NCBI C++ Toolkit Cross Reference

  C++/include/objects/genomecoll/GC_Assembly.hpp


/* $Id: GC_Assembly.hpp 76430 2017-02-07 19:31:53Z mozese2 $ * =========================================================================== * * 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. * * =========================================================================== * */ /// @file GC_Assembly.hpp /// User-defined methods of the data storage class. /// /// This file was originally generated by application DATATOOL /// using the following specifications: /// 'genome_collection.asn'. /// /// New methods or data members can be added to it if needed. /// See also: GC_Assembly_.hpp #ifndef INTERNAL_GPIPE_OBJECTS_GENOMECOLL_GC_ASSEMBLY_HPP #define INTERNAL_GPIPE_OBJECTS_GENOMECOLL_GC_ASSEMBLY_HPP #include <corelib/ncbimtx.hpp> // generated includes #include <objects/genomecoll/GC_Assembly_.hpp> // generated classes #include <objects/genomecoll/GC_TaggedSequences.hpp> #include <objects/genomecoll/GC_Sequence.hpp> #include <objects/seq/seq_id_handle.hpp> BEGIN_NCBI_SCOPE BEGIN_objects_SCOPE // namespace ncbi::objects:: class CGC_AssemblyDesc; class CGC_Sequence; class CGC_Replicon; ///////////////////////////////////////////////////////////////////////////// class NCBI_GENOME_COLLECTION_EXPORT CGC_Assembly : public CGC_Assembly_Base { typedef CGC_Assembly_Base Tparent; public: typedef list< CConstRef<CGC_Sequence> > TSequenceList; typedef list< CConstRef<CGC_AssemblyUnit> > TAssemblyUnits; typedef list< CConstRef<CGC_Assembly> > TFullAssemblies; public: // constructor CGC_Assembly(void); // destructor ~CGC_Assembly(void); /// Retrieve the release id for this assembly int GetReleaseId() const; /// Retrieve the accession for this assembly string GetAccession() const; /// Either accession or submitter-provided id string GetBestIdentifier() const; /// Retrieve the full set of assembly descriptors const CGC_AssemblyDesc& GetDesc() const; /// Retrieve the tax-id for this assembly int GetTaxId() const; /// Retrieve the name of this assembly string GetName() const; /// Is this assembly a RefSeq assembly? bool IsRefSeq() const; /// Is this assembly a GenBank assembly? bool IsGenBank() const; /// Generate the internal up-pointers void CreateHierarchy(CGC_Assembly *target_set = NULL); /// Generate the Seq-id index void CreateIndex(); enum ESubset { eChromosome, eScaffold, eComponent, eTopLevel, eSubmitterPseudoScaffold, eAll }; /// Retrieve a subset of molecules /// void GetMolecules(TSequenceList& molecules, ESubset subset) const; /// Retrieve a list of all assembly units contained in this assembly TAssemblyUnits GetAssemblyUnits() const; /// Retrieve a list of all full assemblies contained in this assembly /// Note that, if the assembly is a full assembly, then it will be the only /// assembly returned; also, if the assembly is not an assembly set, then /// the base assembly will be returned. TFullAssemblies GetFullAssemblies() const; /// Find all references to a given sequence within an assembly void Find(const CSeq_id_Handle& id, TSequenceList& sequences) const; /// Find a single sequence corresponding to the supplied id. /// This variant will throw an exception if the sequence occurs more than /// once CConstRef<CGC_Sequence> Find(const CSeq_id_Handle& id) const; /// Returns replicon type, location and role void GetRepliconTypeLocRole(const CSeq_id_Handle& id, string& type, string& location, set<int>& role) const; /// PreWrite() / PostRead() handle events for indexing of local structures void PreWrite() const; void PostRead(); /// Access the top-level target set that this assemhly belongs to CConstRef<CGC_Assembly> GetTargetSet() const; /// Is this assembly the reference assembly of the target set, or part of it? bool IsTargetSetReference() const; private: // Prohibit copy constructor and assignment operator CGC_Assembly(const CGC_Assembly& value); CGC_Assembly& operator=(const CGC_Assembly& value); CMutex m_Mutex; typedef map<CSeq_id_Handle, TSequenceList> TSequenceIndex; TSequenceIndex m_SequenceMap; CGC_Assembly* m_TargetSet; /// indexing infrastructure void x_Index(CGC_Assembly& assm, CGC_Replicon& replicon); void x_Index(CGC_Assembly& assm, CGC_Sequence& seq); void x_Index(CGC_AssemblyUnit& unit, CGC_Replicon& replicon); void x_Index(CGC_AssemblyUnit& unit, CGC_Sequence& seq); void x_Index(CGC_Replicon& replicon, CGC_Sequence& seq); void x_Index(CGC_Sequence& parent, CGC_Sequence& seq, CGC_TaggedSequences::TState relation); void x_Index(CGC_Sequence& seq, CGC_TaggedSequences::TState relation); void x_Index(CGC_Assembly& root); const list< CRef< CDbtag > >& x_GetId() const; string x_GetSubmitterId() const; }; /////////////////// CGC_Assembly inline methods /////////////////// end of CGC_Assembly inline methods NCBISER_HAVE_PRE_WRITE(CGC_Assembly) NCBISER_HAVE_POST_READ(CGC_Assembly) END_objects_SCOPE // namespace ncbi::objects:: END_NCBI_SCOPE #endif // INTERNAL_GPIPE_OBJECTS_GENOMECOLL_GC_ASSEMBLY_HPP /* Original file checksum: lines: 86, chars: 2546, CRC32: 1afb85e */

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