RandSeqAccess Class Reference

abstract class for quick access to an arbitrary sequence segment in genomes needed for comparative gene finding More...

#include <randseqaccess.hh>

Inheritance diagram for RandSeqAccess:

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

Protected Attributes
int	numSpecies
vector< map< string, int > >	chrLen
vector< string >	speciesNames
map< string, size_t >	speciesIndex
SpeciesCollection	extrinsicFeatures

Detailed Description

abstract class for quick access to an arbitrary sequence segment in genomes needed for comparative gene finding

random acces to sequence data, e.g. get me chr1:1000-2000 from species 'human'

Author

Mario Stanke

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

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