alignment_smear.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: alignment_smear.hpp,v $
 * PRODUCTION Revision 1000.0  2004/06/01 19:54:26  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.3
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_OBJUTILS___ALIGNMENT_SMEAR__HPP
#define GUI_OBJUTILS___ALIGNMENT_SMEAR__HPP

/*  $Id: alignment_smear.hpp,v 1000.0 2004/06/01 19:54:26 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:  Robert G. Smith
 *
 * File Description:
 *
 */

#include <corelib/ncbiobj.hpp>
#include <gui/gui.hpp>
#include <gui/objutils/density_map.hpp>

/** @addtogroup GUI_OBJUTILS
 *
 * @{
 */


BEGIN_NCBI_SCOPE


template <typename T>
struct max_func : public binary_function<T, T, T>
{
    T operator() (T a1, T a2) const {
        return max(a1, a2);
    };
};


/*
class CAlignSmearSeg_CI {
public:
    typedef int     score_type;
    
    CAlignSmearSeg_CI(const CDenMapRunIterator<score_type>& dmr_it, const CDensityMap<score_type>& density);
    
    score_type  Advance();
        
    TSeqPos     GetPosition() const { return m_DMR_it.GetPosition() * m_Window + m_Start; }
    TSeqPos     GetLength() const{ return m_DMR_it.GetRunLength() * m_Window; }
    score_type  GetValue() const { return m_DMR_it.GetValue(); }
        
    operator bool() const { return m_DMR_it.Valid(); }
private:    
    CDenMapRunIterator<score_type>      m_DMR_it;
    TSeqPos                 m_Start;
    TSeqPos                 m_Window;
    
};




class CAlignSmearGap_CI {
public:
    typedef int     score_type;
    
    CAlignSmearGap_CI(const CDenMapRunIterator<score_type>& dmr_it, const CDensityMap<score_type, max_func<score_type> >& density);
    
    void        Advance();
        
    TSeqPos     GetPosition() const { return m_DMR_it.GetPosition() * m_Window + m_Start; }
    TSeqPos     GetLength() const{ return m_DMR_it.GetRunLength() * m_Window; }
        
    operator bool() const { return m_DMR_it.Valid(); }
private:    
    CDensityMap<score_type, max_func<score_type> >      m_DMR_it;
    TSeqPos                 m_Start;
    TSeqPos                 m_Window;
    
};
*/

class objects::CBioseq_Handle;
class objects::CAlnMap;
class objects::CSeq_annot;
struct objects::SAnnotSelector;

class NCBI_GUIOBJUTILS_EXPORT CAlignmentSmear : public CObject {
public:
    enum EAlignSmearStrand {
        eSmearStrand_Both,
        eSmearStrand_Pos,
        eSmearStrand_Neg
    };

    typedef int     score_type;
    typedef CDenMapRunIterator<score_type>  runlen_iterator;
    
    CAlignmentSmear(
        const objects::CBioseq_Handle& handle, 
        TSeqPos start, 
        TSeqPos stop, 
        TSeqPos window = 1,
        EAlignSmearStrand strand_type = eSmearStrand_Both
        );

/// INPUT:
    /// smear all the alignments in this annotation.
    void    AddAnnot(const objects::CSeq_annot& seq_annot);

    /// Smear all the alignments matchec by this selector on my bioseq.
    void    AddAlignments(const objects::SAnnotSelector& sel);
    
    /// Add this one alignment to my smear.    
    void    AddAlignment(objects::CAlnMap& align);

    void MaskGaps();
    
    string      GetLabel() const;
    void        SetLabel(const string& label);
    
    EAlignSmearStrand   GetStrandType() const { return m_StrandType; }
    
    static bool SeparateStrands(const objects::CSeq_annot& seq_annot);
    
/// OUTPUT:
    runlen_iterator  SmearSegBegin() const 
        { return m_AccumSeg.RunLenBegin(); }
    runlen_iterator  SmearGapBegin() const
        { return m_AccumGap.RunLenBegin(); }

    score_type         GetMaxValue() const { return m_AccumSeg.GetMax(); }
private:

    static string   x_GetAnnotName(const objects::CSeq_annot& seq_annot);

    const objects::CBioseq_Handle&  m_BioseqHandle;
    
    typedef CDensityMap<score_type> TSegMap;
    TSegMap     m_AccumSeg;
    
    typedef CDensityMap<score_type, max_func<score_type> >  TGapMap;
    TGapMap     m_AccumGap;

    EAlignSmearStrand   m_StrandType;
    string      m_Label;
};



END_NCBI_SCOPE

/* @} */


/*
 * ===========================================================================
 * $Log: alignment_smear.hpp,v $
 * Revision 1000.0  2004/06/01 19:54:26  gouriano
 * PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.3
 *
 * Revision 1.3  2004/05/03 13:34:53  dicuccio
 * FIxed include guards, doxygen groups
 *
 * Revision 1.2  2004/05/03 12:41:35  dicuccio
 * Fixed #includes and export specifiers
 *
 * Revision 1.1  2004/04/30 11:52:52  dicuccio
 * Split out from gui/utils
 *
 * Revision 1.4  2004/04/16 14:27:17  dicuccio
 * Added doxygen module tag
 *
 * Revision 1.3  2004/03/23 13:34:39  dicuccio
 * Added export specifiers.  Changed predeclaration from class -> struct to match
 * actual definition
 *
 * Revision 1.2  2004/03/22 18:40:10  ucko
 * Fix forward declaration of SAnnotSelector to contain "class".
 *
 * Revision 1.1  2004/03/22 16:35:34  rsmith
 * initial checkin
 *
 *
 * ===========================================================================
 */

#endif  // GUI_OBJUTILS___ALIGNMENT_SMEAR__HPP