BLOSUM 50 Substitution Matrix. More...

#include <Bpp/Seq/AlphabetIndex/BLOSUM50.h>

Inheritance diagram for bpp::BLOSUM50:

Collaboration diagram for bpp::BLOSUM50:

Public Member Functions
	BLOSUM50 ()

	BLOSUM50 (const BLOSUM50 &blosum)

BLOSUM50 &	operator= (const BLOSUM50 &blosum)

BLOSUM50 *	clone () const override

virtual	~BLOSUM50 ()

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...

Methods from the AlphabetIndex2 interface.
double	getIndex (int state1, int state2) const override
	Get the index associated to a pair of states. More...

double	getIndex (const std::string &state1, const std::string &state2) const override
	Get the index associated to a pair of states. More...

const Matrix< double > &	getIndexMatrix () const override

bool	isSymmetric () const override

Private Attributes
LinearMatrix< double >	distanceMatrix_

std::shared_ptr< const ProteicAlphabet >	alpha_

Detailed Description

BLOSUM 50 Substitution Matrix.

Reference: Henikoff, S. and Henikoff, J.G. Amino acid substitution matrices from protein blocks Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992)

Data from AAIndex2 database, Accession Number HENS920104.

Definition at line 29 of file BLOSUM50.h.

Constructor & Destructor Documentation

◆ BLOSUM50() [1/2]

BLOSUM50::BLOSUM50 ( )

Definition at line 14 of file BLOSUM50.cpp.

Referenced by clone().

◆ BLOSUM50() [2/2]

bpp::BLOSUM50::BLOSUM50 ( const BLOSUM50 & blosum )

inline

Definition at line 38 of file BLOSUM50.h.

◆ ~BLOSUM50()

virtual bpp::BLOSUM50::~BLOSUM50 ( )

inlinevirtual

Definition at line 52 of file BLOSUM50.h.

Member Function Documentation

◆ alphabet()

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

inlineoverridevirtualinherited

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 bpp::ProteicAlphabetIndex2::alpha_.

◆ clone()

BLOSUM50* bpp::BLOSUM50::clone ( ) const

inlineoverridevirtual

Implements bpp::ProteicAlphabetIndex2.

Definition at line 50 of file BLOSUM50.h.

References BLOSUM50().

◆ getAlphabet()

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

inlineoverridevirtualinherited

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 bpp::ProteicAlphabetIndex2::alpha_.

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

◆ getIndex() [1/2]

double BLOSUM50::getIndex	(	const std::string &	state1,
		const std::string &	state2
	)		const

overridevirtual

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.

Implements bpp::AlphabetIndex2.

Definition at line 26 of file BLOSUM50.cpp.

References distanceMatrix_, and bpp::ProteicAlphabetIndex2::getAlphabet().

◆ getIndex() [2/2]

double BLOSUM50::getIndex	(	int	state1,
		int	state2
	)		const

overridevirtual

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.

Implements bpp::AlphabetIndex2.

Definition at line 21 of file BLOSUM50.cpp.

References distanceMatrix_, and bpp::ProteicAlphabetIndex2::getAlphabet().

◆ getIndexMatrix()

const Matrix< double > & BLOSUM50::getIndexMatrix ( ) const

overridevirtual

Returns: A matrix object with all indices.

Implements bpp::AlphabetIndex2.

Definition at line 31 of file BLOSUM50.cpp.

References distanceMatrix_.

◆ isSymmetric()

bool bpp::BLOSUM50::isSymmetric ( ) const

inlineoverridevirtual

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

Implements bpp::AlphabetIndex2.

Definition at line 63 of file BLOSUM50.h.

◆ operator=()

BLOSUM50& bpp::BLOSUM50::operator= ( const BLOSUM50 & blosum )

inline

Definition at line 43 of file BLOSUM50.h.

References distanceMatrix_, and bpp::ProteicAlphabetIndex2::operator=().

Member Data Documentation

◆ alpha_

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

privateinherited

Definition at line 84 of file AlphabetIndex2.h.

Referenced by bpp::ProteicAlphabetIndex2::alphabet(), bpp::ProteicAlphabetIndex2::getAlphabet(), and bpp::ProteicAlphabetIndex2::operator=().

◆ distanceMatrix_

LinearMatrix<double> bpp::BLOSUM50::distanceMatrix_

private

Definition at line 33 of file BLOSUM50.h.

Referenced by getIndex(), getIndexMatrix(), and operator=().

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

Bpp/Seq/AlphabetIndex/BLOSUM50.h
Bpp/Seq/AlphabetIndex/BLOSUM50.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ BLOSUM50() [1/2]

◆ BLOSUM50() [2/2]

◆ ~BLOSUM50()

Member Function Documentation

◆ alphabet()

◆ clone()

◆ getAlphabet()

◆ getIndex() [1/2]

◆ getIndex() [2/2]

◆ getIndexMatrix()

◆ isSymmetric()

◆ operator=()

Member Data Documentation

◆ alpha_

◆ distanceMatrix_