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 0.1.0
    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_