Two DNA chains with secondary structures. More...

#include <FoldedPair.h>

Inheritance diagram for faif::dna::FoldedPair:

Collaboration diagram for faif::dna::FoldedPair:

Public Types
typedef boost::scoped_ptr< FoldedMatrix >	FoldedMatrixPtr

typedef boost::scoped_ptr< FoldedMatrixStrategy >	FoldedMatrixStrategyPtr

Public Member Functions
	FoldedPair (const Chain &first_chain, const Chain &second_chain, const EnergyNucleo &energy, unsigned int max_foldings=100)

const Chain &	getFirstChain () const

const Chain &	getSecondChain () const

EnergyValue	getSecStructEnergy () const

SecStruct	findInDepth () const

const SecStructures &	getStructures () const

std::ostream &	printMatrix (std::ostream &os, int print_width=4) const

std::ostream &	printStructures (std::ostream &os, int print_width=4) const

Detailed Description

Two DNA chains with secondary structures.

Two DNA chains with secondary structures (created between them as well as the self-secondary structures)

Member Typedef Documentation

the support class - holding the matrix with energy and secondary structures

the strategy to access for FoldedMatrix (one or two DNA chains)

const Chain& faif::dna::FoldedPair::getFirstChain ( ) const

inline

accessor

const Chain& faif::dna::FoldedPair::getSecondChain ( ) const

inline

accessor

EnergyValue faif::dna::FoldedPair::getSecStructEnergy ( ) const

inline

the second structure energy. Calculated on the first time, when method is called.

SecStruct faif::dna::FoldedPair::findInDepth ( ) const

inline

single second structure, algorithm search graph in depth

const SecStructures& faif::dna::FoldedPair::getStructures ( ) const

inline

collection of second structures, algorithm search graph in width, the max_foldings parameters restricts the number of structures

std::ostream& faif::dna::FoldedPair::printMatrix	(	std::ostream &	os,
		int	print_width = `4`
	)		const

inline

print the matrix (for testing and debugging)

std::ostream& faif::dna::FoldedPair::printStructures	(	std::ostream &	os,
		int	print_width = `4`
	)		const

inline

print the secondary structures (for testing and debugging)

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