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gnSourceSpec.h

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// File:            gnSourceSpec.h
// Purpose:         implements gnBaseSpec for source specs
// 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 _gnSourceSpec_h_
#define _gnSourceSpec_h_

#include "gn/gnDefs.h"

#include <string>
#include "gn/gnContigSpec.h"
#include "gn/gnBaseSource.h"

class GNDLLEXPORT gnSourceSpec : public gnContigSpec
{
public:
        gnSourceSpec();
        gnSourceSpec( gnBaseSource* m_pSource, const uint32 m_ContigIndex=ALL_CONTIGS, const gnSeqI start=0, const gnSeqI endI=GNSEQI_END, const boolean revComp = false);
        gnSourceSpec( const gnSourceSpec& s );
        ~gnSourceSpec();

        gnSourceSpec* Clone() const;
// Source Spec Specific functions
        virtual void Clear();
        virtual gnSeqI GetSourceLength() const; 
        virtual gnBaseSource *GetSource() const;

        virtual gnSourceSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const;

protected:
        virtual boolean Read(const gnSeqI start, gnSeqC* buf, uint32& bufLen ) const;
        gnBaseSource* m_pSource;
        
}; // class gnSourceSpec

inline
gnSourceSpec* gnSourceSpec::Clone() const
{
        return new gnSourceSpec( *this );
}
inline
gnSeqI gnSourceSpec::GetSourceLength() const{
        return m_pSource->GetContigSeqLength(m_SourceContigIndex);
}
inline
gnBaseSource* gnSourceSpec::GetSource() const
{
        return m_pSource;
}

inline
boolean gnSourceSpec::Read(const gnSeqI start, gnSeqC* buf, uint32& bufLen) const{
        return m_pSource->SeqRead(start, buf, bufLen, m_SourceContigIndex);
}

#endif
        // _gnSourceSpec_h_

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