bpp::KD_AAHydropathyIndex Class Reference

Hydropathy index defined in Kyte & Doolitle (1982). More...

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

Inheritance diagram for bpp::KD_AAHydropathyIndex:

Collaboration diagram for bpp::KD_AAHydropathyIndex:

Public Member Functions
	KD_AAHydropathyIndex ()
virtual	~KD_AAHydropathyIndex ()
KD_AAHydropathyIndex *	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 >	hydropathy_
std::shared_ptr< const ProteicAlphabet >	alpha_

Detailed Description

Hydropathy index defined in Kyte & Doolitle (1982).

Kyte, J. and Doolittle, R.F., J. Mol. Biol., 157, 105-132 (1982).

Definition at line 20 of file KD_AAHydropathyIndex.h.

Constructor & Destructor Documentation

KD_AAHydropathyIndex()

bpp::KD_AAHydropathyIndex::KD_AAHydropathyIndex ( )

inline

Definition at line 27 of file KD_AAHydropathyIndex.h.

References hydropathy_.

Referenced by clone().

~KD_AAHydropathyIndex()

virtual bpp::KD_AAHydropathyIndex::~KD_AAHydropathyIndex ( )

inlinevirtual

Definition at line 54 of file KD_AAHydropathyIndex.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()

KD_AAHydropathyIndex* bpp::KD_AAHydropathyIndex::clone ( ) const

inlineoverridevirtual

Implements bpp::ProteicAlphabetIndex1.

Definition at line 56 of file KD_AAHydropathyIndex.h.

References KD_AAHydropathyIndex().

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(), bpp::GranthamAAVolumeIndex::getIndex(), getIndex(), and bpp::KleinAANetChargeIndex::getIndex().

getIndex() [1/2]

double bpp::KD_AAHydropathyIndex::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 64 of file KD_AAHydropathyIndex.h.

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

getIndex() [2/2]

double bpp::KD_AAHydropathyIndex::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 59 of file KD_AAHydropathyIndex.h.

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

indexVector()

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

inlineoverridevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 69 of file KD_AAHydropathyIndex.h.

References hydropathy_.

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=().

hydropathy_

std::vector<double> bpp::KD_AAHydropathyIndex::hydropathy_

private

Definition at line 24 of file KD_AAHydropathyIndex.h.

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

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

• Bpp/Seq/AlphabetIndex/KD_AAHydropathyIndex.h