bpp::AAChouFasmanTurnIndex Class Reference

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

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

Inheritance diagram for bpp::AAChouFasmanTurnIndex:

Collaboration diagram for bpp::AAChouFasmanTurnIndex:

Public Member Functions
	AAChouFasmanTurnIndex ()
virtual	~AAChouFasmanTurnIndex ()
AAChouFasmanTurnIndex *	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 >	turn_

Detailed Description

Turn 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 AAChouFasmanTurnIndex.h.

Constructor & Destructor Documentation

AAChouFasmanTurnIndex()

bpp::AAChouFasmanTurnIndex::AAChouFasmanTurnIndex ( )

inline

Definition at line 61 of file AAChouFasmanTurnIndex.h.

References turn_.

Referenced by clone().

~AAChouFasmanTurnIndex()

virtual bpp::AAChouFasmanTurnIndex::~AAChouFasmanTurnIndex ( )

inlinevirtual

Definition at line 87 of file AAChouFasmanTurnIndex.h.

Member Function Documentation

clone()

AAChouFasmanTurnIndex* bpp::AAChouFasmanTurnIndex::clone ( ) const

inlinevirtual

Implements bpp::AlphabetIndex1.

Definition at line 89 of file AAChouFasmanTurnIndex.h.

References AAChouFasmanTurnIndex().

getAlphabet()

const Alphabet* bpp::AAChouFasmanTurnIndex::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 AAChouFasmanTurnIndex.h.

References bpp::AlphabetTools::PROTEIN_ALPHABET.

getIndex() [1/2]

double bpp::AAChouFasmanTurnIndex::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 AAChouFasmanTurnIndex.h.

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

getIndex() [2/2]

double bpp::AAChouFasmanTurnIndex::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 AAChouFasmanTurnIndex.h.

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

getIndexVector()

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

inlinevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 103 of file AAChouFasmanTurnIndex.h.

References turn_.

Member Data Documentation

turn_

std::vector<double> bpp::AAChouFasmanTurnIndex::turn_

private

Definition at line 58 of file AAChouFasmanTurnIndex.h.

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

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

• Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h