/*  $Id: gff_base_columns.hpp 665737 2023-04-12 18:55:59Z ivanov $
 * ===========================================================================
 *
 *                            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.
 *
 * ===========================================================================
 *
 * Author: Frank Ludwig
 *
 * File Description:
 *   GFF3 transient data structures
 *
 */

#ifndef OBJTOOLS_READERS___GFF_BASE_COLUMNS__HPP
#define OBJTOOLS_READERS___GFF_BASE_COLUMNS__HPP

#include <objects/seqfeat/Cdregion.hpp>

BEGIN_NCBI_SCOPE
BEGIN_objects_SCOPE

//  ============================================================================
class CGffBaseColumns
//  ============================================================================
{
public:
    using TFrame = CCdregion::EFrame;
    using SeqIdResolver = CRef<CSeq_id> (*)(const string&, unsigned int, bool);

    CGffBaseColumns();

    CGffBaseColumns(
        const CGffBaseColumns& rhs);

    virtual ~CGffBaseColumns();

    //
    // accessors:
    const string& Id() const {
        return mSeqId;
    };

    TSeqPos SeqStart() const {
        return m_uSeqStart;
    };

    TSeqPos SeqStop() const {
        return m_uSeqStop;
    };

    const string& Source() const {
        return m_strSource;
    };

    const string& Type() const {
        return m_strType;
    };

    const string& NormalizedType() const {
        return m_strNormalizedType;
    };


    double Score() const {
        return IsSetScore() ? *m_pdScore : 0.0;
    };

    ENa_strand Strand() const {
        return IsSetStrand() ? *m_peStrand : eNa_strand_unknown;
    };

    TFrame Phase() const {
        return IsSetPhase() ? *m_pePhase : CCdregion::eFrame_not_set;
    };

    bool IsSetScore() const {
        return m_pdScore != nullptr;
    }

    bool IsSetStrand() const {
        return m_peStrand != nullptr;
    }

    bool IsSetPhase() const {
        return m_pePhase != nullptr;
    }

    CRef<CSeq_id> GetSeqId(
        int,
        SeqIdResolver = nullptr ) const;

    CRef<CSeq_loc> GetSeqLoc(
        int,
        SeqIdResolver seqidresolve = nullptr) const;

    // feature initialization:
    virtual bool InitializeFeature(
        int,
        CRef<CSeq_feat>,
        SeqIdResolver = nullptr ) const;

    virtual void SetExtent(
        TSeqPos seqStart,
        TSeqPos seqStop) {
        m_uSeqStart = seqStart;
        m_uSeqStop = seqStop;
    }

    virtual void SetType(
        const string& recType) {
        m_strType = m_strNormalizedType =recType;
        NStr::ToLower(m_strNormalizedType);
    }

    virtual bool xInitFeatureId(
        int, //flags
        CRef<CSeq_feat> ) const;

    virtual bool xInitFeatureLocation(
        int,
        CRef<CSeq_feat>,
        SeqIdResolver = nullptr ) const;

    virtual bool xInitFeatureData(
        int,
        CRef<CSeq_feat>) const;

    // utility:
    static unsigned int NextId() {
        return ++msNextId;
    };

    static void ResetId() {
        msNextId = 0;
    };


protected:
    string mSeqId;
    TSeqPos m_uSeqStart;
    TSeqPos m_uSeqStop;
    string m_strSource;
    string m_strType;
    string m_strNormalizedType;
    double* m_pdScore;
    ENa_strand* m_peStrand;
    TFrame* m_pePhase;

    static unsigned int msNextId;
};


END_objects_SCOPE
END_NCBI_SCOPE

#endif // OBJTOOLS_READERS___GFF_BASE_COLUMNS__HPP
