#include <gnDataBaseSource.h>
Inheritance diagram for gnDataBaseSource:
Public Member Functions | |
virtual gnBaseSource * | Clone () const =0 |
virtual gnDataBaseSource * | Clone () const =0 |
virtual boolean | Close ()=0 |
Closes the file or connection this source is reading from. | |
virtual uint32 | GetContigID (const string &name) const =0 |
Get a contig index by name. | |
virtual uint32 | GetContigListLength () const =0 |
Get the number of sequence contigs in this source. | |
virtual string | GetContigName (const uint32 i) const =0 |
Get the name of the specified contig. | |
virtual gnSeqI | GetContigSeqLength (const uint32 i) const =0 |
Get the total number of base pairs in the specified contig. | |
virtual const gnFilter * | GetFilter () const =0 |
Get the filter currently being used to filter unwanted characters out of read sequences. | |
virtual string | GetOpenString () const =0 |
Get the location of the source that is being used. | |
virtual gnGenomeSpec * | GetSpec () const =0 |
Get the annotated sequence data as a gnGenomeSpec. | |
virtual boolean | HasContig (const string &name) const =0 |
Looks for a contig by name. | |
virtual boolean | Open ()=0 |
Opens this source for reading. | |
virtual boolean | Open (string openString)=0 |
Opens the source given in "openString" for reading. | |
virtual boolean | Read (const uint64 pos, char *buf, uint32 &bufLen)=0 |
virtual boolean | SeqRead (const gnSeqI start, char *buf, uint32 &bufLen, const uint32 contigI=ALL_CONTIGS)=0 |
virtual boolean | SetFilter (gnFilter *filter)=0 |
Set the filter that will be used to filter unwanted characters out of the sequence data. | |
virtual | ~gnDataBaseSourcee () |
Private Member Functions | |
gnDataBaseSource () |
Definition at line 23 of file gnDataBaseSource.h.
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Definition at line 26 of file gnDataBaseSource.h. |
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Definition at line 47 of file gnDataBaseSource.h. |
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Implements gnBaseSource.
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Implements gnBaseSource.
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Closes the file or connection this source is reading from.
Implements gnBaseSource.
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Get a contig index by name. If the source does not contain a contig by the specified name GetContigID returns UINT32_MAX.
Implements gnBaseSource.
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Get the number of sequence contigs in this source.
Implements gnBaseSource.
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Get the name of the specified contig. Returns an empty string if the specified contig is out of range.
Implements gnBaseSource.
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Get the total number of base pairs in the specified contig.
Implements gnBaseSource.
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Get the filter currently being used to filter unwanted characters out of read sequences.
Implements gnBaseSource.
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Get the location of the source that is being used.
Implements gnBaseSource.
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Get the annotated sequence data as a gnGenomeSpec. GetSpec returns a gnGenomeSpec which contains the sequence, header, and feature data contained by this source.
Implements gnBaseSource.
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Looks for a contig by name. Returns true if it finds the contig, otherwise false.
Implements gnBaseSource.
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Opens this source for reading.
Implements gnBaseSource.
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Opens the source given in "openString" for reading.
Implements gnBaseSource.
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Set the filter that will be used to filter unwanted characters out of the sequence data.
Implements gnBaseSource.
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