

References alpha_.

clone()

virtual ProteicAlphabetIndex2* bpp::ProteicAlphabetIndex2::clone ( ) const

overridepure virtual

Implements bpp::AlphabetIndex2.

Implemented in bpp::MiyataAAChemicalDistance, bpp::GranthamAAChemicalDistance, bpp::BLOSUM50, and bpp::AAIndex2Entry.

getAlphabet()

std::shared_ptr<const Alphabet> bpp::ProteicAlphabetIndex2::getAlphabet ( ) const

inlineoverridevirtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex2.

Definition at line 102 of file AlphabetIndex2.h.

References alpha_.

Referenced by bpp::AAIndex2Entry::getIndex(), bpp::BLOSUM50::getIndex(), bpp::GranthamAAChemicalDistance::getIndex(), and bpp::MiyataAAChemicalDistance::getIndex().

getIndex() [1/2]

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

pure virtualinherited

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 virtualinherited

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 virtualinherited

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 virtualinherited

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.

operator=()

ProteicAlphabetIndex2& bpp::ProteicAlphabetIndex2::operator= ( const ProteicAlphabetIndex2 &  pt )

inline

Definition at line 96 of file AlphabetIndex2.h.

References alpha_.

Referenced by bpp::AAIndex2Entry::operator=(), bpp::BLOSUM50::operator=(), bpp::GranthamAAChemicalDistance::operator=(), and bpp::MiyataAAChemicalDistance::operator=().

Member Data Documentation

alpha_

std::shared_ptr<const ProteicAlphabet> bpp::ProteicAlphabetIndex2::alpha_

private

Definition at line 84 of file AlphabetIndex2.h.

Referenced by alphabet(), getAlphabet(), and operator=().

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

• Bpp/Seq/AlphabetIndex/AlphabetIndex2.h