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'
The documentation for this class was generated from the following files:
- include/randseqaccess.hh
- src/randseqaccess.cc
