contig_item.cpp

来自「ncbi源码」· C++ 代码 · 共 149 行

/*
 * ===========================================================================
 * PRODUCTION $Log: contig_item.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 19:43:55  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.5
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: contig_item.cpp,v 1000.1 2004/06/01 19:43:55 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:
*   Contig item for flat-file
*
*/
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>

#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Delta_seq.hpp>
#include <objects/seq/Seq_literal.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seq/Seg_ext.hpp>

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


BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)


CContigItem::CContigItem(CBioseqContext& ctx) :
    CFlatItem(&ctx), m_Loc(new CSeq_loc)
{
    x_GatherInfo(ctx);
}


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


void CContigItem::x_GatherInfo(CBioseqContext& ctx)
{
    typedef CRef<CSeq_loc>  TLoc;
    if ( !ctx.GetHandle().IsSetInst_Ext() ) {
        return;
    }

    CSeq_loc_mix::Tdata& data = m_Loc->SetMix().Set();
    //const CSeq_inst& inst = ctx.GetHandle().GetSeq_inst();
    //if ( !inst.CanGetExt() ) {
    //    return;
    //}
    const CSeq_ext& ext = ctx.GetHandle().GetInst_Ext();

    if ( ctx.IsSegmented()  &&  ctx.HasParts() ) {
        ITERATE (CSeg_ext::Tdata, it, ext.GetSeg().Get()) {
            data.push_back(*it);
        }
    } else if ( ctx.IsDelta() ) {
        ITERATE (CDelta_ext::Tdata, it, ext.GetDelta().Get()) {
            if ( (*it)->IsLoc() ) {
                CSeq_loc& l = const_cast<CSeq_loc&>((*it)->GetLoc());
                CRef<CSeq_loc> lr(&l);
                data.push_back(lr);
            } else {  // literal
                const CSeq_literal& lit = (*it)->GetLiteral();
                TSeqPos len = lit.CanGetLength() ? lit.GetLength() : 0;
                if ( lit.CanGetSeq_data() ) {
                    // data with 0 length => gap
                    if ( len == 0 ) {
                        data.push_back(TLoc(new CFlatGapLoc(0)));
                    } else {
                        // !!! don't know what to do here
                    }
                } else {
                    // no data => gap
                    data.push_back(TLoc(new CFlatGapLoc(len)));
                }
            }
        }
    }
}


END_SCOPE(objects)
END_NCBI_SCOPE


/*
* ===========================================================================
*
* $Log: contig_item.cpp,v $
* Revision 1000.1  2004/06/01 19:43:55  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 15:51:43  shomrat
* Changes in context
*
* Revision 1.3  2004/02/19 18:04:01  shomrat
* Implemented Contig item
*
* Revision 1.2  2003/12/18 17:43:32  shomrat
* context.hpp moved
*
* Revision 1.1  2003/12/17 20:19:04  shomrat
* Initial Revision (adapted from flat lib)
*
*
* ===========================================================================
*/