gnDataBaseSource Class Reference

Not yet implemented. More...

#include <gnDataBaseSource.h>

Inheritance diagram for gnDataBaseSource:

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Collaboration diagram for gnDataBaseSource:

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List of all members.

Public Member Functions

virtual gnBaseSourceClone () const =0
virtual gnDataBaseSourceClone () const =0
virtual boolean Close ()=0
 Closes the file or connection this source is reading from.
virtual uint32 GetContigID (const string &name) const =0
 Get a contig index by name.
virtual uint32 GetContigListLength () const =0
 Get the number of sequence contigs in this source.
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 gnFilterGetFilter () const =0
 Get the filter currently being used to filter unwanted characters out of read sequences.
virtual string GetOpenString () const =0
 Get the location of the source that is being used.
virtual gnGenomeSpecGetSpec () const =0
 Get the annotated sequence data as a gnGenomeSpec.
virtual boolean HasContig (const string &name) const =0
 Looks for a contig by name.
virtual boolean Open ()=0
 Opens this source for reading.
virtual boolean Open (string openString)=0
 Opens the source given in "openString" for reading.
virtual boolean Read (const uint64 pos, char *buf, uint32 &bufLen)=0
virtual boolean SeqRead (const gnSeqI start, char *buf, uint32 &bufLen, const uint32 contigI=ALL_CONTIGS)=0
virtual boolean SetFilter (gnFilter *filter)=0
 Set the filter that will be used to filter unwanted characters out of the sequence data.
virtual ~gnDataBaseSourcee ()

Private Member Functions

 gnDataBaseSource ()

Detailed Description

Not yet implemented.

Definition at line 23 of file gnDataBaseSource.h.


Constructor & Destructor Documentation

virtual gnDataBaseSource::~gnDataBaseSourcee  )  [inline, virtual]
 

Definition at line 26 of file gnDataBaseSource.h.

gnDataBaseSource::gnDataBaseSource  )  [inline, private]
 

Definition at line 47 of file gnDataBaseSource.h.


Member Function Documentation

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

Implements gnBaseSource.

virtual gnDataBaseSource* gnDataBaseSource::Clone  )  const [pure virtual]
 

Implements gnBaseSource.

virtual boolean gnDataBaseSource::Close  )  [pure virtual]
 

Closes the file or connection this source is reading from.

Exceptions:
IOStreamError if an error occurs closing the file.

Implements gnBaseSource.

virtual uint32 gnDataBaseSource::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.

Implements gnBaseSource.

virtual uint32 gnDataBaseSource::GetContigListLength  )  const [pure virtual]
 

Get the number of sequence contigs in this source.

Returns:
The number of contigs in this source.

Implements gnBaseSource.

virtual string gnDataBaseSource::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.

Implements gnBaseSource.

virtual gnSeqI gnDataBaseSource::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.

Implements gnBaseSource.

virtual const gnFilter* gnDataBaseSource::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.

Implements gnBaseSource.

virtual string gnDataBaseSource::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.

Implements gnBaseSource.

virtual gnGenomeSpec* gnDataBaseSource::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.

Implements gnBaseSource.

virtual boolean gnDataBaseSource::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.

Implements gnBaseSource.

virtual boolean gnDataBaseSource::Open  )  [pure virtual]
 

Opens this source for reading.

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

Implements gnBaseSource.

virtual boolean gnDataBaseSource::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.

Implements gnBaseSource.

virtual boolean gnDataBaseSource::Read const uint64  pos,
char *  buf,
uint32 bufLen
[pure virtual]
 

virtual boolean gnDataBaseSource::SeqRead const gnSeqI  start,
char *  buf,
uint32 bufLen,
const uint32  contigI = ALL_CONTIGS
[pure virtual]
 

virtual boolean gnDataBaseSource::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.

Implements gnBaseSource.


The documentation for this class was generated from the following file:
Generated on Mon Feb 14 19:29:48 2005 for libGenome by doxygen 1.3.8