gnomon_engine.hpp

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#ifndef ALGO_GNOMON___GNOMON_ENGINE__HPP
#define ALGO_GNOMON___GNOMON_ENGINE__HPP
 
/*  $Id: gnomon_engine.hpp 100690 2023-08-30 14:46:42Z souvorov $
 * ===========================================================================
 *
 *                            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
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Authors:  Alexandre Souvorov
 *
 * File Description:
 *
 */
 
#include <corelib/ncbistd.hpp>
#include "gnomon_seq.hpp"
#include "hmm.hpp"
 
class CTerminal;
class CCodingRegion;
class CNonCodingRegion;
class CSeqScores;
class CParse;
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(gnomon)
 
struct CGnomonEngine::SGnomonEngineImplData {
    SGnomonEngineImplData(CConstRef<CHMMParameters> hmm_params, CResidueVec&& sequence, TSignedSeqRange range, SPhyloCSFSlice* pcsf_slice);
    SGnomonEngineImplData(CConstRef<CHMMParameters> hmm_params, const CResidueVec& sequence, TSignedSeqRange range, SPhyloCSFSlice* pcsf_slice);
    ~SGnomonEngineImplData();
 
    CResidueVec       m_seq;
    CDoubleStrandSeq  m_ds;
    TSignedSeqRange   m_range;
    int               m_gccontent;
 
    CConstRef<CHMMParameters> m_hmm_params;
 
    template<class C>
    void GetHMMParameter(const C*& param)
    {
        param = dynamic_cast<const C*>( & m_hmm_params->GetParameter(C::class_id(),m_gccontent));
    }
 
    const CWAM_Acceptor<2>*       m_acceptor;
    const CWAM_Donor<2>*          m_donor;
    const CWMM_Start*             m_start;
    const CWAM_Stop*              m_stop;
    const CMC3_CodingRegion<5>*   m_cdr;
    const CMC_NonCodingRegion<5>* m_ncdr;
    const CMC_NonCodingRegion<5>* m_intrg;
    const CIntronParameters*      m_intron_params;
    const CIntergenicParameters*  m_intergenic_params;
    const CExonParameters*        m_exon_params;
    const SPhyloCSFSlice*         m_pcsf_slice;
 
    unique_ptr<CSeqScores>        m_ss;
    unique_ptr<CParse>            m_parse;
};
 
END_SCOPE(gnomon)
END_NCBI_SCOPE
 
#endif  // ALGO_GNOMON___GNOMON_ENGINE__HPP