bpp::AAIndex1Entry Class Reference

Create a AlphabetIndex1 object from an AAIndex2 entry. More...

#include <Bpp/Seq/AlphabetIndex/AAIndex1Entry.h>

Inheritance diagram for bpp::AAIndex1Entry:

Collaboration diagram for bpp::AAIndex1Entry:

Public Member Functions
	AAIndex1Entry (std::istream &input)
	Create a new AAIndex1Entry from an input stream. More...
	AAIndex1Entry (const AAIndex1Entry &index)
AAIndex1Entry &	operator= (const AAIndex1Entry &index)
virtual	~AAIndex1Entry ()
AAIndex1Entry *	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 >	property_
std::shared_ptr< const ProteicAlphabet >	alpha_

Detailed Description

Create a AlphabetIndex1 object from an AAIndex2 entry.

Definition at line 16 of file AAIndex1Entry.h.

Constructor & Destructor Documentation

AAIndex1Entry() [1/2]

AAIndex1Entry::AAIndex1Entry

(

std::istream &

input

)

Create a new AAIndex1Entry from an input stream.

Parameters

input

The input stream to use.

Exceptions

IOException

if the stream content does not follow the AAIndex1 database entry format.

Definition at line 14 of file AAIndex1Entry.cpp.

References bpp::FileTools::getNextLine(), bpp::StringTokenizer::nextToken(), bpp::StringTokenizer::numberOfRemainingTokens(), property_, and bpp::TextTools::toDouble().

Referenced by clone().

AAIndex1Entry() [2/2]

bpp::AAIndex1Entry::AAIndex1Entry ( const AAIndex1Entry &  index )

inline

Definition at line 31 of file AAIndex1Entry.h.

~AAIndex1Entry()

virtual bpp::AAIndex1Entry::~AAIndex1Entry ( )

inlinevirtual

Definition at line 43 of file AAIndex1Entry.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()

AAIndex1Entry* bpp::AAIndex1Entry::clone ( ) const

inlineoverridevirtual

Implements bpp::ProteicAlphabetIndex1.

Definition at line 45 of file AAIndex1Entry.h.

References AAIndex1Entry().

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(), 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::AAIndex1Entry::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 53 of file AAIndex1Entry.h.

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

getIndex() [2/2]

double bpp::AAIndex1Entry::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 48 of file AAIndex1Entry.h.

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

indexVector()

const std::vector<double>& bpp::AAIndex1Entry::indexVector ( ) const

inlineoverridevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 58 of file AAIndex1Entry.h.

References property_.

operator=()

AAIndex1Entry& bpp::AAIndex1Entry::operator= ( const AAIndex1Entry &  index )

inline

Definition at line 36 of file AAIndex1Entry.h.

References bpp::ProteicAlphabetIndex1::operator=(), and property_.

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=().

property_

std::vector<double> bpp::AAIndex1Entry::property_

private

Definition at line 20 of file AAIndex1Entry.h.

Referenced by AAIndex1Entry(), getIndex(), indexVector(), and operator=().

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

• Bpp/Seq/AlphabetIndex/AAIndex1Entry.h
• Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp