alnvec_multi_ds.cpp

来自「ncbi源码」· C++ 代码 · 共 194 行

/*
 * ===========================================================================
 * PRODUCTION $Log: alnvec_multi_ds.cpp,v $
 * PRODUCTION Revision 1000.2  2004/06/01 21:07:18  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.8
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: alnvec_multi_ds.cpp,v 1000.2 2004/06/01 21:07:18 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:  Andrey Yazhuk
 *
 * File Description:
 *
 */

#include <ncbi_pch.hpp>
#include <gui/widgets/aln_multiple/alnvec_multi_ds.hpp>

#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>


BEGIN_NCBI_SCOPE
USING_SCOPE(ncbi::objects);


CAlnVecMultiDataSource::CAlnVecMultiDataSource()
{
}

CAlnVecMultiDataSource::~CAlnVecMultiDataSource()
{
    x_ClearHandles();
}

int     CAlnVecMultiDataSource::GetConsensusRow() const
{
    return x_GetConsensusRow();
}

CAlnVecMultiDataSource::TNumrow  CAlnVecMultiDataSource::GetNumRows (void) const 
{
    return (TNumrow) m_AlnMgr->GetNumRows();
}

TSeqPos  CAlnVecMultiDataSource::GetAlnStart (void) const
{
    return m_AlnMgr->GetAlnStart();
}

TSeqPos  CAlnVecMultiDataSource::GetAlnStop (void) const
{
    return m_AlnMgr->GetAlnStop();
}

bool  CAlnVecMultiDataSource::IsSetAnchor (void) const
{
    return m_AlnMgr->IsSetAnchor();
}

CAlnVecMultiDataSource::TNumrow  CAlnVecMultiDataSource::GetAnchor (void) const
{
    return m_AlnMgr->GetAnchor();
}

void  CAlnVecMultiDataSource::SetAnchor (TNumrow anchor)
{
    m_AlnMgr->SetAnchor(anchor);
}

void  CAlnVecMultiDataSource::UnsetAnchor (void)
{
    m_AlnMgr->UnsetAnchor();
}

bool    CAlnVecMultiDataSource::CanGetId(TNumrow row) const
{
    return (row >= 0  &&  row < m_AlnMgr->GetNumRows());
}

const CSeq_id&  CAlnVecMultiDataSource::GetSeqId(TNumrow row) const
{
    return m_AlnMgr->GetSeqId(row);
}

const CBioseq_Handle &  CAlnVecMultiDataSource::GetBioseqHandle(TNumrow row) const
{
    return m_AlnMgr->GetBioseqHandle(row);
}

TSignedSeqPos  CAlnVecMultiDataSource::GetAlnPosFromSeqPos(TNumrow for_row, TSeqPos aln_pos, 
                                                        ESearchDirection dir, 
                                                        bool try_reverse_dir) const 
{
    return m_AlnMgr->GetAlnPosFromSeqPos(for_row, aln_pos, (CAlnVec::ESearchDirection) dir, try_reverse_dir);
}

TSignedSeqPos  CAlnVecMultiDataSource::GetSeqPosFromAlnPos(TNumrow row, TSeqPos seq_pos, 
                                            ESearchDirection dir, 
                                            bool try_reverse_dir) const
{
    return m_AlnMgr->GetSeqPosFromAlnPos(row, seq_pos, (CAlnVec::ESearchDirection) dir, try_reverse_dir);
}

void  CAlnVecMultiDataSource::SetGapChar (TResidue gap_char)
{
    m_AlnMgr->SetGapChar(gap_char);
}

const IAlignRowHandle*  CAlnVecMultiDataSource::GetRowHandle(TNumrow row) const
{
    return static_cast<const IAlignRowHandle*>(m_Handles[row]);
}

void CAlnVecMultiDataSource::x_ClearHandles()
{
    NON_CONST_ITERATE(THandleVector, it, m_Handles) {
        delete *it;
    }
    m_Handles.clear();
}

void CAlnVecMultiDataSource::x_CreateHandles()
{
    TNumrow row_n = m_AlnMgr->GetNumRows();
    m_Handles.resize(row_n);
    for( TNumrow r = 0; r < row_n;  r++ )   {
        m_Handles[r] = new CAlnVecRowHandle(m_AlnMgr, r);
    }
}

END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: alnvec_multi_ds.cpp,v $
 * Revision 1000.2  2004/06/01 21:07:18  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.8
 *
 * Revision 1.8  2004/05/21 22:27:52  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.7  2004/04/06 13:37:31  dicuccio
 * Removed dead code
 *
 * Revision 1.6  2004/03/24 19:20:02  yazhuk
 * Commented traces
 *
 * Revision 1.5  2004/02/11 15:26:55  yazhuk
 * Removed constructors with arguments
 *
 * Revision 1.4  2003/12/10 19:03:46  yazhuk
 * Added const specifier to CanGetId() and GetSeqId().
 *
 * Revision 1.3  2003/12/10 17:04:59  yazhuk
 * Changed row identification from mandatory CBioseqHandle to optional CSeq_id.
 * Clean-up
 *
 * Revision 1.2  2003/12/08 15:13:47  yazhuk
 * Moved constructors from .hpp
 *
 * Revision 1.1  2003/10/29 23:29:48  yazhuk
 * Initial revision
 *
 * ===========================================================================
 */