faif::dna Namespace Reference

primitives for bioinformatics More...

Classes
class	Chain
	The DNA strand (single). More...
class	Codon
	the triplet of nucleotides, codon. More...
class	CodonAminoTable
	codons for given amino, amino for given codon, singleton More...
class	CodonStringTooShortException
	the exception when chain representing codon is shorted than 3 nucleotides More...
struct	ConnectPair
	The pair of nucleotides which are join by Watson-Crick interaction. More...
class	EnergyNucleo
	the maps between pair of nucleotides and its energy More...
class	FoldedChain
	DNA strand with secondary structure. More...
class	FoldedMatrix
class	FoldedMatrixStrategy
class	FoldedPair
	Two DNA chains with secondary structures. More...
struct	lessComplementary
class	Matrix
	matrix - 2D array with indexing More...
class	Nucleotide
	the DNA nucleotide More...
class	NucleotideBadCharException
	the exception thrown when unknown nucleotide (bad letter) occures More...
class	SecStruct
	the secondary structure More...
class	SecStructProxy

Typedefs
typedef int	EnergyValue
typedef std::pair< faif::dna::Nucleotide, faif::dna::Nucleotide >	Complementary
typedef boost::scoped_ptr< SecStructProxy >	SecStructProxyPtr
typedef std::set< SecStruct >	SecStructures

Enumerations
enum	AminoAcid {   PHENYLALANINE = 'F', LEUCINE = 'L', ISOLEUCINE = 'I', METHIONINE = 'M',   VALINE = 'V', SERINE = 'S', PROLINE = 'P', THREONINE = 'T',   ALANINE = 'A', TYROSINE = 'Y', STOP_CODON = '.', HISTIDYNE = 'H',   GLUTAMINE = 'Q', ASPARAGINE = 'N', LYSINE = 'K', ASPARTIC = 'D',   GLUTAMIC = 'E', CYSTEINE = 'C', TRYPTOPHAN = 'W', ARGININE = 'R',   GLYCINE = 'G', UNKNOWN = '?' }
enum	NucleotideValue {   ADENINE = 'A', CYTOSINE = 'C', GUANINE = 'G', THYMINE = 'T',   ANY_NUCLEOTIDE = 'N' }

Functions
Chain	createSubChain (const Chain &chain, int start, int length)
std::ostream &	operator<< (std::ostream &os, const Chain &chain)
std::ostream &	operator<< (std::ostream &os, const Codon &codon)
std::ostream &	operator<< (std::ostream &os, const AminoAcid &n)
	ostream for amino More...
EnergyNucleo	createDefaultEnergy (EnergyValue defaultEnergy=DEFAULT_NUCLEO_ENERGY)
std::ostream &	operator<< (std::ostream &os, const FoldedChain &folded)
std::ostream &	operator<< (std::ostream &os, const FoldedPair &folded)
Nucleotide	create (const char &n)
std::ostream &	operator<< (std::ostream &os, const Nucleotide &n)
std::ostream &	operator<< (std::ostream &os, const ConnectPair &p)
std::ostream &	operator<< (std::ostream &os, const SecStruct &sec_struct)

Detailed Description

primitives for bioinformatics

Typedef Documentation

typedef int faif::dna::EnergyValue

the energy value

typedef std::pair<faif::dna::Nucleotide, faif::dna::Nucleotide> faif::dna::Complementary

the pair of nucleotides

typedef std::set<SecStruct> faif::dna::SecStructures

secondary structure collection

Enumeration Type Documentation

enum faif::dna::AminoAcid

the enum represents amino

enum faif::dna::NucleotideValue

the nucleotide value (enum)

Function Documentation

Chain faif::dna::createSubChain ( const Chain &  chain, int  start, int  length  )

inline

creator (support): sub-chain, using index). Returns the largest chain starting from given index and having length less or equal given length.

References faif::dna::Chain::begin(), faif::dna::Chain::end(), and faif::dna::Chain::getLength().

std::ostream& faif::dna::operator<< ( std::ostream &  os, const Chain &  chain  )

inline

stream operator (support for debugging)

References faif::dna::Chain::getString().

Referenced by faif::dna::FoldedMatrix::findInDepth(), and faif::dna::SecStruct::getFoldings().

std::ostream& faif::dna::operator<< ( std::ostream &  os, const Codon &  codon  )

inline

ostream operator for codon

References faif::dna::Codon::getFirst(), faif::dna::Codon::getSecond(), and faif::dna::Codon::getThird().

std::ostream& faif::dna::operator<< ( std::ostream &  os, const AminoAcid &  n  )

inline

ostream for amino

EnergyNucleo faif::dna::createDefaultEnergy ( EnergyValue  defaultEnergy = DEFAULT_NUCLEO_ENERGY )

inline

default energy object: GC pair: energy = 3, AT pair: energy = 2, GT pair: energy = 1, otherwise energy = -1000

References faif::dna::EnergyNucleo::addPair().

std::ostream& faif::dna::operator<< ( std::ostream &  os, const FoldedChain &  folded  )

inline

print the chain sequence and one secondary structure

References faif::dna::FoldedChain::findInDepth(), faif::dna::FoldedChain::getChain(), and faif::dna::Chain::getString().

Nucleotide faif::dna::create ( const char &  n )

inline

creates from the char representing nucleotide

References faif::dna::Nucleotide::Nucleotide().

Referenced by faif::dna::Codon::Codon(), and faif::dna::Chain::const_iterator::operator==().

std::ostream& faif::dna::operator<< ( std::ostream &  os, const Nucleotide &  n  )

inline

stream operator, support, for debugging

References faif::dna::Nucleotide::get().

std::ostream& faif::dna::operator<< ( std::ostream &  os, const ConnectPair &  p  )

inline

support - to debuggiog

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

inline

support - to debugging