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gnSourceSpec.h

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/////////////////////////////////////////////////////////////////////////////
// File:            gnSourceSpec.h
// Purpose:         implements gnBaseSpec for source specs
// Description:     
// Changes:        
// Version:         libGenome 0.5.1 
// Author:          Aaron Darling 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        See COPYING file for details 
/////////////////////////////////////////////////////////////////////////////
#ifndef _gnSourceSpec_h_
#define _gnSourceSpec_h_

#include "gn/gnDefs.h"

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

/**
 * gnSourceSpec stores sequence and annotation data from another source.
 * @see gnContigSpec
 * @see gnBaseSpec
 */
class GNDLLEXPORT gnSourceSpec : public gnContigSpec
{
public:
        /**
         * Empty constructor.
         */
        gnSourceSpec();
        /**
         * Constructor, creates a gnSourceSpec using sequence data in the given source.
         * A circular spec will be created if the end index is greater than the start.
         * @param m_pSource The source to read base pairs from.
         * @param m_ContigIndex The index of the contig in the source, ALL_CONTIGS by default.
         * @param startI The index to start reading base pairs from the source.
         * @param endI The index to stop reading base pairs from the source.
         * @param revComp True if the sequence is read reverse complement.
         */
        gnSourceSpec( gnBaseSource* m_pSource, const uint32 m_ContigIndex=ALL_CONTIGS, const gnSeqI startI=0, const gnSeqI endI=GNSEQI_END, const boolean revComp = false);
        /**
         * Copy constructor.
         * @param s the gnSourceSpec to copy.
         */
        gnSourceSpec( const gnSourceSpec& s );
        ~gnSourceSpec();

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

        /**
         * Copies a specified range of bases and returns a pointer to
         * the resulting gnSourceSpec.  You must delete the copy when you
         * are finished with it.
         * @param startI The first base pair to copy
         * @param len The length of the piece to copy
         * @return A copy of the gnSourceSpec containing only the specified bases
         */
        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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