gnRAWSource Class Reference

gnRAWSource reads raw sequence data from a text file. More...

#include <gnRAWSource.h>

Inheritance diagram for gnRAWSource:

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Collaboration diagram for gnRAWSource:

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List of all members.

Public Member Functions

gnRAWSourceClone () 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.
gnFileContigGetFileContig (const uint32 contigI) const
 Returns a pointer to the file contig corresponding to contigI or null if none exists.
gnGenomeSpecGetSpec () const
 Get the annotated sequence data as a gnGenomeSpec.
 gnRAWSource (const gnRAWSource &s)
 Clone Constructor copies the specified gnRAWSource.
 gnRAWSource ()
 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.
 ~gnRAWSource ()
 Destructor, frees memory.

Static Public Member Functions

boolean CheckRawData (boolean set=false, boolean check=false)
boolean Write (gnBaseSource *source, const string &filename)
 Writes the specified source to a raw file named "filename".
boolean Write (gnSequence &sequence, const string &filename)
 Writes the specified gnSequence to a raw 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

gnFileContigm_contig
gnGenomeSpecm_spec

Detailed Description

gnRAWSource reads raw sequence data from a text file.

This class reads and writes raw sequence to and from files. A raw sequence does not contain any newlines, fragment delimiters, or other type of annotation. gnRAWSource is used by gnSourceFactory to read files and should only be used directly.when writing out raw files by calling gnRAWSource::Write( mySpec, "C:\\myFile.txt");

Definition at line 35 of file gnRAWSource.h.


Constructor & Destructor Documentation

gnRAWSource::gnRAWSource  ) 
 

Empty Constructor, does nothing.

Definition at line 20 of file gnRAWSource.cpp.

References m_contig.

Referenced by Clone().

gnRAWSource::gnRAWSource const gnRAWSource s  ) 
 

Clone Constructor copies the specified gnRAWSource.

Parameters:
s The gnRAWSource to copy.
Definition at line 27 of file gnRAWSource.cpp.

References gnFileContig::Clone(), and m_contig.

gnRAWSource::~gnRAWSource  ) 
 

Destructor, frees memory.

Definition at line 34 of file gnRAWSource.cpp.

References m_contig.


Member Function Documentation

boolean gnRAWSource::CheckRawData boolean  set = false,
boolean  check = false
[inline, static]
 

Definition at line 109 of file gnRAWSource.h.

Referenced by ParseStream().

gnRAWSource * gnRAWSource::Clone  )  const [inline, virtual]
 

Returns an exact copy of this class.

Implements gnFileSource.

Definition at line 92 of file gnRAWSource.h.

References gnRAWSource().

uint32 gnRAWSource::GetContigID const string &  name  )  const [virtual]
 

Get a contig index by name.

If the source does not contain a contig by the specified name GetContigID returns UINT32_MAX.

Parameters:
name The name of the contig to look for.
Returns:
The index of the named contig or UINT32_MAX.

Implements gnBaseSource.

Definition at line 47 of file gnRAWSource.cpp.

References uint32.

uint32 gnRAWSource::GetContigListLength  )  const [inline, virtual]
 

Get the number of sequence contigs in this source.

Returns:
The number of contigs in this source.

Implements gnBaseSource.

Definition at line 98 of file gnRAWSource.h.

References m_contig, and uint32.

string gnRAWSource::GetContigName const uint32  i  )  const [virtual]
 

Get the name of the specified contig.

Returns an empty string if the specified contig is out of range.

Parameters:
i The index of the contig or ALL_CONTIGS.
Returns:
The name of the contig or an empty string.

Implements gnBaseSource.

Definition at line 52 of file gnRAWSource.cpp.

References uint32.

gnSeqI gnRAWSource::GetContigSeqLength const uint32  i  )  const [virtual]
 

Get the total number of base pairs in the specified contig.

Parameters:
i The index of the contig or ALL_CONTIGS.
Returns:
The length in base pairs of the specified contig.

Implements gnBaseSource.

Definition at line 57 of file gnRAWSource.cpp.

References gnFileContig::GetSeqLength(), gnSeqI, GNSEQI_ERROR, m_contig, and uint32.

gnFileContig * gnRAWSource::GetFileContig const uint32  contigI  )  const [virtual]
 

Returns a pointer to the file contig corresponding to contigI or null if none exists.

Implements gnFileSource.

Definition at line 94 of file gnRAWSource.cpp.

References m_contig, and uint32.

gnGenomeSpec * gnRAWSource::GetSpec  )  const [virtual]
 

Get the annotated sequence data as a gnGenomeSpec.

GetSpec returns a gnGenomeSpec which contains the sequence, header, and feature data contained by this source.

Returns:
The annotated sequence data.

Implements gnBaseSource.

Definition at line 68 of file gnRAWSource.cpp.

References gnGenomeSpec::Clone(), and m_spec.

boolean gnRAWSource::HasContig const string &  name  )  const [virtual]
 

Looks for a contig by name.

Returns true if it finds the contig, otherwise false.

Parameters:
name The name of the contig to look for.
Returns:
True if the named contig exists, false otherwise.

Implements gnBaseSource.

Definition at line 40 of file gnRAWSource.cpp.

boolean gnRAWSource::ParseStream istream &  fin  )  [private, virtual]
 

Implements gnFileSource.

Definition at line 101 of file gnRAWSource.cpp.

References gnMultiSpec< SubSpec >::AddSpec(), CheckRawData(), gnContigSequence, gnSeqI, gnFilter::IsValid(), m_contig, m_spec, gnFileContig::SetName(), gnFileContig::SetRepeatSeqGap(), gnFileContig::SetSectEnd(), gnFileContig::SetSectStart(), gnFileContig::SetSeqLength(), gnContigSpec::SetSourceName(), uint32, and uint64.

boolean gnRAWSource::SeqRead const gnSeqI  start,
char *  buf,
gnSeqI bufLen,
const uint32  contigI = ALL_CONTIGS
[virtual]
 

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.

Parameters:
start The base pair to start reading at.
buf The character array to store base pairs into.
bufLen The number of base pairs to read.
contigI The index of the contig to read or ALL_CONTIGS by default.
Returns:
True if the operation was successful.

Implements gnBaseSource.

Definition at line 64 of file gnRAWSource.cpp.

References gnSeqI, gnFileSource::Read(), and uint32.

boolean gnRAWSource::SeqSeek const gnSeqI  start,
const uint32 contigI,
uint64 startPos,
uint64 readableBytes
[private]
 

boolean gnRAWSource::SeqStartPos const gnSeqI  start,
gnFileContig contig,
uint64 startPos,
uint64 readableBytes
[private]
 

boolean gnRAWSource::Write gnBaseSource source,
const string &  filename
[inline, static]
 

Writes the specified source to a raw file named "filename".

Parameters:
source The source to write out.
filename The name of the file to write.
Returns:
True if successful, false otherwise.
Definition at line 103 of file gnRAWSource.h.

References gnBaseSource::GetSpec(), and Write().

boolean gnRAWSource::Write gnSequence sequence,
const string &  filename
[static]
 

Writes the specified gnSequence to a raw file named "filename".

Parameters:
sequence The gnSequence to write out.
filename The name of the file to write.
Returns:
True if successful, false otherwise.
Definition at line 72 of file gnRAWSource.cpp.

References gnSeqC, gnSeqI, gnSequence::length(), and gnSequence::ToArray().

Referenced by Write().


Member Data Documentation

gnFileContig* gnRAWSource::m_contig [private]
 

Definition at line 87 of file gnRAWSource.h.

Referenced by GetContigListLength(), GetContigSeqLength(), GetFileContig(), gnRAWSource(), ParseStream(), and ~gnRAWSource().

gnGenomeSpec* gnRAWSource::m_spec [private]
 

Definition at line 88 of file gnRAWSource.h.

Referenced by GetSpec(), and ParseStream().


The documentation for this class was generated from the following files:
Generated on Mon Feb 14 19:29:55 2005 for libGenome by doxygen 1.3.8