bpp::BLOSUM50 Class Reference

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)
virtual	~BLOSUM50 ()
Methods from the AlphabetIndex2 interface.
double	getIndex (int state1, int state2) const throw (BadIntException)
	Get the index associated to a pair of states. More...
double	getIndex (const std::string &state1, const std::string &state2) const throw (BadCharException)
	Get the index associated to a pair of states. More...
const Alphabet *	getAlphabet () const
	Get the alphabet associated to this index. More...
BLOSUM50 *	clone () const
LinearMatrix< double > *	getIndexMatrix () const
bool	isSymmetric () const

Private Attributes
LinearMatrix< double >	distanceMatrix_
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 64 of file BLOSUM50.h.

Constructor & Destructor Documentation

BLOSUM50() [1/2]

BLOSUM50::BLOSUM50

(

)

Definition at line 51 of file BLOSUM50.cpp.

Referenced by clone().

BLOSUM50() [2/2]

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

inline

Definition at line 74 of file BLOSUM50.h.

~BLOSUM50()

virtual bpp::BLOSUM50::~BLOSUM50 ( )

inlinevirtual

Definition at line 86 of file BLOSUM50.h.

Member Function Documentation

clone()

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

inlinevirtual

Implements bpp::AlphabetIndex2.

Definition at line 97 of file BLOSUM50.h.

References BLOSUM50().

getAlphabet()

const Alphabet* bpp::BLOSUM50::getAlphabet ( ) const

inlinevirtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex2.

Definition at line 96 of file BLOSUM50.h.

References alpha_.

getIndex() [1/2]

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

virtual

Get the index associated to a pair of states.

Parameters

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

Returns

The index associated to the pair of states.

Implements bpp::AlphabetIndex2.

Definition at line 58 of file BLOSUM50.cpp.

getIndex() [2/2]

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

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.

Implements bpp::AlphabetIndex2.

Definition at line 66 of file BLOSUM50.cpp.

getIndexMatrix()

LinearMatrix< double > * BLOSUM50::getIndexMatrix ( ) const

virtual

Returns

A matrix object with all indices.

Implements bpp::AlphabetIndex2.

Definition at line 74 of file BLOSUM50.cpp.

References distanceMatrix_.

isSymmetric()

bool bpp::BLOSUM50::isSymmetric ( ) const

inlinevirtual

Returns

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

Implements bpp::AlphabetIndex2.

Definition at line 99 of file BLOSUM50.h.

operator=()

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

inline

Definition at line 79 of file BLOSUM50.h.

References alpha_, and distanceMatrix_.

Member Data Documentation

alpha_

const ProteicAlphabet* bpp::BLOSUM50::alpha_

private

Definition at line 69 of file BLOSUM50.h.

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

distanceMatrix_

LinearMatrix<double> bpp::BLOSUM50::distanceMatrix_

private

Definition at line 68 of file BLOSUM50.h.

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

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

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