coor.hpp File Reference

Reference sequence coordinates. More...

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Classes
struct	shore::refseq_coor
	Reference sequence coordinates. More...
struct	shore::refseq_region
	Range on a reference sequence with start and end on the same chromosome. More...
struct	shore::refseq_range
	Range on a reference sequence where start and end may be on different chromosomes. More...
struct	shore::genomic_coor
	Genomic coordinates. More...
struct	shore::genomic_region
	Range on a genomic sequence with start and end on the same chromosome. More...
struct	shore::genomic_range
	Range on a genomic sequence where start and end may be on different chromosomes. More...

Namespaces
	shore
	SHORE core API.

Constant Groups
	shore
	SHORE core API.

Enumerations
enum	shore::Strand { STR_FWD =1, STR_REV =2 }
	Strand.
enum	shore::OptionalStrand { STR_NA_OPT =0, STR_FWD_OPT =STR_FWD, STR_REV_OPT =STR_REV }
	Strand with an additional value NA.
enum	shore::ExtendedStrand { STR_NA_EXT =STR_NA_OPT, STR_FWD_EXT =STR_FWD, STR_REV_EXT =STR_REV, STR_UNKNOWN_EXT =3 }
	As OptionalStrand, with additional value UNKNOWN (e.g. as in GFF). More...

Functions
refseq_coor	shore::operator+ (const refseq_coor &c0, const refseq_coor::diff_t d)
refseq_coor	shore::operator- (const refseq_coor &c0, const refseq_coor::diff_t d)
refseq_coor::diff_t	shore::operator- (const refseq_coor &c0, const refseq_coor &c1)
bool	shore::operator< (const refseq_coor &gc1, const refseq_coor &gc2)
bool	shore::operator> (const refseq_coor &gc1, const refseq_coor &gc2)
bool	shore::operator<= (const refseq_coor &gc1, const refseq_coor &gc2)
bool	shore::operator>= (const refseq_coor &gc1, const refseq_coor &gc2)
bool	shore::operator== (const refseq_coor &gc1, const refseq_coor &gc2)
bool	shore::operator!= (const refseq_coor &gc1, const refseq_coor &gc2)
std::ostream &	shore::operator<< (std::ostream &os, const refseq_coor &gc)
std::istream &	shore::operator>> (std::istream &is, refseq_coor &gc)
bool	shore::operator== (const refseq_region &gc1, const refseq_region &gc2)
bool	shore::operator!= (const refseq_region &gc1, const refseq_region &gc2)
bool	shore::operator== (const refseq_range &gc1, const refseq_range &gc2)
bool	shore::operator!= (const refseq_range &gc1, const refseq_range &gc2)
std::ostream &	shore::operator<< (std::ostream &os, const refseq_range &gr)
std::istream &	shore::operator>> (std::istream &is, refseq_range &gr)
std::istream &	shore::operator>> (std::istream &in, Strand &s)
	Parse Strand.
std::ostream &	shore::operator<< (std::ostream &out, const Strand &s)
	Print Strand.
Strand	shore::other_strand (const Strand strand)
	Get the opposite strand.
std::istream &	shore::operator>> (std::istream &in, OptionalStrand &s)
	Parse OptionalStrand.
std::ostream &	shore::operator<< (std::ostream &out, const OptionalStrand &s)
	Print OptionalStrand.
OptionalStrand	shore::other_strand (const OptionalStrand strand)
	Get the opposite strand.
std::istream &	shore::operator>> (std::istream &in, ExtendedStrand &s)
	Parse ExtendedStrand.
std::ostream &	shore::operator<< (std::ostream &out, const ExtendedStrand &s)
	Print ExtendedStrand.
ExtendedStrand	shore::other_strand (const ExtendedStrand strand)
	Get the opposite strand.
std::istream &	shore::operator>> (std::istream &is, genomic_range &gr)
	Parse genomic_range. More...
std::ostream &	shore::operator<< (std::ostream &os, const genomic_range &gr)
	Print a genomic_range. More...

Detailed Description

Reference sequence coordinates.

Author

Felix Ott