seq_annot_info.cpp

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void CSeq_annot_Info::x_UpdateAnnotIndexContents(CTSE_Info& tse)
{
    m_ObjectInfos.SetName(GetName());

    const CSeq_annot::C_Data& data = m_Object->GetData();
    switch ( data.Which() ) {
    case CSeq_annot::C_Data::e_Ftable:
        x_MapAnnotObjects(tse, data.GetFtable());
        break;
    case CSeq_annot::C_Data::e_Align:
        x_MapAnnotObjects(tse, data.GetAlign());
        break;
    case CSeq_annot::C_Data::e_Graph:
        x_MapAnnotObjects(tse, data.GetGraph());
        break;
    default:
        break;
    }
    if ( m_SNP_Info ) {
        m_SNP_Info->x_UpdateAnnotIndex(tse);
    }
    TParent::x_UpdateAnnotIndexContents(tse);
}


void
CSeq_annot_Info::x_MapAnnotObjects(CTSE_Info& tse,
                                   const CSeq_annot::C_Data::TFtable& objs)
{
    m_ObjectInfos.Reserve(objs.size(), 1.1);

    CTSE_Info::TAnnotObjs& index = tse.x_SetAnnotObjs(GetName());

    SAnnotObject_Key key;
    SAnnotObject_Index annotRef;
    vector<CHandleRangeMap> hrmaps;
    ITERATE ( CSeq_annot::C_Data::TFtable, fit, objs ) {
        const CSeq_feat& feat = **fit;

        CAnnotObject_Info* info =
            m_ObjectInfos.AddInfo(CAnnotObject_Info(feat, *this));
        key.m_AnnotObject_Info = annotRef.m_AnnotObject_Info = info;

        info->GetMaps(hrmaps);
        annotRef.m_AnnotLocationIndex = 0;
        ITERATE ( vector<CHandleRangeMap>, hrmit, hrmaps ) {
            ITERATE ( CHandleRangeMap, hrit, *hrmit ) {
                key.m_Handle = hrit->first;
                const CHandleRange& hr = hrit->second;
                key.m_Range = hr.GetOverlappingRange();
                if ( hr.HasGaps() ) {
                    annotRef.m_HandleRange.Reset(new CObjectFor<CHandleRange>);
                    annotRef.m_HandleRange->GetData() = hr;
                }
                else {
                    annotRef.m_HandleRange.Reset();
                }
                
                tse.x_MapAnnotObject(index, key, annotRef, m_ObjectInfos);
            }
            ++annotRef.m_AnnotLocationIndex;
        }
    }
}


void CSeq_annot_Info::x_MapAnnotObjects(CTSE_Info& tse,
                                        const CSeq_annot::C_Data::TGraph& objs)
{
    m_ObjectInfos.Reserve(objs.size());

    CTSE_Info::TAnnotObjs& index = tse.x_SetAnnotObjs(GetName());

    SAnnotObject_Key key;
    SAnnotObject_Index annotRef;
    vector<CHandleRangeMap> hrmaps;
    ITERATE ( CSeq_annot::C_Data::TGraph, git, objs ) {
        const CSeq_graph& graph = **git;

        CAnnotObject_Info* info =
            m_ObjectInfos.AddInfo(CAnnotObject_Info(graph, *this));
        key.m_AnnotObject_Info = annotRef.m_AnnotObject_Info = info;

        info->GetMaps(hrmaps);
        annotRef.m_AnnotLocationIndex = 0;
        ITERATE ( vector<CHandleRangeMap>, hrmit, hrmaps ) {
            ITERATE ( CHandleRangeMap, hrit, *hrmit ) {
                key.m_Handle = hrit->first;
                const CHandleRange& hr = hrit->second;
                key.m_Range = hr.GetOverlappingRange();
                if ( hr.HasGaps() ) {
                    annotRef.m_HandleRange.Reset(new CObjectFor<CHandleRange>);
                    annotRef.m_HandleRange->GetData() = hr;
                }
                else {
                    annotRef.m_HandleRange.Reset();
                }

                tse.x_MapAnnotObject(index, key, annotRef, m_ObjectInfos);
            }
            ++annotRef.m_AnnotLocationIndex;
        }
    }
}


void CSeq_annot_Info::x_MapAnnotObjects(CTSE_Info& tse,
                                        const CSeq_annot::C_Data::TAlign& objs)
{
    m_ObjectInfos.Reserve(objs.size());

    CTSE_Info::TAnnotObjs& index = tse.x_SetAnnotObjs(GetName());

    SAnnotObject_Key key;
    SAnnotObject_Index annotRef;
    vector<CHandleRangeMap> hrmaps;
    ITERATE ( CSeq_annot::C_Data::TAlign, ait, objs ) {
        const CSeq_align& align = **ait;

        CAnnotObject_Info* info =
            m_ObjectInfos.AddInfo(CAnnotObject_Info(align, *this));
        key.m_AnnotObject_Info = annotRef.m_AnnotObject_Info = info;

        info->GetMaps(hrmaps);
        annotRef.m_AnnotLocationIndex = 0;
        ITERATE ( vector<CHandleRangeMap>, hrmit, hrmaps ) {
            ITERATE ( CHandleRangeMap, hrit, *hrmit ) {
                key.m_Handle = hrit->first;
                const CHandleRange& hr = hrit->second;
                key.m_Range = hr.GetOverlappingRange();
                if ( hr.HasGaps() ) {
                    annotRef.m_HandleRange.Reset(new CObjectFor<CHandleRange>);
                    annotRef.m_HandleRange->GetData() = hr;
                }
                else {
                    annotRef.m_HandleRange.Reset();
                }

                tse.x_MapAnnotObject(index, key, annotRef, m_ObjectInfos);
            }
            ++annotRef.m_AnnotLocationIndex;
        }
    }
}


void CSeq_annot_Info::x_UnmapAnnotObjects(CTSE_Info& tse)
{
    if ( m_SNP_Info ) {
        m_SNP_Info->x_UnmapAnnotObjects(tse);
    }
    tse.x_UnmapAnnotObjects(m_ObjectInfos);
}


void CSeq_annot_Info::x_DropAnnotObjects(CTSE_Info& tse)
{
    if ( m_SNP_Info ) {
        m_SNP_Info->x_DropAnnotObjects(tse);
    }
    m_ObjectInfos.Clear();
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
 * ===========================================================================
 * $Log: seq_annot_info.cpp,v $
 * Revision 1000.4  2004/06/01 19:23:51  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.16
 *
 * Revision 1.16  2004/05/21 21:42:13  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.15  2004/03/26 19:42:04  vasilche
 * Fixed premature deletion of SNP annot info object.
 * Removed obsolete references to chunk info.
 *
 * Revision 1.14  2004/03/24 18:30:30  vasilche
 * Fixed edit API.
 * Every *_Info object has its own shallow copy of original object.
 *
 * Revision 1.13  2004/03/16 15:47:28  vasilche
 * Added CBioseq_set_Handle and set of EditHandles
 *
 * Revision 1.12  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 1.11  2003/11/26 17:56:00  vasilche
 * Implemented ID2 split in ID1 cache.
 * Fixed loading of splitted annotations.
 *
 * Revision 1.10  2003/11/19 22:18:03  grichenk
 * All exceptions are now CException-derived. Catch "exception" rather
 * than "runtime_error".
 *
 * Revision 1.9  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 1.8  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 1.7  2003/08/27 14:29:52  vasilche
 * Reduce object allocations in feature iterator.
 *
 * Revision 1.6  2003/07/18 19:41:46  vasilche
 * Removed unused variable.
 *
 * Revision 1.5  2003/07/17 22:51:31  vasilche
 * Fixed unused variables warnings.
 *
 * Revision 1.4  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 1.3  2003/07/09 17:54:29  dicuccio
 * Fixed uninitialized variables in CDataSource and CSeq_annot_Info
 *
 * Revision 1.2  2003/06/02 16:06:38  dicuccio
 * Rearranged src/objects/ subtree.  This includes the following shifts:
 *     - src/objects/asn2asn --> arc/app/asn2asn
 *     - src/objects/testmedline --> src/objects/ncbimime/test
 *     - src/objects/objmgr --> src/objmgr
 *     - src/objects/util --> src/objmgr/util
 *     - src/objects/alnmgr --> src/objtools/alnmgr
 *     - src/objects/flat --> src/objtools/flat
 *     - src/objects/validator --> src/objtools/validator
 *     - src/objects/cddalignview --> src/objtools/cddalignview
 * In addition, libseq now includes six of the objects/seq... libs, and libmmdb
 * replaces the three libmmdb? libs.
 *
 * Revision 1.1  2003/04/24 16:12:38  vasilche
 * Object manager internal structures are splitted more straightforward.
 * Removed excessive header dependencies.
 *
 *
 * ===========================================================================
 */