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gnABISource Class Reference

gnABISource is not implemented. More...

#include <gnABISource.h>

Inheritance diagram for gnABISource::

Public Methods
	gnABISource ()
	gnABISource (const gnABISource &s)
	Clone Constructor copies the specified gnSEQSource. More...
	~gnABISource ()
gnABISource*	Clone () const
uint32	GetContigListLength () const
	Get the number of sequence contigs in this source. More...
boolean	HasContig (const string &name) const
	Looks for a contig by name. More...
uint32	GetContigID (const string &name) const
	Get a contig index by name. More...
string	GetContigName (uint32 i) const
	Get the name of the specified contig. More...
gnSeqI	GetContigSeqLength (uint32 i) const
	Get the total number of base pairs in the specified contig. More...
gnFileContig*	GetContig (const uint32 i) const
boolean	SeqRead (const gnSeqI start, char *buf, uint32 &bufLen, const uint32 contigI=ALL_CONTIGS)
	Gets sequence data from this source. More...
gnGenomeSpec*	GetSpec () const
	Get the annotated sequence data as a gnGenomeSpec. More...
gnFileContig*	GetFileContig (const uint32 contigI) const
	Returns a pointer to the file contig corresponding to contigI or null if none exists. More...
Static Public Methods
boolean	Write (gnSequence &sequence, const string &filename)
	Writes the specified gnSequence to an ABI file named "filename". More...
Private Methods
boolean	SeqSeek (const gnSeqI start, const uint32 &contigI, uint64 &startPos, uint64 &readableBytes)
boolean	SeqStartPos (const gnSeqI start, gnFileContig &contig, uint64 &startPos, uint64 &readableBytes)
boolean	ParseStream (istream &fin)
Private Attributes
gnGenomeSpec*	m_spec
vector< gnFileContig* >	m_contigList

Detailed Description

gnABISource is not implemented.

Definition at line 27 of file gnABISource.h.

Constructor & Destructor Documentation

gnABISource::gnABISource ( )

Definition at line 15 of file gnABISource.cpp.
Referenced by Clone().

gnABISource::gnABISource ( const gnABISource & s )

Clone Constructor copies the specified gnSEQSource.

Parameters:

s The gnABISource to copy.

Definition at line 20 of file gnABISource.cpp.

gnABISource::~gnABISource ( )

Definition at line 28 of file gnABISource.cpp.

Member Function Documentation

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

Reimplemented from gnFileSource.
Definition at line 69 of file gnABISource.h.

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.

Reimplemented from gnBaseSource.
Definition at line 51 of file gnABISource.cpp.

uint32 gnABISource::GetContigListLength ( ) const [inline, virtual]

Get the number of sequence contigs in this source.

Returns:
The number of contigs in this source.

Reimplemented from gnBaseSource.
Definition at line 74 of file gnABISource.h.

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.

Reimplemented from gnBaseSource.
Definition at line 62 of file gnABISource.cpp.

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.

Reimplemented from gnBaseSource.
Definition at line 69 of file gnABISource.cpp.

gnFileContig * gnABISource::GetFileContig ( const uint32 contigI ) const [virtual]

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

Reimplemented from gnFileSource.
Definition at line 96 of file gnABISource.cpp.

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.

Reimplemented from gnBaseSource.
Definition at line 79 of file gnABISource.h.

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.

Reimplemented from gnBaseSource.
Definition at line 41 of file gnABISource.cpp.

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

Reimplemented from gnFileSource.
Definition at line 102 of file gnABISource.cpp.

boolean gnABISource::SeqRead ( const gnSeqI start,

char * buf,

uint32 & 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.

len 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.

Reimplemented from gnBaseSource.
Definition at line 82 of file gnABISource.cpp.

boolean gnABISource::SeqSeek ( const gnSeqI start,

const uint32 & contigI,

uint64 & startPos,

uint64 & readableBytes ) [private]

Definition at line 87 of file gnABISource.cpp.

boolean gnABISource::SeqStartPos ( const gnSeqI start,

gnFileContig & contig,

uint64 & startPos,

uint64 & readableBytes ) [private]

Definition at line 91 of file gnABISource.cpp.
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< gnFileContig* > [private]

Definition at line 64 of file gnABISource.h.

gnGenomeSpec * gnABISource::m_spec [private]

Definition at line 63 of file gnABISource.h.

The documentation for this class was generated from the following files:

Generated at Thu Apr 4 01:52:04 2002 for libGenome by

gnABISource Class Reference

Public Methods

Static Public Methods

Private Methods

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation