accession_item.cpp

来自「ncbi源码」· C++ 代码 · 共 167 行

/*
 * ===========================================================================
 * PRODUCTION $Log: accession_item.cpp,v $
 * PRODUCTION Revision 1000.2  2004/06/01 19:43:44  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.5
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: accession_item.cpp,v 1000.2 2004/06/01 19:43:44 gouriano Exp $
* ===========================================================================
*
*                            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 "utils.hpp"


BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)


CAccessionItem::CAccessionItem(CBioseqContext& ctx) :
    CFlatItem(&ctx), m_ExtraAccessions(0), m_IsSetRegion(false)
{
    x_GatherInfo(ctx);
}


void CAccessionItem::Format
(IFormatter& formatter,
 IFlatTextOStream& text_os) const
{
    formatter.FormatAccession(*this, text_os);
}



/***************************************************************************/
/*                                  PRIVATE                                */
/***************************************************************************/


void CAccessionItem::x_GatherInfo(CBioseqContext& ctx)
{
    if ( ctx.GetPrimaryId() == 0 ) {
        x_SetSkip();
        return;
    }

    m_Accession = ctx.GetPrimaryId()->GetSeqIdString();

    if ( ctx.IsWGS()  && ctx.GetLocation().IsWhole() ) {
        size_t acclen = m_Accession.length();
        m_WGSAccession = m_Accession;
        if ( acclen == 12  &&  !NStr::EndsWith(m_WGSAccession, "000000") ) {
            m_WGSAccession.replace(acclen - 6, 6, 6, '0');
        } else if ( acclen == 13  &&  !NStr::EndsWith(m_WGSAccession, "0000000") ) {
            m_WGSAccession.replace(acclen - 7, 7, 7, '0');
        } else if ( acclen == 15  &&  !NStr::EndsWith(m_WGSAccession, "00000000") ) {
            m_WGSAccession.replace(acclen - 8, 8, 8, '0');
        } else {
            m_WGSAccession.erase();
        }
    }
    
    const list<string>* xtra = 0;
    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);
        xtra = &embl_desc->GetEmbl().GetExtra_acc();
    }

    if ( xtra != 0 ) {
        ITERATE (list<string>, it, *xtra) {
            if ( ValidateAccession(*it) ) {
                m_ExtraAccessions.push_back(*it);
            }
        }
    }

    if ( !ctx.GetLocation().IsWhole() ) {
        // specific region is set
        const CSeq_loc& loc = ctx.GetLocation();
        m_Region.SetFrom(loc.GetStart(kInvalidSeqPos) + 1);
        m_Region.SetTo(loc.GetEnd(kInvalidSeqPos) + 1);
        m_IsSetRegion = true;
    }
}


END_SCOPE(objects)
END_NCBI_SCOPE


/*
* ===========================================================================
*
* $Log: accession_item.cpp,v $
* Revision 1000.2  2004/06/01 19:43:44  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.5
*
* Revision 1.5  2004/05/21 21:42:54  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.4  2004/04/22 15:50:40  shomrat
* Changes in context; + Region
*
* Revision 1.3  2004/04/13 16:44:59  shomrat
* Added WGS accession
*
* Revision 1.2  2003/12/18 17:43:31  shomrat
* context.hpp moved
*
* Revision 1.1  2003/12/17 20:17:45  shomrat
* Initial Revision (adapted from flat lib)
*
*
* ===========================================================================
*/