cross_aln_ds.cpp

来自「ncbi源码」· C++ 代码 · 共 159 行

/*
 * ===========================================================================
 * PRODUCTION $Log: cross_aln_ds.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 21:06:26  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: cross_aln_ds.cpp,v 1000.1 2004/06/01 21:06:26 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
 *
 */



#include <ncbi_pch.hpp>
#include <gui/widgets/aln_crossaln/cross_aln_ds.hpp>


BEGIN_NCBI_SCOPE
USING_SCOPE(ncbi::objects);



CCrossAlnDataSource::CCrossAlnDataSource(const CSeq_annot& annot, CScope& scope)
    : CHitMatrixDataSource(annot, scope)
{
}

CCrossAlnDataSource::CCrossAlnDataSource(const CSeq_align_set& aset, CScope& scope)
    : CHitMatrixDataSource(aset, scope)
{
}

CCrossAlnDataSource::~CCrossAlnDataSource()
{
}



bool CCrossAlnDataSource::SelectIds(const TIdRef& q_id, const TIdRef& s_id)
{
    bool b_ok = CHitMatrixDataSource::SelectIds(q_id, s_id);
    const THitAdapterCont& hit_adapts = GetHits();

    TSignedSeqPos off1  = INT_MAX, off2  = INT_MAX;
    TSeqPos start1 = INT_MAX, start2 = INT_MAX;
    TSeqPos stop1  = 0, stop2 = 0;

    ITERATE(THitAdapterCont, iter, hit_adapts) {
        for (int idx = 0;  idx != (*iter).GetElemsCount();  idx++) {
            TSignedSeqPos qs = (*iter).GetQueryStart  (idx);
            TSignedSeqPos ss = (*iter).GetSubjectStart(idx);
            TSeqPos      len = (*iter).GetLength(idx);
            
            off1 = min(off1, qs);
            off2 = min(off2, ss);
            
            start1 = min(start1, TSeqPos(qs));
            start2 = min(start2, TSeqPos(ss));
            
            stop1 = max(stop1, qs+len);
            stop2 = max(stop2, ss+len);
        }
    }
    // FixMe: Only Totalrange is really needed
    m_Offset = off1 - off2;
    m_QueryRange   = TSeqRange(start1, stop1);
    m_SubjectRange = TSeqRange(start2, stop2);
    m_TotalRange   = TSeqRange(min(start1, start2),
                            max(stop1, stop2) );

    if (m_Offset < 0) {
        m_QueryRange   = TSeqRange(start1 - m_Offset, stop1 - m_Offset);
        m_SubjectRange = TSeqRange(start2, stop2);
    } else {
        m_QueryRange   = TSeqRange(start1, stop1);
        m_SubjectRange = TSeqRange(start2 + m_Offset, stop2 + m_Offset);
    }
    
    m_TotalRange   = TSeqRange(min(m_QueryRange.GetFrom(), m_SubjectRange.GetFrom()),
                            max(m_QueryRange.GetTo(), m_SubjectRange.GetTo()) );
    return b_ok;
}


TSignedSeqPos CCrossAlnDataSource::GetOffset() const
{
    return m_Offset;
}                      

const TSeqRange& CCrossAlnDataSource::GetQueryRange() const
{
    return m_QueryRange;
}                      

const TSeqRange& CCrossAlnDataSource::GetSubjectRange() const
{
    return m_SubjectRange;
}                      

const TSeqRange& CCrossAlnDataSource::GetTotalRange() const
{
    return m_TotalRange;
}                      


END_NCBI_SCOPE



/*
 * ===========================================================================
 * $Log: cross_aln_ds.cpp,v $
 * Revision 1000.1  2004/06/01 21:06:26  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
 *
 * Revision 1.4  2004/05/21 22:27:51  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.3  2004/03/11 17:50:41  dicuccio
 * Updated typedefs: dropped TDimension, TPosition, TIndex, TColor; use TSeqRange
 * instead of TRange
 *
 * Revision 1.2  2003/12/22 21:44:34  ucko
 * Avoid deque<>::const_iterator::operator->, which fails to compile on
 * GCC 2.95.x due to a typo in its STL implementation. :-/
 *
 * Revision 1.1  2003/12/22 13:12:32  lebedev
 * Initial revision
 *
 * ===========================================================================
 */