GenomeLocus Struct Reference

#include <genesis/population/genome_locus.hpp>

Detailed Description

A single locus, that is, a position (or coordinate) on a chromosome.

For our purposes here, we define a locus to be one position (1-based) on one chromosome exactly.

When working with multiple loci, we here often expect their chromosome names to be sorted in lexicographical order. Hence, for example, when comparing two loci on different chromosomes, we also take the ordering of their chromosome names into account.

There are some special cases:

• We use an empty chromosome with position 0 to denote an empty(), unspecified locus.
• A non-empty chromosome with position 0 means "any position" on the chromosome; this is however not considered to be a specified() locus.
• An empty chromosome with a position other than 0 is an invalid state, and will throw.

See also

GenomeLocusSet

GenomeRegion

GenomeRegionList

Definition at line 64 of file genome_locus.hpp.

Public Member Functions
	GenomeLocus (GenomeLocus &&)=default
	GenomeLocus (GenomeLocus const &)=default
	GenomeLocus (std::string const &chr="", size_t pos=0)
	~GenomeLocus ()=default
void	clear ()
bool	empty () const
GenomeLocus &	operator= (GenomeLocus &&)=default
GenomeLocus &	operator= (GenomeLocus const &)=default
bool	specified () const

Public Attributes
std::string	chromosome
size_t	position = 0

Constructor & Destructor Documentation

GenomeLocus() [1/3]

GenomeLocus ( std::string const &  chr = "", size_t  pos = 0  )

inline

Definition at line 69 of file genome_locus.hpp.

~GenomeLocus()

~GenomeLocus ( )

default

GenomeLocus() [2/3]

GenomeLocus ( GenomeLocus const &  )

default

GenomeLocus() [3/3]

GenomeLocus ( GenomeLocus &&  )

default

Member Function Documentation

clear()

void clear ( )

inline

Definition at line 96 of file genome_locus.hpp.

empty()

bool empty ( ) const

inline

Definition at line 84 of file genome_locus.hpp.

operator=() [1/2]

GenomeLocus& operator= ( GenomeLocus &&  )

default

operator=() [2/2]

GenomeLocus& operator= ( GenomeLocus const &  )

default

specified()

bool specified ( ) const

inline

Definition at line 90 of file genome_locus.hpp.

Member Data Documentation

chromosome

std::string chromosome

Definition at line 66 of file genome_locus.hpp.

position

size_t position = 0

Definition at line 67 of file genome_locus.hpp.

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

• genome_locus.hpp