#include <gnGBKSource.h>
Inheritance diagram for gnGBKSource:
Public Member Functions | |
gnGBKSource * | Clone () const |
Returns an exact copy of this class. | |
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 (const uint32 i) const |
Get the name of the specified contig. | |
gnSeqI | GetContigSeqLength (const 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. | |
gnGBKSource (const gnGBKSource &s) | |
Clone Constructor copies the specified gnGBKSource. | |
gnGBKSource () | |
Empty Constructor, does nothing. | |
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. | |
~gnGBKSource () | |
Destructor, frees memory. | |
Static Public Member Functions | |
boolean | Write (gnBaseSource *source, const string &filename) |
Writes the specified source to a .GBK file named "filename". | |
boolean | Write (gnSequence &seq, const string &filename) |
Writes the specified gnSequence to a .GBK 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) |
Static Private Member Functions | |
string & | Filler (uint32 length) |
void | FormatString (string &data, uint32 offset, uint32 width) |
Private Attributes | |
vector< gnFileContig * > | m_contigList |
gnGenomeSpec * | m_spec |
This class reads and writes the GenBank file format. gnGBKSource is used by gnSourceFactory to read files and should only be used directly when writing out files in GBK file format by calling gnGBKSource::Write( mySpec, "C:\\mySeqFile.gbk");
Definition at line 50 of file gnGBKSource.h.
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Empty Constructor, does nothing. Definition at line 24 of file gnGBKSource.cpp. References DebugMsg(), and gnFilter::proteinSeqFilter(). Referenced by Clone(). |
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Clone Constructor copies the specified gnGBKSource.
References m_contigList. |
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Destructor, frees memory. Definition at line 40 of file gnGBKSource.cpp. References m_contigList. |
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Returns an exact copy of this class.
Implements gnFileSource. Definition at line 113 of file gnGBKSource.h. References gnGBKSource(). |
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Definition at line 255 of file gnGBKSource.cpp. References uint32. |
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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 60 of file gnGBKSource.cpp. References m_contigList, and uint32. |
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Get the number of sequence contigs in this source.
Implements gnBaseSource. Definition at line 119 of file gnGBKSource.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 69 of file gnGBKSource.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 77 of file gnGBKSource.cpp. References gnMultiSpec< SubSpec >::GetLength(), gnSeqI, GNSEQI_ERROR, m_contigList, m_spec, 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 557 of file gnGBKSource.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 129 of file gnGBKSource.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 51 of file gnGBKSource.cpp. References m_contigList, and uint32. |
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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 88 of file gnGBKSource.cpp. References gnSeqC, gnSeqI, gnFilter::IsValid(), m_contigList, SeqSeek(), uint32, and uint64. |
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Definition at line 171 of file gnGBKSource.cpp. References gnSeqI, m_contigList, SeqStartPos(), uint32, and uint64. Referenced by SeqRead(). |
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Definition at line 198 of file gnGBKSource.cpp. References ErrorMsg(), gnFileContig::GetSectStartEnd(), gnContigSequence, gnSeqI, gnFileContig::HasRepeatSeqGap(), gnFilter::IsValid(), uint32, and uint64. Referenced by SeqSeek(). |
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Writes the specified source to a .GBK file named "filename".
References gnBaseSource::GetSpec(), and Write(). |
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Definition at line 105 of file gnGBKSource.h. Referenced by GetContigID(), GetContigListLength(), GetContigName(), GetContigSeqLength(), GetFileContig(), gnGBKSource(), HasContig(), ParseStream(), SeqRead(), SeqSeek(), and ~gnGBKSource(). |
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Definition at line 104 of file gnGBKSource.h. Referenced by GetContigSeqLength(), GetSpec(), and ParseStream(). |