bpp::AAVolumeIndex Class Reference

Volume (Angström^3) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html. More...

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

Inheritance diagram for bpp::AAVolumeIndex:

Collaboration diagram for bpp::AAVolumeIndex:

Public Member Functions
	AAVolumeIndex ()
virtual	~AAVolumeIndex ()
AAVolumeIndex *	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 >	volume_

Detailed Description

Volume (Angström^3) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html.

Definition at line 54 of file AAVolumeIndex.h.

Constructor & Destructor Documentation

AAVolumeIndex()

bpp::AAVolumeIndex::AAVolumeIndex ( )

inline

Definition at line 61 of file AAVolumeIndex.h.

References volume_.

Referenced by clone().

~AAVolumeIndex()

virtual bpp::AAVolumeIndex::~AAVolumeIndex ( )

inlinevirtual

Definition at line 87 of file AAVolumeIndex.h.

Member Function Documentation

clone()

AAVolumeIndex* bpp::AAVolumeIndex::clone ( ) const

inlinevirtual

Implements bpp::AlphabetIndex1.

Definition at line 89 of file AAVolumeIndex.h.

References AAVolumeIndex().

getAlphabet()

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

inlinevirtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex1.

Definition at line 105 of file AAVolumeIndex.h.

References bpp::AlphabetTools::PROTEIN_ALPHABET.

getIndex() [1/2]

double bpp::AAVolumeIndex::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 92 of file AAVolumeIndex.h.

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

getIndex() [2/2]

double bpp::AAVolumeIndex::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 98 of file AAVolumeIndex.h.

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

getIndexVector()

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

inlinevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 103 of file AAVolumeIndex.h.

References volume_.

Member Data Documentation

volume_

std::vector<double> bpp::AAVolumeIndex::volume_

private

Definition at line 58 of file AAVolumeIndex.h.

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

---

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

• Bpp/Seq/AlphabetIndex/AAVolumeIndex.h