#include <gnABISource.h>
Inheritance diagram for gnABISource:
Public Member Functions | |
gnABISource * | Clone () const |
gnFileContig * | GetContig (const uint32 i) const |
uint32 | GetContigID (const string &name) const |
Get a contig index by name. | |
uint32 | GetContigListLength () const |
Get the number of sequence contigs in this source. | |
string | GetContigName (uint32 i) const |
Get the name of the specified contig. | |
gnSeqI | GetContigSeqLength (uint32 i) const |
Get the total number of base pairs in the specified contig. | |
gnFileContig * | GetFileContig (const uint32 contigI) const |
Returns a pointer to the file contig corresponding to contigI or null if none exists. | |
gnGenomeSpec * | GetSpec () const |
Get the annotated sequence data as a gnGenomeSpec. | |
gnABISource (const gnABISource &s) | |
Clone Constructor copies the specified gnSEQSource. | |
gnABISource () | |
boolean | HasContig (const string &name) const |
Looks for a contig by name. | |
boolean | SeqRead (const gnSeqI start, char *buf, gnSeqI &bufLen, const uint32 contigI=ALL_CONTIGS) |
Gets sequence data from this source. | |
~gnABISource () | |
Static Public Member Functions | |
boolean | Write (gnSequence &sequence, const string &filename) |
Writes the specified gnSequence to an ABI file named "filename". | |
Private Member Functions | |
boolean | ParseStream (istream &fin) |
boolean | SeqSeek (const gnSeqI start, const uint32 &contigI, uint64 &startPos, uint64 &readableBytes) |
boolean | SeqStartPos (const gnSeqI start, gnFileContig &contig, uint64 &startPos, uint64 &readableBytes) |
Private Attributes | |
vector< gnFileContig * > | m_contigList |
gnGenomeSpec * | m_spec |
Definition at line 26 of file gnABISource.h.
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Definition at line 14 of file gnABISource.cpp. References gnFilter::fullDNASeqFilter(). Referenced by Clone(). |
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Clone Constructor copies the specified gnSEQSource.
References m_contigList. |
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Definition at line 27 of file gnABISource.cpp. References m_contigList. |
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Implements gnFileSource. Definition at line 68 of file gnABISource.h. References gnABISource(). |
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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. Definition at line 50 of file gnABISource.cpp. References m_contigList, and uint32. |
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Get the number of sequence contigs in this source.
Implements gnBaseSource. Definition at line 73 of file gnABISource.h. References m_contigList, and uint32. |
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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. Definition at line 61 of file gnABISource.cpp. References m_contigList, and uint32. |
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Get the total number of base pairs in the specified contig.
Implements gnBaseSource. Definition at line 68 of file gnABISource.cpp. References gnSeqI, GNSEQI_ERROR, m_contigList, and uint32. |
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Returns a pointer to the file contig corresponding to contigI or null if none exists.
Implements gnFileSource. Definition at line 95 of file gnABISource.cpp. References m_contigList, and uint32. |
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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. Definition at line 78 of file gnABISource.h. References gnGenomeSpec::Clone(), and m_spec. |
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Looks for a contig by name. Returns true if it finds the contig, otherwise false.
Implements gnBaseSource. Definition at line 40 of file gnABISource.cpp. References m_contigList. |
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Implements gnFileSource. Definition at line 101 of file gnABISource.cpp. |
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Gets sequence data from this source. SeqRead will attempt to read "bufLen" base pairs starting at "start", an offset into the sequence. Reading inside a specific contig can be accomplished by supplying the "contigI" parameter with a valid contig index. SeqRead stores the sequence data in "buf" and returns the actual number of bases read in "bufLen". SeqRead will return false if a serious error occurs.
Implements gnBaseSource. Definition at line 81 of file gnABISource.cpp. |
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Definition at line 86 of file gnABISource.cpp. References gnSeqI, m_contigList, SeqStartPos(), uint32, and uint64. |
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Definition at line 90 of file gnABISource.cpp. References gnSeqI, and uint64. Referenced by SeqSeek(). |
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Writes the specified gnSequence to an ABI file named "filename".
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Definition at line 63 of file gnABISource.h. Referenced by GetContigID(), GetContigListLength(), GetContigName(), GetContigSeqLength(), GetFileContig(), gnABISource(), HasContig(), SeqSeek(), and ~gnABISource(). |
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Definition at line 62 of file gnABISource.h. Referenced by GetSpec(). |