accession_item.cpp

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/*  $Id: accession_item.cpp 99483 2023-04-04 17:43:43Z 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:  Mati Shomrat, NCBI
*
* File Description:
*   flat-file generator -- accession item implementation
*
*/
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
 
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seqblock/GB_block.hpp>
#include <objects/seqblock/EMBL_block.hpp>
#include <objects/seqloc/Textseq_id.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/seqdesc_ci.hpp>
 
#include <objtools/format/formatter.hpp>
#include <objtools/format/text_ostream.hpp>
#include <objtools/format/items/accession_item.hpp>
#include <objtools/format/context.hpp>
#include <objmgr/util/objutil.hpp>
#include <algorithm>
 
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
 
 
CAccessionItem::CAccessionItem(CBioseqContext& ctx) :
    CFlatItem(&ctx), m_ExtraAccessions(), m_IsSetRegion(false)
{
    x_GatherInfo(ctx);
}
 
IFlatItem::EItem CAccessionItem::GetItemType(void) const
{
    return eItem_Accession;
}
 
 
void CAccessionItem::Format
(IFormatter& formatter,
 IFlatTextOStream& text_os) const
{
    formatter.FormatAccession(*this, text_os);
}
 
 
 
/***************************************************************************/
/*                                  PRIVATE                                */
/***************************************************************************/
 
 
void CAccessionItem::x_GatherInfo(CBioseqContext& ctx)
{
    if (! ctx.GetPrimaryId()) {
        x_SetSkip();
        return;
    }
 
    m_IsNuc = ctx.IsNuc();
 
    const CSeq_id& id = *ctx.GetPrimaryId();
 
    if (!ctx.GetLocation().IsWhole()) {
        // specific region is set
        m_Region.Reset(&ctx.GetLocation());
        m_IsSetRegion = true;
    }
 
    bool okay = true;
    // if no accession, do not show local or general in ACCESSION
    if ((id.IsGeneral()  ||  id.IsLocal())  &&
        (ctx.Config().IsModeEntrez()  ||  ctx.Config().IsModeGBench())) {
            okay = false;
    }
 
    if (okay) {
        m_Accession = id.GetSeqIdString();
 
        if ( ctx.IsWGS()  && ctx.GetLocation().IsWhole() && ctx.GetTech() == CMolInfo::eTech_wgs ) {
            size_t acclen = m_Accession.length();
            size_t nz_len = (m_Accession.substr(0,3) == "NZ_" ? 3 : 0);
            if (acclen >= 12+nz_len) {
                size_t pos = m_Accession.find_first_of("0123456789");
                if (pos == 4+nz_len || pos == 6+nz_len) {
                    size_t stem_len = pos + 2;
                    size_t tail_len = acclen - stem_len;
                    m_WGSAccession = m_Accession;
                    if (m_Accession.find_first_not_of("0", stem_len) != NPOS) {
                        m_WGSAccession.replace(stem_len, tail_len, tail_len, '0');
                    } else {
                        m_WGSAccession.erase();
                    }
                }
            }
        }
    }
 
    // extra accessions not done if we're taking a slice
    // (i.e. command-line args "-from" and "-to" )
    if( ctx.GetLocation().IsWhole() ) {
 
        const list<string>* xtra = nullptr;
        CSeqdesc_CI gb_desc(ctx.GetHandle(), CSeqdesc::e_Genbank);
        if ( gb_desc ) {
            x_SetObject(*gb_desc);
            xtra = &gb_desc->GetGenbank().GetExtra_accessions();
        }
 
        CSeqdesc_CI embl_desc(ctx.GetHandle(), CSeqdesc::e_Embl);
        if ( embl_desc ) {
            x_SetObject(*embl_desc);
            if( embl_desc->GetEmbl().GetExtra_acc().size() > 0 ) {
                xtra = &embl_desc->GetEmbl().GetExtra_acc();
            }
        }
 
        if (xtra) {
            // no validation done if less than a certain number of accessions
            // TODO: When we've switched completely away from C, we should
            //       probably *always* validate accessions.
            const int kAccessionValidationCutoff = 20;
            ITERATE (list<string>, it, *xtra) {
                if( xtra->size() >= kAccessionValidationCutoff ) {
                    if ( ! IsValidAccession(*it) ) {
                        continue;
                    }
                }
                m_ExtraAccessions.push_back(*it);
            }
        }
 
        /// add GPipe accessions as extra if no RefSeq accession
        if (okay && ! id.IsOther() && ! id.IsGpipe()) {
            ITERATE (CBioseq::TId, it, ctx.GetHandle().GetBioseqCore()->GetId()) {
                if ((*it)->IsGpipe()) {
                    m_ExtraAccessions.push_back((*it)->GetGpipe().GetAccession());
                }
            }
        }
 
        sort(m_ExtraAccessions.begin(), m_ExtraAccessions.end());
 
    }
}
 
 
END_SCOPE(objects)
END_NCBI_SCOPE