NCBI C++ Toolkit Cross Reference

  C++/include/objmgr/scope.hpp


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#ifndef OBJMGR_SCOPE__HPP #define OBJMGR_SCOPE__HPP /* $Id: scope.hpp 61952 2014-03-03 17:35:59Z 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. * * =========================================================================== * * 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 <objects/seq/seq_id_handle.hpp> #include <objmgr/tse_handle.hpp> #include <objmgr/scope_transaction.hpp> #include <objmgr/seq_entry_handle.hpp> #include <objmgr/bioseq_set_handle.hpp> #include <objmgr/bioseq_handle.hpp> #include <objmgr/seq_annot_handle.hpp> #include <objmgr/seq_feat_handle.hpp> #include <objmgr/gc_assembly_parser.hpp> #include <objects/genomecoll/GC_Assembly.hpp> BEGIN_NCBI_SCOPE BEGIN_SCOPE(objects) /** @addtogroup ObjectManagerCore * * @{ */ // 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; class CBlobIdKey; class CDataLoader; ///////////////////////////////////////////////////////////////////////////// /// /// CScope -- /// /// Scope of cache visibility and reference resolution /// class NCBI_XOBJMGR_EXPORT CScope : public CObject { public: explicit CScope(CObjectManager& objmgr); virtual ~CScope(void); /// priority type and special value for added objects typedef int TPriority; enum EPriority { kPriority_Default = -1, ///< Use default priority for added data kPriority_NotSet = -1 ///< Deprecated: use kPriority_Default instead }; /// Get object manager controlling this scope CObjectManager& GetObjectManager(void); // CBioseq_Handle methods: /// Get bioseq handle by seq-id CBioseq_Handle GetBioseqHandle(const CSeq_id& id); /// Get bioseq handle by seq-id handle CBioseq_Handle GetBioseqHandle(const CSeq_id_Handle& id); /// Get bioseq handle by seq-loc. /// If the seq-loc contains no seq-ids or there's a single seq-id which /// can not be resolved, returns empty handle. /// If the seq-loc references only parts of a segmented set, the method /// returns bioseq handle for the master bioseq. /// If the seq-loc contains a single seq-id, the bioseq handle for this /// id is returned. /// If there are multiple seq-ids not belonging to the same seg-set, /// the method throws CObjMgrException. CBioseq_Handle GetBioseqHandle(const CSeq_loc& loc); 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 }; /// Get bioseq handle without loading new data CBioseq_Handle GetBioseqHandle(const CSeq_id& id, EGetBioseqFlag get_flag); /// Get bioseq handle without loading new data CBioseq_Handle GetBioseqHandle(const CSeq_id_Handle& id, EGetBioseqFlag get_flag); /// Check if two seq-ids are resolved to the same Bioseq bool IsSameBioseq(const CSeq_id_Handle& id1, const CSeq_id_Handle& id2, EGetBioseqFlag get_flag); typedef CBioseq_Handle::TId TIds; typedef vector<CBioseq_Handle> TBioseqHandles; /// Get bioseq handles for all ids. The returned vector contains /// bioseq handles for all requested ids in the same order. TBioseqHandles GetBioseqHandles(const TIds& ids); /// GetXxxHandle control values. enum EMissing { eMissing_Throw, eMissing_Null, eMissing_Default = eMissing_Throw }; typedef CBlobIdKey TBlobId; /// Get Seq-entry handle by its blob-id, with possible loading. /// The blob-id can be obtained from CTSE_Handle::GetBlobId() or /// from specific data loader (see CGBDataLoader::GetBlobId()). CSeq_entry_Handle GetSeq_entryHandle(CDataLoader* loader, const TBlobId& blob_id, EMissing action = eMissing_Default); // Deprecated interface /// Find object in scope /// If object is not found GetXxxHandle() methods will either /// throw an exception or return null handle depending on argument. CTSE_Handle GetTSE_Handle(const CSeq_entry& tse, EMissing action = eMissing_Default); CBioseq_Handle GetBioseqHandle(const CBioseq& bioseq, EMissing action = eMissing_Default); CBioseq_set_Handle GetBioseq_setHandle(const CBioseq_set& seqset, EMissing action = eMissing_Default); CSeq_entry_Handle GetSeq_entryHandle(const CSeq_entry& entry, EMissing action = eMissing_Default); CSeq_annot_Handle GetSeq_annotHandle(const CSeq_annot& annot, EMissing action = eMissing_Default); CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat& feat, EMissing action = eMissing_Default); CBioseq_Handle GetObjectHandle(const CBioseq& bioseq, EMissing action = eMissing_Default); CBioseq_set_Handle GetObjectHandle(const CBioseq_set& seqset, EMissing action = eMissing_Default); CSeq_entry_Handle GetObjectHandle(const CSeq_entry& entry, EMissing action = eMissing_Default); CSeq_annot_Handle GetObjectHandle(const CSeq_annot& annot, EMissing action = eMissing_Default); CSeq_feat_Handle GetObjectHandle(const CSeq_feat& feat, EMissing action = eMissing_Default); /// Get edit handle for the specified object /// Throw an exception if object is not found, or non-editable CBioseq_EditHandle GetBioseqEditHandle(const CBioseq& bioseq); CSeq_entry_EditHandle GetSeq_entryEditHandle(const CSeq_entry& entry); CSeq_annot_EditHandle GetSeq_annotEditHandle(const CSeq_annot& annot); CBioseq_set_EditHandle GetBioseq_setEditHandle(const CBioseq_set& seqset); CBioseq_EditHandle GetObjectEditHandle(const CBioseq& bioseq); CBioseq_set_EditHandle GetObjectEditHandle(const CBioseq_set& seqset); CSeq_entry_EditHandle GetObjectEditHandle(const CSeq_entry& entry); CSeq_annot_EditHandle GetObjectEditHandle(const CSeq_annot& annot); /// Get bioseq handle for sequence withing one TSE CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id& id, const CTSE_Handle& tse); CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id_Handle& id, const CTSE_Handle& tse); CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id& id, const CBioseq_Handle& bh); /// Get bioseq handle for sequence withing one TSE CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id& id, const CSeq_entry_Handle& seh); /// Get bioseq handle for sequence withing one TSE CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id_Handle& id, const CBioseq_Handle& bh); /// Get bioseq handle for sequence withing one TSE CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id_Handle& id, const CSeq_entry_Handle& seh); // CScope contents modification methods /// Add default data loaders from object manager void AddDefaults(TPriority pri = kPriority_Default); /// 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_Default); /// Add the scope's datasources as a single group with the given priority /// All data sources (data loaders and explicitly added data) have /// priorities. The scope scans data sources in order of increasing /// priorities to find the sequence you've requested. By default, /// explicitly added data have priority 9, and data loaders - priority /// 99, so the scope will first look in explicit data, then in data /// loaders. If you have conflicting data or loaders (e.g. GenBank and /// BLAST), you may need different priorities to make scope first look, /// for example, in BLAST, and then if sequence is not found - in GenBank. /// Note, that the priority you've specified for a data loader at /// registration time (RegisterInObjectManager()) is a new default for /// it, and can be overridden when you add the data loader to a scope. void AddScope(CScope& scope, TPriority pri = kPriority_Default); /// AddXxx() control values enum EExist { eExist_Throw, eExist_Get, eExist_Default = eExist_Throw }; /// Add seq_entry, default priority is higher than for defaults or loaders /// Add object to the score with possibility to edit it directly. /// If the object is already in the scope the AddXxx() methods will /// throw an exception or return handle to existent object depending /// on the action argument. CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry& top_entry, TPriority pri = kPriority_Default, EExist action = eExist_Default); /// Add shared Seq-entry, scope will not modify it. /// If edit handle is requested, scope will create a copy object. /// If the object is already in the scope the AddXxx() methods will /// throw an exception or return handle to existent object depending /// on the action argument. CSeq_entry_Handle AddTopLevelSeqEntry(const CSeq_entry& top_entry, TPriority pri = kPriority_Default, EExist action = eExist_Throw); /// Add bioseq, return bioseq handle. Try to use unresolved seq-id /// from the bioseq, fail if all ids are already resolved to /// other sequences. /// Add object to the score with possibility to edit it directly. /// If the object is already in the scope the AddXxx() methods will /// throw an exception or return handle to existent object depending /// on the action argument. CBioseq_Handle AddBioseq(CBioseq& bioseq, TPriority pri = kPriority_Default, EExist action = eExist_Throw); /// Add shared Bioseq, scope will not modify it. /// If edit handle is requested, scope will create a copy object. /// If the object is already in the scope the AddXxx() methods will /// throw an exception or return handle to existent object depending /// on the action argument. CBioseq_Handle AddBioseq(const CBioseq& bioseq, TPriority pri = kPriority_Default, EExist action = eExist_Throw); /// Add GC-Assembly. Sequences from the assembly are converted /// to bioseqs and added to the scope as a new top level seq-entry. CSeq_entry_Handle AddGC_Assembly(const CGC_Assembly& gc_assembly, CGC_Assembly_Parser::FParserFlags flags = CGC_Assembly_Parser::fDefault, TPriority pri = kPriority_Default, EExist action = eExist_Throw); /// Add Seq-annot, return its CSeq_annot_Handle. /// Add object to the score with possibility to edit it directly. /// If the object is already in the scope the AddXxx() methods will /// throw an exception or return handle to existent object depending /// on the action argument. CSeq_annot_Handle AddSeq_annot(CSeq_annot& annot, TPriority pri = kPriority_Default, EExist action = eExist_Throw); /// Add shared Seq-annot, scope will not modify it. /// If edit handle is requested, scope will create a copy object. /// If the object is already in the scope the AddXxx() methods will /// throw an exception or return handle to existent object depending /// on the action argument. CSeq_annot_Handle AddSeq_annot(const CSeq_annot& annot, TPriority pri = kPriority_Default, EExist action = eExist_Throw); /// Get editable Biosec handle by regular one CBioseq_EditHandle GetEditHandle(const CBioseq_Handle& seq); /// Get editable SeqEntry handle by regular one CSeq_entry_EditHandle GetEditHandle(const CSeq_entry_Handle& entry); /// Get editable Seq-annot handle by regular one CSeq_annot_EditHandle GetEditHandle(const CSeq_annot_Handle& annot); /// Get editable Biosec-set handle by regular one CBioseq_set_EditHandle GetEditHandle(const CBioseq_set_Handle& seqset); enum EActionIfLocked { eKeepIfLocked, eThrowIfLocked, eRemoveIfLocked }; /// Clean all unused TSEs from the scope's cache and release the memory. /// TSEs referenced by any handles are not removed. /// Explicitly added entries are not removed. /// Edited entries retrieved from a data loader are removed, /// so that their unmodified version will be visible. void ResetHistory(EActionIfLocked action = eKeepIfLocked); /// Clear all information in the scope except added data loaders. void ResetDataAndHistory(void); /// Clear all information in the scope including data loaders. enum ERemoveDataLoaders { eRemoveDataLoaders }; void ResetDataAndHistory(ERemoveDataLoaders remove_data_loaders); /// Remove single TSE from the scope's history. If there are other /// live handles referencing the TSE, nothing is removed. /// @param tse /// TSE to be removed from the cache. void RemoveFromHistory(const CTSE_Handle& tse); /// Remove the bioseq's TSE from the scope's history. If there are other /// live handles referencing the TSE, nothing is removed. /// @param bioseq /// Bioseq, which TSE is to be removed from the cache. void RemoveFromHistory(const CBioseq_Handle& bioseq); /// Revoke data loader from the scope. Throw exception if the /// operation fails (e.g. data source is in use or not found). void RemoveDataLoader(const string& loader_name, EActionIfLocked action = eThrowIfLocked); /// Revoke TSE previously added using AddTopLevelSeqEntry() or /// AddBioseq(). Throw exception if the TSE is still in use or /// not found in the scope. void RemoveTopLevelSeqEntry(const CTSE_Handle& entry); void RemoveTopLevelSeqEntry(const CSeq_entry_Handle& entry); /// Revoke Bioseq previously added using AddBioseq(). /// Throw exception if the Bioseq is still in use or /// not found in the scope. void RemoveBioseq(const CBioseq_Handle& seq); /// Revoke Seq-annot previously added using AddSeq_annot(). /// Throw exception if the Bioseq is still in use or /// not found in the scope. void RemoveSeq_annot(const CSeq_annot_Handle& annot); /// Get "native" bioseq ids without filtering and matching. TIds GetIds(const CSeq_id& id ); TIds GetIds(const CSeq_id_Handle& idh); CSeq_id_Handle GetAccVer(const CSeq_id_Handle& idh); TGi GetGi(const CSeq_id_Handle& idh); static CSeq_id_Handle x_GetAccVer(const TIds& ids); static TGi x_GetGi(const TIds& ids); /// Get short description of bioseq, usually "accession.version" enum EForceLabelLoad { eNoForceLabelLoad, eForceLabelLoad }; string GetLabel(const CSeq_id& id, EForceLabelLoad force_load = eNoForceLabelLoad); string GetLabel(const CSeq_id_Handle& idh, EForceLabelLoad force_load = eNoForceLabelLoad); /// Get taxonomy id of bioseq /// -1 means failure to determine the taxonomy id /// 0 means absence of the taxonomy id for the sequence enum EForceLoad { eNoForceLoad, eForceLoad }; int GetTaxId(const CSeq_id& id, EForceLoad force_load = eNoForceLoad); int GetTaxId(const CSeq_id_Handle& idh, EForceLoad force_load = eNoForceLoad); // returns kInvalidSeqPos if sequence is not known TSeqPos GetSequenceLength(const CSeq_id& id, EForceLoad force_load = eNoForceLoad); TSeqPos GetSequenceLength(const CSeq_id_Handle& id, EForceLoad force_load = eNoForceLoad); // returns CSeq_inst::eMol_not_set if sequence is not known CSeq_inst::TMol GetSequenceType(const CSeq_id& id, EForceLoad force_load = eNoForceLoad); CSeq_inst::TMol GetSequenceType(const CSeq_id_Handle& id, EForceLoad force_load = eNoForceLoad); // returns (fState_not_found|fState_no_data) if sequence is not known CBioseq_Handle::TBioseqStateFlags GetSequenceState(const CSeq_id& id, EForceLoad force_load = eNoForceLoad); CBioseq_Handle::TBioseqStateFlags GetSequenceState(const CSeq_id_Handle& id, EForceLoad force_load = eNoForceLoad); /// Bulk retrieval methods typedef vector<CSeq_id_Handle> TSeq_id_Handles; TSeq_id_Handles GetAccVers(const TSeq_id_Handles& idhs, EForceLoad force_load = eNoForceLoad); void GetAccVers(TSeq_id_Handles* results, const TSeq_id_Handles& idhs, EForceLoad force_load = eNoForceLoad); typedef vector<TGi> TGIs; TGIs GetGis(const TSeq_id_Handles& idhs, EForceLoad force_load = eNoForceLoad); void GetGis(TGIs* results, const TSeq_id_Handles& idhs, EForceLoad force_load = eNoForceLoad); typedef vector<string> TLabels; TLabels GetLabels(const TSeq_id_Handles& idhs, EForceLoad force_load = eNoForceLoad); void GetLabels(TLabels* results, const TSeq_id_Handles& idhs, EForceLoad force_load = eNoForceLoad); typedef vector<int> TTaxIds; TTaxIds GetTaxIds(const TSeq_id_Handles& idhs, EForceLoad force_load = eNoForceLoad); void GetTaxIds(TTaxIds* results, const TSeq_id_Handles& idhs, EForceLoad force_load = eNoForceLoad); typedef vector<TSeqPos> TSequenceLengths; TSequenceLengths GetSequenceLengths(const TSeq_id_Handles& idhs, EForceLoad force_load = eNoForceLoad); void GetSequenceLengths(TSequenceLengths* results, const TSeq_id_Handles& idhs, EForceLoad force_load = eNoForceLoad); typedef vector<CSeq_inst::TMol> TSequenceTypes; TSequenceTypes GetSequenceTypes(const TSeq_id_Handles& idhs, EForceLoad force_load = eNoForceLoad); void GetSequenceTypes(TSequenceTypes* results, const TSeq_id_Handles& idhs, EForceLoad force_load = eNoForceLoad); typedef vector<CBioseq_Handle::TBioseqStateFlags> TSequenceStates; TSequenceStates GetSequenceStates(const TSeq_id_Handles& idhs, EForceLoad force_load = eNoForceLoad); void GetSequenceStates(TSequenceStates* results, const TSeq_id_Handles& idhs, EForceLoad force_load = eNoForceLoad); /// Get bioseq synonyms, resolving to the bioseq in this scope. CConstRef<CSynonymsSet> GetSynonyms(const CSeq_id& id); /// Get bioseq synonyms, resolving to the bioseq in this scope. CConstRef<CSynonymsSet> GetSynonyms(const CSeq_id_Handle& id); /// Get bioseq synonyms, resolving to the bioseq in this scope. 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); CScopeTransaction GetTransaction(); void UpdateAnnotIndex(void); 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 CPrefetchTokenOld_Impl; friend class CScopeTransaction; CRef<CScope> m_HeapScope; CRef<CScope_Impl> m_Impl; }; ///////////////////////////////////////////////////////////////////////////// // CScope inline methods ///////////////////////////////////////////////////////////////////////////// inline CScope_Impl& CScope::GetImpl(void) { return *m_Impl; } inline CBioseq_Handle CScope::GetObjectHandle(const CBioseq& obj, EMissing action) { return GetBioseqHandle(obj, action); } inline CBioseq_set_Handle CScope::GetObjectHandle(const CBioseq_set& obj, EMissing action) { return GetBioseq_setHandle(obj, action); } inline CSeq_entry_Handle CScope::GetObjectHandle(const CSeq_entry& obj, EMissing action) { return GetSeq_entryHandle(obj, action); } inline CSeq_annot_Handle CScope::GetObjectHandle(const CSeq_annot& obj, EMissing action) { return GetSeq_annotHandle(obj, action); } inline CSeq_feat_Handle CScope::GetObjectHandle(const CSeq_feat& feat, EMissing action) { return GetSeq_featHandle(feat, action); } inline CBioseq_EditHandle CScope::GetObjectEditHandle(const CBioseq& obj) { return GetBioseqEditHandle(obj); } inline CBioseq_set_EditHandle CScope::GetObjectEditHandle(const CBioseq_set& obj) { return GetBioseq_setEditHandle(obj); } inline CSeq_entry_EditHandle CScope::GetObjectEditHandle(const CSeq_entry& obj) { return GetSeq_entryEditHandle(obj); } inline CSeq_annot_EditHandle CScope::GetObjectEditHandle(const CSeq_annot& obj) { return GetSeq_annotEditHandle(obj); } inline void CScope::RemoveTopLevelSeqEntry(const CSeq_entry_Handle& entry) { RemoveTopLevelSeqEntry(entry.GetTSE_Handle()); } /* @} */ END_SCOPE(objects) END_NCBI_SCOPE #endif//OBJMGR_SCOPE__HPP

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