/*===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's official duties as a United States Government employee and
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*
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*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
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* ===========================================================================
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*/

#ifndef _hpp_ngs_itf_fragmentitf_
#define _hpp_ngs_itf_fragmentitf_

#ifndef _hpp_ngs_itf_refcount_
#include <ngs/itf/Refcount.hpp>
#endif

struct NGS_Fragment_v1;

namespace ngs
{

    /*----------------------------------------------------------------------
     * forwards
     */
    class StringItf;

    /*----------------------------------------------------------------------
     * FragmentItf
     */
    class   FragmentItf : public Refcount < FragmentItf, NGS_Fragment_v1 >
    {
    public:

        StringItf * getFragmentId () const
            NGS_THROWS ( ErrorMsg );
        StringItf * getFragmentBases () const
            NGS_THROWS ( ErrorMsg );
        StringItf * getFragmentBases ( uint64_t offset ) const
            NGS_THROWS ( ErrorMsg );
        StringItf * getFragmentBases ( uint64_t offset, uint64_t length ) const
            NGS_THROWS ( ErrorMsg );
        StringItf * getFragmentQualities () const
            NGS_THROWS ( ErrorMsg );
        StringItf * getFragmentQualities ( uint64_t offset ) const
            NGS_THROWS ( ErrorMsg );
        StringItf * getFragmentQualities ( uint64_t offset, uint64_t length ) const
            NGS_THROWS ( ErrorMsg );
        bool nextFragment ()
            NGS_THROWS ( ErrorMsg );
        bool isPaired () const
            NGS_THROWS ( ErrorMsg );
        bool isAligned () const
            NGS_THROWS ( ErrorMsg );
    };


} // namespace ngs

#endif // _hpp_ngs_itf_fragmentitf_
