#include <gnSEQSource.h>
Inheritance diagram for gnSEQSource:
Public Member Functions | |
gnSEQSource * | 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. | |
gnSEQSource (const gnSEQSource &s) | |
Clone Constructor copies the specified gnSEQSource. | |
gnSEQSource () | |
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. | |
~gnSEQSource () | |
Destructor, frees memory. | |
Static Public Member Functions | |
boolean | Write (gnGenomeSpec *spec, const string &filename) |
Writes the given spec to a .SEQ file named "filename". | |
boolean | Write (gnBaseSource *source, const string &filename) |
Writes the specified source to a .SEQ file named "filename". | |
boolean | Write (gnSequence &sequence, const string &filename) |
Writes the specified gnSequence to a .SEQ 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 | |
void | BaseCount (const string &bases, gnSeqI &a_count, gnSeqI &c_count, gnSeqI &g_count, gnSeqI &t_count, gnSeqI &other_count) |
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 DNAStar SEQ file format. gnSEQSource is used by gnSourceFactory to read files and should only be used directly.when writing out files in SEQ file format by calling gnSEQSource::Write( mySpec, "C:\\mySeqFile.seq");
Definition at line 34 of file gnSEQSource.h.
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Empty Constructor, does nothing. Definition at line 23 of file gnSEQSource.cpp. References DebugMsg(), and gnFilter::fullDNASeqFilter(). Referenced by Clone(). |
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Clone Constructor copies the specified gnSEQSource.
References m_contigList. |
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Destructor, frees memory. Definition at line 39 of file gnSEQSource.cpp. References m_contigList. |
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Definition at line 262 of file gnSEQSource.cpp. |
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Returns an exact copy of this class.
Implements gnFileSource. Definition at line 101 of file gnSEQSource.h. References gnSEQSource(). |
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Definition at line 282 of file gnSEQSource.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 59 of file gnSEQSource.cpp. References m_contigList, and uint32. |
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Get the number of sequence contigs in this source.
Implements gnBaseSource. Definition at line 107 of file gnSEQSource.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 68 of file gnSEQSource.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 76 of file gnSEQSource.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 328 of file gnSEQSource.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 120 of file gnSEQSource.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 50 of file gnSEQSource.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 87 of file gnSEQSource.cpp. References gnSeqC, gnSeqI, gnFilter::IsValid(), m_contigList, SeqSeek(), uint32, and uint64. |
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Definition at line 170 of file gnSEQSource.cpp. References gnSeqI, m_contigList, SeqStartPos(), uint32, and uint64. Referenced by SeqRead(). |
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Definition at line 197 of file gnSEQSource.cpp. References DebugMsg(), ErrorMsg(), gnFileContig::GetRepeatSeqGapSize(), gnFileContig::GetSectStartEnd(), gnContigSequence, gnSeqI, gnFileContig::HasRepeatSeqGap(), gnFilter::IsValid(), uint32, and uint64. Referenced by SeqSeek(). |
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Writes the given spec to a .SEQ file named "filename".
References ErrorMsg(). |
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Writes the specified source to a .SEQ file named "filename".
References gnBaseSource::GetSpec(), and Write(). |
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Writes the specified gnSequence to a .SEQ file named "filename".
References gnSequence::GetSpec(). Referenced by Write(). |
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Definition at line 97 of file gnSEQSource.h. Referenced by GetContigID(), GetContigListLength(), GetContigName(), GetContigSeqLength(), GetFileContig(), gnSEQSource(), HasContig(), ParseStream(), SeqRead(), SeqSeek(), and ~gnSEQSource(). |
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Definition at line 96 of file gnSEQSource.h. Referenced by GetContigSeqLength(), GetSpec(), and ParseStream(). |