gnDataBaseSource.h Source File

00001 
00002 // DataBase:        gnDataBaseSource.h
00003 // Purpose:         Implements gnBaseSource for .DataBase files
00004 // Description:     
00005 // Changes:        
00006 // Version:         libGenome 0.1.0 
00007 // Author:          Aaron Darling 
00008 // Last Edited:     April 15, 2001, 10:34:50pm 
00009 // Modified by:     
00010 // Copyright:       (c) Aaron Darling 
00011 // Licenses:        Proprietary 
00013 #ifndef _gnDataBaseSource_h_
00014 #define _gnDataBaseSource_h_
00015 
00016 #include "gn/gnDefs.h"
00017 
00018 #include <string>
00019 #include "gnBaseSource.h"
00020 
00024 class gnDataBaseSource : public gnBaseSource
00025 {
00026 public:
00027         virtual ~gnDataBaseSourcee(){}
00028 
00029         virtual gnDataBaseSource* Clone() const = 0;
00030 
00031         virtual gnBaseSource* Clone() const = 0;
00032 
00033         virtual boolean Open( string openString ) = 0;
00034         virtual boolean Open() = 0;
00035         virtual boolean Close() = 0;
00036         virtual string GetOpenString() const = 0;
00037         virtual uint32 GetContigListLength() const = 0;
00038         virtual boolean HasContig( const string& name ) const = 0;
00039         virtual uint32 GetContigID( const string& name ) const = 0;
00040         virtual string GetContigName( const uint32 i ) const = 0;
00041         virtual gnSeqI GetContigSeqLength( const uint32 i ) const = 0;
00042         virtual const gnFilter* GetFilter() const = 0;
00043         virtual boolean SetFilter( gnFilter* pFilter ) = 0;
00044         virtual boolean Read( const uint64 pos, char* buf, uint32& len) = 0;
00045         virtual boolean SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI=ALL_CONTIGS ) = 0;
00046         virtual gnGenomeSpec *GetSpec() const = 0;
00047 private:
00048         gnDataBaseSource(){}
00049 };// class gnDataBaseSource
00050 
00051 #endif
00052         // _gnDataBaseSource_h_