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/////////////////////////////////////////////////////////////////////////////
// DataBase: gnDataBaseSource.h
// Purpose: Implements gnBaseSource for .DataBase files
// Description:
// Changes:
// Version: libGenome 0.5.1
// Author: Aaron Darling
// Modified by:
// Copyright: (c) Aaron Darling
// Licenses: See COPYING file for details
/////////////////////////////////////////////////////////////////////////////
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#ifndef _gnDataBaseSource_h_
#define _gnDataBaseSource_h_
#include "libGenome/gnDefs.h"
#include <string>
#include "gnBaseSource.h"
namespace genome {
/**
* Not yet implemented.
*/
class gnDataBaseSource : public gnBaseSource
{
public:
virtual ~gnDataBaseSourcee(){}
virtual gnDataBaseSource* Clone() const = 0;
virtual gnBaseSource* Clone() const = 0;
virtual boolean Open( std::string openString ) = 0;
virtual boolean Open() = 0;
virtual boolean Close() = 0;
virtual std::string GetOpenString() const = 0;
virtual uint32 GetContigListLength() const = 0;
virtual boolean HasContig( const std::string& name ) const = 0;
virtual uint32 GetContigID( const std::string& name ) const = 0;
virtual std::string GetContigName( const uint32 i ) const = 0;
virtual gnSeqI GetContigSeqLength( const uint32 i ) const = 0;
virtual const gnFilter* GetFilter() const = 0;
virtual boolean SetFilter( gnFilter* filter ) = 0;
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 gnGenomeSpec *GetSpec() const = 0;
private:
gnDataBaseSource(){}
};// class gnDataBaseSource
} // end namespace genome
#endif
// _gnDataBaseSource_h_
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