seq_id_handle.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: seq_id_handle.hpp,v $
- * PRODUCTION Revision 1000.2 2004/04/12 17:27:42 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.22
- * PRODUCTION
- * ===========================================================================
- */
- #ifndef OBJECTS_OBJMGR___SEQ_ID_HANDLE__HPP
- #define OBJECTS_OBJMGR___SEQ_ID_HANDLE__HPP
- /* $Id: seq_id_handle.hpp,v 1000.2 2004/04/12 17:27:42 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.
- *
- * ===========================================================================
- *
- * Author: Aleksey Grichenko, Eugene Vasilchenko
- *
- * File Description:
- * Seq-id handle for Object Manager
- *
- */
- #include <objects/seqloc/Seq_id.hpp>
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(objects)
- ////////////////////////////////////////////////////////////////////
- //
- // CSeq_id_Handle::
- //
- // Handle to be used instead of CSeq_id. Supports different
- // methods of comparison: exact equality or match of seq-ids.
- //
- // forward declaration
- class CSeq_id;
- class CSeq_id_Handle;
- class CSeq_id_Mapper;
- class CSeq_id_Which_Tree;
- class NCBI_XOBJMGR_EXPORT CSeq_id_Info
- {
- public:
- explicit CSeq_id_Info(CSeq_id_Which_Tree* tree);
- CSeq_id_Info(CSeq_id_Which_Tree* tree, const CConstRef<CSeq_id>& seq_id);
- ~CSeq_id_Info(void);
- CConstRef<CSeq_id> GetSeqId(void) const
- {
- return m_Seq_id;
- }
- CConstRef<CSeq_id> GetGiSeqId(int gi) const;
- void AddReference(void) const;
- void RemoveReference(void) const;
- int GetCounter(void) const;
- CSeq_id_Which_Tree* GetTree(void) const;
- protected:
- void x_RemoveLastReference(void) const;
- mutable CAtomicCounter m_Counter;
- CSeq_id_Which_Tree* m_Tree;
- CConstRef<CSeq_id> m_Seq_id;
- private:
- CSeq_id_Info(const CSeq_id_Info&);
- const CSeq_id_Info& operator=(const CSeq_id_Info&);
- };
- class NCBI_XOBJMGR_EXPORT CSeq_id_Handle
- {
- public:
- // 'ctors
- CSeq_id_Handle(void);
- explicit CSeq_id_Handle(const CSeq_id_Info* info, int gi = 0);
- static CSeq_id_Handle GetGiHandle(int gi);
- static CSeq_id_Handle GetHandle(const CSeq_id& id);
- bool operator== (const CSeq_id_Handle& handle) const;
- bool operator!= (const CSeq_id_Handle& handle) const;
- bool operator< (const CSeq_id_Handle& handle) const;
- bool operator== (const CSeq_id& id) const;
- // Check if the handle is a valid or an empty one
- operator bool(void) const;
- bool operator! (void) const;
- // Reset the handle (remove seq-id reference)
- void Reset(void);
- // True if "this" is a better bioseq than "h".
- bool IsBetter(const CSeq_id_Handle& h) const;
- string AsString(void) const;
- bool IsGi(void) const;
- int GetGi(void) const;
- unsigned GetHash(void) const;
- CConstRef<CSeq_id> GetSeqId(void) const;
- CConstRef<CSeq_id> GetSeqIdOrNull(void) const;
- static void DumpRegister(const char* msg);
- private:
- void x_Register(void);
- void x_Deregister(void);
-
- friend class CSeq_id_Mapper;
- CSeq_id_Which_Tree* x_GetTree(void) const;
- // Comparison methods
- // True if handles are strictly equal
- bool x_Equal(const CSeq_id_Handle& handle) const;
- // True if "this" may be resolved to "handle"
- bool x_Match(const CSeq_id_Handle& handle) const;
- // Seq-id info
- CConstRef<CSeq_id_Info> m_Info;
- int m_Gi;
- };
- /////////////////////////////////////////////////////////////////////
- //
- // Inline methods
- //
- /////////////////////////////////////////////////////////////////////
- /////////////////////////////////////////////////////////////////////////////
- // CSeq_id_Info
- /////////////////////////////////////////////////////////////////////////////
- inline
- CSeq_id_Info::CSeq_id_Info(CSeq_id_Which_Tree* tree)
- : m_Tree(tree)
- {
- _ASSERT(tree);
- m_Counter.Set(0);
- }
- inline
- CSeq_id_Info::CSeq_id_Info(CSeq_id_Which_Tree* tree, const CConstRef<CSeq_id>& seq_id)
- : m_Tree(tree),
- m_Seq_id(seq_id)
- {
- _ASSERT(tree);
- m_Counter.Set(0);
- }
- inline
- void CSeq_id_Info::AddReference(void) const
- {
- _VERIFY(m_Counter.Add(1) > 0);
- }
- inline
- void CSeq_id_Info::RemoveReference(void) const
- {
- if ( m_Counter.Add(-1) <= 0 ) {
- x_RemoveLastReference();
- }
- }
- inline
- int CSeq_id_Info::GetCounter(void) const
- {
- int counter = m_Counter.Get();
- _ASSERT(counter >= 0);
- return counter;
- }
- inline
- CSeq_id_Which_Tree* CSeq_id_Info::GetTree(void) const
- {
- _ASSERT(m_Tree);
- return m_Tree;
- }
- /////////////////////////////////////////////////////////////////////////////
- // CSeq_id_Handle
- /////////////////////////////////////////////////////////////////////////////
- inline
- CSeq_id_Handle::operator bool (void) const
- {
- return m_Info;
- }
- inline
- bool CSeq_id_Handle::operator!(void) const
- {
- return !m_Info;
- }
- inline
- CSeq_id_Handle::CSeq_id_Handle(void)
- : m_Info(0), m_Gi(0)
- {
- }
- inline
- CSeq_id_Handle::CSeq_id_Handle(const CSeq_id_Info* info, int gi)
- : m_Info(info), m_Gi(gi)
- {
- _ASSERT(info);
- }
- inline
- void CSeq_id_Handle::Reset(void)
- {
- m_Info.Reset();
- m_Gi = 0;
- }
- inline
- bool CSeq_id_Handle::operator==(const CSeq_id_Handle& handle) const
- {
- return m_Gi == handle.m_Gi && m_Info == handle.m_Info;
- }
- inline
- bool CSeq_id_Handle::operator!=(const CSeq_id_Handle& handle) const
- {
- return m_Gi != handle.m_Gi || m_Info != handle.m_Info;
- }
- inline
- bool CSeq_id_Handle::operator<(const CSeq_id_Handle& handle) const
- {
- return m_Gi < handle.m_Gi ||
- m_Gi == handle.m_Gi && m_Info < handle.m_Info;
- }
- inline
- bool CSeq_id_Handle::IsGi(void) const
- {
- return m_Gi != 0;
- }
- inline
- int CSeq_id_Handle::GetGi(void) const
- {
- return m_Gi;
- }
- inline
- unsigned CSeq_id_Handle::GetHash(void) const
- {
- unsigned hash = m_Gi;
- if ( !hash ) {
- hash = unsigned((unsigned long)(m_Info)>>3);
- }
- return hash;
- }
- END_SCOPE(objects)
- END_NCBI_SCOPE
- /*
- * ---------------------------------------------------------------------------
- * $Log: seq_id_handle.hpp,v $
- * Revision 1000.2 2004/04/12 17:27:42 gouriano
- * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.22
- *
- * Revision 1.22 2004/02/19 17:25:33 vasilche
- * Use CRef<> to safely hold pointer to CSeq_id_Info.
- * CSeq_id_Info holds pointer to owner CSeq_id_Which_Tree.
- * Reduce number of calls to CSeq_id_Handle.GetSeqId().
- *
- * Revision 1.21 2004/01/22 20:10:38 vasilche
- * 1. Splitted ID2 specs to two parts.
- * ID2 now specifies only protocol.
- * Specification of ID2 split data is moved to seqsplit ASN module.
- * For now they are still reside in one resulting library as before - libid2.
- * As the result split specific headers are now in objects/seqsplit.
- * 2. Moved ID2 and ID1 specific code out of object manager.
- * Protocol is processed by corresponding readers.
- * ID2 split parsing is processed by ncbi_xreader library - used by all readers.
- * 3. Updated OBJMGR_LIBS correspondingly.
- *
- * Revision 1.20 2004/01/07 20:42:00 grichenk
- * Fixed matching of accession to accession.version
- *
- * Revision 1.19 2003/11/26 17:55:54 vasilche
- * Implemented ID2 split in ID1 cache.
- * Fixed loading of splitted annotations.
- *
- * Revision 1.18 2003/10/07 13:43:22 vasilche
- * Added proper handling of named Seq-annots.
- * Added feature search from named Seq-annots.
- * Added configurable adaptive annotation search (default: gene, cds, mrna).
- * Fixed selection of blobs for loading from GenBank.
- * Added debug checks to CSeq_id_Mapper for easier finding lost CSeq_id_Handles.
- * Fixed leaked split chunks annotation stubs.
- * Moved some classes definitions in separate *.cpp files.
- *
- * Revision 1.17 2003/09/30 16:21:59 vasilche
- * Updated internal object manager classes to be able to load ID2 data.
- * SNP blobs are loaded as ID2 split blobs - readers convert them automatically.
- * Scope caches results of requests for data to data loaders.
- * Optimized CSeq_id_Handle for gis.
- * Optimized bioseq lookup in scope.
- * Reduced object allocations in annotation iterators.
- * CScope is allowed to be destroyed before other objects using this scope are
- * deleted (feature iterators, bioseq handles etc).
- * Optimized lookup for matching Seq-ids in CSeq_id_Mapper.
- * Added 'adaptive' option to objmgr_demo application.
- *
- * Revision 1.16 2003/07/17 20:07:55 vasilche
- * Reduced memory usage by feature indexes.
- * SNP data is loaded separately through PUBSEQ_OS.
- * String compression for SNP data.
- *
- * Revision 1.15 2003/06/19 18:23:44 vasilche
- * Added several CXxx_ScopeInfo classes for CScope related information.
- * CBioseq_Handle now uses reference to CBioseq_ScopeInfo.
- * Some fine tuning of locking in CScope.
- *
- * Revision 1.14 2003/06/10 19:06:34 vasilche
- * Simplified CSeq_id_Mapper and CSeq_id_Handle.
- *
- * Revision 1.13 2003/04/24 16:12:37 vasilche
- * Object manager internal structures are splitted more straightforward.
- * Removed excessive header dependencies.
- *
- * Revision 1.12 2003/02/24 18:57:21 vasilche
- * Make feature gathering in one linear pass using CSeqMap iterator.
- * Do not use feture index by sub locations.
- * Sort features at the end of gathering in one vector.
- * Extracted some internal structures and classes in separate header.
- * Delay creation of mapped features.
- *
- * Revision 1.11 2003/02/21 14:33:50 grichenk
- * Display warning but don't crash on uninitialized seq-ids.
- *
- * Revision 1.10 2002/12/26 20:44:02 dicuccio
- * Added Win32 export specifier. Added #include for seq_id_mapper - at bottom of
- * file to skirt circular include dependency.
- *
- * Revision 1.9 2002/07/08 20:50:56 grichenk
- * Moved log to the end of file
- * Replaced static mutex (in CScope, CDataSource) with the mutex
- * pool. Redesigned CDataSource data locking.
- *
- * Revision 1.8 2002/05/29 21:19:57 gouriano
- * added debug dump
- *
- * Revision 1.7 2002/05/02 20:42:35 grichenk
- * throw -> THROW1_TRACE
- *
- * Revision 1.6 2002/03/18 17:26:32 grichenk
- * +CDataLoader::x_GetSeq_id(), x_GetSeq_id_Key(), x_GetSeq_id_Handle()
- *
- * Revision 1.5 2002/03/15 18:10:05 grichenk
- * Removed CRef<CSeq_id> from CSeq_id_Handle, added
- * key to seq-id map th CSeq_id_Mapper
- *
- * Revision 1.4 2002/02/21 19:27:00 grichenk
- * Rearranged includes. Added scope history. Added searching for the
- * best seq-id match in data sources and scopes. Updated tests.
- *
- * Revision 1.3 2002/02/12 19:41:40 grichenk
- * Seq-id handles lock/unlock moved to CSeq_id_Handle 'ctors.
- *
- * Revision 1.2 2002/01/29 17:06:12 grichenk
- * + operator !()
- *
- * Revision 1.1 2002/01/23 21:56:35 grichenk
- * Splitted id_handles.hpp
- *
- *
- * ===========================================================================
- */
- #endif /* OBJECTS_OBJMGR___SEQ_ID_HANDLE__HPP */