#include <gnDNXSource.h>
Inheritance diagram for gnDNXSource:
Public Member Functions | |
gnDNXSource * | Clone () 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 (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. | |
gnDNXSource (const gnDNXSource &s) | |
The copy constructor copies the given gnDNXSource. | |
gnDNXSource () | |
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. | |
~gnDNXSource () | |
Destructor, frees memory. | |
Static Public Member Functions | |
boolean | Write (gnGenomeSpec *spec, const string &filename) |
Writes the given gnGenomeSpec to a DNX file named "filename". | |
boolean | Write (gnBaseSource *source, const string &filename) |
This method is deprecated. | |
boolean | Write (gnSequence &sequence, const string &filename) |
Writes the given gnSequence to a DNX file named "filename". | |
Private Member Functions | |
boolean | ParseStream (istream &fin) |
Static Private Member Functions | |
void | ValidateName (string &name) |
Private Attributes | |
gnGenomeSpec * | m_DNXSpec |
This class reads and writes the Blattner Lab DNX file format. DNX files may be written by calling: gnDNXSource::Write( mySpec, "C:\\myFile.dnx");
Definition at line 35 of file gnDNXSource.h.
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Empty Constructor, does nothing. Definition at line 24 of file gnDNXSource.cpp. References DebugMsg(), gnFilter::fullDNASeqFilter(), and m_DNXSpec. Referenced by Clone(). |
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The copy constructor copies the given gnDNXSource.
References gnGenomeSpec::Clone(), and m_DNXSpec. |
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Destructor, frees memory. Definition at line 39 of file gnDNXSource.cpp. References m_DNXSpec. |
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Implements gnFileSource. Definition at line 101 of file gnDNXSource.h. References gnDNXSource(). |
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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 52 of file gnDNXSource.cpp. References gnBaseSpec::GetName(), gnMultiSpec< SubSpec >::GetSpec(), gnMultiSpec< SubSpec >::GetSpecListLength(), m_DNXSpec, and uint32. |
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Get the number of sequence contigs in this source.
Implements gnBaseSource. Definition at line 107 of file gnDNXSource.h. References gnMultiSpec< SubSpec >::GetSpecListLength(), m_DNXSpec, 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 60 of file gnDNXSource.cpp. References gnBaseSpec::GetName(), gnMultiSpec< SubSpec >::GetSpec(), gnMultiSpec< SubSpec >::GetSpecListLength(), m_DNXSpec, 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 gnDNXSource.cpp. References gnBaseSpec::GetLength(), gnMultiSpec< SubSpec >::GetLength(), gnMultiSpec< SubSpec >::GetSpec(), gnMultiSpec< SubSpec >::GetSpecListLength(), gnSeqI, m_DNXSpec, 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 136 of file gnDNXSource.cpp. References 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 127 of file gnDNXSource.h. References gnGenomeSpec::Clone(), and m_DNXSpec. |
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Looks for a contig by name. Returns true if it finds the contig, otherwise false.
Implements gnBaseSource. Definition at line 44 of file gnDNXSource.cpp. References gnBaseSpec::GetName(), gnMultiSpec< SubSpec >::GetSpec(), gnMultiSpec< SubSpec >::GetSpecListLength(), m_DNXSpec, 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 113 of file gnDNXSource.h. References gnSeqI, m_DNXSpec, gnMultiSpec< SubSpec >::SeqRead(), and uint32. |
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Definition at line 80 of file gnDNXSource.cpp. Referenced by Write(). |
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Writes the given gnGenomeSpec to a DNX file named "filename". Actual sequence and annotation data will be written to GenBank files. The DNX file will then reference any created GenBank files.
References gnBaseHeader::GetHeader(), gnMultiSpec< SubSpec >::GetHeader(), gnBaseSpec::GetName(), gnSourceFactory::GetSourceFactory(), gnMultiSpec< SubSpec >::GetSourceName(), gnMultiSpec< SubSpec >::GetSpec(), gnMultiSpec< SubSpec >::GetSpecListLength(), gnSourceFactory::HasSource(), uint32, ValidateName(), and gnGBKSource::Write(). |
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This method is deprecated. Writes the given gnBaseSource to a DNX file named "filename". Actual sequence and annotation data will be written to GenBank files. The DNX file will then reference any created GenBank files.
References gnBaseSource::GetSpec(), and Write(). |
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Writes the given gnSequence to a DNX file named "filename". Actual sequence and annotation data will be written to GenBank files. The DNX file will then reference any created GenBank files.
References gnSequence::GetSpec(). Referenced by Write(). |
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Definition at line 97 of file gnDNXSource.h. Referenced by GetContigID(), GetContigListLength(), GetContigName(), GetContigSeqLength(), GetSpec(), gnDNXSource(), HasContig(), ParseStream(), SeqRead(), and ~gnDNXSource(). |