faif::hapl Namespace Reference

Population genetics (haplotype and marker analyzis) primitives and algorithms. More...

Classes
struct	AlleleImpl
	the helping structure, implements the Allele members More...

Typedefs
typedef ValueNominal< AlleleImpl >	Allele
	Allele, variant of a gene. More...
typedef DomainEnumerate< Allele >	Locus
	Locus, place on DNA contatining the Allele. More...
typedef std::vector< Locus >	Loci
	Loci, the collection(sequence) of Locus, e.g. genotype. More...

Functions
std::ostream &	operator<< (std::ostream &os, const AlleleImpl &a)
	ostream operator More...
std::string	getName (const Allele &a)
	accessor More...
bool	isSilent (const Allele &a)
	accessor More...
Locus	createLocus (const std::string &name, int num_variants, bool has_silent)
	helping method - create the entire locus, with number variants. More...
std::ostream &	operator<< (std::ostream &os, const Loci &loci)

Detailed Description

Population genetics (haplotype and marker analyzis) primitives and algorithms.

Typedef Documentation

typedef ValueNominal<AlleleImpl> faif::hapl::Allele

Allele, variant of a gene.

typedef DomainEnumerate<Allele> faif::hapl::Locus

Locus, place on DNA contatining the Allele.

typedef std::vector<Locus> faif::hapl::Loci

Loci, the collection(sequence) of Locus, e.g. genotype.

Function Documentation

std::ostream& faif::hapl::operator<< ( std::ostream &  os, const AlleleImpl &  a  )

inline

ostream operator

std::string faif::hapl::getName ( const Allele &  a )

inline

accessor

References faif::ValueNominal< Val >::get().

bool faif::hapl::isSilent ( const Allele &  a )

inline

accessor

References faif::ValueNominal< Val >::get().

Locus faif::hapl::createLocus	(	const std::string &	name,
		int	num_variants,
		bool	has_silent
	)

helping method - create the entire locus, with number variants.

Variants name are the locus name and the variant number, i.e. silent variant has name 'name0', first non silent variant has name 'name1' etc.

References faif::hapl::AlleleImpl::AlleleImpl(), and faif::DomainEnumerate< Val >::insert().

std::ostream& faif::hapl::operator<< ( std::ostream &  os, const Loci &  loci  )

inline

ostream operator for loci