bpp::AAChouFasmanAHelixIndex Class Reference

A-Helix score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm. More...

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

Inheritance diagram for bpp::AAChouFasmanAHelixIndex:

Collaboration diagram for bpp::AAChouFasmanAHelixIndex:

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

Detailed Description

A-Helix score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm.

Definition at line 18 of file AAChouFasmanAHelixIndex.h.

Constructor & Destructor Documentation

AAChouFasmanAHelixIndex()

bpp::AAChouFasmanAHelixIndex::AAChouFasmanAHelixIndex ( )

inline

Definition at line 25 of file AAChouFasmanAHelixIndex.h.

References aHelix_.

Referenced by clone().

~AAChouFasmanAHelixIndex()

virtual bpp::AAChouFasmanAHelixIndex::~AAChouFasmanAHelixIndex ( )

inlinevirtual

Definition at line 52 of file AAChouFasmanAHelixIndex.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()

AAChouFasmanAHelixIndex* bpp::AAChouFasmanAHelixIndex::clone ( ) const

inlineoverridevirtual

Implements bpp::ProteicAlphabetIndex1.

Definition at line 54 of file AAChouFasmanAHelixIndex.h.

References AAChouFasmanAHelixIndex().

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(), 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]

double bpp::AAChouFasmanAHelixIndex::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 65 of file AAChouFasmanAHelixIndex.h.

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

getIndex() [2/2]

double bpp::AAChouFasmanAHelixIndex::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 60 of file AAChouFasmanAHelixIndex.h.

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

indexVector()

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

inlineoverridevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 70 of file AAChouFasmanAHelixIndex.h.

References aHelix_.

Member Data Documentation

aHelix_

std::vector<double> bpp::AAChouFasmanAHelixIndex::aHelix_

private

Definition at line 22 of file AAChouFasmanAHelixIndex.h.

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

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=().

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

• Bpp/Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h