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gnDataBaseSource Class Reference Not yet implemented. More... #include <gnDataBaseSource.h> Inheritance diagram for gnDataBaseSource:: List of all members. Public Methods virtual  ~gnDataBaseSourcee () virtual gnDataBaseSource*  Clone () const=0 virtual gnBaseSource*  Clone () const=0 virtual boolean  Open (string openString)=0   Opens the source given in "openString" for reading. More... virtual boolean  Open ()=0   Opens this source for reading. More... virtual boolean  Close ()=0   Closes the file or connection this source is reading from. More... virtual string  GetOpenString () const=0   Get the location of the source that is being used. More... virtual uint32  GetContigListLength () const=0   Get the number of sequence contigs in this source. More... virtual boolean  HasContig (const string &name) const=0   Looks for a contig by name. More... virtual uint32  GetContigID (const string &name) const=0   Get a contig index by name. More... virtual string  GetContigName (const uint32 i) const=0   Get the name of the specified contig. More... virtual gnSeqI  GetContigSeqLength (const uint32 i) const=0   Get the total number of base pairs in the specified contig. More... virtual const gnFilter*  GetFilter () const=0   Get the filter currently being used to filter unwanted characters out of read sequences. More... virtual boolean  SetFilter (gnFilter *pFilter)=0   Set the filter that will be used to filter unwanted characters out of the sequence data. More... virtual boolean  Read (const uint64 pos, char *buf, uint32 &len)=0   Gets raw input from this source. More... virtual boolean  SeqRead (const gnSeqI start, char *buf, uint32 &bufLen, const uint32 contigI=ALL_CONTIGS)=0   Gets sequence data from this source. More... virtual gnGenomeSpec*  GetSpec () const=0   Get the annotated sequence data as a gnGenomeSpec. More... Private Methods   gnDataBaseSource () Detailed Description Not yet implemented. Definition at line 24 of file gnDataBaseSource.h. Constructor & Destructor Documentation gnDataBaseSource::~gnDataBaseSourcee ( ) [inline, virtual]   Definition at line 27 of file gnDataBaseSource.h. gnDataBaseSource::gnDataBaseSource ( ) [inline, private]   Definition at line 48 of file gnDataBaseSource.h. Member Function Documentation gnBaseSource * gnDataBaseSource::Clone ( ) const [pure virtual]   Reimplemented from gnBaseSource. gnBaseSource * gnDataBaseSource::Clone ( ) const [pure virtual]   Reimplemented from gnBaseSource. boolean gnDataBaseSource::Close ( ) [pure virtual]   Closes the file or connection this source is reading from. Exceptions: IOStreamError   if an error occurs closing the file. Reimplemented from gnBaseSource. 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. Reimplemented from gnBaseSource. uint32 gnDataBaseSource::GetContigListLength ( ) const [pure virtual]   Get the number of sequence contigs in this source. Returns: The number of contigs in this source. Reimplemented from gnBaseSource. 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. Reimplemented from gnBaseSource. 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. Reimplemented from gnBaseSource. 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. Reimplemented from gnBaseSource. 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. Reimplemented from gnBaseSource. 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. Reimplemented from gnBaseSource. 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. Reimplemented from gnBaseSource. 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. Reimplemented from gnBaseSource. 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. Reimplemented from gnBaseSource. boolean gnDataBaseSource::Read ( const uint64 pos, char * buf, uint32 & len ) [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. len   The number of bytes to read. Returns: True if the operation was successful. Reimplemented from gnBaseSource. boolean gnDataBaseSource::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. 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. boolean gnDataBaseSource::SetFilter ( gnFilter * pFilter ) [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. Reimplemented from gnBaseSource. The documentation for this class was generated from the following file: gnDataBaseSource.h