tse_split_info.hpp

Go to the documentation of this file.

Go to the SVN repository for this file.

#ifndef OBJECTS_OBJMGR_IMPL___TSE_SPLIT_INFO__HPP
#define OBJECTS_OBJMGR_IMPL___TSE_SPLIT_INFO__HPP
 
/*  $Id: tse_split_info.hpp 100045 2023-06-06 20:50:22Z 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: Eugene Vasilchenko
*
* File Description:
*   Split TSE info
*
*/
 
 
#include <corelib/ncbiobj.hpp>
#include <corelib/ncbimtx.hpp>
 
#include <objects/seq/seq_id_handle.hpp>
 
#include <objmgr/impl/tse_chunk_info.hpp>
 
#include <vector>
#include <map>
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
 
class CTSE_Info;
class CTSE_Chunk_Info;
class CBioseq_Info;
class CSeq_entry_Info;
class CDataSource;
class CDataLoader;
class CTSE_SetObjectInfo;
 
class ITSE_Assigner;
class CBioseqUpdater;
 
struct SAnnotObjectsIndex;
 
class NCBI_XOBJMGR_EXPORT CTSE_Split_Info : public CObject
{
public:
    typedef CBlobIdKey                              TBlobId;
    typedef int                                     TBlobVersion;
    typedef int                                     TSplitVersion;
    typedef CTSE_Chunk_Info::TChunkId               TChunkId;
    typedef vector<TChunkId>                        TChunkIds;
    typedef map<CTSE_Info*, CRef<ITSE_Assigner> >   TTSE_Set;
    typedef vector<pair<CSeq_id_Handle, TChunkId> > TSeqIdToChunks;
    typedef map<TChunkId, CRef<CTSE_Chunk_Info> >   TChunks;
    typedef CTSE_Chunk_Info::TBioseqId              TBioseqId;
    typedef CTSE_Chunk_Info::TBioseq_setId          TBioseq_setId;
    typedef CTSE_Chunk_Info::TPlace                 TPlace;
    typedef CTSE_Chunk_Info::TDescInfo              TDescInfo;
    typedef CTSE_Chunk_Info::TSequence              TSequence;
    typedef CTSE_Chunk_Info::TAssembly              TAssembly;
    typedef CTSE_Chunk_Info::TLocationSet           TLocationSet;
    typedef vector<CSeq_id_Handle>                  TSeqIds;
    typedef CTSE_Chunk_Info::TAssemblyInfo          TAssemblyInfo;
 
    CTSE_Split_Info(void);
    CTSE_Split_Info(TBlobId, TBlobVersion);
    ~CTSE_Split_Info(void);
 
    // interface to TSE
    TBlobId GetBlobId(void) const;
    TBlobVersion GetBlobVersion(void) const;
    TSplitVersion GetSplitVersion(void) const;
    void SetSplitVersion(TSplitVersion version);
    CInitMutexPool& GetMutexPool(void);
    CDataLoader& GetDataLoader(void) const;
 
    // TSE connection
    void x_DSAttach(CDataSource& ds);
    void x_DSDetach(CDataSource& ds);
    void x_TSEAttach(CTSE_Info& tse_info, CRef<ITSE_Assigner>& assigner);
    void x_TSEDetach(CTSE_Info& tse_info);
 
    CRef<ITSE_Assigner> GetAssigner(const CTSE_Info& tse);
 
    // chunk connection
    void AddChunk(CTSE_Chunk_Info& chunk_info);
    CTSE_Chunk_Info& GetChunk(TChunkId chunk_id);
    const CTSE_Chunk_Info& GetChunk(TChunkId chunk_id) const;
    CTSE_Chunk_Info& GetSkeletonChunk(void);
    void LoadChunk(TChunkId id) const;
    void LoadChunks(const TChunkIds& ids) const;
 
    bool x_HasDelayedMainChunk(void) const;
    bool x_NeedsDelayedMainChunk(void) const;
    void x_LoadDelayedMainChunk(void) const;
 
    // split information
    void x_AddDescInfo(const TDescInfo& info, TChunkId chunk_id);
    void x_AddAnnotPlace(const TPlace& place, TChunkId chunk_id);
    void x_AddBioseqPlace(TBioseq_setId place_id, TChunkId chunk_id);
    void x_AddSeq_data(const TLocationSet& location, CTSE_Chunk_Info& chunk);
    void x_AddAssemblyInfo(const TAssemblyInfo& info, TChunkId chunk_id);
 
    // id indexing
    void x_UpdateCore(void);
    void x_SetBioseqChunkId(TChunkId chunk_id);
    void x_SetContainedId(const TBioseqId& id, TChunkId chunk_id, bool bioseq);
    void x_SetContainedSeqIds(const vector<TBioseqId>& seq_ids,
                              const set<TBioseqId>& annot_ids,
                              TChunkId chunk_id);
 
    bool x_CanAddBioseq(const TBioseqId& id) const;
 
    void x_UpdateAnnotIndex(void);
    void x_UpdateAnnotIndex(CTSE_Chunk_Info& chunk);
    void x_UpdateFeatIdIndex(CSeqFeatData::E_Choice type,
                             EFeatIdType id_type);
    void x_UpdateFeatIdIndex(CSeqFeatData::ESubtype subtype,
                             EFeatIdType id_type);
    
    // append ids with all Bioseqs Seq-ids from this Split-Info
    void GetBioseqsIds(TSeqIds& ids) const;
 
    // bioseq lookup
    bool ContainsBioseqs() const { return m_ContainsBioseqs.load(memory_order_relaxed); }
    bool ContainsBioseq(const CSeq_id_Handle& id) const;
 
    // loading requests
    void x_GetRecords(const CSeq_id_Handle& id, bool bioseq) const;
    void x_LoadChunk(TChunkId chunk_id) const;
    void x_LoadChunks(const TChunkIds& chunk_ids) const;
    void x_AddChunksForGetRecords(vector<CConstRef<CTSE_Chunk_Info>>& chunks,
                                  const CSeq_id_Handle& id) const;
    static void x_LoadChunks(CDataLoader* loader,
                             const vector<CConstRef<CTSE_Chunk_Info>>& chunks);
 
    // loading results
    void x_LoadDescr(const TPlace& place, const CSeq_descr& descr);
    void x_LoadAnnot(const TPlace& place, const CSeq_annot& annot, int chunk_id);
    void x_LoadBioseqs(const TPlace& place, const list< CRef<CBioseq> >& bioseqs, int chunk_id);
    void x_LoadSequence(const TPlace& place, TSeqPos pos,
                        const TSequence& sequence);
    void x_LoadAssembly(const TBioseqId& seq_id,
                        const TAssembly& assembly);
    void x_LoadSeq_entry(CSeq_entry& entry, CTSE_SetObjectInfo* set_info = 0);
 
    // update in-memory size
    void x_AddUsedMemory(size_t size);
 
    void x_SetBioseqUpdater(CRef<CBioseqUpdater> updater);
 
protected:
    TSeqIdToChunks::const_iterator x_FindChunk(const CSeq_id_Handle& id) const;
 
private:
    // identification of the blob
    CDataSource*           m_DataLoader;
    TBlobId                m_BlobId;
    TBlobVersion           m_BlobVersion;
    TSplitVersion          m_SplitVersion;
 
    // all TSEs using this split info
    TTSE_Set               m_TSE_Set;
 
    // mutex to serialize chunk addition
    mutable CMutex         m_AttachMutex;
    
    // Split chunks
    mutable CMutex         m_ChunksMutex;
    TChunks                m_Chunks;
    TChunkId               m_BioseqChunkId;
 
    // loading
    CInitMutexPool         m_MutexPool;
    mutable CMutex         m_SeqIdToChunksMutex;
    mutable bool           m_SeqIdToChunksSorted;
    atomic<bool>           m_ContainsBioseqs;
    mutable TSeqIdToChunks m_SeqIdToChunks;
 
private:
    CTSE_Split_Info(const CTSE_Split_Info&);
    CTSE_Split_Info& operator=(const CTSE_Split_Info&);
};
 
 
inline
void CTSE_Split_Info::LoadChunk(TChunkId id) const
{
    x_LoadChunk(id);
}
 
 
inline
void CTSE_Split_Info::LoadChunks(const TChunkIds& ids) const
{
    x_LoadChunks(ids);
}
 
 
END_SCOPE(objects)
END_NCBI_SCOPE
 
#endif//OBJECTS_OBJMGR_IMPL___TSE_SPLIT_INFO__HPP