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gnFASSource Class Reference

gnFASSource reads and writes FastA files. More...

#include <gnFASSource.h>

Inheritance diagram for gnFASSource::

Public Methods
	gnFASSource ()
	Empty Constructor, does nothing. More...
	gnFASSource (const gnFASSource &s)
	Clone Constructor copies the specified gnFASSource. More...
	~gnFASSource ()
	Destructor, frees memory. More...
gnFASSource*	Clone () const
	Returns an exact copy of this class. More...
uint32	GetContigListLength () const
	Get the number of sequence contigs in this source. More...
boolean	HasContig (const string &nameStr) const
	Looks for a contig by name. More...
uint32	GetContigID (const string &nameStr) const
	Get a contig index by name. More...
string	GetContigName (const uint32 i) const
	Get the name of the specified contig. More...
gnSeqI	GetContigSeqLength (const 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
	deprecated - do not use Writes the given spec to a FastA file named "filename". 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
void	Write (gnSequence &sequence, const string &filename, boolean write_coords=true, boolean enforce_unique_names=true)
	Write the given gnSequence to a FastA file. More...
void	Write (gnSequence &sequence, ostream &m_ostream, boolean write_coords=true, boolean enforce_unique_names=true)
	Write the given gnSequence to an ostream. More...
boolean	Write (gnBaseSource *source, const string &filename)
	Deprecated - do not use. 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
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 33 of file gnFASSource.h.

Constructor & Destructor Documentation

gnFASSource::gnFASSource ( )

Empty Constructor, does nothing.

Definition at line 21 of file gnFASSource.cpp.
Referenced by Clone().

gnFASSource::gnFASSource ( const gnFASSource & s )

Clone Constructor copies the specified gnFASSource.

Parameters:

s The gnFASSource to copy.

Definition at line 29 of file gnFASSource.cpp.

gnFASSource::~gnFASSource ( )

Destructor, frees memory.

Definition at line 37 of file gnFASSource.cpp.

Member Function Documentation

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

Returns an exact copy of this class.

Reimplemented from gnFileSource.
Definition at line 121 of file gnFASSource.h.

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

Definition at line 85 of file gnFASSource.cpp.
Referenced by main().

uint32 gnFASSource::GetContigID ( const string & nameStr ) 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 57 of file gnFASSource.cpp.

uint32 gnFASSource::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 127 of file gnFASSource.h.
Referenced by main().

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.

Reimplemented from gnBaseSource.
Definition at line 66 of file gnFASSource.cpp.

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.

Reimplemented from gnBaseSource.
Definition at line 73 of file gnFASSource.cpp.

gnFileContig * gnFASSource::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 384 of file gnFASSource.cpp.

gnGenomeSpec * gnFASSource::GetSpec ( ) const [virtual]

deprecated - do not use Writes the given spec to a FastA file named "filename".

Parameters:

spec The spec to write out.

filename The name of the file to write.

Returns:
True if successful, false otherwise.

Reimplemented from gnBaseSource.
Definition at line 360 of file gnFASSource.cpp.

boolean gnFASSource::HasContig ( const string & nameStr ) 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 48 of file gnFASSource.cpp.

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

Reimplemented from gnFileSource.
Definition at line 390 of file gnFASSource.cpp.

boolean gnFASSource::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 93 of file gnFASSource.cpp.
Referenced by main().

boolean gnFASSource::SeqSeek ( const gnSeqI start,

const uint32 contigI,

uint64 & startPos,

uint64 & readableBytes ) [private]

Definition at line 178 of file gnFASSource.cpp.
Referenced by SeqRead().

boolean gnFASSource::SeqStartPos ( const gnSeqI start,

gnFileContig & contig,

uint64 & startPos,

uint64 & readableBytes ) [private]

Definition at line 206 of file gnFASSource.cpp.
Referenced by SeqSeek().

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 261 of file gnFASSource.cpp.

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.

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)

Definition at line 295 of file gnFASSource.cpp.

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 287 of file gnFASSource.cpp.
Referenced by WriteData(), and main().

Member Data Documentation

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

Definition at line 117 of file gnFASSource.h.

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

Generated at Thu Apr 4 01:52:05 2002 for libGenome by

gnFASSource Class Reference

Public Methods

Static Public Methods

Private Methods

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation