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gnRAWSource Class Reference

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

#include <gnRAWSource.h>

Inheritance diagram for gnRAWSource:


Public Member Functions
	gnRAWSource ()
	Empty Constructor, does nothing.
	gnRAWSource (const gnRAWSource &s)
	Clone Constructor copies the specified gnRAWSource.
	~gnRAWSource ()
	Destructor, frees memory.
gnRAWSource *	Clone () const
	Returns an exact copy of this class.
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 (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.
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 a raw file named "filename".
boolean	Write (gnBaseSource *source, const string &filename)
	Writes the specified source to a raw 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
gnFileContig *	m_contig
gnGenomeSpec *	m_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, and gnFileSource::m_openString.
Referenced by Clone().

gnRAWSource::gnRAWSource ( const gnRAWSource & s )

Clone Constructor copies the specified gnRAWSource.

Parameters:

s The gnRAWSource to copy.

Definition at line 26 of file gnRAWSource.cpp.
References gnFileContig::Clone(), and m_contig.

gnRAWSource::~gnRAWSource ( )

Destructor, frees memory.

Definition at line 32 of file gnRAWSource.cpp.
References m_contig, and gnFileSource::m_ifstream.

Member Function Documentation

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

Returns an exact copy of this class.

Implements gnFileSource.
Definition at line 90 of file gnRAWSource.h.
References gnRAWSource().

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().

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 45 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 96 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 50 of file gnRAWSource.cpp.

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 55 of file gnRAWSource.cpp.
References gnFileContig::GetSeqLength(), gnSeqI, GNSEQI_ERROR, and m_contig.

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 92 of file gnRAWSource.cpp.
References m_contig.

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 * 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 66 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 38 of file gnRAWSource.cpp.

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

Implements gnFileSource.
Definition at line 99 of file gnRAWSource.cpp.
References gnFragmentSpec::AddSpec(), gnGenomeSpec::AddSpec(), Array< T >::data, gnSeqI, gnFilter::IsValid(), m_contig, gnFileSource::m_ifstream, gnFileSource::m_pFilter, m_spec, gnFileContig::SetRepeatSeqGap(), gnFileContig::SetSectEnd(), gnFileContig::SetSectStart(), gnFileContig::SetSeqLength(), gnContigSpec::SetSourceName(), uint32, and uint64.

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 SeqRead().

boolean gnRAWSource::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 62 of file gnRAWSource.cpp.
References gnFileSource::Read().

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]

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 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 101 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 70 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 85 of file gnRAWSource.h.
Referenced by GetContigListLength(), GetContigSeqLength(), GetFileContig(), gnRAWSource(), ParseStream(), and ~gnRAWSource().

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(), ParseStream(), gnGBKSource::ParseStream(), gnFASSource::ParseStream(), gnFileSource::Read(), gnSEQSource::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), gnSEQSource::SeqStartPos(), gnGBKSource::SeqStartPos(), gnFASSource::SeqStartPos(), gnABISource::~gnABISource(), gnDNXSource::~gnDNXSource(), gnFASSource::~gnFASSource(), gnGBKSource::~gnGBKSource(), ~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::gnABISource(), gnFASSource::gnFASSource(), gnFileSource::gnFileSource(), gnGBKSource::gnGBKSource(), 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::gnABISource(), gnDNXSource::gnDNXSource(), gnFASSource::gnFASSource(), gnFileSource::gnFileSource(), gnGBKSource::gnGBKSource(), gnSEQSource::gnSEQSource(), gnSEQSource::ParseStream(), ParseStream(), gnGBKSource::ParseStream(), gnFASSource::ParseStream(), gnSEQSource::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), gnSEQSource::SeqStartPos(), gnGBKSource::SeqStartPos(), gnFASSource::SeqStartPos(), and gnFileSource::SetFilter().

gnGenomeSpec* gnRAWSource::m_spec [private]

Definition at line 86 of file gnRAWSource.h.
Referenced by GetSpec(), and ParseStream().

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

Generated on Mon Feb 3 02:34:51 2003 for libGenome by

1.3-rc3

gnRAWSource 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