gnDataBaseSource.h Source File

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# gnDataBaseSource.h

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    00001 /////////////////////////////////////////////////////////////////////////////
    00002 // DataBase:        gnDataBaseSource.h
    00003 // Purpose:         Implements gnBaseSource for .DataBase files
    00004 // Description:
    00005 // Changes:
    00006 // Version:         libGenome 0.5.1
    00007 // Author:          Aaron Darling
    00008 // Modified by:
    00009 // Copyright:       (c) Aaron Darling
    00010 // Licenses:        See COPYING file for details
    00011 /////////////////////////////////////////////////////////////////////////////
    00012 #ifndef _gnDataBaseSource_h_
    00013 #define _gnDataBaseSource_h_
    00014
    00015 #include "gn/gnDefs.h"
    00016
    00017 #include <string>
    00018 #include "gnBaseSource.h"
    00019
    00020 /**
    00021  * Not yet implemented.
    00022  */
    00023 class gnDataBaseSource : public gnBaseSource
    00024 {
    00025 public:
    00026         virtual ~gnDataBaseSourcee(){}
    00027
    00028         virtual gnDataBaseSource* Clone() const = 0;
    00029
    00030         virtual gnBaseSource* Clone() const = 0;
    00031
    00032         virtual boolean Open( string openString ) = 0;
    00033         virtual boolean Open() = 0;
    00034         virtual boolean Close() = 0;
    00035         virtual string GetOpenString() const = 0;
    00036         virtual uint32 GetContigListLength() const = 0;
    00037         virtual boolean HasContig( const string& name ) const = 0;
    00038         virtual uint32 GetContigID( const string& name ) const = 0;
    00039         virtual string GetContigName( const uint32 i ) const = 0;
    00040         virtual gnSeqI GetContigSeqLength( const uint32 i ) const = 0;
    00041         virtual const gnFilter* GetFilter() const = 0;
    00042         virtual boolean SetFilter( gnFilter* filter ) = 0;
    00043         virtual boolean Read( const uint64 pos, char* buf, uint32& bufLen) = 0;
    00044         virtual boolean SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI=ALL_CONTIGS ) = 0;
    00045         virtual gnGenomeSpec *GetSpec() const = 0;
    00046 private:
    00047         gnDataBaseSource(){}
    00048 };// class gnDataBaseSource
    00049
    00050 #endif
    00051         // _gnDataBaseSource_h_