alnvec_row_handle.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: alnvec_row_handle.hpp,v $
 * PRODUCTION Revision 1000.1  2004/04/12 18:16:07  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.4
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_WIDGETS_ALN_MULTIPLE___ALNVEC_ROW_HANDLE__HPP
#define GUI_WIDGETS_ALN_MULTIPLE___ALNVEC_ROW_HANDLE__HPP

/*  $Id: alnvec_row_handle.hpp,v 1000.1 2004/04/12 18:16:07 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 <corelib/ncbiobj.hpp>
#include <objtools/alnmgr/alnvec.hpp>
#include <gui/widgets/aln_multiple/alnmulti_ds.hpp>

BEGIN_NCBI_SCOPE

/// CAlnVecRowHandle is inherited from IAlignRowHandle and represents a row
/// of CAlnVec-based alignment. 
class CAlnVecRowHandle : public IAlignRowHandle
{
public:
    typedef objects::CAlnVec    TAlnVec;
    typedef TAlnVec::TNumrow    TNumrow;
    typedef TAlnVec::TRange     TRange;
    typedef TAlnVec::TSignedRange   TSignedRange;


    CAlnVecRowHandle(const TAlnVec* aln_vec, TNumrow row)
        : m_AlnVec(aln_vec), m_Row(row) {}

    TNumrow     GetRowNum() const;
    const objects::CBioseq_Handle&  GetBioseqHandle() const;
    
    TSignedSeqPos   GetSeqAlnStart() const;
    TSignedSeqPos   GetSeqAlnStop() const;
    TSignedRange    GetSeqAlnRange() const;
    TSignedSeqPos   GetSeqStop() const;  
    bool            IsNegativeStrand() const;  

    string&  GetSeqString (string &buffer, const TRange &seq_rng) const;
    string&  GetAlnSeqString(string &buffer, const TSignedRange &aln_rng) const;    

    TSignedSeqPos  GetAlnPosFromSeqPos(TSeqPos seq_pos, 
                        TAlnVec::ESearchDirection dir = TAlnVec::eNone, 
                        bool try_reverse_dir = true) const;
    TSignedSeqPos  GetSeqPosFromAlnPos(TSeqPos aln_pos, 
                        TAlnVec::ESearchDirection dir = TAlnVec::eNone, 
                        bool try_reverse_dir = true) const;
    
    CRef<TAlnVec::CAlnChunkVec>     GetAlnChunks(const TSignedRange& range,
                                    TAlnVec::TGetChunkFlags flags) const;

protected:
    const objects::CAlnVec* m_AlnVec;
    TNumrow m_Row;
};


inline CAlnVecRowHandle::TNumrow CAlnVecRowHandle::GetRowNum() const
{
    return m_Row;
}
inline const objects::CBioseq_Handle&  CAlnVecRowHandle::GetBioseqHandle() const
{
    return m_AlnVec->GetBioseqHandle(m_Row);
}
inline TSignedSeqPos  CAlnVecRowHandle::GetSeqAlnStart() const
{
    return m_AlnVec->GetSeqAlnStart(m_Row);
}
inline TSignedSeqPos  CAlnVecRowHandle::GetSeqAlnStop() const
{
    return m_AlnVec->GetSeqAlnStop(m_Row);
}
inline TSignedSeqPos  CAlnVecRowHandle::GetSeqStop() const
{
    return m_AlnVec->GetSeqStop(m_Row);
}
inline bool CAlnVecRowHandle::IsNegativeStrand() const
{
    return m_AlnVec->IsNegativeStrand(m_Row);
}
inline CAlnVecRowHandle::TSignedRange  CAlnVecRowHandle::GetSeqAlnRange() const
{
    return m_AlnVec->GetSeqAlnRange(m_Row);
}
inline string&  CAlnVecRowHandle::GetSeqString (string &buffer, 
                                                const TRange &seq_rng) const
{
    return m_AlnVec->GetSeqString(buffer, m_Row, seq_rng);
}

inline string &  CAlnVecRowHandle::GetAlnSeqString(string &buffer, 
                                          const TSignedRange &aln_rng) const
{
    return m_AlnVec->GetAlnSeqString(buffer, m_Row, aln_rng);
}

inline TSignedSeqPos  CAlnVecRowHandle::GetAlnPosFromSeqPos(TSeqPos seq_pos, 
                        TAlnVec::ESearchDirection dir, 
                        bool try_reverse_dir) const
{
    return m_AlnVec->GetAlnPosFromSeqPos(m_Row, seq_pos, dir, try_reverse_dir);
}
    
inline TSignedSeqPos  CAlnVecRowHandle::GetSeqPosFromAlnPos (TSeqPos aln_pos, 
                    TAlnVec::ESearchDirection dir, 
                    bool try_reverse_dir) const
{
    return m_AlnVec->GetSeqPosFromAlnPos(m_Row, aln_pos, dir, try_reverse_dir);
}

inline CRef<CAlnVecRowHandle::TAlnVec::CAlnChunkVec>     
    CAlnVecRowHandle::GetAlnChunks(const TSignedRange& range, 
                                    TAlnVec::TGetChunkFlags flags) const
{
    return m_AlnVec->GetAlnChunks(m_Row, range, flags);
}


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: alnvec_row_handle.hpp,v $
 * Revision 1000.1  2004/04/12 18:16:07  gouriano
 * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.4
 *
 * Revision 1.4  2004/03/08 17:15:04  yazhuk
 * Added GetAlnPosFromSeqPos()
 *
 * Revision 1.3  2004/03/02 15:11:21  yazhuk
 * Added IsNegativeStrand()
 *
 * Revision 1.2  2004/01/08 19:38:48  yazhuk
 * Added GetSeqString()
 *
 * Revision 1.1  2003/10/29 23:29:38  yazhuk
 * Initial revision
 *
 * ===========================================================================
 */

#endif  // GUI_WIDGETS_ALN_MULTIPLE___ALNVEC_ROW_HANDLE__HPP