bpp::GranthamAAVolumeIndex Class Reference

Volume index used in Grantham (1974). More...

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

Inheritance diagram for bpp::GranthamAAVolumeIndex:

Collaboration diagram for bpp::GranthamAAVolumeIndex:

List of all members.

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

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Detailed Description

Volume index used in Grantham (1974).

 Database: AAindex1
 Entry: GRAR740103

 H GRAR740103
 D Volume (Grantham, 1974)
 R LIT:2004143b PMID:4843792
 A Grantham, R.
 T Amino acid difference formula to help explain protein evolution
 J Science 185, 862-864 (1974)
 I    A/L     R/K     N/M     D/F     C/P     Q/S     E/T     G/W     H/Y     I/V
      31.    124.     56.     54.     55.     85.     83.      3.     96.    111.
     111.    119.    105.    132.    32.5     32.     61.    170.    136.     84.
 //

Definition at line 70 of file GranthamAAVolumeIndex.h.

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Constructor & Destructor Documentation

bpp::GranthamAAVolumeIndex::GranthamAAVolumeIndex

(

)

[inline]

Definition at line 77 of file GranthamAAVolumeIndex.h.

References volume_.

Referenced by clone().

virtual bpp::GranthamAAVolumeIndex::~GranthamAAVolumeIndex

(

)

[inline, virtual]

Definition at line 103 of file GranthamAAVolumeIndex.h.

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Member Function Documentation

GranthamAAVolumeIndex* bpp::GranthamAAVolumeIndex::clone

(

)

const [inline, virtual]

Implements bpp::Clonable.

Definition at line 105 of file GranthamAAVolumeIndex.h.

References GranthamAAVolumeIndex().

const Alphabet* bpp::GranthamAAVolumeIndex::getAlphabet

(

)

const [inline, virtual]

Get the alphabet associated to this index.

Returns:

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex1.

Definition at line 121 of file GranthamAAVolumeIndex.h.

References bpp::AlphabetTools::PROTEIN_ALPHABET.

double bpp::GranthamAAVolumeIndex::getIndex

(

int

state

)

const throw (BadIntException) [inline, virtual]

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 108 of file GranthamAAVolumeIndex.h.

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

double bpp::GranthamAAVolumeIndex::getIndex

(

const std::string &

state

)

const throw (BadCharException) [inline, virtual]

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 114 of file GranthamAAVolumeIndex.h.

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

std::vector<double>* bpp::GranthamAAVolumeIndex::getIndexVector

(

)

const [inline, virtual]

Returns:

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 119 of file GranthamAAVolumeIndex.h.

References volume_.

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Member Data Documentation

std::vector<double> bpp::GranthamAAVolumeIndex::volume_ [private]

Definition at line 74 of file GranthamAAVolumeIndex.h.

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

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

• Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h