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 =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 const Alphabet *	getAlphabet () const =0
	Get the alphabet associated to this index. More...
virtual std::vector< double > *	getIndexVector () const =0

Detailed Description

One dimensionnal alphabet index interface.

Derivatives of this interface implement properties for a single state.

Definition at line 58 of file AlphabetIndex1.h.

Constructor & Destructor Documentation

AlphabetIndex1()

bpp::AlphabetIndex1::AlphabetIndex1 ( )

inline

Definition at line 62 of file AlphabetIndex1.h.

~AlphabetIndex1()

virtual bpp::AlphabetIndex1::~AlphabetIndex1 ( )

inlinevirtual

Definition at line 63 of file AlphabetIndex1.h.

Member Function Documentation

clone()

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

pure virtual

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

getAlphabet()

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

getIndex() [1/2]

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

getIndex() [2/2]

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

getIndexVector()

virtual std::vector<double>* bpp::AlphabetIndex1::getIndexVector ( ) const

pure virtual

Returns

A vector object with all indices.

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

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

• Bpp/Seq/AlphabetIndex/AlphabetIndex1.h