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gnRAWSource.h

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// File:            gnRAWSource.h
// Purpose:         Implements gnBaseSource for raw data files
// Description:     
// Changes:        
// Version:         libGenome 0.1.0 
// Author:          Aaron Darling 
// Last Edited:     April 15, 2001, 10:34:50pm 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        Proprietary 

#ifndef _gnRAWSource_h_
#define _gnRAWSource_h_

#include "gn/gnDefs.h"

#include <string>
#include <fstream>
#include <vector>
#include "gn/gnFileSource.h"
#include "gn/gnFileContig.h"
#include "gn/gnSourceSpec.h"
#include "gn/gnSequence.h"


class GNDLLEXPORT gnRAWSource : public gnFileSource
{
public:
        gnRAWSource();  
        gnRAWSource( const gnRAWSource& s );
        ~gnRAWSource();
        gnRAWSource* Clone() const;
// Contig Access methods        
        uint32 GetContigListLength() const;
        boolean HasContig( const string& name ) const;
        uint32 GetContigID( const string& name ) const;
        string GetContigName( const uint32 i ) const;
        gnSeqI GetContigSeqLength( const uint32 i ) const;

        boolean SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI=ALL_CONTIGS );

        static boolean Write(gnSequence& sequence, const string& filename);
        static boolean Write(gnBaseSource *source, const string& filename);
        gnGenomeSpec *GetSpec() const;
        gnFileContig* GetFileContig( const uint32 contigI ) const;
private:
        boolean SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes );
        boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes );
        boolean ParseStream( istream& fin );
        
        gnFileContig* m_contig; 
        gnGenomeSpec* m_spec;
};// class gnRAWSource
// Clone        
inline
gnRAWSource* gnRAWSource::Clone() const
{
        return new gnRAWSource( *this );
}
// Contig Access methods        
inline
uint32 gnRAWSource::GetContigListLength() const
{
        return m_contig == NULL? 0 : 1;
}
inline
boolean gnRAWSource::Write(gnBaseSource *source, const string& filename){
        gnSequence gns(*source->GetSpec());
        return Write(gns, filename);
}

#endif
        // _gnRAWSource_h_

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