alignment.cpp

来自「ncbi源码」· C++ 代码 · 共 111 行

/*
 * ===========================================================================
 * PRODUCTION $Log: alignment.cpp,v $
 * PRODUCTION Revision 1000.0  2004/06/01 21:19:48  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.3
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: alignment.cpp,v 1000.0 2004/06/01 21:19:48 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.
 *
 * ===========================================================================
 *
 * Authors:  Vlad Lebedev
 *
 * File Description:
 *   CLayoutAlign -- utility class to layout alignments and hold CAlnVec objects
 */

#include <ncbi_pch.hpp>
#include <gui/objutils/alignment.hpp>



BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


CLayoutAlign::CLayoutAlign(const CAlnVec& aln_mgr,
                           const CSeq_align& align)
    : m_AlnMgr(&aln_mgr),
      m_SeqAlign(&align)
{
    TSignedSeqPos start = m_AlnMgr->GetSeqStart(m_AlnMgr->GetAnchor());
    TSignedSeqPos stop  = m_AlnMgr->GetSeqStop (m_AlnMgr->GetAnchor());

    m_Location.Reset(new CSeq_loc());
    m_Location->SetInt().SetFrom(start);
    m_Location->SetInt().SetTo  (stop);

    const CSeq_id& id = m_AlnMgr->GetSeqId(m_AlnMgr->GetAnchor());
    m_Location->SetId(id);
}


END_NCBI_SCOPE



/*
 * ===========================================================================
 * $Log: alignment.cpp,v $
 * Revision 1000.0  2004/06/01 21:19:48  gouriano
 * PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.3
 *
 * Revision 1.3  2004/05/21 22:27:43  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.2  2004/05/14 14:25:20  dicuccio
 * Formatting changes
 *
 * Revision 1.1  2004/04/30 11:48:15  dicuccio
 * Initial commit - split out from src/gui/utils
 *
 * Revision 1.7  2004/04/12 16:50:21  dicuccio
 * Derive alignment range from alignment manager.  Set ID field on location
 *
 * Revision 1.6  2004/03/11 17:49:40  dicuccio
 * Use TSeqRange instead of TRange
 *
 * Revision 1.5  2003/09/19 00:28:59  ucko
 * CLayoutAlign: use an unsigned range per CAlnMap::GetSeqRange's new rettype.
 *
 * Revision 1.4  2003/08/22 15:48:12  dicuccio
 * Added 'USING_SCOPE(objects)'
 *
 * Revision 1.3  2003/08/18 14:47:08  dicuccio
 * Changed nales: CFeature -> CLayoutFeat; CAlignment -> CLayoutAlign; CGraph ->
 * CLayoutGraph; CProtProduct -> CLayoutProtProd.
 *
 * Revision 1.2  2003/07/21 19:35:21  dicuccio
 * Changed storage mechanism - CLayoutObject::GetObject() is now pure virtual.
 * Changed CFeature to wrap a CMappedFeat instead of a CSeq_feat / CSeq_loc pair
 *
 * Revision 1.1  2003/07/18 13:36:41  lebedev
 * Initial revision
 *
 * ===========================================================================
 */