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gnFASSource Class Reference

gnFASSource reads and writes FastA files. More...

#include <gnFASSource.h>

Inheritance diagram for gnFASSource:


Public Member Functions
	gnFASSource ()
	Empty Constructor, does nothing.
	gnFASSource (const gnFASSource &s)
	Clone Constructor copies the specified gnFASSource.
	~gnFASSource ()
	Destructor, frees memory.
gnFASSource *	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.
gnFileContig *	GetContig (const uint32 i) const
boolean	SeqRead (const gnSeqI start, char *buf, gnSeqI &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, gnSeqI &bufLen)
	Gets raw input from this source.
Static Public Member Functions
void	Write (gnSequence &sequence, const string &filename, boolean write_coords=true, boolean enforce_unique_names=true)
	Write the given gnSequence to a FastA file.
void	Write (gnSequence &sequence, ostream &m_ostream, boolean write_coords=true, boolean enforce_unique_names=true)
	Write the given gnSequence to an ostream.
boolean	Write (gnBaseSource *source, const string &filename)
	Deprecated - do not use.
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
vector< gnFileContig * >	m_contigList

Detailed Description

gnFASSource reads and writes FastA files.

gnFASSource is used by gnSourceFactory to read files. Files can be written in the FastA file format by calling gnFASSource::Write( mySpec, "C:\myFasFile.fas");

Definition at line 32 of file gnFASSource.h.

Constructor & Destructor Documentation

gnFASSource::gnFASSource ( )

Empty Constructor, does nothing.

Definition at line 20 of file gnFASSource.cpp.
References DebugMsg(), gnFilter::fullDNASeqFilter(), gnFileSource::m_openString, and gnFileSource::m_pFilter.
Referenced by Clone().

gnFASSource::gnFASSource ( const gnFASSource & s )

Clone Constructor copies the specified gnFASSource.

Parameters:

s The gnFASSource to copy.

Definition at line 28 of file gnFASSource.cpp.
References m_contigList.

gnFASSource::~gnFASSource ( )

Destructor, frees memory.

Definition at line 36 of file gnFASSource.cpp.
References m_contigList, and gnFileSource::m_ifstream.

Member Function Documentation

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

Returns an exact copy of this class.

Implements gnFileSource.
Definition at line 113 of file gnFASSource.h.
References gnFASSource().

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 ParseStream().

gnFileContig * gnFASSource::GetContig ( const uint32 i ) const

Definition at line 84 of file gnFASSource.cpp.
References m_contigList.

uint32 gnFASSource::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 56 of file gnFASSource.cpp.
References m_contigList, and uint32.

uint32 gnFASSource::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 119 of file gnFASSource.h.
References m_contigList, and uint32.

string gnFASSource::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 65 of file gnFASSource.cpp.
References m_contigList.

gnSeqI gnFASSource::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 72 of file gnFASSource.cpp.
References gnSeqI, GNSEQI_ERROR, m_contigList, and uint32.

gnFileContig * gnFASSource::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 382 of file gnFASSource.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 * gnFASSource::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 358 of file gnFASSource.cpp.
References gnMultiSpec::AddHeader(), gnFragmentSpec::AddSpec(), gnGenomeSpec::AddSpec(), m_contigList, gnBaseSpec::SetName(), gnContigSpec::SetSourceName(), gnMultiSpec::SetSourceName(), and uint32.

boolean gnFASSource::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 47 of file gnFASSource.cpp.
References m_contigList, and uint32.

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

Implements gnFileSource.
Definition at line 388 of file gnFASSource.cpp.
References gnFileContig::AddToSeqLength(), Array< T >::data, gnFileSource::DetermineNewlineType(), ErrorMsg(), isNewLine(), isSpace(), gnFilter::IsValid(), m_contigList, gnFileSource::m_ifstream, gnFileSource::m_newlineSize, gnFileSource::m_pFilter, gnFileContig::SetFileEnd(), gnFileContig::SetFileStart(), gnFileContig::SetName(), gnFileContig::SetRepeatGapSize(), gnFileContig::SetRepeatSeqGap(), gnFileContig::SetRepeatSeqSize(), gnFileContig::SetSectEnd(), gnFileContig::SetSectStart(), uint32, and uint64.

boolean gnFileSource::Read ( const uint64 pos,

char * buf,

gnSeqI & 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 gnFASSource::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 92 of file gnFASSource.cpp.
References Array< T >::data, gnSeqC, gnSeqI, gnFilter::IsValid(), m_contigList, gnFileSource::m_ifstream, gnFileSource::m_pFilter, SeqSeek(), uint32, and uint64.

boolean gnFASSource::SeqSeek ( const gnSeqI start,

const uint32 contigI,

uint64 & startPos,

uint64 & readableBytes

) [private]

Definition at line 178 of file gnFASSource.cpp.
References gnSeqI, m_contigList, SeqStartPos(), and uint64.
Referenced by SeqRead().

boolean gnFASSource::SeqStartPos ( const gnSeqI start,

gnFileContig & contig,

uint64 & startPos,

uint64 & readableBytes

) [private]

Definition at line 206 of file gnFASSource.cpp.
References Array< T >::data, ErrorMsg(), gnFileContig::GetRepeatSeqGapSize(), gnFileContig::GetSectStartEnd(), gnFileContig::HasRepeatSeqGap(), gnFilter::IsValid(), gnFileSource::m_ifstream, gnFileSource::m_pFilter, and uint32.
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 gnFASSource::Write ( gnBaseSource * source,

const string & filename

) [static]

Deprecated - do not use.
Write the given source to a FastA file.
Parameters:

source The spec to write out.

filename The name of the file to write.

Definition at line 259 of file gnFASSource.cpp.
References Array< T >::data, gnBaseSource::GetContigListLength(), gnBaseSource::GetContigName(), gnBaseSource::GetContigSeqLength(), gnSeqC, gnSeqI, gnBaseSource::SeqRead(), and uint32.

void gnFASSource::Write ( gnSequence & sequence,

ostream & m_ostream,

boolean write_coords = true,

boolean enforce_unique_names = true

) [static]

Write the given gnSequence to an ostream.

Parameters:

sequence The gnSequence to write out.

m_ostream The output stream to write to.

write_coords If true each entry's name will be followed by the coordinates of the entry in the context of the entrire file.

enforce_unique_names If true each entry's name will be recorded as they are written. Each successive duplicate name that is found will have an underscore and a number appended to it, indicating the number of entries by the same name which have already been written. Turning this off will yield a slight performance improvement when writing files with a large number of entries. (More than 1000)

Definition at line 293 of file gnFASSource.cpp.
References gnSequence::contigLength(), gnSequence::contigListLength(), gnSequence::contigName(), Array< T >::data, FAS_LINE_WIDTH, gnBaseHeader::GetHeader(), gnMultiSpec::GetHeader(), gnGenomeSpec::GetSpec(), gnSequence::GetSpec(), gnSeqC, gnSeqI, gnSequence::ToArray(), uint32, and uintToString().

void gnFASSource::Write ( gnSequence & sequence,

const string & filename,

boolean write_coords = true,

boolean enforce_unique_names = true

) [static]

Write the given gnSequence to a FastA file.

Parameters:

sequence The gnSequence to write out.

filename The name of the file to write.

write_coords If true each entry's name will be followed by the coordinates of the entry in the context of the entrire file.

enforce_unique_names If true each entry's name will be recorded as they are written. Each successive duplicate name that is found will have an underscore and a number appended to it, indicating the number of entries by the same name which have already been written. Turning this off will yield a slight performance improvement when writing files with a large number of entries. (More than 1000)

Exceptions:

A FileNotOpened() exception may be thrown.

Definition at line 285 of file gnFASSource.cpp.
References FileNotOpened(), and Throw_gnEx.