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gnDNXSource.h

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// File:            gnDNXSource.h
// Purpose:         Implements gnBaseSource for .DNX 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 _gnDNXSource_h_
#define _gnDNXSource_h_

#include "gn/gnDefs.h"


#include <string>
#include <vector>
#include <fstream>
#include <time.h>

#include "gn/gnSetup.h"
#include "gn/gnFileSource.h"
#include "gn/gnSourceSpec.h"
#include "gn/gnSequence.h"


class GNDLLEXPORT gnDNXSource : public gnFileSource
{
public:
        gnDNXSource();  
        gnDNXSource( const gnDNXSource& s );
        ~gnDNXSource();

        gnDNXSource* Clone() const;

        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);
        static boolean Write(gnGenomeSpec *spec, const string& filename);

        gnGenomeSpec* GetSpec() const;
        gnFileContig* GetFileContig( const uint32 contigI ) const;
private:
        boolean ParseStream( istream& fin );
        static void ValidateName(string& name);

        gnGenomeSpec *m_DNXSpec;
};// class gnDNXSource

inline
gnDNXSource* gnDNXSource::Clone() const
{
        return new gnDNXSource( *this );
}

inline
uint32 gnDNXSource::GetContigListLength() const
{
        return m_DNXSpec->GetSpecListLength();
}
//read sequence data from the file
inline
boolean gnDNXSource::SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI ) 
{
        return m_DNXSpec->SeqRead(start, buf, bufLen, contigI);
}

inline
boolean gnDNXSource::Write(gnSequence& sequence, const string& filename){
        return Write(sequence.GetSpec(), filename);
}
inline
boolean gnDNXSource::Write(gnBaseSource *source, const string& filename){
        return Write(source->GetSpec(), filename);
}
inline
gnGenomeSpec *gnDNXSource::GetSpec() const{
        return m_DNXSpec->Clone();
}

#endif
        // _gnDNXSource_h_

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