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gnBaseSource Class Reference

gnBaseSource defines a standard interface for derived classes to provide access to file, database, and network sources of genetic data. More...

#include <gnBaseSource.h>

Inheritance diagram for gnBaseSource:

List of all members.

Public Member Functions
	gnBaseSource ()
virtual	~gnBaseSource ()
	Destructor, frees memory used by this source class.
virtual gnBaseSource *	Clone () const=0
virtual void	Open (string openString)=0
	Opens the source given in "openString" for reading.
virtual void	Open ()=0
	Opens this source for reading.
virtual void	Close ()=0
	Closes the file or connection this source is reading from.
virtual string	GetOpenString () const=0
	Get the location of the source that is being used.
virtual uint32	GetContigListLength () const=0
	Get the number of sequence contigs in this source.
virtual boolean	HasContig (const string &name) const=0
	Looks for a contig by name.
virtual uint32	GetContigID (const string &name) const=0
	Get a contig index by name.
virtual string	GetContigName (const uint32 i) const=0
	Get the name of the specified contig.
virtual gnSeqI	GetContigSeqLength (const uint32 i) const=0
	Get the total number of base pairs in the specified contig.
virtual const gnFilter *	GetFilter () const=0
	Get the filter currently being used to filter unwanted characters out of read sequences.
virtual void	SetFilter (gnFilter *filter)=0
	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)=0
	Gets raw input from this source.
virtual boolean	SeqRead (const gnSeqI start, char *buf, uint32 &bufLen, const uint32 contigI=ALL_CONTIGS)=0
	Gets sequence data from this source.
virtual gnGenomeSpec *	GetSpec () const=0
	Get the annotated sequence data as a gnGenomeSpec.

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Detailed Description

gnBaseSource defines a standard interface for derived classes to provide access to file, database, and network sources of genetic data.

First the data source is opened and parsed, using the open() function. The source class then creates and a gnGenomeSpec containing references to its sequence data. The gnGenomeSpec can then be used by gnSequence to give programmer friendly access to the sequence data.

Definition at line 31 of file gnBaseSource.h.

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Constructor & Destructor Documentation

gnBaseSource::gnBaseSource (    )  [inline]

Definition at line 34 of file gnBaseSource.h.

virtual gnBaseSource::~gnBaseSource (    )  [inline, virtual]

Destructor, frees memory used by this source class. Definition at line 38 of file gnBaseSource.h.

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Member Function Documentation

virtual gnBaseSource* gnBaseSource::Clone (    )  const [pure virtual]

Implements gnClone. Implemented in gnABISource, gnDataBaseSource, gnDataBaseSource, gnDNXSource, gnFASSource, gnFileSource, gnGBKSource, gnRAWSource, and gnSEQSource. Referenced by gnSourceFactory::AddSource(), gnSourceFactory::SetDefaultSourceClass(), and gnSourceFactory::SetSourceClass().

virtual void gnBaseSource::Close (    )  [pure virtual]

Closes the file or connection this source is reading from. Exceptions: IOStreamError  if an error occurs closing the file. Implemented in gnDataBaseSource, and gnFileSource. Referenced by gnSourceFactory::DelSource().

virtual uint32 gnBaseSource::GetContigID (  const string &    name )  const [pure 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. Implemented in gnABISource, gnDataBaseSource, gnDNXSource, gnFASSource, gnGBKSource, gnRAWSource, and gnSEQSource. Referenced by gnDNXSource::ParseStream().

virtual uint32 gnBaseSource::GetContigListLength (    )  const [pure virtual]

Get the number of sequence contigs in this source. Returns: The number of contigs in this source. Implemented in gnABISource, gnDataBaseSource, gnDNXSource, gnFASSource, gnGBKSource, gnRAWSource, and gnSEQSource. Referenced by gnFASSource::Write().

virtual string gnBaseSource::GetContigName (  const uint32    i )  const [pure 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. Implemented in gnABISource, gnDataBaseSource, gnDNXSource, gnFASSource, gnGBKSource, gnRAWSource, and gnSEQSource. Referenced by gnFASSource::Write().

virtual gnSeqI gnBaseSource::GetContigSeqLength (  const uint32    i )  const [pure 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. Implemented in gnABISource, gnDataBaseSource, gnDNXSource, gnFASSource, gnGBKSource, gnRAWSource, and gnSEQSource. Referenced by gnSourceSpec::GetSourceLength(), and gnFASSource::Write().

virtual const gnFilter* gnBaseSource::GetFilter (    )  const [pure virtual]

Get the filter currently being used to filter unwanted characters out of read sequences. Returns: A pointer to the gnFilter currently in use. Implemented in gnDataBaseSource, and gnFileSource.

virtual string gnBaseSource::GetOpenString (    )  const [pure virtual]

Get the location of the source that is being used. Returns: The location string describing this source, usually a file name. Implemented in gnDataBaseSource, and gnFileSource.

virtual gnGenomeSpec* gnBaseSource::GetSpec (    )  const [pure 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. Implemented in gnABISource, gnDataBaseSource, gnDNXSource, gnFASSource, gnGBKSource, gnRAWSource, and gnSEQSource. Referenced by gnSequence::LoadSource(), gnSEQSource::Write(), gnRAWSource::Write(), gnGBKSource::Write(), and gnDNXSource::Write().

virtual boolean gnBaseSource::HasContig (  const string &    name )  const [pure 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. Implemented in gnABISource, gnDataBaseSource, gnDNXSource, gnFASSource, gnGBKSource, gnRAWSource, and gnSEQSource.

virtual void gnBaseSource::Open (    )  [pure virtual]

Opens this source for reading. Exceptions: Will  throw a FileNotOpened exception if the file was not found or was not accessible. Implemented in gnDataBaseSource, and gnFileSource.

virtual void gnBaseSource::Open (  string    openString )  [pure virtual]

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. Implemented in gnDataBaseSource, and gnFileSource. Referenced by gnSourceFactory::AddSource().

virtual boolean gnBaseSource::Read (  const uint64    pos, char *    buf, uint32 &    bufLen )  [pure virtual]

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. Implemented in gnDataBaseSource, and gnFileSource. Referenced by gnSourceHeader::GetHeader(), and gnSourceQualifier::GetValue().

virtual boolean gnBaseSource::SeqRead (  const gnSeqI    start, char *    buf, uint32 &    bufLen, const uint32    contigI = ALL_CONTIGS )  [pure 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. Implemented in gnABISource, gnDataBaseSource, gnDNXSource, gnFASSource, gnGBKSource, gnRAWSource, and gnSEQSource. Referenced by gnSourceSpec::Read(), and gnFASSource::Write().

virtual void gnBaseSource::SetFilter (  gnFilter *    filter )  [pure virtual]

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. Implemented in gnDataBaseSource, and gnFileSource.

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

• gnBaseSource.h

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