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gnABISource Class Reference

gnABISource is not implemented. More...

#include <gnABISource.h>

Inheritance diagram for gnABISource:


Public Member Functions
	gnABISource ()
	gnABISource (const gnABISource &s)
	Clone Constructor copies the specified gnSEQSource.
	~gnABISource ()
gnABISource *	Clone () const
uint32	GetContigListLength () const
	Get the number of sequence contigs in this source.
boolean	HasContig (const string &name) const
	Looks for a contig by name.
uint32	GetContigID (const string &name) const
	Get a contig index by name.
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.
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.
gnGenomeSpec *	GetSpec () const
	Get the annotated sequence data as a gnGenomeSpec.
gnFileContig *	GetFileContig (const uint32 contigI) const
	Returns a pointer to the file contig corresponding to contigI or null if none exists.
virtual void	Open (string openString)
	Opens the source given in "openString" for reading.
virtual void	Open ()
	Opens this source for reading.
virtual void	Close ()
	Closes the file or connection this source is reading from.
virtual string	GetOpenString () const
	Get the location of the source that is being used.
virtual const gnFilter *	GetFilter () const
	Get the filter currently being used to filter unwanted characters out of read sequences.
virtual void	SetFilter (gnFilter *filter)
	Set the filter that will be used to filter unwanted characters out of the sequence data.
virtual boolean	Read (const uint64 pos, char *buf, uint32 &bufLen)
	Gets raw input from this source.
Static Public Member Functions
boolean	Write (gnSequence &sequence, const string &filename)
	Writes the specified gnSequence to an ABI file named "filename".
Protected Member Functions
void	DetermineNewlineType ()
Protected Attributes
string	m_openString
ifstream	m_ifstream
const gnFilter *	m_pFilter
gnNewlineType	m_newlineType
uint32	m_newlineSize
Private Member Functions
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 26 of file gnABISource.h.

Constructor & Destructor Documentation

gnABISource::gnABISource ( )

Definition at line 14 of file gnABISource.cpp.
References gnFilter::fullDNASeqFilter(), gnFileSource::m_openString, and gnFileSource::m_pFilter.
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, and gnFileSource::m_ifstream.

Member Function Documentation

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

Implements gnFileSource.
Definition at line 68 of file gnABISource.h.
References gnABISource().

void gnFileSource::Close ( ) [virtual, inherited]

Closes the file or connection this source is reading from.

Exceptions:

IOStreamError if an error occurs closing the file.

Implements gnBaseSource.
Definition at line 56 of file gnFileSource.cpp.
References IOStreamFailed(), gnFileSource::m_ifstream, and Throw_gnEx.

void gnFileSource::DetermineNewlineType ( ) [protected, inherited]

Definition at line 74 of file gnFileSource.cpp.
References gnNewlineMac, gnNewlineUnix, gnNewlineWindows, gnFileSource::m_ifstream, gnFileSource::m_newlineSize, and gnFileSource::m_newlineType.
Referenced by gnGBKSource::ParseStream(), and gnFASSource::ParseStream().

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.

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, and m_contigList.

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.

const gnFilter * gnFileSource::GetFilter ( ) const [inline, virtual, inherited]

Get the filter currently being used to filter unwanted characters out of read sequences.

Returns:
A pointer to the gnFilter currently in use.

Implements gnBaseSource.
Definition at line 68 of file gnFileSource.h.
References gnFileSource::m_pFilter.

string gnFileSource::GetOpenString ( ) const [inline, virtual, inherited]

Get the location of the source that is being used.

Returns:
The location string describing this source, usually a file name.

Implements gnBaseSource.
Definition at line 62 of file gnFileSource.h.
References gnFileSource::m_openString.

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.

void gnFileSource::Open ( ) [virtual, inherited]

Opens this source for reading.

Exceptions:

Will throw a FileNotOpened exception if the file was not found or was not accessible.

Implements gnBaseSource.
Definition at line 48 of file gnFileSource.cpp.
References FileNotOpened(), gnFileSource::m_ifstream, gnFileSource::m_openString, and Throw_gnEx.

void gnFileSource::Open ( string openString ) [virtual, inherited]

Opens the source given in "openString" for reading.

Parameters:

openString The name of the source (file, network URL, or database) to open.

Exceptions:

Will throw a FileNotOpened exception if the file was not found or was not accessible. Will propagate a FileUnreadable exception if the file format was invalid.

Implements gnBaseSource.
Definition at line 29 of file gnFileSource.cpp.
References FileNotOpened(), gnFileSource::m_ifstream, gnFileSource::m_openString, gnFileSource::ParseStream(), and Throw_gnEx.

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

Implements gnFileSource.
Definition at line 101 of file gnABISource.cpp.

boolean gnFileSource::Read ( const uint64 pos,

char * buf,

uint32 & bufLen

) [virtual, inherited]

Gets raw input from this source.
Read will attempt to read "bufLen" bytes starting at "pos" directly from the source. It stores the data in "buf", and returns the actual number of bytes read in bufLen. Read will return false if a serious error occurs.
Parameters:

pos The position in the file to start reading.

buf The character array to store data into.

bufLen The number of bytes to read.

Returns:
True if the operation was successful.

Implements gnBaseSource.
Definition at line 63 of file gnFileSource.cpp.
References gnFileSource::m_ifstream.
Referenced by gnRAWSource::SeqRead().

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.

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.

boolean gnABISource::SeqSeek ( const gnSeqI start,

const uint32 & contigI,

uint64 & startPos,

uint64 & readableBytes

) [private]

Definition at line 86 of file gnABISource.cpp.
References SeqStartPos().

boolean gnABISource::SeqStartPos ( const gnSeqI start,

gnFileContig & contig,

uint64 & startPos,

uint64 & readableBytes

) [private]

Definition at line 90 of file gnABISource.cpp.
Referenced by SeqSeek().

void gnFileSource::SetFilter ( gnFilter * filter ) [inline, virtual, inherited]

Set the filter that will be used to filter unwanted characters out of the sequence data.

Parameters:

filter The filter to remove unwanted characters from the sequence.

Exceptions:

NullPointer is thrown if the specified filter pointer is null.

Implements gnBaseSource.
Definition at line 74 of file gnFileSource.h.
References gnFileSource::m_pFilter, NullPointer(), and Throw_gnEx.

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(), and ~gnABISource().

ifstream gnFileSource::m_ifstream [protected, inherited]

Definition at line 53 of file gnFileSource.h.
Referenced by gnFileSource::Close(), gnFileSource::DetermineNewlineType(), gnFileSource::gnFileSource(), gnFileSource::Open(), gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), gnFASSource::ParseStream(), gnFileSource::Read(), gnSEQSource::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), gnSEQSource::SeqStartPos(), gnGBKSource::SeqStartPos(), gnFASSource::SeqStartPos(), ~gnABISource(), gnDNXSource::~gnDNXSource(), gnFASSource::~gnFASSource(), gnGBKSource::~gnGBKSource(), gnRAWSource::~gnRAWSource(), and gnSEQSource::~gnSEQSource().

uint32 gnFileSource::m_newlineSize [protected, inherited]

Definition at line 56 of file gnFileSource.h.
Referenced by gnFileSource::DetermineNewlineType(), gnFileSource::gnFileSource(), gnGBKSource::ParseStream(), gnFASSource::ParseStream(), and gnGBKSource::SeqStartPos().

gnNewlineType gnFileSource::m_newlineType [protected, inherited]

Definition at line 55 of file gnFileSource.h.
Referenced by gnFileSource::DetermineNewlineType(), and gnFileSource::gnFileSource().

string gnFileSource::m_openString [protected, inherited]

Definition at line 52 of file gnFileSource.h.
Referenced by gnFileSource::GetOpenString(), gnABISource(), gnFASSource::gnFASSource(), gnFileSource::gnFileSource(), gnGBKSource::gnGBKSource(), gnRAWSource::gnRAWSource(), gnSEQSource::gnSEQSource(), and gnFileSource::Open().

const gnFilter* gnFileSource::m_pFilter [protected, inherited]

Definition at line 54 of file gnFileSource.h.
Referenced by gnFileSource::GetFilter(), gnABISource(), gnDNXSource::gnDNXSource(), gnFASSource::gnFASSource(), gnFileSource::gnFileSource(), gnGBKSource::gnGBKSource(), gnSEQSource::gnSEQSource(), gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), gnFASSource::ParseStream(), gnSEQSource::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), gnSEQSource::SeqStartPos(), gnGBKSource::SeqStartPos(), gnFASSource::SeqStartPos(), and gnFileSource::SetFilter().

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 3 02:34:43 2003 for libGenome by

1.3-rc3

gnABISource Class Reference

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation