scope.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: scope.hpp,v $
 * PRODUCTION Revision 1000.6  2004/04/16 16:59:56  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.78
 * PRODUCTION
 * ===========================================================================
 */

#ifndef OBJMGR_SCOPE__HPP
#define OBJMGR_SCOPE__HPP

/*  $Id: scope.hpp,v 1000.6 2004/04/16 16:59:56 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 <corelib/ncbiobj.hpp>
#include <objmgr/seq_id_handle.hpp>
#include <objmgr/seq_entry_handle.hpp>
#include <objmgr/bioseq_set_handle.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/seq_annot_handle.hpp>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)


// fwd decl
// objects
class CSeq_entry;
class CBioseq_set;
class CBioseq;
class CSeq_annot;
class CSeq_id;
class CSeq_loc;

// objmgr
class CSeq_id_Handle;
class CObjectManager;
class CScope_Impl;
class CSynonymsSet;


/////////////////////////////////////////////////////////////////////////////
// CScope
/////////////////////////////////////////////////////////////////////////////

class NCBI_XOBJMGR_EXPORT CScope : public CObject
{
public:
    explicit CScope(CObjectManager& objmgr);
    virtual ~CScope(void);

    // CBioseq_Handle methods:
    // Get bioseq handle by seq-id
    CBioseq_Handle GetBioseqHandle(const CSeq_id& id);
    CBioseq_Handle GetBioseqHandle(const CSeq_id_Handle& id);
    CBioseq_Handle GetBioseqHandle(const CSeq_loc& loc);

    // Get bioseq handle without loading new data
    enum EGetBioseqFlag {
        eGetBioseq_Resolved, // Search only in already resolved ids
        eGetBioseq_Loaded,   // Search in all loaded TSEs in the scope
        eGetBioseq_All       // Search bioseq, load if not loaded yet
    };
    CBioseq_Handle GetBioseqHandle(const CSeq_id& id,
                                   EGetBioseqFlag get_flag);
    CBioseq_Handle GetBioseqHandle(const CSeq_id_Handle& id,
                                   EGetBioseqFlag get_flag);

    // Deprecated interface
    CBioseq_Handle GetBioseqHandle(const CBioseq& bioseq);
    CSeq_entry_Handle GetSeq_entryHandle(const CSeq_entry& entry);
    CSeq_annot_Handle GetSeq_annotHandle(const CSeq_annot& annot);

    // Get bioseq handle for sequence withing one TSE
    CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id& id,
                                          const CBioseq_Handle& bh);
    CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id& id,
                                          const CSeq_entry_Handle& seh);
    CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id_Handle& id,
                                          const CBioseq_Handle& bh);
    CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id_Handle& id,
                                          const CSeq_entry_Handle& seh);

    // CScope contents modification methods
    typedef int TPriority;
    enum EPriority {
        kPriority_NotSet = -1
    };

    // Add default data loaders from object manager
    void AddDefaults(TPriority pri = kPriority_NotSet);
    // Add data loader by name.
    // The loader (or its factory) must be known to Object Manager.
    void AddDataLoader(const string& loader_name,
                       TPriority pri = kPriority_NotSet);
    // Add the scope's datasources as a single group with the given priority
    void AddScope(CScope& scope,
                  TPriority pri = kPriority_NotSet);


    // Add seq_entry, default priority is higher than for defaults or loaders
    CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry& top_entry,
                                          TPriority pri = kPriority_NotSet);
    // Add bioseq, return bioseq handle. Try to use unresolved seq-id
    // from the bioseq, fail if all ids are already resolved to
    // other sequences.
    CBioseq_Handle AddBioseq(CBioseq& bioseq,
                             TPriority pri = kPriority_NotSet);
    // Add Seq-annot
    CSeq_annot_Handle AddSeq_annot(const CSeq_annot& annot,
                                   TPriority pri = kPriority_NotSet);

    CBioseq_EditHandle GetEditHandle(const CBioseq_Handle& seq);
    CSeq_entry_EditHandle GetEditHandle(const CSeq_entry_Handle& entry);
    CSeq_annot_EditHandle GetEditHandle(const CSeq_annot_Handle& annot);
    CBioseq_set_EditHandle GetEditHandle(const CBioseq_set_Handle& seqset);

    void ResetHistory(void);

    CConstRef<CSynonymsSet> GetSynonyms(const CSeq_id& id);
    CConstRef<CSynonymsSet> GetSynonyms(const CSeq_id_Handle& id);
    CConstRef<CSynonymsSet> GetSynonyms(const CBioseq_Handle& bh);

    // deprecated interface
    void AttachEntry(CSeq_entry& parent, CSeq_entry& entry);
    void RemoveEntry(CSeq_entry& entry);

    void AttachAnnot(CSeq_entry& parent, CSeq_annot& annot);
    void RemoveAnnot(CSeq_entry& parent, CSeq_annot& annot);
    void ReplaceAnnot(CSeq_entry& entry,
                      CSeq_annot& old_annot, CSeq_annot& new_annot);

    CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id& id,
                                          const CSeq_entry& tse);
    CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id_Handle& id,
                                          const CSeq_entry& tse);

    enum ETSEKind {
        eManualTSEs,
        eAllTSEs
    };
    typedef vector<CSeq_entry_Handle> TTSE_Handles;
    void GetAllTSEs(TTSE_Handles& tses, enum ETSEKind kind = eManualTSEs);

protected:
    CScope_Impl& GetImpl(void);

private:
    // to prevent copying
    CScope(const CScope&);
    CScope& operator=(const CScope&);

    friend class CSeqMap_CI;
    friend class CSeq_annot_CI;
    friend class CAnnot_Collector;
    friend class CBioseq_CI;
    friend class CHeapScope;
    friend class CPrefetchToken_Impl;

    CRef<CScope>      m_HeapScope;
    CRef<CScope_Impl> m_Impl;
};


/////////////////////////////////////////////////////////////////////////////
// CScope inline methods
/////////////////////////////////////////////////////////////////////////////


inline
CScope_Impl& CScope::GetImpl(void)
{
    return *m_Impl;
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: scope.hpp,v $
* Revision 1000.6  2004/04/16 16:59:56  gouriano
* PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.78
*
* Revision 1.78  2004/04/16 13:31:46  grichenk
* Added data pre-fetching functions.
*
* Revision 1.77  2004/04/13 16:39:36  grichenk
* Corrected comments
*
* Revision 1.76  2004/04/13 15:59:35  grichenk
* Added CScope::GetBioseqHandle() with id resolving flag.
*
* Revision 1.75  2004/04/12 18:40:24  grichenk
* Added GetAllTSEs()
*
* Revision 1.74  2004/04/05 15:56:13  grichenk
* Redesigned CAnnotTypes_CI: moved all data and data collecting
* functions to CAnnotDataCollector. CAnnotTypes_CI is no more
* inherited from SAnnotSelector.
*
* Revision 1.73  2004/03/24 18:30:28  vasilche
* Fixed edit API.
* Every *_Info object has its own shallow copy of original object.
*
* Revision 1.72  2004/03/16 15:47:26  vasilche
* Added CBioseq_set_Handle and set of EditHandles
*
* Revision 1.71  2004/02/19 17:23:00  vasilche
* Changed order of deletion of heap scope and scope impl objects.
* Reduce number of calls to x_ResetHistory().
*
* Revision 1.70  2004/02/02 14:46:42  vasilche
* Several performance fixed - do not iterate whole tse set in CDataSource.
*
* Revision 1.69  2004/01/29 20:33:27  vasilche
* Do not resolve any Seq-ids in CScope::GetSynonyms() -