annot_types_ci.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: annot_types_ci.cpp,v $
 * PRODUCTION Revision 1000.5  2004/06/01 19:22:48  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.121
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: annot_types_ci.cpp,v 1000.5 2004/06/01 19:22:48 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, Eugene Vasilchenko
*
* File Description:
*   Object manager iterators
*
*/

#include <ncbi_pch.hpp>
#include <objmgr/annot_types_ci.hpp>
#include <objmgr/impl/handle_range_map.hpp>
#include <objmgr/impl/snp_annot_info.hpp>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)


/////////////////////////////////////////////////////////////////////////////
// CAnnotTypes_CI
/////////////////////////////////////////////////////////////////////////////


CAnnotTypes_CI::CAnnotTypes_CI(void)
    : m_DataCollector(0)
{
    return;
}


CAnnotTypes_CI::CAnnotTypes_CI(TAnnotType type,
                               CScope& scope,
                               const CSeq_loc& loc,
                               const SAnnotSelector& params)
    : m_DataCollector(new CAnnot_Collector(params, scope))
{
    m_DataCollector->GetSelector().CheckAnnotType(type);
    CHandleRangeMap master_loc;
    master_loc.AddLocation(loc);
    m_DataCollector->x_Initialize(master_loc);
    Rewind();
}


CAnnotTypes_CI::CAnnotTypes_CI(TAnnotType type,
                               const CBioseq_Handle& bioseq,
                               TSeqPos start, TSeqPos stop,
                               const SAnnotSelector& params)
    : m_DataCollector(new CAnnot_Collector(params, bioseq.GetScope()))
{
    m_DataCollector->GetSelector().CheckAnnotType(type);
    m_DataCollector->x_Initialize(bioseq, start, stop);
    Rewind();
}


CAnnotTypes_CI::CAnnotTypes_CI(TAnnotType type,
                               const CSeq_annot_Handle& annot)
    : m_DataCollector(new CAnnot_Collector(SAnnotSelector(type),
                                              annot.GetScope()))
{
    m_DataCollector->GetSelector()
        .SetResolveNone() // nothing to resolve
        .SetLimitSeqAnnot(annot);
    m_DataCollector->x_Initialize();
    Rewind();
}


CAnnotTypes_CI::CAnnotTypes_CI(TAnnotType type,
                               const CSeq_annot_Handle& annot,
                               const SAnnotSelector& params)
    : m_DataCollector(new CAnnot_Collector(params, annot.GetScope()))
{
    m_DataCollector->GetSelector()
        .CheckAnnotType(type)
        .SetResolveNone() // nothing to resolve
        .SetLimitSeqAnnot(annot);
    m_DataCollector->x_Initialize();
    Rewind();
}


CAnnotTypes_CI::CAnnotTypes_CI(TAnnotType type,
                               const CSeq_entry_Handle& entry)
    : m_DataCollector(new CAnnot_Collector(SAnnotSelector(type),
                                              entry.GetScope()))
{
    m_DataCollector->GetSelector()
        .SetResolveNone() // nothing to resolve
        .SetSortOrder(SAnnotSelector::eSortOrder_None)
        .SetLimitSeqEntry(entry);
    m_DataCollector->x_Initialize();
    Rewind();
}


CAnnotTypes_CI::CAnnotTypes_CI(TAnnotType type,
                               const CSeq_entry_Handle& entry,
                               const SAnnotSelector& params)
    : m_DataCollector(new CAnnot_Collector(params, entry.GetScope()))
{
    m_DataCollector->GetSelector()
        .CheckAnnotType(type)
        .SetResolveNone() // nothing to resolve
        .SetSortOrder(SAnnotSelector::eSortOrder_None)
        .SetLimitSeqEntry(entry);
    m_DataCollector->x_Initialize();
    Rewind();
}


CAnnotTypes_CI::CAnnotTypes_CI(TAnnotType type,
                               CScope& scope,
                               const CSeq_loc& loc,
                               //const SAnnotSelector& selector,
                               SAnnotSelector::EOverlapType overlap_type,
                               SAnnotSelector::EResolveMethod resolve_method)
    : m_DataCollector(new CAnnot_Collector(SAnnotSelector(), scope))
{
    m_DataCollector->GetSelector()
        .CheckAnnotType(type)
        .SetOverlapType(overlap_type)
        .SetResolveMethod(resolve_method);
    CHandleRangeMap master_loc;
    master_loc.AddLocation(loc);
    m_DataCollector->x_Initialize(master_loc);
    Rewind();
}


CAnnotTypes_CI::CAnnotTypes_CI(TAnnotType type,
                               const CBioseq_Handle& bioseq,
                               TSeqPos start, TSeqPos stop,
                               //const SAnnotSelector& selector,
                               SAnnotSelector::EOverlapType overlap_type,
                               SAnnotSelector::EResolveMethod resolve_method)
    : m_DataCollector(new CAnnot_Collector(SAnnotSelector(),
                                              bioseq.GetScope()))
{
    m_DataCollector->GetSelector()
        .CheckAnnotType(type)
        .SetOverlapType(overlap_type)
        .SetResolveMethod(resolve_method);
    m_DataCollector->x_Initialize(bioseq, start, stop);
    Rewind();
}


CSeq_annot_Handle CAnnotTypes_CI::GetAnnot(void) const
{
    const CAnnotObject_Ref& ref = Get();
    const CSeq_annot_Info* info;
    if ( ref.GetObjectType() == ref.eType_Seq_annot_SNP_Info ) {
        info = &ref.GetSeq_annot_SNP_Info().GetParentSeq_annot_Info();
    }
    else {
        info = &ref.GetSeq_annot_Info();
    }
    return CSeq_annot_Handle(GetScope(), *info);
}


const CSeq_annot& CAnnotTypes_CI::GetSeq_annot(void) const
{
    ERR_POST_ONCE(Warning<<
                  "CAnnotTypes_CI::GetSeq_annot() is deprecated, "
                  "use GetAnnot()");
    return *GetAnnot().GetCompleteSeq_annot();
}


CAnnotTypes_CI::~CAnnotTypes_CI(void)
{
    return;
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: annot_types_ci.cpp,v $
* Revision 1000.5  2004/06/01 19:22:48  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.121
*
* Revision 1.121  2004/05/21 21:42:12  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.120  2004/04/05 15:56:14  grichenk
* Redesigned CAnnotTypes_CI: moved all data and data collecting
* functions to CAnnotDataCollector. CAnnotTypes_CI is no more
* inherited from SAnnotSelector.
*
* Revision 1.119  2004/04/01 20:18:12  grichenk
* Added initialization of m_MultiId member.
*
* Revision 1.118  2004/03/31 20:43:29  grichenk
* Fixed mapping of seq-locs containing both master sequence
* and its segments.
*
* Revision 1.117  2004/03/30 15:42:33  grichenk
* Moved alignment mapper to separate file, added alignment mapping
* to CSeq_loc_Mapper.
*
* Revision 1.116  2004/03/24 18:30:29  vasilche
* Fixed edit API.
* Every *_Info object has its own shallow copy of original object.
*
* Revision 1.115  2004/03/16 15:47:27  vasilche
* Added CBioseq_set_Handle and set of EditHandles
*
* Revision 1.114  2004/02/26 14:41:41  grichenk
* Fixed types excluding in SAnnotSelector and multiple types search
* in CAnnotTypes_CI.
*
* Revision 1.113  2004/02/19 19:25:08  vasilche
* Hidded implementation of CAnnotObject_Ref.
* Added necessary access methods.
*
* Revision 1.112  2004/02/09 14:48:37  vasilche
* Got rid of performance warning on MSVC.
*
* Revision 1.111  2004/02/06 18:31:54  vasilche
* Fixed annot sorting class - deal with different annot types (graph align feat).
*
* Revision 1.110  2004/02/05 19:53:40  grichenk
* Fixed type matching in SAnnotSelector. Added IncludeAnnotType().
*
* Revision 1.109  2004/02/04 18:05:38  grichenk
* Added annotation filtering by set of types/subtypes.
* Renamed *Choice to *Type in SAnnotSelector.
*
* Revision 1.108  2004/01/30 15:25:45  grichenk
* Fixed alignments mapping and sorting
*
* Revision 1.107  2004/01/28 20:54:36  vasilche
* Fixed mapping of annotations.
*
* Revision 1.106  2004/01/26 17:50:55  vasilche
* Do assert check only when object is non-null.
*
* Revision 1.105  2004/01/23 16:14:47  grichenk
* Implemented alignment mapping
*
* Revision 1.104  2004/01/22 20:10:40  vasilche
* 1. Splitted ID2 specs to two parts.
* ID2 now specifies only protocol.
* Specification of ID2 split data is moved to seqsplit ASN module.
* For now they are still reside in one resulting library as before - libid2.
* As the result split specific headers are now in objects/seqsplit.
* 2. Moved ID2 and ID1 specific code out of object manager.
* Protocol is processed by corresponding readers.
* ID2 split parsing is processed by ncbi_xreader library - used by all readers.
* 3. Updated OBJMGR_LIBS correspondingly.
*
* Revision 1.103  2003/11/26 17:55:56  vasilche
* Implemented ID2 split in ID1 cache.
* Fixed loading of splitted annotations.
*
* Revision 1.102  2003/11/13 19:12:53  grichenk
* Added possibility to exclude TSEs from annotations request.
*
* Revision 1.101  2003/11/10 18:11:03  grichenk
* Moved CSeq_loc_Conversion_Set to seq_loc_cvt
*
* Revision 1.100  2003/11/05 00:33:53  ucko
* Un-inline CSeq_loc_Conversion_Set::Add due to use before definition.
*
* Revision 1.99  2003/11/04 21:10:01  grichenk
* Optimized feature mapping through multiple segments.
* Fixed problem with CAnnotTypes_CI not releasing scope
* when exception is thrown from constructor.
*
* Revision 1.98  2003/11/04 16:21:37  grichenk
* Updated CAnnotTypes_CI to map whole features instead of splitting
* them by sequence segments.
*
* Revision 1.97  2003/10/28 14:46:29  vasilche
* Fixed wrong _ASSERT().
*
* Revision 1.96  2003/10/27 20:07:10  vasilche
* Started implementation of full annotations' mapping.
*
* Revision 1.95  2003/10/10 12:47:24  dicuccio
* Fixed off-by-one error in x_Search() - allocate correct size for array
*
* Revision 1.94  2003/10/09 20:20:58  vasilche
* Added possibility to include and exclude Seq-annot names to annot iterator.
* Fixed adaptive search. It looked only on selected set of annot names before.
*
* Revision 1.93  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 1.92  2003/09/30 16:22:02  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.