handle_range.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: handle_range.hpp,v $
 * PRODUCTION Revision 1000.0  2003/10/29 20:24:43  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.18
 * PRODUCTION
 * ===========================================================================
 */

#ifndef OBJECTS_OBJMGR_IMPL___HANDLE_RANGE__HPP
#define OBJECTS_OBJMGR_IMPL___HANDLE_RANGE__HPP

/*  $Id: handle_range.hpp,v 1000.0 2003/10/29 20:24:43 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.
 *
 * ===========================================================================
 *
 * Author: Aleksey Grichenko, Michael Kimelman, Eugene Vasilchenko
 *
 * File Description:
 *
 */

#include <objects/seqloc/Na_strand.hpp>
#include <util/range.hpp>
#include <vector>
#include <utility>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)

// Locations list for a particular bioseq handle
class NCBI_XOBJMGR_EXPORT CHandleRange
{
public:
    typedef CRange<TSeqPos> TRange;
    typedef COpenRange<TSeqPos> TOpenRange;
    typedef pair<TRange, ENa_strand> TRangeWithStrand;
    typedef vector<TRangeWithStrand> TRanges;
    typedef TRanges::const_iterator const_iterator;

    CHandleRange(void);
    CHandleRange(const CHandleRange& hr);
    ~CHandleRange(void);
    CHandleRange& operator=(const CHandleRange& hr);

    bool Empty(void) const;
    const_iterator begin(void) const;
    const_iterator end(void) const;

    // Add a new range
    void AddRange(TRange range, ENa_strand strand/* = eNa_strand_unknown*/);
    // Merge a new range with the existing ranges
    void MergeRange(TRange range, ENa_strand strand);

    void AddRanges(const CHandleRange& hr);

    // return true if there is a gap between some intervals
    bool HasGaps(void) const;
    // Get the range including all ranges in the list (with any strand)
    TRange GetOverlappingRange(void) const;
    
    // Get the range including all ranges in the list which (with any strand)
    // filter the list through 'range' argument
    TRange GetOverlappingRange(const TRange& range) const;

    // Check if the two sets of ranges do intersect
    bool IntersectingWith(const CHandleRange& hr) const;

    // Check if the two sets of ranges do intersect
    bool IntersectingWith(const TRange& range,
                          ENa_strand strand = eNa_strand_unknown) const;

private:
    static bool x_IntersectingStrands(ENa_strand str1, ENa_strand str2);

    TRanges        m_Ranges;

    // friend class CDataSource;
    friend class CHandleRangeMap;
};


inline
bool CHandleRange::Empty(void) const
{
    return m_Ranges.empty();
}


inline
CHandleRange::const_iterator CHandleRange::begin(void) const
{
    return m_Ranges.begin();
}


inline
CHandleRange::const_iterator CHandleRange::end(void) const
{
    return m_Ranges.end();
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
 * ---------------------------------------------------------------------------
 * $Log: handle_range.hpp,v $
 * Revision 1000.0  2003/10/29 20:24:43  gouriano
 * PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.18
 *
 * Revision 1.18  2003/07/17 20:07:55  vasilche
 * Reduced memory usage by feature indexes.
 * SNP data is loaded separately through PUBSEQ_OS.
 * String compression for SNP data.
 *
 * Revision 1.17  2003/04/24 16:12:37  vasilche
 * Object manager internal structures are splitted more straightforward.
 * Removed excessive header dependencies.
 *
 * Revision 1.16  2003/02/25 14:48:07  vasilche
 * Added Win32 export modifier to object manager classes.
 *
 * Revision 1.15  2003/02/05 17:57:41  dicuccio
 * Moved into include/objects/objmgr/impl to permit data loaders to be defined
 * outside of xobjmgr.
 *
 * Revision 1.14  2003/02/04 21:45:43  grichenk
 * Removed CDataSource from friends
 *
 * Revision 1.13  2003/01/22 20:11:54  vasilche
 * Merged functionality of CSeqMapResolved_CI to CSeqMap_CI.
 * CSeqMap_CI now supports resolution and iteration over sequence range.
 * Added several caches to CScope.
 * Optimized CSeqVector().
 * Added serveral variants of CBioseqHandle::GetSeqVector().
 * Tried to optimize annotations iterator (not much success).
 * Rewritten CHandleRange and CHandleRangeMap classes to avoid sorting of list.
 *
 * Revision 1.12  2002/08/07 17:51:54  grichenk
 * Removed debug message
 *
 * Revision 1.11  2002/07/31 16:52:36  grichenk
 * Fixed bug in IntersectingWith()
 *
 * Revision 1.10  2002/07/08 20:51:01  grichenk
 * Moved log to the end of file
 * Replaced static mutex (in CScope, CDataSource) with the mutex
 * pool. Redesigned CDataSource data locking.
 *
 * Revision 1.9  2002/06/12 14:40:47  grichenk
 * Made some methods inline
 *
 * Revision 1.8  2002/05/06 03:28:47  vakatov
 * OM/OM1 renaming
 *
 * Revision 1.7  2002/05/03 21:28:10  ucko
 * Introduce T(Signed)SeqPos.
 *
 * Revision 1.6  2002/04/22 20:05:35  grichenk
 * +MergeRange()
 *
 * Revision 1.5  2002/02/21 19:27:05  grichenk
 * Rearranged includes. Added scope history. Added searching for the
 * best seq-id match in data sources and scopes. Updated tests.
 *
 * Revision 1.4  2002/02/15 20:35:38  gouriano
 * changed implementation of HandleRangeMap
 *
 * Revision 1.3  2002/01/23 21:59:31  grichenk
 * Redesigned seq-id handles and mapper
 *
 * Revision 1.2  2002/01/16 16:25:58  gouriano
 * restructured objmgr
 *
 * Revision 1.1  2002/01/11 19:06:20  gouriano
 * restructured objmgr
 *
 *
 * ===========================================================================
 */

#endif  // OBJECTS_OBJMGR_IMPL___HANDLE_RANGE__HPP