tse_assigner.hpp

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#ifndef OBJECTS_OBJMGR_IMPL___TSE_ASSIGNER__HPP
#define OBJECTS_OBJMGR_IMPL___TSE_ASSIGNER__HPP
 
/*  $Id: tse_assigner.hpp 75695 2016-12-07 16:40:59Z vasilche $
* ===========================================================================
*
*                            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: Maxim Didenko
*
* File Description:
*
*/
 
#include <objmgr/impl/tse_chunk_info.hpp>
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
 
static const int kTSE_Place_id = 0;
 
class NCBI_XOBJMGR_EXPORT ITSE_Assigner : public CObject
{
public:
    typedef CTSE_Chunk_Info::TPlace          TPlace;
    typedef CTSE_Chunk_Info::TSequence       TSequence;
    typedef CTSE_Chunk_Info::TAssembly       TAssembly;
    typedef CTSE_Chunk_Info::TChunkId        TChunkId;
    typedef CTSE_Chunk_Info::TLocationSet    TLocationSet;
    typedef CTSE_Chunk_Info::TDescInfo       TDescInfo;
    typedef CTSE_Chunk_Info::TBioseq_setId   TBioseq_setId;
    typedef CTSE_Chunk_Info::TAssemblyInfo   TAssemblyInfo;
    typedef CTSE_Chunk_Info::TBioseqId       TBioseqId;
 
    virtual ~ITSE_Assigner() {}
 
    virtual void AddDescInfo(CTSE_Info&, const TDescInfo& info,
                             TChunkId chunk_id) = 0;
    virtual void AddAnnotPlace(CTSE_Info&, const TPlace& place, 
                               TChunkId chunk_id) = 0;
    virtual void AddBioseqPlace(CTSE_Info&, TBioseq_setId place_id, 
                                TChunkId chunk_id) = 0;
    virtual void AddSeq_data(CTSE_Info&, const TLocationSet& location, 
                             CTSE_Chunk_Info& chunk) = 0;
    virtual void AddAssemblyInfo(CTSE_Info&, const TAssemblyInfo& info, 
                                 TChunkId chunk_id) = 0;
 
    virtual void UpdateAnnotIndex(CTSE_Info&, CTSE_Chunk_Info& chunk) = 0;
 
    // loading results
    virtual void LoadDescr(CTSE_Info&, const TPlace& place, 
                           const CSeq_descr& descr) = 0;
    virtual void LoadAnnot(CTSE_Info&, const TPlace& place, 
                           CRef<CSeq_annot> annot,
                           int chunk_id) = 0;
    virtual void LoadBioseq(CTSE_Info&, const TPlace& place, 
                            CRef<CSeq_entry> entry,
                            int chunk_id) = 0;
    virtual void LoadChunkBioseqs(CTSE_Info&, const TPlace& place, 
                                  const list< CRef<CBioseq> >& bioseqs,
                                  int chunk_id) = 0;
    virtual void LoadSequence(CTSE_Info&, const TPlace& place, TSeqPos pos,
                              const TSequence& sequence) = 0;
    virtual void LoadAssembly(CTSE_Info&, const TBioseqId& seq_id,
                              const TAssembly& assembly) = 0;
    virtual void LoadSeq_entry(CTSE_Info&, CSeq_entry& entry, 
                               CTSE_SetObjectInfo* set_info) = 0;
 
    // get attach points from CTSE_Info
    static CBioseq_Base_Info& x_GetBase(CTSE_Info& tse, const TPlace& place);
    static CBioseq_Info& x_GetBioseq(CTSE_Info& tse, const TPlace& place);
    static CBioseq_set_Info& x_GetBioseq_set(CTSE_Info& tse, const TPlace& place);
    static CBioseq_Info& x_GetBioseq(CTSE_Info& tse, const TBioseqId& id);
    static CBioseq_set_Info& x_GetBioseq_set(CTSE_Info& tse, TBioseq_setId id);
 
};
 
 
class NCBI_XOBJMGR_EXPORT CTSE_Default_Assigner : public ITSE_Assigner
{
public:
 
    CTSE_Default_Assigner();
 
    virtual ~CTSE_Default_Assigner();
 
    virtual void AddDescInfo(CTSE_Info&, const TDescInfo& info, TChunkId chunk_id);
    virtual void AddAnnotPlace(CTSE_Info&, const TPlace& place, TChunkId chunk_id);
    virtual void AddBioseqPlace(CTSE_Info&, TBioseq_setId place_id, 
                                TChunkId chunk_id);
    virtual void AddSeq_data(CTSE_Info&, const TLocationSet& location, 
                             CTSE_Chunk_Info& chunk);
    virtual void AddAssemblyInfo(CTSE_Info&, const TAssemblyInfo& info, 
                                 TChunkId chunk_id);
 
    virtual void UpdateAnnotIndex(CTSE_Info&, CTSE_Chunk_Info& chunk);
 
    // loading results
    virtual void LoadDescr(CTSE_Info&, const TPlace& place, 
                           const CSeq_descr& descr);
    virtual void LoadAnnot(CTSE_Info&, const TPlace& place, 
                           CRef<CSeq_annot> annot,
                           int chunk_id);
    virtual void LoadBioseq(CTSE_Info&, const TPlace& place, 
                            CRef<CSeq_entry> entry,
                            int chunk_id);
    virtual void LoadChunkBioseqs(CTSE_Info&, const TPlace& place, 
                                  const list< CRef<CBioseq> >& bioseqs,
                                  int chunk_id);
    virtual void LoadSequence(CTSE_Info&, const TPlace& place, TSeqPos pos,
                              const TSequence& sequence);
    virtual void LoadAssembly(CTSE_Info&, const TBioseqId& seq_id,
                              const TAssembly& assembly);
    virtual void LoadSeq_entry(CTSE_Info&, CSeq_entry& entry, 
                               CTSE_SetObjectInfo* set_info);
 
private:
    CTSE_Default_Assigner(const CTSE_Default_Assigner&);
    CTSE_Default_Assigner& operator=(const CTSE_Default_Assigner&);
};
 
 
 
/////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////
 
 
END_SCOPE(objects)
END_NCBI_SCOPE
 
#endif //OBJECTS_OBJMGR_IMPL___TSE_ASSIGNER__HPP