bpp::AlphabetIndex1 Class Reference

One dimensionnal alphabet index interface. More...

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

Inheritance diagram for bpp::AlphabetIndex1:

Collaboration diagram for bpp::AlphabetIndex1:

Public Member Functions
	AlphabetIndex1 ()
virtual	~AlphabetIndex1 ()
virtual AlphabetIndex1 *	clone () const override=0
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 std::shared_ptr< const Alphabet >	getAlphabet () const =0
	Get the alphabet associated to this index. More...
virtual const Alphabet &	alphabet () const =0
	Get the alphabet associated to this index. More...
virtual const std::vector< double > &	indexVector () const =0

Detailed Description

One dimensionnal alphabet index interface.

Derivatives of this interface implement properties for a single state.

Definition at line 24 of file AlphabetIndex1.h.

Constructor & Destructor Documentation

AlphabetIndex1()

bpp::AlphabetIndex1::AlphabetIndex1 ( )

inline

Definition at line 28 of file AlphabetIndex1.h.

~AlphabetIndex1()

virtual bpp::AlphabetIndex1::~AlphabetIndex1 ( )

inlinevirtual

Definition at line 29 of file AlphabetIndex1.h.

Member Function Documentation

alphabet()

virtual const Alphabet& bpp::AlphabetIndex1::alphabet ( ) const

pure virtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implemented in bpp::CodonFromProteicAlphabetIndex1, bpp::ProteicAlphabetIndex1, and bpp::UserAlphabetIndex1.

clone()

virtual AlphabetIndex1* bpp::AlphabetIndex1::clone ( ) const

overridepure virtual

Implements bpp::Clonable.

Implemented in bpp::ProteicAlphabetIndex1, bpp::UserAlphabetIndex1, 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, and bpp::AAChargeIndex.

getAlphabet()

virtual std::shared_ptr<const Alphabet> bpp::AlphabetIndex1::getAlphabet ( ) const

pure virtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implemented in bpp::CodonFromProteicAlphabetIndex1, bpp::ProteicAlphabetIndex1, and bpp::UserAlphabetIndex1.

getIndex() [1/2]

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

pure 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

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 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

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 virtual

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.

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

• Bpp/Seq/AlphabetIndex/AlphabetIndex1.h