mate_pair.hpp

来自「ncbi源码」· HPP 代码 · 共 267 行

/*
 * ===========================================================================
 * PRODUCTION $Log: mate_pair.hpp,v $
 * PRODUCTION Revision 1000.0  2004/06/01 19:55:32  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.5
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_OBJUTILS___MATE_PAIR__HPP
#define GUI_OBJUTILS___MATE_PAIR__HPP

/*  $Id: mate_pair.hpp,v 1000.0 2004/06/01 19:55:32 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:  Vlad Lebedev
 *
 * File Description:
 *   CLayoutMatePair -- utility class to layout mate pairs (a special type of
 *      pairwise alignments and hold a set of CLayoutPWAlign
 */


#include <corelib/ncbiobj.hpp>
#include <gui/gui.hpp>
#include <gui/objutils/layout.hpp>
#include <gui/objutils/pw_alignment.hpp>

#include <objects/seqalign/Seq_align.hpp>

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


BEGIN_NCBI_SCOPE


class NCBI_GUIOBJUTILS_EXPORT CLayoutMatePair : public CLayoutObject
{
public:
    typedef vector< CRef<CLayoutPWAlign> > TAlignList;
    
    // ctors
    CLayoutMatePair(const TAlignList& aligns);

    // Access the alignment as a CObject
    const CObject* GetObject(TSeqPos pos) const;
    bool HasObject(const CObject* obj) const;

    bool IsSelected(const CLayoutPWAlign* pw_aln) const;
    
    // Access the alignments's remapped location
    const objects::CSeq_loc& GetLocation(void) const;
    const TAlignList&        GetSeqAligns() const;

    // retrieve the type of this object
    EType GetType() const;

    // matepair specifics

    // library information
    enum ELibraryId {
        eLibrary_NotSet = -1,
        eLibrary_NotFound = 0
    };
    size_t GetLibraryId() const;

    // matepair errors
    enum EErrorType {

        // no error found (initial state)
        eError_NotSet = -1,

        // no error
        eError_NoError = 0,

        // the mate is not aligned with the correct otientation
        eError_Orientation = 1,

        // the mate aligns to multiple locations
        eError_NonUnique = 2,

        // the mate is not in the expected distance range
        eError_Distance = 3
    };
    EErrorType GetError() const;

    //
    // pure virtual requirements
    //    
    // Comparators
    bool LessByPos (const CLayoutObject& obj) const;
    bool LessBySize(const CLayoutObject& obj) const;

protected:
    TAlignList              m_SeqAligns;
    CRef<objects::CSeq_loc> m_Location;

    // parsed matepair library (-1 = not set, 0 = not found)
    int m_LibraryId;

    // parsed mate pair error code
    EErrorType m_ErrorType;
    
    // store the selected object (if any)
    mutable vector<const CObject*> m_ObjSel;
};


inline
bool CLayoutMatePair::LessByPos(const CLayoutObject& obj) const
{
    TSeqRange r0 = GetLocation().GetTotalRange();
    TSeqRange r1 = obj.GetLocation().GetTotalRange();
    return (r0.GetFrom() < r1.GetFrom());
}


inline
bool CLayoutMatePair::LessBySize(const CLayoutObject& obj) const
{
    TSeqRange r0 = GetLocation().GetTotalRange();
    TSeqRange r1 = obj.GetLocation().GetTotalRange();
    return (r0.GetLength() < r1.GetLength());
}




inline
bool CLayoutMatePair::HasObject(const CObject* obj) const
{
    ITERATE(TAlignList, iter, m_SeqAligns)
    {
        if ( (*iter)->HasObject(obj) ) {
            m_ObjSel.push_back(obj);
            return true;
        }
    }
    return false;
}


inline
bool CLayoutMatePair::IsSelected(const CLayoutPWAlign* pw_aln) const
{
    ITERATE(vector<const CObject*>, iter, m_ObjSel) {
        if (pw_aln->HasObject(*iter))
            return true;
    }
    return false;
}

            
inline
const CLayoutMatePair::TAlignList&
CLayoutMatePair::GetSeqAligns(void) const
{
    return m_SeqAligns;
}


inline
const objects::CSeq_loc& CLayoutMatePair::GetLocation(void) const
{
    return *m_Location;
}


inline
size_t CLayoutMatePair::GetLibraryId() const
{
    return m_LibraryId;
}


inline
CLayoutMatePair::EErrorType CLayoutMatePair::GetError() const
{
    return m_ErrorType;
}


inline
CLayoutMatePair::EType CLayoutMatePair::GetType() const
{
    return eMatepair;
}




END_NCBI_SCOPE

/* @} */


/*
 * ===========================================================================
 * $Log: mate_pair.hpp,v $
 * Revision 1000.0  2004/06/01 19:55:32  gouriano
 * PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.5
 *
 * Revision 1.5  2004/05/14 14:24:47  dicuccio
 * Added new pure virtual requirement on CLayoutObject(): GetType(), returns enum
 * defined in CLayoutObject
 *
 * Revision 1.4  2004/05/10 18:24:29  dicuccio
 * Added identification of mate pair library and error codes
 *
 * Revision 1.3  2004/05/03 13:34:54  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 11:52:53  dicuccio
 * Split out from gui/utils
 *
 * Revision 1.6  2004/04/20 19:15:04  dicuccio
 * Converted to store a set of pairwise alignments
 *
 * Revision 1.5  2004/04/16 14:27:17  dicuccio
 * Added doxygen module tag
 *
 * Revision 1.4  2004/04/15 12:57:43  lebedev
 * Changed GetObject to return NULL or const pointer based on given position
 *
 * Revision 1.3  2004/04/12 16:49:02  dicuccio
 * Redesign CLayoutMatePair - use alignment manager internally, store a set of
 * alignments
 *
 * Revision 1.2  2004/04/07 12:39:09  dicuccio
 * Formatting changes
 *
 * Revision 1.1  2004/04/05 16:10:06  lebedev
 * Initial revision
 *
 * ===========================================================================
 */

#endif  // GUI_OBJUTILS___MATE_PAIR__HPP