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
double	getIndex (int state) const throw (BadIntException)
	Get the index associated to a state. More...
double	getIndex (const std::string &state) const throw (BadCharException)
	Get the index associated to a state. More...
std::vector< double > *	getIndexVector () const
const Alphabet *	getAlphabet () const
	Get the alphabet associated to this index. More...

Private Attributes
std::vector< double >	aHelix_

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 54 of file AAChouFasmanAHelixIndex.h.

Constructor & Destructor Documentation

AAChouFasmanAHelixIndex()

bpp::AAChouFasmanAHelixIndex::AAChouFasmanAHelixIndex ( )

inline

Definition at line 61 of file AAChouFasmanAHelixIndex.h.

References aHelix_.

Referenced by clone().

~AAChouFasmanAHelixIndex()

virtual bpp::AAChouFasmanAHelixIndex::~AAChouFasmanAHelixIndex ( )

inlinevirtual

Definition at line 87 of file AAChouFasmanAHelixIndex.h.

Member Function Documentation

clone()

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

inlinevirtual

Implements bpp::AlphabetIndex1.

Definition at line 89 of file AAChouFasmanAHelixIndex.h.

References AAChouFasmanAHelixIndex().

getAlphabet()

const Alphabet* bpp::AAChouFasmanAHelixIndex::getAlphabet ( ) const

inlinevirtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex1.

Definition at line 105 of file AAChouFasmanAHelixIndex.h.

References bpp::AlphabetTools::PROTEIN_ALPHABET.

getIndex() [1/2]

double bpp::AAChouFasmanAHelixIndex::getIndex ( int  state ) const throw ( BadIntException )

inlinevirtual

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 92 of file AAChouFasmanAHelixIndex.h.

References aHelix_, and bpp::AlphabetTools::PROTEIN_ALPHABET.

getIndex() [2/2]

double bpp::AAChouFasmanAHelixIndex::getIndex ( const std::string &  state ) const throw ( BadCharException )

inlinevirtual

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 98 of file AAChouFasmanAHelixIndex.h.

References aHelix_, bpp::LetterAlphabet::charToInt(), and bpp::AlphabetTools::PROTEIN_ALPHABET.

getIndexVector()

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

inlinevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 103 of file AAChouFasmanAHelixIndex.h.

References aHelix_.

Member Data Documentation

aHelix_

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

private

Definition at line 58 of file AAChouFasmanAHelixIndex.h.

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

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

• Bpp/Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h