mate_pair.cpp

来自「ncbi源码」· C++ 代码 · 共 141 行

/*
 * ===========================================================================
 * PRODUCTION $Log: mate_pair.cpp,v $
 * PRODUCTION Revision 1000.0  2004/06/01 21:20:56  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.3
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: mate_pair.cpp,v 1000.0 2004/06/01 21:20:56 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:
 *   CLayoutMatePair -- utility class to layout mate pairs (a special type of
 *      pairwise alignments and hold a set of CLayoutPWAlign
 */


#include <ncbi_pch.hpp>
#include <gui/objutils/mate_pair.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objtools/alnmgr/alnvec.hpp>


BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


CLayoutMatePair::CLayoutMatePair(const TAlignList& aligns)
    : m_SeqAligns(aligns)
    , m_LibraryId(eLibrary_NotSet)
    , m_ErrorType(eError_NotSet)
{
    if (m_SeqAligns.size() != 1) {
        m_ErrorType = eError_NoError;
    }

    const CSeq_id* id = NULL;
    TSeqRange range;
    ITERATE (TAlignList, iter, m_SeqAligns) {
        const CLayoutPWAlign& pw = **iter;
        range += pw.GetLocation().GetTotalRange();
        id = &pw.GetAlignMgr().GetSeqId(pw.GetAlignMgr().GetAnchor());

        const CSeq_align& align = pw.GetAlignment();
        int type = 0;
        if (m_ErrorType != eError_NoError  &&
            align.GetNamedScore("bad matepair code", type)) {
            m_ErrorType = static_cast<EErrorType>(type);
        }
        align.GetNamedScore("matepair library", m_LibraryId);
    }

    if (m_LibraryId == eLibrary_NotSet) {
        m_LibraryId = eLibrary_NotFound;
    }

    if (m_ErrorType == eError_NotSet) {
        m_ErrorType = eError_NoError;
    }

    if (id) {
        m_Location.Reset(new CSeq_loc());
        m_Location->SetInt().SetFrom(range.GetFrom());
        m_Location->SetInt().SetTo  (range.GetTo());
        m_Location->SetId(*id);
    }
}


const CObject* CLayoutMatePair::GetObject(TSeqPos pos) const
{
    ITERATE (TAlignList, iter, m_SeqAligns) {
        const CObject* obj = (*iter)->GetObject(pos);
        if (obj) {
            return obj;
        }
    }
    return NULL;
}



END_NCBI_SCOPE



/*
 * ===========================================================================
 * $Log: mate_pair.cpp,v $
 * Revision 1000.0  2004/06/01 21:20:56  gouriano
 * PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.3
 *
 * Revision 1.3  2004/05/21 22:27:44  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.2  2004/05/10 18:22:10  dicuccio
 * Added recognition of mate pair library and error codes
 *
 * Revision 1.1  2004/04/30 11:48:16  dicuccio
 * Initial commit - split out from src/gui/utils
 *
 * Revision 1.4  2004/04/20 19:16:08  dicuccio
 * Converted to use a set of pairwise alignments
 *
 * Revision 1.3  2004/04/15 13:00:11  lebedev
 * Changed GetObject to return NULL or const pointer based on given position
 *
 * Revision 1.2  2004/04/12 16:50:54  dicuccio
 * Redesign CLayoutMatePair to store an alignment manager internally
 *
 * Revision 1.1  2004/04/05 16:11:00  lebedev
 * Initial revision
 *
 * ===========================================================================
 */