gff_base_columns.cpp

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/*  $Id: gff_base_columns.cpp 99211 2023-02-27 16:15:10Z ludwigf $
 * ===========================================================================
 *
 *                            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:
 *   GFF file reader
 *
 */
 
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <objects/seq/so_map.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seqfeat/Feat_id.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objects/seqfeat/RNA_gen.hpp>
 
#include <objtools/readers/read_util.hpp>
#include <objtools/readers/gff_base_columns.hpp>
#include <objtools/readers/gff2_reader.hpp>
 
BEGIN_NCBI_SCOPE
 
BEGIN_objects_SCOPE // namespace ncbi::objects::
 
unsigned int CGffBaseColumns::msNextId = 0;
 
//  ============================================================================
CGffBaseColumns::CGffBaseColumns():
//  ============================================================================
    mSeqId(""),
    m_uSeqStart(0),
    m_uSeqStop(0),
    m_strSource(""),
    m_strType(""),
    m_strNormalizedType(""),
    m_pdScore(nullptr),
    m_peStrand(nullptr),
    m_pePhase(nullptr)
{
};
 
//  ============================================================================
CGffBaseColumns::CGffBaseColumns(
//  ============================================================================
    const CGffBaseColumns& rhs):
    mSeqId(rhs.mSeqId),
    m_uSeqStart(rhs.m_uSeqStart),
    m_uSeqStop(rhs.m_uSeqStop),
    m_strSource(rhs.m_strSource),
    m_strType(rhs.m_strType),
    m_strNormalizedType(rhs.m_strNormalizedType),
    m_pdScore(nullptr),
    m_peStrand(nullptr),
    m_pePhase(nullptr)
{
    if (rhs.m_pdScore) {
        m_pdScore = new double(rhs.Score());
    }
    if (rhs.m_peStrand) {
        m_peStrand = new ENa_strand(rhs.Strand());
    }
    if (rhs.m_pePhase) {
        m_pePhase = new TFrame(rhs.Phase());
    }
};
 
//  ============================================================================
CGffBaseColumns::~CGffBaseColumns()
//  ============================================================================
{
    delete m_pdScore;
    delete m_peStrand;
    delete m_pePhase;
};
 
//  ============================================================================
CRef<CSeq_id> CGffBaseColumns::GetSeqId(
    TReaderFlags flags,
    SeqIdResolver seqidresolve ) const
//  ============================================================================
{
    if (!seqidresolve) {
        seqidresolve = CReadUtil::AsSeqId;
    }
    return seqidresolve(Id(), flags, true);
}
 
//  ============================================================================
CRef<CSeq_loc> CGffBaseColumns::GetSeqLoc(
    TReaderFlags flags,
    SeqIdResolver seqidresolve ) const
//  ============================================================================
{
    CRef<CSeq_loc> pLocation(new CSeq_loc);
    pLocation->SetInt().SetId(*GetSeqId(flags, seqidresolve));
    pLocation->SetInt().SetFrom(static_cast<TSeqPos>(SeqStart()));
    pLocation->SetInt().SetTo(static_cast<TSeqPos>(SeqStop()));
    if (IsSetStrand()) {
        pLocation->SetInt().SetStrand(Strand());
    }
    return pLocation;
}
 
//  ----------------------------------------------------------------------------
bool CGffBaseColumns::InitializeFeature(
    TReaderFlags flags,
    CRef<CSeq_feat> pFeature,
    SeqIdResolver seqidresolve ) const
    //  ----------------------------------------------------------------------------
{
    if (!xInitFeatureLocation(flags, pFeature, seqidresolve)) {
        return false;
    }
    if (!xInitFeatureData(flags, pFeature)) {
        return false;
    }
    return xInitFeatureId(flags, pFeature);
}
 
//  ============================================================================
bool CGffBaseColumns::xInitFeatureId(
    TReaderFlags,
    CRef<CSeq_feat> pFeature ) const
//  ============================================================================
{
    unsigned int featId = NextId();
    CRef<CFeat_id> pFeatId(new CFeat_id);
    pFeatId->SetLocal().SetId(featId);
    pFeature->SetId(*pFeatId);
    return true;
}
 
//  ============================================================================
bool CGffBaseColumns::xInitFeatureLocation(
    TReaderFlags flags,
    CRef<CSeq_feat> pFeature,
    SeqIdResolver seqidresolve ) const
//  ============================================================================
{
    pFeature->SetLocation(*GetSeqLoc(flags, seqidresolve));
    return true;
}
 
//  ----------------------------------------------------------------------------
bool CGffBaseColumns::xInitFeatureData(
    TReaderFlags flags,
    CRef<CSeq_feat> pFeature ) const
    //  ----------------------------------------------------------------------------
{
    CSeqFeatData::ESubtype subtype = pFeature->GetData().GetSubtype();
    if (subtype == CSeqFeatData::eSubtype_cdregion) {
        CCdregion::EFrame frame = Phase();
        if (frame == CCdregion::eFrame_not_set) {
            frame = CCdregion::eFrame_one;
        }
        pFeature->SetData().SetCdregion().SetFrame(frame);
        return true;
    }
 
    return true;
}
 
END_objects_SCOPE
END_NCBI_SCOPE