alignment.hpp

来自「ncbi源码」· HPP 代码 · 共 235 行

/*
 * ===========================================================================
 * PRODUCTION $Log: alignment.hpp,v $
 * PRODUCTION Revision 1000.0  2004/06/01 19:54:21  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.4
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_OBJUTILS___ALIGNMENT__HPP
#define GUI_OBJUTILS___ALIGNMENT__HPP

/*  $Id: alignment.hpp,v 1000.0 2004/06/01 19:54:21 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:
 *   CLayoutAlign -- utility class to layout alignments and hold CAlnVec objects
 */


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

#include <objects/seqloc/Seq_interval.hpp>
#include <objtools/alnmgr/alnmix.hpp>


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


BEGIN_NCBI_SCOPE


class NCBI_GUIOBJUTILS_EXPORT CLayoutAlign : public CLayoutObject
{
public:
    typedef vector< CRef<CLayoutAlign> > TAlnList;
    
    // ctors
    CLayoutAlign(const objects::CAlnVec& aln_mgr,
                 const objects::CSeq_align& align);

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

    // Access the alignments's remapped location
    const objects::CSeq_loc&   GetLocation(void) const;
    const objects::CAlnVec&    GetAlignMgr(void) const;
    const objects::CSeq_align& GetAlignment(void) const;
    
    //
    // pure virtual requirements
    //    
    // Comparators
    bool LessByPos (const CLayoutObject& obj) const;
    bool LessBySize(const CLayoutObject& obj) const;

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


protected:
    // pointer to the actual alignment information
    CConstRef<objects::CAlnVec>     m_AlnMgr;
    CConstRef<objects::CSeq_align>  m_SeqAlign;
    CRef<objects::CSeq_loc> 	    m_Location;
};


inline
bool CLayoutAlign::LessByPos(const CLayoutObject& obj) const
{
    TSeqRange r0 = GetLocation().GetTotalRange();
    TSeqRange r1 = obj.GetLocation().GetTotalRange();
    if (r0.GetFrom() < r1.GetFrom()) {
        return true;
    }
    if (r0.GetFrom() > r1.GetFrom()) {
        return false;
    }
    if (r0.GetTo() > r1.GetTo()) {
        return true;
    }
    return false;
}


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


inline
const CObject* CLayoutAlign::GetObject(TSeqPos pos) const
{
    TSeqRange r = GetLocation().GetTotalRange();
    if (pos >= r.GetFrom()  &&  pos <= r.GetTo()) {
        return m_SeqAlign.GetPointer();
    }
    return NULL;
}


inline
bool CLayoutAlign::HasObject(const CObject* obj) const
{
    return m_SeqAlign.GetPointer() == obj;
}


inline
const objects::CAlnVec& CLayoutAlign::GetAlignMgr(void) const
{
    return *m_AlnMgr;
}


inline
const objects::CSeq_align& CLayoutAlign::GetAlignment(void) const
{
    return *m_SeqAlign;
}


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


inline
CLayoutAlign::EType CLayoutAlign::GetType() const
{
    return eAlign;
}



END_NCBI_SCOPE

/* @} */


/*
 * ===========================================================================
 * $Log: alignment.hpp,v $
 * Revision 1000.0  2004/06/01 19:54:21  gouriano
 * PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.4
 *
 * Revision 1.4  2004/05/14 14:24:47  dicuccio
 * Added new pure virtual requirement on CLayoutObject(): GetType(), returns enum
 * defined in CLayoutObject
 *
 * 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 1.10  2004/04/20 19:14:45  dicuccio
 * Expose underlying seq-align
 *
 * Revision 1.9  2004/04/16 14:27:17  dicuccio
 * Added doxygen module tag
 *
 * Revision 1.8  2004/04/15 12:57:43  lebedev
 * Changed GetObject to return NULL or const pointer based on given position
 *
 * Revision 1.7  2004/04/12 16:48:13  dicuccio
 * Changed variable m_AlignMgr to m_AlnMgr.  Changed ctor signature - no longer
 * require an externally computed alignment range.
 *
 * Revision 1.6  2004/03/11 17:19:32  dicuccio
 * Use TSeqRange instead of TRange.  Use gui/gui instead of gui/types
 *
 * Revision 1.5  2003/09/29 15:20:08  dicuccio
 * Deprecated gui/scope.hpp.  Merged gui/core/types.hpp into gui/types.hpp
 *
 * Revision 1.4  2003/09/19 00:28:59  ucko
 * CLayoutAlign: use an unsigned range per CAlnMap::GetSeqRange's new rettype.
 *
 * Revision 1.3  2003/08/18 14:53:26  dicuccio
 * Changed nales: CFeature -> CLayoutFeat; CAlignment -> CLayoutAlign; CGraph ->
 * CLayoutGraph; CProtProduct -> CLayoutProtProd.
 * Removed USING_SCOPE(objects);
 *
 * Revision 1.2  2003/07/21 19:24:09  dicuccio
 * Changed storage mechanism: CLayoutObject::GetObject() is pure virtual.  Also,
 * CFeature now stores a CMappedFeat object instead of a CSeq_feat / CSeq_loc pair
 *
 * Revision 1.1  2003/07/18 13:33:52  lebedev
 * Initial revision
 *
 * ===========================================================================
 */

#endif  // GUI_OBJUTILS___ALIGNMENT__HPP