heap_scope.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: heap_scope.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 19:23:24  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.3
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: heap_scope.cpp,v 1000.1 2004/06/01 19:23:24 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:
*           Andrei Gourianov
*           Aleksey Grichenko
*           Michael Kimelman
*           Denis Vakatov
*           Eugene Vasilchenko
*
* File Description:
*           Scope is top-level object available to a client.
*           Its purpose is to define a scope of visibility and reference
*           resolution and provide access to the bio sequence data
*
*/

#include <ncbi_pch.hpp>
#include <objmgr/impl/heap_scope.hpp>
#include <objmgr/impl/scope_impl.hpp>
#include <objmgr/scope.hpp>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)


/////////////////////////////////////////////////////////////////////////////
//
// CHeapScope
//
/////////////////////////////////////////////////////////////////////////////


void CHeapScope::Set(CScope* scope)
{
    if ( scope ) {
        m_Scope.Reset(scope->m_Impl->m_HeapScope);
        _ASSERT(m_Scope);
    }
    else {
        m_Scope.Reset();
    }
}


CScope& CHeapScope::GetScope(void) const
{
    return static_cast<CScope&>(const_cast<CObject&>(*m_Scope));
}


CScope* CHeapScope::GetScopeOrNull(void) const
{
    return static_cast<CScope*>
        (const_cast<CObject*>(m_Scope.GetPointerOrNull()));
}


CScope_Impl* CHeapScope::GetImpl(void) const
{
    return GetScope().m_Impl.GetPointer();
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: heap_scope.cpp,v $
* Revision 1000.1  2004/06/01 19:23:24  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.3
*
* Revision 1.3  2004/05/21 21:42:12  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.2  2004/04/12 16:49:16  vasilche
* Allow null scope in CSeqMap_CI and CSeqVector.
*
* Revision 1.1  2004/03/16 15:47:27  vasilche
* Added CBioseq_set_Handle and set of EditHandles
*
* Revision 1.101  2004/02/19 17:23:01  vasilche
* Changed order of deletion of heap scope and scope impl objects.
* Reduce number of calls to x_ResetHistory().
*
* Revision 1.100  2004/02/10 21:15:16  grichenk
* Added reverse ID matching.
*
* Revision 1.99  2004/02/09 14:42:46  vasilche
* Temporary fix in GetSynonyms() to get accession without version.
*
* Revision 1.98  2004/02/02 14:46:43  vasilche
* Several performance fixed - do not iterate whole tse set in CDataSource.
*
* Revision 1.97  2004/01/29 20:33:28  vasilche
* Do not resolve any Seq-ids in CScope::GetSynonyms() -
* assume all not resolved Seq-id as synonym.
* Seq-id conflict messages made clearer.
*
* Revision 1.96  2004/01/28 20:50:49  vasilche
* Fixed NULL pointer exception in GetSynonyms() when matching Seq-id w/o version.
*
* Revision 1.95  2004/01/07 20:42:01  grichenk
* Fixed matching of accession to accession.version
*
* Revision 1.94  2003/12/18 16:38:07  grichenk
* Added CScope::RemoveEntry()
*
* Revision 1.93  2003/12/12 16:59:51  grichenk
* Fixed conflicts resolving (ask data source).
*
* Revision 1.92  2003/12/03 20:55:12  grichenk
* Check value returned by x_GetBioseq_Info()
*
* Revision 1.91  2003/11/21 20:33:03  grichenk
* Added GetBioseqHandleFromTSE(CSeq_id, CSeq_entry)
*
* Revision 1.90  2003/11/19 22:18:03  grichenk
* All exceptions are now CException-derived. Catch "exception" rather
* than "runtime_error".
*
* Revision 1.89  2003/11/12 15:49:39  vasilche
* Added loading annotations on non gi Seq-id.
*
* Revision 1.88  2003/10/23 13:47:27  vasilche
* Check CSeq_id_Handle for null in CScope::GetBioseqHandle().
*
* Revision 1.87  2003/10/22 14:08:15  vasilche
* Detach all CBbioseq_Handle objects from scope in CScope::ResetHistory().
*
* Revision 1.86  2003/10/22 13:54:36  vasilche
* All CScope::GetBioseqHandle() methods return 'null' CBioseq_Handle object
* instead of throwing an exception.
*
* Revision 1.85  2003/10/20 18:23:54  vasilche
* Make CScope::GetSynonyms() to skip conflicting ids.
*
* Revision 1.84  2003/10/09 13:58:21  vasilche
* Fixed conflict when the same datasource appears twice with equal priorities.
*
* Revision 1.83  2003/10/07 13:43:23  vasilche
* Added proper handling of named Seq-annots.
* Added feature search from named Seq-annots.
* Added configurable adaptive annotation search (default: gene, cds, mrna).
* Fixed selection of blobs for loading from GenBank.
* Added debug checks to CSeq_id_Mapper for easier finding lost CSeq_id_Handles.
* Fixed leaked split chunks annotation stubs.
* Moved some classes definitions in separate *.cpp files.
*
* Revision 1.82  2003/09/30 16:22:03  vasilche
* Updated internal object manager classes to be able to load ID2 data.
* SNP blobs are loaded as ID2 split blobs - readers convert them automatically.
* Scope caches results of requests for data to data loaders.
* Optimized CSeq_id_Handle for gis.
* Optimized bioseq lookup in scope.
* Reduced object allocations in annotation iterators.
* CScope is allowed to be destroyed before other objects using this scope are
* deleted (feature iterators, bioseq handles etc).
* Optimized lookup for matching Seq-ids in CSeq_id_Mapper.
* Added 'adaptive' option to objmgr_demo application.
*
* Revision 1.81  2003/09/05 20:50:26  grichenk
* +AddBioseq(CBioseq&)
*
* Revision 1.80  2003/09/05 17:29:40  grichenk
* Structurized Object Manager exceptions
*
* Revision 1.79  2003/09/03 20:00:02  grichenk
* Added sequence filtering by level (mains/parts/all)
*
* Revision 1.78  2003/08/04 17:03:01  grichenk
* Added constructors to iterate all annotations from a
* seq-entry or seq-annot.
*
* Revision 1.77  2003/07/25 15:25:25  grichenk
* Added CSeq_annot_CI class
*
* Revision 1.76  2003/07/17 20:07:56  vasilche
* Reduced memory usage by feature indexes.
* SNP data is loaded separately through PUBSEQ_OS.
* String compression for SNP data.
*
* Revision 1.75  2003/07/14 21:13:59  grichenk
* Added seq-loc dump in GetBioseqHandle(CSeqLoc)
*
* Revision 1.74  2003/06/30 18:42:10  vasilche
* CPriority_I made to use less memory allocations/deallocations.
*
* Revision 1.73  2003/06/24 14:25:18  vasilche
* Removed obsolete CTSE_Guard class.
* Used separate mutexes for bioseq and annot maps.
*
* Revision 1.72  2003/06/19 18:23:46  vasilche
* Added several CXxx_ScopeInfo classes for CScope related information.
* CBioseq_Handle now uses reference to CBioseq_ScopeInfo.
* Some fine tuning of locking in CScope.
*
* Revision 1.69  2003/05/27 19:44:06  grichenk
* Added CSeqVector_CI class
*
* Revision 1.68  2003/05/20 15:44:37  vasilche
* Fixed interaction of CDataSource and CDataLoader in multithreaded app.