bpp::ProteicAlphabetIndex1 Class Reference

#include <Bpp/Seq/AlphabetIndex/AlphabetIndex1.h>

Inheritance diagram for bpp::ProteicAlphabetIndex1:

Collaboration diagram for bpp::ProteicAlphabetIndex1:

Public Member Functions
	ProteicAlphabetIndex1 ()
virtual	~ProteicAlphabetIndex1 ()
virtual ProteicAlphabetIndex1 *	clone () const override=0
	ProteicAlphabetIndex1 (const ProteicAlphabetIndex1 &pt)
ProteicAlphabetIndex1 &	operator= (const ProteicAlphabetIndex1 &pt)
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...
virtual double	getIndex (int state) const =0
	Get the index associated to a state. More...
virtual double	getIndex (const std::string &state) const =0
	Get the index associated to a state. More...
virtual const std::vector< double > &	indexVector () const =0

Private Attributes
std::shared_ptr< const ProteicAlphabet >	alpha_

Detailed Description

Definition at line 75 of file AlphabetIndex1.h.

Constructor & Destructor Documentation

ProteicAlphabetIndex1() [1/2]

bpp::ProteicAlphabetIndex1::ProteicAlphabetIndex1 ( )

inline

Definition at line 82 of file AlphabetIndex1.h.

~ProteicAlphabetIndex1()

virtual bpp::ProteicAlphabetIndex1::~ProteicAlphabetIndex1 ( )

inlinevirtual

Definition at line 83 of file AlphabetIndex1.h.

ProteicAlphabetIndex1() [2/2]

bpp::ProteicAlphabetIndex1::ProteicAlphabetIndex1 ( const ProteicAlphabetIndex1 &  pt )

inline

Definition at line 87 of file AlphabetIndex1.h.

Member Function Documentation

alphabet()

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

inlineoverridevirtual

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 alpha_.

clone()

virtual ProteicAlphabetIndex1* bpp::ProteicAlphabetIndex1::clone ( ) const

overridepure virtual

Implements bpp::AlphabetIndex1.

Implemented in bpp::KleinAANetChargeIndex, bpp::KD_AAHydropathyIndex, bpp::GranthamAAVolumeIndex, bpp::GranthamAAPolarityIndex, bpp::AAVolumeIndex, bpp::AASurfaceIndex, bpp::AASEASup30Index, bpp::AASEAInf10Index, bpp::AASEA1030Index, bpp::AAMassIndex, bpp::AAIndex1Entry, bpp::AAChouFasmanTurnIndex, bpp::AAChouFasmanBSheetIndex, bpp::AAChouFasmanAHelixIndex, bpp::AAChenGuHuangHydrophobicityIndex, and bpp::AAChargeIndex.

getAlphabet()

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

inlineoverridevirtual

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

getIndex() [1/2]

virtual double bpp::AlphabetIndex1::getIndex ( const std::string &  state ) const

pure virtualinherited

Get the index associated to a state.

Parameters

state

The state to consider, as a string value.

Returns

The index associated to the state

Implemented in bpp::KleinAANetChargeIndex, bpp::KD_AAHydropathyIndex, bpp::GranthamAAVolumeIndex, bpp::GranthamAAPolarityIndex, bpp::CodonFromProteicAlphabetIndex1, bpp::AAVolumeIndex, bpp::AASurfaceIndex, bpp::AASEASup30Index, bpp::AASEAInf10Index, bpp::AASEA1030Index, bpp::AAMassIndex, bpp::AAIndex1Entry, bpp::AAChouFasmanTurnIndex, bpp::AAChouFasmanBSheetIndex, bpp::AAChouFasmanAHelixIndex, bpp::AAChenGuHuangHydrophobicityIndex, bpp::AAChargeIndex, and bpp::UserAlphabetIndex1.

getIndex() [2/2]

virtual double bpp::AlphabetIndex1::getIndex ( int  state ) const

pure virtualinherited

Get the index associated to a state.

Parameters

state

The state to consider, as a int value.

Returns

The index associated to the state

Implemented in bpp::KleinAANetChargeIndex, bpp::KD_AAHydropathyIndex, bpp::GranthamAAVolumeIndex, bpp::GranthamAAPolarityIndex, bpp::CodonFromProteicAlphabetIndex1, bpp::AAVolumeIndex, bpp::AASurfaceIndex, bpp::AASEASup30Index, bpp::AASEAInf10Index, bpp::AASEA1030Index, bpp::AAMassIndex, bpp::AAIndex1Entry, bpp::AAChouFasmanTurnIndex, bpp::AAChouFasmanBSheetIndex, bpp::AAChouFasmanAHelixIndex, bpp::AAChenGuHuangHydrophobicityIndex, bpp::AAChargeIndex, and bpp::UserAlphabetIndex1.

indexVector()

virtual const std::vector<double>& bpp::AlphabetIndex1::indexVector ( ) const

pure virtualinherited

Returns

A vector object with all indices.

Implemented in bpp::KleinAANetChargeIndex, bpp::KD_AAHydropathyIndex, bpp::GranthamAAVolumeIndex, bpp::GranthamAAPolarityIndex, bpp::CodonFromProteicAlphabetIndex1, bpp::AAVolumeIndex, bpp::AASurfaceIndex, bpp::AASEASup30Index, bpp::AASEAInf10Index, bpp::AASEA1030Index, bpp::AAMassIndex, bpp::AAIndex1Entry, bpp::AAChouFasmanTurnIndex, bpp::AAChouFasmanBSheetIndex, bpp::AAChouFasmanAHelixIndex, bpp::AAChenGuHuangHydrophobicityIndex, bpp::AAChargeIndex, and bpp::UserAlphabetIndex1.

operator=()

ProteicAlphabetIndex1& bpp::ProteicAlphabetIndex1::operator= ( const ProteicAlphabetIndex1 &  pt )

inline

Definition at line 91 of file AlphabetIndex1.h.

References alpha_.

Referenced by bpp::AAIndex1Entry::operator=().

Member Data Documentation

alpha_

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

private

Definition at line 79 of file AlphabetIndex1.h.

Referenced by alphabet(), getAlphabet(), and operator=().

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

• Bpp/Seq/AlphabetIndex/AlphabetIndex1.h