annot_ci.cpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: annot_ci.cpp,v $
- * PRODUCTION Revision 1000.2 2004/06/01 19:22:29 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.32
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: annot_ci.cpp,v 1000.2 2004/06/01 19:22:29 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:
- * Object manager iterators
- *
- */
- #include <ncbi_pch.hpp>
- #include <objmgr/annot_ci.hpp>
- #include <objmgr/seq_entry_handle.hpp>
- #include <objmgr/seq_annot_handle.hpp>
- #include <objmgr/impl/annot_object.hpp>
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(objects)
- CAnnot_CI::CAnnot_CI(void)
- {
- }
- CAnnot_CI::CAnnot_CI(const CAnnot_CI& iter)
- : CAnnotTypes_CI(iter)
- {
- m_SeqAnnotSet = iter.m_SeqAnnotSet;
- if (iter) {
- m_Iterator = m_SeqAnnotSet.find(*iter.m_Iterator);
- }
- else {
- m_Iterator = m_SeqAnnotSet.end();
- }
- }
- CAnnot_CI::CAnnot_CI(CScope& scope, const CSeq_loc& loc,
- const SAnnotSelector& sel)
- : CAnnotTypes_CI(CSeq_annot::C_Data::e_not_set,
- scope, loc,
- SAnnotSelector(sel)
- .SetNoMapping(true)
- .SetSortOrder(SAnnotSelector::eSortOrder_None))
- {
- x_Collect();
- }
- CAnnot_CI::CAnnot_CI(const CBioseq_Handle& bioseq,
- TSeqPos start, TSeqPos stop,
- const SAnnotSelector& sel)
- : CAnnotTypes_CI(CSeq_annot::C_Data::e_not_set,
- bioseq, start, stop,
- SAnnotSelector(sel)
- .SetNoMapping(true)
- .SetSortOrder(SAnnotSelector::eSortOrder_None))
- {
- x_Collect();
- }
- CAnnot_CI& CAnnot_CI::operator= (const CAnnot_CI& iter)
- {
- CAnnotTypes_CI::operator=(iter);
- m_SeqAnnotSet.clear();
- m_SeqAnnotSet = iter.m_SeqAnnotSet;
- if (iter) {
- m_Iterator = m_SeqAnnotSet.find(*iter.m_Iterator);
- }
- else {
- m_Iterator = m_SeqAnnotSet.end();
- }
- return *this;
- }
- CAnnot_CI::CAnnot_CI(CScope& scope,
- const CSeq_loc& loc,
- SAnnotSelector::EOverlapType overlap_type,
- SAnnotSelector::EResolveMethod resolve)
- : CAnnotTypes_CI(CSeq_annot::C_Data::e_not_set,
- scope, loc,
- SAnnotSelector()
- .SetNoMapping(true)
- .SetSortOrder(SAnnotSelector::eSortOrder_None)
- .SetOverlapType(overlap_type)
- .SetResolveMethod(resolve))
- {
- x_Collect();
- }
- CAnnot_CI::CAnnot_CI(const CBioseq_Handle& bioseq, TSeqPos start, TSeqPos stop,
- SAnnotSelector::EOverlapType overlap_type,
- SAnnotSelector::EResolveMethod resolve)
- : CAnnotTypes_CI(CSeq_annot::C_Data::e_not_set,
- bioseq, start, stop,
- SAnnotSelector()
- .SetNoMapping(true)
- .SetSortOrder(SAnnotSelector::eSortOrder_None)
- .SetOverlapType(overlap_type)
- .SetResolveMethod(resolve))
- {
- x_Collect();
- }
- CAnnot_CI::~CAnnot_CI(void)
- {
- return;
- }
- void CAnnot_CI::x_Collect(void)
- {
- while ( IsValid() ) {
- if (Get().GetObjectType() != CAnnotObject_Ref::eType_Seq_annot_Info) {
- Next();
- continue;
- }
- CSeq_annot_Handle h(GetScope(),
- Get().GetAnnotObject_Info().GetSeq_annot_Info());
- m_SeqAnnotSet.insert(h);
- Next();
- }
- m_Iterator = m_SeqAnnotSet.begin();
- }
- END_SCOPE(objects)
- END_NCBI_SCOPE
- /*
- * ---------------------------------------------------------------------------
- * $Log: annot_ci.cpp,v $
- * Revision 1000.2 2004/06/01 19:22:29 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.32
- *
- * Revision 1.32 2004/05/21 21:42:12 gorelenk
- * Added PCH ncbi_pch.hpp
- *
- * Revision 1.31 2004/05/10 18:26:37 grichenk
- * Fixed 'not used' warnings
- *
- * Revision 1.30 2004/04/05 15:56:14 grichenk
- * Redesigned CAnnotTypes_CI: moved all data and data collecting
- * functions to CAnnotDataCollector. CAnnotTypes_CI is no more
- * inherited from SAnnotSelector.
- *
- * Revision 1.29 2004/03/16 15:47:27 vasilche
- * Added CBioseq_set_Handle and set of EditHandles
- *
- * Revision 1.28 2003/09/11 17:45:07 grichenk
- * Added adaptive-depth option to annot-iterators.
- *
- * Revision 1.27 2003/08/27 14:29:52 vasilche
- * Reduce object allocations in feature iterator.
- *
- * Revision 1.26 2003/08/22 15:00:49 grichenk
- * Redesigned CAnnot_CI to iterate over seq-annots, containing
- * given location.
- *
- * Revision 1.25 2003/08/15 15:22:00 grichenk
- * Initial revision
- *
- *
- * ===========================================================================
- */