faif::dna::FoldedChain Class Reference

DNA strand with secondary structure. More...

#include <FoldedChain.h>

Inheritance diagram for faif::dna::FoldedChain:

Collaboration diagram for faif::dna::FoldedChain:

Public Types
typedef boost::scoped_ptr< FoldedMatrix >	FoldedMatrixPtr
typedef boost::scoped_ptr< FoldedMatrixStrategy >	FoldedMatrixStrategyPtr

Public Member Functions
	FoldedChain (const Chain &chain, const EnergyNucleo &energy, unsigned int max_foldings=100)
const Chain &	getChain () 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

DNA strand with secondary structure.

Single DNA strand with secondary structures calculated by given algorithm.

Member Typedef Documentation

typedef boost::scoped_ptr<FoldedMatrix> faif::dna::FoldedChain::FoldedMatrixPtr

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

typedef boost::scoped_ptr<FoldedMatrixStrategy> faif::dna::FoldedChain::FoldedMatrixStrategyPtr

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

Member Function Documentation

const Chain& faif::dna::FoldedChain::getChain ( ) const

inline

accessor

Referenced by faif::dna::operator<<().

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

inline

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

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

inline

single second structure, algorithm search graph in depth

Referenced by faif::dna::operator<<().

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

inline

print the matrix (for testing and debugging)

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

inline

print the secondary structures (for testing and debugging)

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

• faif/dna/FoldedChain.h