gnABISource Class Reference

gnABISource is not implemented. More...

#include <gnABISource.h>

Inheritance diagram for gnABISource:

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Collaboration diagram for gnABISource:

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List of all members.

Public Member Functions

gnABISourceClone () const
gnFileContigGetContig (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.
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.
 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
gnGenomeSpecm_spec

Detailed Description

gnABISource is not implemented.

Definition at line 26 of file gnABISource.h.


Constructor & Destructor Documentation

gnABISource::gnABISource  ) 
 

Definition at line 14 of file gnABISource.cpp.

References gnFilter::fullDNASeqFilter().

Referenced by Clone().

gnABISource::gnABISource const gnABISource s  ) 
 

Clone Constructor copies the specified gnSEQSource.

Parameters:
s The gnABISource to copy.
Definition at line 19 of file gnABISource.cpp.

References m_contigList.

gnABISource::~gnABISource  ) 
 

Definition at line 27 of file gnABISource.cpp.

References m_contigList.


Member Function Documentation

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

Implements gnFileSource.

Definition at line 68 of file gnABISource.h.

References gnABISource().

gnFileContig* gnABISource::GetContig const uint32  i  )  const
 

uint32 gnABISource::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 50 of file gnABISource.cpp.

References m_contigList, and uint32.

uint32 gnABISource::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 73 of file gnABISource.h.

References m_contigList, and uint32.

string gnABISource::GetContigName 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 61 of file gnABISource.cpp.

References m_contigList, and uint32.

gnSeqI gnABISource::GetContigSeqLength 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 68 of file gnABISource.cpp.

References gnSeqI, GNSEQI_ERROR, m_contigList, and uint32.

gnFileContig * gnABISource::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 95 of file gnABISource.cpp.

References m_contigList, and uint32.

gnGenomeSpec * gnABISource::GetSpec  )  const [inline, 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 78 of file gnABISource.h.

References gnGenomeSpec::Clone(), and m_spec.

boolean gnABISource::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 gnABISource.cpp.

References m_contigList.

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

Implements gnFileSource.

Definition at line 101 of file gnABISource.cpp.

boolean gnABISource::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 81 of file gnABISource.cpp.

References gnSeqI, and uint32.

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

Definition at line 86 of file gnABISource.cpp.

References gnSeqI, m_contigList, SeqStartPos(), uint32, and uint64.

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

Definition at line 90 of file gnABISource.cpp.

References gnSeqI, and uint64.

Referenced by SeqSeek().

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

Writes the specified gnSequence to an ABI file named "filename".

Parameters:
sequence The gnSequence to write out.
filename The name of the file to write.
Returns:
True if successful, false otherwise.


Member Data Documentation

vector< gnFileContig* > gnABISource::m_contigList [private]
 

Definition at line 63 of file gnABISource.h.

Referenced by GetContigID(), GetContigListLength(), GetContigName(), GetContigSeqLength(), GetFileContig(), gnABISource(), HasContig(), SeqSeek(), and ~gnABISource().

gnGenomeSpec* gnABISource::m_spec [private]
 

Definition at line 62 of file gnABISource.h.

Referenced by GetSpec().


The documentation for this class was generated from the following files:
Generated on Mon Feb 14 19:29:44 2005 for libGenome by doxygen 1.3.8