Random access to sequence segments through a database. More...

Inheritance diagram for DbSeqAccess:

Public Member Functions
virtual AnnoSequence *	getSeq (string speciesname, string chrName, int start, int end, Strand strand)=0

virtual SequenceFeatureCollection *	getFeatures (string speciesname, string chrName, int start, int end, Strand strand)=0

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)

Protected Member Functions
	DbSeqAccess (vector< string > s=vector< string >())

Protected Attributes
string	dbaccess

Protected Attributes inherited from RandSeqAccess
int	numSpecies

vector< map< string, int > >	chrLen

vector< string >	speciesNames

map< string, size_t >	speciesIndex

SpeciesCollection	extrinsicFeatures

Detailed Description

Random access to sequence segments through a database.

The sequences must be stored in a database.

Member Function Documentation

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

pure virtual

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

pure virtual

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