bpp::AASurfaceIndex Class Reference

Surface (Angström^2) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html. More...

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

Inheritance diagram for bpp::AASurfaceIndex:

Collaboration diagram for bpp::AASurfaceIndex:

Public Member Functions
	AASurfaceIndex ()
virtual	~AASurfaceIndex ()
AASurfaceIndex *	clone () const
double	getIndex (int state) const throw (BadIntException)
	Get the index associated to a state. More...
double	getIndex (const std::string &state) const throw (BadCharException)
	Get the index associated to a state. More...
std::vector< double > *	getIndexVector () const
const Alphabet *	getAlphabet () const
	Get the alphabet associated to this index. More...

Private Attributes
std::vector< double >	surface_

Detailed Description

Surface (Angström^2) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html.

Definition at line 52 of file AASurfaceIndex.h.

Constructor & Destructor Documentation

AASurfaceIndex()

bpp::AASurfaceIndex::AASurfaceIndex ( )

inline

Definition at line 59 of file AASurfaceIndex.h.

References surface_.

Referenced by clone().

~AASurfaceIndex()

virtual bpp::AASurfaceIndex::~AASurfaceIndex ( )

inlinevirtual

Definition at line 85 of file AASurfaceIndex.h.

Member Function Documentation

clone()

AASurfaceIndex* bpp::AASurfaceIndex::clone ( ) const

inlinevirtual

Implements bpp::AlphabetIndex1.

Definition at line 87 of file AASurfaceIndex.h.

References AASurfaceIndex().

getAlphabet()

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

inlinevirtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex1.

Definition at line 103 of file AASurfaceIndex.h.

References bpp::AlphabetTools::PROTEIN_ALPHABET.

getIndex() [1/2]

double bpp::AASurfaceIndex::getIndex ( int  state ) const throw ( BadIntException )

inlinevirtual

Get the index associated to a state.

Parameters

state

The state to consider, as a int value.

Returns

The index associated to the state

Implements bpp::AlphabetIndex1.

Definition at line 90 of file AASurfaceIndex.h.

References bpp::AlphabetTools::PROTEIN_ALPHABET, and surface_.

getIndex() [2/2]

double bpp::AASurfaceIndex::getIndex ( const std::string &  state ) const throw ( BadCharException )

inlinevirtual

Get the index associated to a state.

Parameters

state

The state to consider, as a string value.

Returns

The index associated to the state

Implements bpp::AlphabetIndex1.

Definition at line 96 of file AASurfaceIndex.h.

References bpp::LetterAlphabet::charToInt(), bpp::AlphabetTools::PROTEIN_ALPHABET, and surface_.

getIndexVector()

std::vector<double>* bpp::AASurfaceIndex::getIndexVector ( ) const

inlinevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 101 of file AASurfaceIndex.h.

References surface_.

Member Data Documentation

surface_

std::vector<double> bpp::AASurfaceIndex::surface_

private

Definition at line 56 of file AASurfaceIndex.h.

Referenced by AASurfaceIndex(), getIndex(), and getIndexVector().

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

• Bpp/Seq/AlphabetIndex/AASurfaceIndex.h