aln_scoring.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: aln_scoring.hpp,v $
 * PRODUCTION Revision 1000.2  2004/04/12 18:15:46  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.6
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_WIDGETS_ALN_MULTIPLE___ALN_SCORING__HPP
#define GUI_WIDGETS_ALN_MULTIPLE___ALN_SCORING__HPP

/*  $Id: aln_scoring.hpp,v 1000.2 2004/04/12 18:15:46 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
 *
 */

#include <corelib/ncbistd.hpp>
#include <corelib/ncbistl.hpp>

#include <gui/opengl/glcolor.hpp>
#include <gui/widgets/aln_multiple/attr_range_coll.hpp>
#include <objtools/alnmgr/alnvec.hpp>

BEGIN_NCBI_SCOPE


/// IScoringMethod represents an abstract algorithm for calculating alignment
/// scores and assigning colors.
class IScoringMethod
{
public:
    typedef float   TScore;
    typedef vector<TScore>  TScoreVector;

    virtual ~IScoringMethod()   {};

    /// returns unique name of the method that can be used in UI to identify it
    virtual string  GetName() = 0;

    /// calculates scores for a column
    virtual void    CalculateScores(char cons, const string& column, 
                            TScore& col_score, TScoreVector& scores) = 0;    

    /// returns a color corresponding to a given score value. It  is recommended
    /// that this method be implemented using color table, on-the-fly creation
    /// of colors is expensive.
    virtual const CGlColor& GetColorForScore(TScore score) const = 0;
};


/// CSimpleScoringMethod - trivial implementation of IScoringMethod.
///
/// Scores are calculated as frequences of symbols normalized to fit in range
/// [0, 1]. CreateColorTable() must be called once before any GetColorForScore()
/// cals.
class CSimpleScoringMethod : public IScoringMethod
{
public:
    enum    EOptions    {
        //fAnchorAsConsensus  = 0x01,
        fIgnoreEmptySpace   = 0x02,
        fIgnoreGaps         = 0x04
    };

    CSimpleScoringMethod();
    virtual ~CSimpleScoringMethod();

    void    SetOptions(int options); // takes as argument combination of EOptions flags
    void    CreateColorTable(int size);

    virtual string  GetName();
    virtual void    CalculateScores(char cons, const string& column,
                             TScore& col_score, TScoreVector& scores);
    virtual const CGlColor& GetColorForScore(TScore score) const;

protected:
    int m_Options; /// combination of EOptions flags
    vector<CGlColor>    m_vColors;

    vector<int>     m_vCharCounts; /// histogramm of characters
    char    m_Space;
    char    m_Gap;
};


class CSNPScoringMethod : public CSimpleScoringMethod
{
public:
    virtual string  GetName();
    virtual void    CalculateScores(char cons, const string& column,
                                    TScore& col_score, TScoreVector& scores);
};


/// CScoreCache class uses given scoring method to calculate scores for
/// CAlnVec-type alignment. CScoreCache stores scores in compressed form
/// as CAttrRangeCollection. To make fetching of sequence and calculation
/// of scores more effective CScoreCache uses sequence buffer.
class CScoreCache
{
public:
    typedef objects::CAlnVec::TNumrow    TNumrow;
    typedef IScoringMethod::TScore  TScore;
    typedef IScoringMethod::TScoreVector  TScoreVector;
    typedef CAttrRangeCollection<TScore, TSeqPos>   TScoreColl;

    CScoreCache();
    
    /// Sets the number of score gradations.
    void    SetGradNumber(int grad_n);
    
    void    SetScoringMethod(IScoringMethod *method);
    IScoringMethod*    GetScoringMethod();
    const IScoringMethod*    GetScoringMethod() const;
    void    SetAlnVec(const objects::CAlnVec* aln_vec);    

    void    CalculateScores();
    
    const TScoreColl&   GetScores(TNumrow row) const;
    const CGlColor&     GetColorForScore(TScore score) const;
    
protected:
    // Sequence buffer routins.
    char x_BufferGetSeq(TSeqPos pos, TNumrow row) const;
    void x_BufferGetColumn(TSeqPos pos, string& column) const;

    void x_AllocBuffer(TSeqPos row_len);
    void x_FreeBuffer(); 
    /// Fetches sequence from CAlnVec.
    void x_UpdateBuffer(TSeqPos start, TSeqPos stop); 
    
    TSeqPos x_GetStart() const;
    TSeqPos x_GetStop() const;
    TSeqPos x_GetRowLength() const;

protected:
    typedef vector<TScoreColl>  TScoreCollVector;
    TScoreCollVector    m_vScoreColls; /// score storage

    const objects::CAlnVec*      m_pAlnVec;
    IScoringMethod*     m_pMethod;
    int     m_GradNumber;

    /// Sequence buffer data members. 

    vector<string> m_vRows;    
    TSeqPos m_BufferStart; /// Aln position corresponding to the first column of the buffer
    TSeqPos m_RowLength;   /// buffer row length
};


inline const CGlColor& CScoreCache::GetColorForScore(TScore score) const
{
    return m_pMethod->GetColorForScore(score);        
}

END_NCBI_SCOPE

/*
 * ===========================================================================
 * $Log: aln_scoring.hpp,v $
 * Revision 1000.2  2004/04/12 18:15:46  gouriano
 * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.6
 *
 * Revision 1.6  2004/04/02 16:37:39  yazhuk
 * Added to CSimpleScoringMethod options for ignoring empty space and gaps;
 * Added CSNPScoringMethod .
 *
 * Revision 1.5  2004/03/18 17:08:50  yazhuk
 * Added GetScoringMethod()
 *
 * Revision 1.4  2004/02/11 17:42:30  yazhuk
 * Added GetName() to IScoringMethod interface; added comments
 *
 * Revision 1.3  2003/11/06 20:01:09  dicuccio
 * Removed USING_SCOPE(objects)
 *
 * Revision 1.2  2003/10/29 23:25:33  yazhuk
 * Changed comments
 *
 * Revision 1.1  2003/10/10 19:03:53  yazhuk
 * Initial revision
 *
 * ===========================================================================
 */

#endif  // GUI_WIDGETS_ALN_MULTIPLE___ALN_SCORING__HPP