gff_base_columns.hpp

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/*  $Id: gff_base_columns.hpp 99481 2023-04-04 13:16:28Z stakhovv $
 * ===========================================================================
 *
 *                            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 TReaderFlags = long; //technical debt: duplicated in reader_base
    using SeqIdResolver = CRef<CSeq_id> (*)(const string&, TReaderFlags, 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(
        TReaderFlags,
        SeqIdResolver = nullptr ) const;
 
    CRef<CSeq_loc> GetSeqLoc(
        TReaderFlags,
        SeqIdResolver seqidresolve = nullptr) const;
 
    // feature initialization:
    virtual bool InitializeFeature(
        TReaderFlags,
        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(
        TReaderFlags,
        CRef<CSeq_feat> ) const;
 
    virtual bool xInitFeatureLocation(
        TReaderFlags,
        CRef<CSeq_feat>,
        SeqIdResolver = nullptr ) const;
 
    virtual bool xInitFeatureData(
        TReaderFlags,
        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