hit_data_adapter.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: hit_data_adapter.hpp,v $
 * PRODUCTION Revision 1000.1  2004/04/12 18:16:40  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.3
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_WIDGETS_HIT_MATRIX___HIT_DATA_ADAPTER__HPP
#define GUI_WIDGETS_HIT_MATRIX___HIT_DATA_ADAPTER__HPP

/*  $Id: hit_data_adapter.hpp,v 1000.1 2004/04/12 18:16:40 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/ncbistd.hpp>

#include <objects/seq/Seq_annot.hpp>
#include <objmgr/scope.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqalign/Score.hpp>
#include <objects/general/Object_id.hpp>
#include <serial/iterator.hpp>

BEGIN_NCBI_SCOPE
USING_SCOPE(objects);

class CHitElemDataAdapter;

/// Wraps a CSeq_align containing CDense_seg and provides a simple API for 
/// interpreting it as a pairwaise alignment of two sequences.
///
    
class CHitDataAdapter
{
public:
    typedef CDense_seg::TDim     TDim;
    typedef list< CRef< CScore > >  TScore; 

    CHitDataAdapter(const CSeq_align& align, const CDense_seg& denseg, 
                            int q_index, int s_index)
    :   m_pSeqAlign(&align),
        m_pDenseSeg(&denseg),
        m_QueryIndex(q_index),
        m_SubjectIndex(s_index)
    {
    }
    
    CHitDataAdapter&    operator=(const CHitDataAdapter& hit)
    {
        m_pSeqAlign = hit.m_pSeqAlign;
        m_pDenseSeg = hit.m_pDenseSeg;
        m_QueryIndex = hit.m_QueryIndex;
        m_SubjectIndex = hit.m_SubjectIndex;
        return *this;
    }

    inline  TDim   GetElemsCount() const
    {
        return m_pDenseSeg->GetNumseg();
    }
    
    inline CHitElemDataAdapter GetElem(TDim elem_index);
    
    inline const CHitElemDataAdapter GetElem(TDim elem_index)   const;
    
    inline TSignedSeqPos  GetQueryStart(TDim elem_index) const
    {
        TDim index = m_QueryIndex + elem_index * m_pDenseSeg->GetDim();
        return m_pDenseSeg->GetStarts()[index];
    }
    inline TSignedSeqPos  GetSubjectStart(TDim elem_index) const
    {
        TDim index = m_SubjectIndex + elem_index * m_pDenseSeg->GetDim();
        return m_pDenseSeg->GetStarts()[index];
    }
    inline TSeqPos      GetLength(TDim elem_index) const
    {
        return m_pDenseSeg->GetLens()[elem_index];
    }
    inline ENa_strand  GetQueryStrand(TDim elem_index) const
    {
        TDim index = m_QueryIndex + elem_index * m_pDenseSeg->GetDim();
        return m_pDenseSeg->GetStrands()[index];
    }
    inline ENa_strand  GetSubjectStrand(TDim elem_index) const
    {
        TDim index = m_SubjectIndex + elem_index * m_pDenseSeg->GetDim();
        return m_pDenseSeg->GetStrands()[index];
    }    
    inline double   GetScoreValue(const CObject_id& id) const
    {
        const CSeq_align::TScore&   scores = m_pSeqAlign->GetScore();
        ITERATE(CSeq_align::TScore, itS, scores)   {
            const CScore&   score = **itS;
            _ASSERT(score.CanGetId());
            if(score.GetId().Compare(id) == 0)  { // Match
                const CScore::C_Value& val = score.GetValue();
                switch(val.Which()) {
                case CScore::C_Value::e_Real: return val.GetReal();
                case CScore::C_Value::e_Int: return val.GetInt();
                default:    _ASSERT(false);
                }    
            }
        }
        _ASSERT(false);
        return -1;
    }
protected:
    const CSeq_align*   m_pSeqAlign;
    const CDense_seg*   m_pDenseSeg;
    TDim    m_QueryIndex;
    TDim    m_SubjectIndex;
    
};


/// CHitElemDataAdapter represents a single element of a Hit.
///
class CHitElemDataAdapter
{
public:
    typedef CDense_seg::TDim     TDim;

    CHitElemDataAdapter()
    :   m_pHit(NULL),
        m_ElemIndex(-1)    
    {
    }
    CHitElemDataAdapter(const CHitDataAdapter& hit, TDim elem_index)
    :   m_pHit(&hit),
        m_ElemIndex(elem_index)
    {
    }
    inline const CHitDataAdapter&  GetHit()    const
    {
        return *m_pHit;
    }
    inline TSignedSeqPos  GetQueryStart() const
    {
        return m_pHit->GetQueryStart(m_ElemIndex);
    }
    inline TSignedSeqPos  GetSubjectStart() const
    {
        return m_pHit->GetSubjectStart(m_ElemIndex);
    }
    inline TSeqPos        GetLength() const
    {
        return m_pHit->GetLength(m_ElemIndex);
    }
    inline  ENa_strand     GetQueryStrand() const
    {
        return m_pHit->GetQueryStrand(m_ElemIndex);
    }
    inline  ENa_strand     GetSubjectStrand() const
    {
        return m_pHit->GetSubjectStrand(m_ElemIndex);
    }
protected:
    const CHitDataAdapter*    m_pHit; /// 
    TDim     m_ElemIndex; /// index of a segment in dense-seg
};


CHitElemDataAdapter  CHitDataAdapter::GetElem(TDim elem_index)
{
    return CHitElemDataAdapter(*this, elem_index);
}

const CHitElemDataAdapter  CHitDataAdapter::GetElem(TDim elem_index) const
{
    return CHitElemDataAdapter(*this, elem_index);
}

END_NCBI_SCOPE

/*
 * ===========================================================================
 * $Log: hit_data_adapter.hpp,v $
 * Revision 1000.1  2004/04/12 18:16:40  gouriano
 * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.3
 *
 * Revision 1.3  2004/02/04 20:04:45  yazhuk
 * Clean-up
 *
 * Revision 1.2  2003/12/05 17:52:56  yazhuk
 * Added functions for retrieving strand information
 *
 * Revision 1.1  2003/12/01 17:01:13  yazhuk
 * Initial revision
 *
 * ===========================================================================
 */

#endif  // GUI_WIDGETS_HIT_MATRIX___HIT_DATA_ADAPTER__HPP