Achieve random access by simply storing all genomes in memory and then retrieving the required substrings when desired. This may need a lot of RAM. More...

#include <randseqaccess.hh>

Inheritance diagram for MemSeqAccess:

Public Member Functions
	MemSeqAccess (vector< string > s)

AnnoSequence *	getSeq (string speciesname, string chrName, int start, int end, Strand strand)

SequenceFeatureCollection *	getFeatures (string speciesname, string chrName, int start, int end, Strand strand)

void	open ()

Public Member Functions inherited from RandSeqAccess
int	getNumSpecies ()

void	setLength (int idx, string chrName, int len)

int	getChrLen (int idx, string chrName)

void	setSpeciesNames (vector< string > speciesNames)

string	getSname (size_t idx)

int	getMaxSnameLen ()

int	getIdx (string speciesname)

void	printStats ()

bool	withEvidence (string speciesname)

AnnoSequence *	getSeq (size_t speciesIdx, string chrName, int start, int end, Strand strand)

Additional Inherited Members
Protected Attributes inherited from RandSeqAccess
int	numSpecies

vector< map< string, int > >	chrLen

vector< string >	speciesNames

map< string, size_t >	speciesIndex

SpeciesCollection	extrinsicFeatures

Detailed Description

Achieve random access by simply storing all genomes in memory and then retrieving the required substrings when desired. This may need a lot of RAM.

Author: Mario Stanke

Member Function Documentation

◆ getFeatures()

SequenceFeatureCollection * MemSeqAccess::getFeatures	(	string	speciesname,
		string	chrName,
		int	start,
		int	end,
		Strand	strand
	)

virtual

Implements RandSeqAccess.

◆ getSeq()

AnnoSequence * MemSeqAccess::getSeq	(	string	speciesname,
		string	chrName,
		int	start,
		int	end,
		Strand	strand
	)

virtual

Implements RandSeqAccess.

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

include/randseqaccess.hh
src/randseqaccess.cc

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ getFeatures()

◆ getSeq()