MemSeqAccess Class Reference

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 Member Functions inherited from RandSeqAccess
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.

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

• include/randseqaccess.hh
• src/randseqaccess.cc