aln_scoring.hpp
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- /*
- * ===========================================================================
- * 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