sequence_item.cpp

来自「ncbi源码」· C++ 代码 · 共 171 行

/*
 * ===========================================================================
 * PRODUCTION $Log: sequence_item.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 19:45:28  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.7
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: sequence_item.cpp,v 1000.1 2004/06/01 19:45:28 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 -- origin item implementation
*
*/
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>

#include <objects/seq/Bioseq.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objmgr/util/sequence.hpp>

#include <objtools/format/formatter.hpp>
#include <objtools/format/text_ostream.hpp>
#include <objtools/format/items/sequence_item.hpp>
#include <objtools/format/context.hpp>


BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)


CSequenceItem::CSequenceItem
(TSeqPos from,
 TSeqPos to,
 bool first, 
 CBioseqContext& ctx) :
    CFlatItem(&ctx),
    m_From(from), m_To(to - 1), m_First(first)
{
    x_GatherInfo(ctx);
}


void CSequenceItem::Format
(IFormatter& formatter,
 IFlatTextOStream& text_os) const

{
    formatter.FormatSequence(*this, text_os);
}


const CSeqVector& CSequenceItem::GetSequence(void) const
{
    return m_Sequence;
}


TSeqPos CSequenceItem::GetFrom(void) const
{
    return m_From + 1;
}


TSeqPos CSequenceItem::GetTo(void) const
{
    return m_To + 1;
}


bool CSequenceItem::IsFirst(void) const
{
    return m_First;
}


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


void CSequenceItem::x_GatherInfo(CBioseqContext& ctx)
{
    x_SetObject(*ctx.GetHandle().GetCompleteBioseq());

    const CSeq_loc& loc = ctx.GetLocation();
    TSeqPos offset = loc.GetStart(kInvalidSeqPos);
    TSeqPos start = m_From + offset;
    TSeqPos end   = min(m_To + offset, ctx.GetHandle().GetInst_Length() - 1);
    
    CSeq_loc region;
    CSeq_loc::TInt& ival = region.SetInt();
    region.SetId(*ctx.GetPrimaryId());
    ival.SetFrom(start);
    ival.SetTo(end);
    
    m_Sequence = 
        ctx.GetHandle().GetSequenceView(region, CBioseq_Handle::eViewConstructed);

    CSeqVector::TCoding code = CSeq_data::e_Iupacna;
    if ( ctx.IsProt() ) {
        code = ctx.Config().IsModeRelease() ?
            CSeq_data::e_Iupacaa : CSeq_data::e_Ncbieaa;
    }
    m_Sequence.SetCoding(code);
}


END_SCOPE(objects)
END_NCBI_SCOPE


/*
* ===========================================================================
*
* $Log: sequence_item.cpp,v $
* Revision 1000.1  2004/06/01 19:45:28  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.7
*
* Revision 1.7  2004/05/21 21:42:54  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.6  2004/05/07 15:23:51  shomrat
* Removed unreferenced varaible
*
* Revision 1.5  2004/04/27 15:14:36  shomrat
* Bug fix
*
* Revision 1.4  2004/04/22 15:56:17  shomrat
* Support partial region
*
* Revision 1.3  2004/02/11 22:56:37  shomrat
* use IsModeRelease method
*
* Revision 1.2  2003/12/18 17:43:36  shomrat
* context.hpp moved
*
* Revision 1.1  2003/12/17 20:24:39  shomrat
* Initial Revision (adapted from flat lib)
*
*
* ===========================================================================
*/