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:

Public Member Functions
	GranthamAAVolumeIndex ()
virtual	~GranthamAAVolumeIndex ()
GranthamAAVolumeIndex *	clone () const override
double	getIndex (int state) const override
	Get the index associated to a state. More...
double	getIndex (const std::string &state) const override
	Get the index associated to a state. More...
const std::vector< double > &	indexVector () const override
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...

Private Attributes
std::vector< double >	volume_
std::shared_ptr< const ProteicAlphabet >	alpha_

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 35 of file GranthamAAVolumeIndex.h.

Constructor & Destructor Documentation

GranthamAAVolumeIndex()

bpp::GranthamAAVolumeIndex::GranthamAAVolumeIndex ( )

inline

Definition at line 42 of file GranthamAAVolumeIndex.h.

References volume_.

Referenced by clone().

~GranthamAAVolumeIndex()

virtual bpp::GranthamAAVolumeIndex::~GranthamAAVolumeIndex ( )

inlinevirtual

Definition at line 69 of file GranthamAAVolumeIndex.h.

Member Function Documentation

alphabet()

const Alphabet& bpp::ProteicAlphabetIndex1::alphabet ( ) const

inlineoverridevirtualinherited

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex1.

Definition at line 99 of file AlphabetIndex1.h.

References bpp::ProteicAlphabetIndex1::alpha_.

clone()

GranthamAAVolumeIndex* bpp::GranthamAAVolumeIndex::clone ( ) const

inlineoverridevirtual

Implements bpp::ProteicAlphabetIndex1.

Definition at line 71 of file GranthamAAVolumeIndex.h.

References GranthamAAVolumeIndex().

getAlphabet()

std::shared_ptr<const Alphabet> bpp::ProteicAlphabetIndex1::getAlphabet ( ) const

inlineoverridevirtualinherited

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex1.

Definition at line 97 of file AlphabetIndex1.h.

References bpp::ProteicAlphabetIndex1::alpha_.

Referenced by bpp::AAChargeIndex::getIndex(), bpp::AAChenGuHuangHydrophobicityIndex::getIndex(), bpp::AAChouFasmanAHelixIndex::getIndex(), bpp::AAChouFasmanBSheetIndex::getIndex(), bpp::AAChouFasmanTurnIndex::getIndex(), bpp::AAIndex1Entry::getIndex(), bpp::AAMassIndex::getIndex(), bpp::AASEA1030Index::getIndex(), bpp::AASEAInf10Index::getIndex(), bpp::AASEASup30Index::getIndex(), bpp::AASurfaceIndex::getIndex(), bpp::AAVolumeIndex::getIndex(), bpp::GranthamAAPolarityIndex::getIndex(), getIndex(), bpp::KD_AAHydropathyIndex::getIndex(), and bpp::KleinAANetChargeIndex::getIndex().

getIndex() [1/2]

double bpp::GranthamAAVolumeIndex::getIndex ( const std::string &  state ) const

inlineoverridevirtual

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 79 of file GranthamAAVolumeIndex.h.

References bpp::ProteicAlphabetIndex1::getAlphabet(), and volume_.

getIndex() [2/2]

double bpp::GranthamAAVolumeIndex::getIndex ( int  state ) const

inlineoverridevirtual

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 74 of file GranthamAAVolumeIndex.h.

References bpp::ProteicAlphabetIndex1::getAlphabet(), and volume_.

indexVector()

const std::vector<double>& bpp::GranthamAAVolumeIndex::indexVector ( ) const

inlineoverridevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 84 of file GranthamAAVolumeIndex.h.

References volume_.

Member Data Documentation

alpha_

std::shared_ptr<const ProteicAlphabet> bpp::ProteicAlphabetIndex1::alpha_

privateinherited

Definition at line 79 of file AlphabetIndex1.h.

Referenced by bpp::ProteicAlphabetIndex1::alphabet(), bpp::ProteicAlphabetIndex1::getAlphabet(), and bpp::ProteicAlphabetIndex1::operator=().

volume_

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

private

Definition at line 39 of file GranthamAAVolumeIndex.h.

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

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

• Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h