faif::dna::SecStruct Class Reference

the secondary structure More...

#include <SecStruct.h>

Collaboration diagram for faif::dna::SecStruct:

Public Types
typedef std::set< ConnectPair >	Foldings

Public Member Functions
	SecStruct ()
	SecStruct (const SecStruct &s)
	~SecStruct ()
SecStruct &	operator= (const SecStruct &s)
void	addPair (const ConnectPair &p)
void	append (const SecStruct &s)
bool	operator== (const SecStruct &s) const
bool	operator< (const SecStruct &s) const
int	size () const
EnergyValue	energy (const EnergyNucleo &energy_matrix) const
const Foldings &	getFoldings () const

Friends
std::ostream &	operator<< (std::ostream &os, const SecStruct &sec_struct)

Detailed Description

the secondary structure

The collection of ConnectPair, represents the secondary structure.

Member Typedef Documentation

typedef std::set<ConnectPair> faif::dna::SecStruct::Foldings

the folded pairs collection - secondary structure

Constructor & Destructor Documentation

faif::dna::SecStruct::SecStruct ( )

inline

constructor

faif::dna::SecStruct::SecStruct ( const SecStruct &  s )

inline

copy constructor

faif::dna::SecStruct::~SecStruct ( )

inline

destructor

Member Function Documentation

SecStruct& faif::dna::SecStruct::operator= ( const SecStruct &  s )

inline

assign operator

void faif::dna::SecStruct::addPair ( const ConnectPair &  p )

inline

adds the pair to secondary structure

Referenced by faif::dna::FoldedMatrix::getStructures().

void faif::dna::SecStruct::append ( const SecStruct &  s )

inline

append the collection of pairs to secondary structure

Referenced by faif::dna::FoldedMatrix::getStructures().

bool faif::dna::SecStruct::operator== ( const SecStruct &  s ) const

inline

identity

bool faif::dna::SecStruct::operator< ( const SecStruct &  s ) const

inline

comparison

int faif::dna::SecStruct::size ( ) const

inline

number of folded pairs

EnergyValue faif::dna::SecStruct::energy ( const EnergyNucleo &  energy_matrix ) const

inline

calculates the energy of secondary structure. Summarizes all pairs.

const Foldings& faif::dna::SecStruct::getFoldings ( ) const

inline

accessor - returns the pair collection

References faif::dna::operator<<().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os, const SecStruct &  sec_struct  )

friend

support - to debugging

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

• faif/dna/SecStruct.h