bioseq_ci.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: bioseq_ci.hpp,v $
- * PRODUCTION Revision 1000.1 2004/04/12 17:27:03 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.15
- * PRODUCTION
- * ===========================================================================
- */
- #ifndef BIOSEQ_CI__HPP
- #define BIOSEQ_CI__HPP
- /* $Id: bioseq_ci.hpp,v 1000.1 2004/04/12 17:27:03 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
- *
- * File Description:
- * Iterates over bioseqs from a given seq-entry and scope
- *
- */
- #include <corelib/ncbiobj.hpp>
- #include <objmgr/bioseq_handle.hpp>
- #include <objmgr/impl/heap_scope.hpp>
- #include <objects/seq/Seq_inst.hpp>
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(objects)
- class CScope;
- class CBioseq_Handle;
- class CSeq_entry;
- class CSeq_entry_Handle;
- // Base class for CBioseq_CI to make enums visible in CScope
- class CBioseq_CI_Base {
- public:
- enum EBioseqLevelFlag {
- eLevel_All,
- eLevel_Mains,
- eLevel_Parts
- };
- };
- class NCBI_XOBJMGR_EXPORT CBioseq_CI : public CBioseq_CI_Base
- {
- public:
- // 'ctors
- CBioseq_CI(void);
- // Iterate over bioseqs from the entry taken from the scope. Use optional
- // filter to iterate over selected bioseq types only.
- CBioseq_CI(const CSeq_entry_Handle& entry,
- CSeq_inst::EMol filter = CSeq_inst::eMol_not_set,
- EBioseqLevelFlag level = eLevel_All);
- CBioseq_CI(CScope& scope, const CSeq_entry& entry,
- CSeq_inst::EMol filter = CSeq_inst::eMol_not_set,
- EBioseqLevelFlag level = eLevel_All);
- CBioseq_CI(const CBioseq_CI& bioseq_ci);
- ~CBioseq_CI(void);
- CScope& GetScope(void) const;
- CBioseq_CI& operator= (const CBioseq_CI& bioseq_ci);
- CBioseq_CI& operator++ (void);
- operator bool (void) const;
- const CBioseq_Handle& operator* (void) const;
- const CBioseq_Handle* operator-> (void) const;
- private:
- typedef vector<CBioseq_Handle> TBioseq_HandleSet;
- typedef TBioseq_HandleSet::const_iterator THandleIterator;
- CHeapScope m_Scope;
- TBioseq_HandleSet m_Handles;
- THandleIterator m_Current;
- };
- inline
- CBioseq_CI& CBioseq_CI::operator++ (void)
- {
- if ( m_Current != m_Handles.end() ) {
- m_Current++;
- }
- return *this;
- }
- inline
- CBioseq_CI::operator bool (void) const
- {
- return m_Current != m_Handles.end();
- }
- inline
- const CBioseq_Handle& CBioseq_CI::operator* (void) const
- {
- return *m_Current;
- }
- inline
- const CBioseq_Handle* CBioseq_CI::operator-> (void) const
- {
- return &(*m_Current);
- }
- inline
- CScope& CBioseq_CI::GetScope(void) const
- {
- return m_Scope;
- }
- END_SCOPE(objects)
- END_NCBI_SCOPE
- /*
- * ---------------------------------------------------------------------------
- * $Log: bioseq_ci.hpp,v $
- * Revision 1000.1 2004/04/12 17:27:03 gouriano
- * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.15
- *
- * Revision 1.15 2004/03/16 15:47:25 vasilche
- * Added CBioseq_set_Handle and set of EditHandles
- *
- * Revision 1.14 2004/02/19 17:15:02 vasilche
- * Removed unused include.
- *
- * Revision 1.13 2003/10/01 19:24:36 vasilche
- * Added export specifier to CBioseq_CI as it's not completely inlined anymore.
- *
- * Revision 1.12 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 1.11 2003/09/16 14:38:13 dicuccio
- * Removed export specifier - the entire class is inlined, and the export
- * specifier confuses MSVC in such cases. Added #include for scope.hpp, which
- * contains the base class (previously undefined without this).
- *
- * Revision 1.10 2003/09/03 19:59:59 grichenk
- * Added sequence filtering by level (mains/parts/all)
- *
- * Revision 1.9 2003/06/02 16:01:36 dicuccio
- * Rearranged include/objects/ subtree. This includes the following shifts:
- * - include/objects/alnmgr --> include/objtools/alnmgr
- * - include/objects/cddalignview --> include/objtools/cddalignview
- * - include/objects/flat --> include/objtools/flat
- * - include/objects/objmgr/ --> include/objmgr/
- * - include/objects/util/ --> include/objmgr/util/
- * - include/objects/validator --> include/objtools/validator
- *
- * Revision 1.8 2003/03/10 17:51:36 kuznets
- * iterate->ITERATE
- *
- * Revision 1.7 2003/02/25 14:48:06 vasilche
- * Added Win32 export modifier to object manager classes.
- *
- * Revision 1.6 2003/02/04 16:01:48 dicuccio
- * Removed export specification so that MSVC won't try to export an inlined class
- *
- * Revision 1.5 2002/12/26 20:42:55 dicuccio
- * Added Win32 export specifier. Removed unimplemented (private) operator++(int)
- *
- * Revision 1.4 2002/12/05 19:28:29 grichenk
- * Prohibited postfix operator ++()
- *
- * Revision 1.3 2002/10/15 13:37:28 grichenk
- * Fixed inline declarations
- *
- * Revision 1.2 2002/10/02 17:58:21 grichenk
- * Added sequence type filter to CBioseq_CI
- *
- * Revision 1.1 2002/09/30 20:00:48 grichenk
- * Initial revision
- *
- *
- * ===========================================================================
- */
- #endif // BIOSEQ_CI__HPP