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feat_ci.cpp
资源名称：ncbi_cxx_win--Jul_08_2004.zip　[点击查看]
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上传日期：2007-06-13
资源大小：13604k
文件大小：20k
源码类别：

生物技术

开发平台：

C/C++

feat_ci.cpp：源码内容
  1. /*
  2.  * ===========================================================================
  3.  * PRODUCTION $Log: feat_ci.cpp,v $
  4.  * PRODUCTION Revision 1000.2  2004/06/01 19:23:14  gouriano
  5.  * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.32
  6.  * PRODUCTION
  7.  * ===========================================================================
  8.  */
  10. /*  $Id: feat_ci.cpp,v 1000.2 2004/06/01 19:23:14 gouriano Exp $
  11. * ===========================================================================
  12. *
  13. *                            PUBLIC DOMAIN NOTICE
  14. *               National Center for Biotechnology Information
  15. *
  16. *  This software/database is a "United States Government Work" under the
  17. *  terms of the United States Copyright Act.  It was written as part of
  18. *  the author's official duties as a United States Government employee and
  19. *  thus cannot be copyrighted.  This software/database is freely available
  20. *  to the public for use. The National Library of Medicine and the U.S.
  21. *  Government have not placed any restriction on its use or reproduction.
  22. *
  23. *  Although all reasonable efforts have been taken to ensure the accuracy
  24. *  and reliability of the software and data, the NLM and the U.S.
  25. *  Government do not and cannot warrant the performance or results that
  26. *  may be obtained by using this software or data. The NLM and the U.S.
  27. *  Government disclaim all warranties, express or implied, including
  28. *  warranties of performance, merchantability or fitness for any particular
  29. *  purpose.
  30. *
  31. *  Please cite the author in any work or product based on this material.
  32. *
  33. * ===========================================================================
  34. *
  35. * Author: Aleksey Grichenko, Eugene Vasilchenko
  36. *
  37. * File Description:
  38. *   Object manager iterators
  39. *
  40. */
  42. #include <ncbi_pch.hpp>
  43. #include <objmgr/feat_ci.hpp>
  44. #include <objmgr/bioseq_handle.hpp>
  45. #include <objmgr/seq_entry_handle.hpp>
  46. #include <objmgr/seq_annot_handle.hpp>
  47. #include <objmgr/impl/annot_object.hpp>
  48. #include <objmgr/impl/seq_annot_info.hpp>
  49. #include <objmgr/impl/snp_annot_info.hpp>
  50. #include <objects/seqfeat/Gb_qual.hpp>
  51. #include <objects/seqfeat/SeqFeatXref.hpp>
  52. #include <objects/general/Dbtag.hpp>
  53. #include <objects/seqloc/Seq_id.hpp>
  54. #include <objects/seqloc/Na_strand.hpp>
  55. #include <objects/seqloc/Seq_loc.hpp>
  56. #include <objects/seqloc/Seq_point.hpp>
  57. #include <objects/seqloc/Seq_interval.hpp>
  59. BEGIN_NCBI_SCOPE
  60. BEGIN_SCOPE(objects)
  63. CFeat_CI::CFeat_CI(void)
  64. {
  65. }
  68. CFeat_CI::CFeat_CI(const CFeat_CI& iter)
  69.     : CAnnotTypes_CI(iter)
  70. {
  71.     Update();
  72. }
  75. CFeat_CI::~CFeat_CI(void)
  76. {
  77. }
  80. CFeat_CI& CFeat_CI::operator= (const CFeat_CI& iter)
  81. {
  82.     CAnnotTypes_CI::operator=(iter);
  83.     Update();
  84.     return *this;
  85. }
  88. CFeat_CI::CFeat_CI(const CBioseq_Handle& bioseq,
  89.                    TSeqPos start, TSeqPos stop,
  90.                    TFeatType feat_type,
  91.                    SAnnotSelector::EOverlapType overlap_type,
  92.                    SAnnotSelector::EResolveMethod resolve,
  93.                    EFeat_Location loc_type)
  94.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  95.                      bioseq, start, stop,
  96.                      SAnnotSelector(feat_type)
  97.                      .SetByProduct(loc_type == e_Product)
  98.                      .SetOverlapType(overlap_type)
  99.                      .SetResolveMethod(resolve))
  100. {
  101.     Update();
  102. }
  105. CFeat_CI::CFeat_CI(const CBioseq_Handle& bioseq,
  106.                    TSeqPos start, TSeqPos stop,
  107.                    TFeatType feat_type,
  108.                    SAnnotSelector::EOverlapType overlap_type,
  109.                    SAnnotSelector::EResolveMethod resolve,
  110.                    EFeat_Location loc_type,
  111.                    const CSeq_entry_Handle& limitEntry)
  112.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  113.                      bioseq, start, stop,
  114.                      SAnnotSelector(feat_type)
  115.                      .SetByProduct(loc_type == e_Product)
  116.                      .SetOverlapType(overlap_type)
  117.                      .SetResolveMethod(resolve)
  118.                      .SetLimitSeqEntry(limitEntry))
  119. {
  120.     Update();
  121. }
  124. CFeat_CI::CFeat_CI(const CBioseq_Handle& bioseq,
  125.                    TSeqPos start, TSeqPos stop,
  126.                    TFeatType feat_type,
  127.                    SAnnotSelector::EOverlapType overlap_type,
  128.                    SAnnotSelector::EResolveMethod resolve,
  129.                    EFeat_Location loc_type,
  130.                    const CSeq_entry* limitEntry)
  131.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  132.                      bioseq, start, stop,
  133.                      SAnnotSelector(feat_type)
  134.                      .SetByProduct(loc_type == e_Product)
  135.                      .SetOverlapType(overlap_type)
  136.                      .SetResolveMethod(resolve)
  137.                      .SetLimitSeqEntry(limitEntry))
  138. {
  139.     Update();
  140. }
  143. CFeat_CI::CFeat_CI(CScope& scope,
  144.                    const CSeq_loc& loc,
  145.                    TFeatType feat_type,
  146.                    SAnnotSelector::EOverlapType overlap_type,
  147.                    SAnnotSelector::EResolveMethod resolve,
  148.                    EFeat_Location loc_type)
  149.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  150.                      scope, loc,
  151.                      SAnnotSelector(feat_type)
  152.                      .SetByProduct(loc_type == e_Product)
  153.                      .SetOverlapType(overlap_type)
  154.                      .SetResolveMethod(resolve))
  155. {
  156.     Update();
  157. }
  160. CFeat_CI::CFeat_CI(CScope& scope,
  161.                    const CSeq_loc& loc)
  162.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  163.                      scope, loc,
  164.                      SAnnotSelector::eOverlap_Intervals,
  165.                      SAnnotSelector::eResolve_TSE)
  166. {
  167.     Update();
  168. }
  171. CFeat_CI::CFeat_CI(const CBioseq_Handle& bioseq,
  172.                    TSeqPos start, TSeqPos stop)
  173.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  174.                      bioseq, start, stop,
  175.                      SAnnotSelector::eOverlap_Intervals,
  176.                      SAnnotSelector::eResolve_TSE)
  177. {
  178.     Update();
  179. }
  182. CFeat_CI::CFeat_CI(CScope& scope,
  183.                    const CSeq_loc& loc,
  184.                    const SAnnotSelector& sel)
  185.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  186.                      scope, loc,
  187.                      sel)
  188. {
  189.     Update();
  190. }
  193. CFeat_CI::CFeat_CI(const CBioseq_Handle& bioseq,
  194.                    TSeqPos start, TSeqPos stop,
  195.                    const SAnnotSelector& sel)
  196.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  197.                      bioseq, start, stop,
  198.                      sel)
  199. {
  200.     Update();
  201. }
  204. CFeat_CI::CFeat_CI(const CSeq_annot_Handle& annot)
  205.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  206.                      annot)
  207. {
  208.     Update();
  209. }
  212. CFeat_CI::CFeat_CI(const CSeq_annot_Handle& annot,
  213.                    const SAnnotSelector& sel)
  214.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  215.                      annot,
  216.                      sel)
  217. {
  218.     Update();
  219. }
  222. CFeat_CI::CFeat_CI(const CSeq_entry_Handle& entry)
  223.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  224.                      entry)
  225. {
  226.     Update();
  227. }
  230. CFeat_CI::CFeat_CI(const CSeq_entry_Handle& entry,
  231.                    const SAnnotSelector& sel)
  232.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  233.                      entry,
  234.                      sel)
  235. {
  236.     Update();
  237. }
  240. CFeat_CI::CFeat_CI(CScope& scope, const CSeq_annot& annot)
  241.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  242.                      scope.GetSeq_annotHandle(annot))
  243. {
  244.     Update();
  245. }
  248. CFeat_CI::CFeat_CI(CScope& scope, const CSeq_annot& annot,
  249.                    const SAnnotSelector& sel)
  250.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  251.                      scope.GetSeq_annotHandle(annot),
  252.                      sel)
  253. {
  254.     Update();
  255. }
  258. CFeat_CI::CFeat_CI(CScope& scope, const CSeq_entry& entry)
  259.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  260.                      scope.GetSeq_entryHandle(entry))
  261. {
  262.     Update();
  263. }
  266. CFeat_CI::CFeat_CI(CScope& scope, const CSeq_entry& entry,
  267.                    const SAnnotSelector& sel)
  268.     : CAnnotTypes_CI(CSeq_annot::C_Data::e_Ftable,
  269.                      scope.GetSeq_entryHandle(entry),
  270.                      sel)
  271. {
  272.     Update();
  273. }
  276. CMappedFeat::CMappedFeat(void)
  277. {
  278. }
  281. CMappedFeat::CMappedFeat(const CMappedFeat& feat)
  282. {
  283.     *this = feat;
  284. }
  287. CMappedFeat& CMappedFeat::operator=(const CMappedFeat& feat)
  288. {
  289.     if ( this != &feat ) {
  290.         m_Collector = feat.m_Collector;
  291.         m_FeatRef = feat.m_FeatRef;
  292.         m_OriginalSeq_feat = feat.m_OriginalSeq_feat;
  293.         m_MappedSeq_feat = feat.m_MappedSeq_feat;
  294.         m_MappedSeq_loc = feat.m_MappedSeq_loc;
  295.     }
  296.     return *this;
  297. }
  300. CMappedFeat::~CMappedFeat(void)
  301. {
  302. }
  305. CSeq_feat_Handle CMappedFeat::GetSeq_feat_Handle(void) const
  306. {
  307.     if ( m_FeatRef->IsSNPFeat() ) {
  308.         return CSeq_feat_Handle(m_Collector->GetScope(),
  309.             m_FeatRef->GetSeq_annot_SNP_Info(),
  310.             m_FeatRef->GetAnnotObjectIndex());
  311.     }
  312.     return CSeq_feat_Handle(m_Collector->GetScope(),
  313.         m_FeatRef->GetSeq_annot_Info(),
  314.         m_FeatRef->GetAnnotObjectIndex());
  315. }
  318. CSeq_annot_Handle CMappedFeat::GetAnnot(void) const
  319. {
  320.     return CSeq_annot_Handle(m_Collector->GetScope(),
  321.         m_FeatRef->GetSeq_annot_Info());
  322. }
  325. const CSeq_annot& CMappedFeat::GetSeq_annot(void) const
  326. {
  327.     ERR_POST_ONCE(Warning<<
  328.                   "CMappedFeat::GetSeq_annot() is deprecated, "
  329.                   "use GetAnnot().");
  330.     return *m_FeatRef->GetSeq_annot_Info().GetCompleteSeq_annot();
  331. }
  334. void CMappedFeat::Reset(void)
  335. {
  336.     m_Collector.Reset();
  337.     m_OriginalSeq_feat.Reset();
  338.     m_MappedSeq_feat.Reset();
  339.     m_MappedSeq_loc.Reset();
  340. }
  343. CMappedFeat& CMappedFeat::Set(CAnnot_Collector& collector,
  344.                               const TIterator& annot)
  345. {
  346.     m_Collector.Reset(&collector);
  347.     _ASSERT(annot->IsFeat());
  348.     m_FeatRef = annot;
  349.     m_OriginalSeq_feat.Reset();
  350.     m_MappedSeq_feat.Reset();
  351.     m_MappedSeq_loc.Reset();
  352.     return *this;
  353. }
  356. const CSeq_feat& CMappedFeat::x_MakeOriginalFeature(void) const
  357. {
  358.     if ( m_FeatRef->IsSNPFeat() ) {
  359.         _ASSERT(!m_OriginalSeq_feat);
  360.         const CSeq_annot_SNP_Info& snp_annot =
  361.             m_FeatRef->GetSeq_annot_SNP_Info();
  362.         const SSNP_Info& snp_info =
  363.             snp_annot.GetSNP_Info(m_FeatRef->GetAnnotObjectIndex());
  364.         CRef<CSeq_feat> orig_feat;
  365.         m_Collector->m_CreatedOriginalSeq_feat.AtomicReleaseTo(orig_feat);
  366.         CRef<CSeq_point> created_point;
  367.         m_Collector->m_CreatedOriginalSeq_point.AtomicReleaseTo(created_point);
  368.         CRef<CSeq_interval> created_interval;
  369.         m_Collector->m_CreatedOriginalSeq_interval.
  370.             AtomicReleaseTo(created_interval);
  371.         snp_info.UpdateSeq_feat(orig_feat,
  372.                                 created_point,
  373.                                 created_interval,
  374.                                 snp_annot);
  375.         m_OriginalSeq_feat = orig_feat;
  376.         m_Collector->m_CreatedOriginalSeq_feat.AtomicResetFrom(orig_feat);
  377.         m_Collector->m_CreatedOriginalSeq_point.AtomicResetFrom(created_point);
  378.         m_Collector->m_CreatedOriginalSeq_interval.
  379.             AtomicResetFrom(created_interval);
  380.     }
  381.     else {
  382.         m_OriginalSeq_feat.Reset(&m_FeatRef->GetFeat());
  383.     }
  384.     return *m_OriginalSeq_feat;
  385. }
  388. const CSeq_loc& CMappedFeat::x_MakeMappedLocation(void) const
  389. {
  390.     _ASSERT(!m_MappedSeq_loc);
  391.     if ( m_FeatRef->MappedSeq_locNeedsUpdate() ) {
  392.         _ASSERT(!m_MappedSeq_feat);
  393.         // need to covert Seq_id to Seq_loc
  394.         // clear references to mapped location from mapped feature
  395.         // Can not use m_MappedSeq_feat since it's a const-ref
  396.         CRef<CSeq_feat> mapped_feat;
  397.         m_Collector->m_CreatedMappedSeq_feat.AtomicReleaseTo(mapped_feat);
  398.         if ( mapped_feat ) {
  399.             if ( !mapped_feat->ReferencedOnlyOnce() ) {
  400.                 mapped_feat.Reset();
  401.             }
  402.             else {
  403.                 // hack with null pointer as ResetLocation doesn't reset CRef<>
  404.                 CSeq_loc* loc = 0;
  405.                 mapped_feat->SetLocation(*loc);
  406.                 mapped_feat->ResetProduct();
  407.             }
  408.         }
  409.         m_MappedSeq_feat = mapped_feat;
  410.         m_Collector->m_CreatedMappedSeq_feat.AtomicResetFrom(mapped_feat);
  412.         CRef<CSeq_loc> mapped_loc;
  413.         m_Collector->m_CreatedMappedSeq_loc.AtomicReleaseTo(mapped_loc);
  414.         CRef<CSeq_point> created_point;
  415.         m_Collector->m_CreatedMappedSeq_point.AtomicReleaseTo(created_point);
  416.         CRef<CSeq_interval> created_interval;
  417.         m_Collector->m_CreatedMappedSeq_interval.
  418.             AtomicReleaseTo(created_interval);
  419.         m_FeatRef->UpdateMappedSeq_loc(mapped_loc,
  420.                                        created_point,
  421.                                        created_interval);
  422.         m_MappedSeq_loc = mapped_loc;
  423.         m_Collector->m_CreatedMappedSeq_loc.AtomicResetFrom(mapped_loc);
  424.         m_Collector->m_CreatedMappedSeq_point.AtomicResetFrom(created_point);
  425.         m_Collector->m_CreatedMappedSeq_interval.
  426.             AtomicResetFrom(created_interval);
  427.     }
  428.     else if ( m_FeatRef->IsMapped() ) {
  429.         _ASSERT(!m_MappedSeq_feat);
  430.         m_MappedSeq_loc.Reset(&m_FeatRef->GetMappedSeq_loc());
  431.     }
  432.     return *m_MappedSeq_loc;
  433. }
  436. const CSeq_feat& CMappedFeat::x_MakeMappedFeature(void) const
  437. {
  438.     if ( m_FeatRef->IsMapped() ) {
  439.         _ASSERT(!m_MappedSeq_feat);
  440.         // some Seq-loc object is mapped
  441.         CRef<CSeq_feat> mapped_feat;
  442.         m_Collector->m_CreatedMappedSeq_feat.AtomicReleaseTo(mapped_feat);
  443.         if ( !mapped_feat || !mapped_feat->ReferencedOnlyOnce() ) {
  444.             mapped_feat.Reset(new CSeq_feat);
  445.         }
  446.         CSeq_feat& dst = *mapped_feat;
  447.         CSeq_feat& src = const_cast<CSeq_feat&>(GetOriginalFeature());
  449.         if ( src.IsSetId() )
  450.             dst.SetId(src.SetId());
  451.         else
  452.             dst.ResetId();
  454.         dst.SetData(src.SetData());
  456.         if ( GetPartial() )
  457.             dst.SetPartial(true);
  458.         else
  459.             dst.ResetPartial();
  461.         if ( src.IsSetExcept() )
  462.             dst.SetExcept(src.GetExcept());
  463.         else
  464.             dst.ResetExcept();
  465.         
  466.         if ( src.IsSetComment() )
  467.             dst.SetComment(src.GetComment());
  468.         else
  469.             dst.ResetComment();
  471.         GetMappedLocation();
  473.         dst.SetLocation(const_cast<CSeq_loc&>(GetLocation()));
  475.         if ( src.IsSetProduct() ) {
  476.             dst.SetProduct(const_cast<CSeq_loc&>(GetProduct()));
  477.         }
  478.         else {
  479.             dst.ResetProduct();
  480.         }
  482.         if ( src.IsSetQual() )
  483.             dst.SetQual() = src.SetQual();
  484.         else
  485.             dst.ResetQual();
  487.         if ( src.IsSetTitle() )
  488.             dst.SetTitle(src.GetTitle());
  489.         else
  490.             dst.ResetTitle();
  492.         if ( src.IsSetExt() )
  493.             dst.SetExt(src.SetExt());
  494.         else
  495.             dst.ResetExt();
  497.         if ( src.IsSetCit() )
  498.             dst.SetCit(src.SetCit());
  499.         else
  500.             dst.ResetCit();
  502.         if ( src.IsSetExp_ev() )
  503.             dst.SetExp_ev(src.GetExp_ev());
  504.         else
  505.             dst.ResetExp_ev();
  507.         if ( src.IsSetXref() )
  508.             dst.SetXref() = src.SetXref();
  509.         else
  510.             dst.ResetXref();
  512.         if ( src.IsSetDbxref() )
  513.             dst.SetDbxref() = src.SetDbxref();
  514.         else
  515.             dst.ResetDbxref();
  517.         if ( src.IsSetPseudo() )
  518.             dst.SetPseudo(src.GetPseudo());
  519.         else
  520.             dst.ResetPseudo();
  522.         if ( src.IsSetExcept_text() )
  523.             dst.SetExcept_text(src.GetExcept_text());
  524.         else
  525.             dst.ResetExcept_text();
  526.         m_MappedSeq_feat = mapped_feat;
  527.         m_Collector->m_CreatedMappedSeq_feat.AtomicResetFrom(mapped_feat);
  528.     }
  529.     else {
  530.         m_MappedSeq_feat.Reset(&GetOriginalFeature());
  531.     }
  532.     return *m_MappedSeq_feat;
  533. }
  536. END_SCOPE(objects)
  537. END_NCBI_SCOPE
  539. /*
  540. * ---------------------------------------------------------------------------
  541. * $Log: feat_ci.cpp,v $
  542. * Revision 1000.2  2004/06/01 19:23:14  gouriano
  543. * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.32
  544. *
  545. * Revision 1.32  2004/05/21 21:42:12  gorelenk
  546. * Added PCH ncbi_pch.hpp
  547. *
  548. * Revision 1.31  2004/05/04 18:08:48  grichenk
  549. * Added CSeq_feat_Handle, CSeq_align_Handle and CSeq_graph_Handle
  550. *
  551. * Revision 1.30  2004/04/07 13:20:17  grichenk
  552. * Moved more data from iterators to CAnnot_Collector
  553. *
  554. * Revision 1.29  2004/04/05 15:56:14  grichenk
  555. * Redesigned CAnnotTypes_CI: moved all data and data collecting
  556. * functions to CAnnotDataCollector. CAnnotTypes_CI is no more
  557. * inherited from SAnnotSelector.
  558. *
  559. * Revision 1.28  2004/03/16 15:47:27  vasilche
  560. * Added CBioseq_set_Handle and set of EditHandles
  561. *
  562. * Revision 1.27  2004/02/11 22:19:24  grichenk
  563. * Fixed annot type initialization in iterators
  564. *
  565. * Revision 1.26  2004/02/05 19:53:40  grichenk
  566. * Fixed type matching in SAnnotSelector. Added IncludeAnnotType().
  567. *
  568. * Revision 1.25  2004/02/04 18:05:39  grichenk
  569. * Added annotation filtering by set of types/subtypes.
  570. * Renamed *Choice to *Type in SAnnotSelector.
  571. *
  572. * Revision 1.24  2004/01/28 20:54:36  vasilche
  573. * Fixed mapping of annotations.
  574. *
  575. * Revision 1.23  2003/08/27 19:44:06  vasilche
  576. * Avoid error on IRIX with null reference cast.
  577. *
  578. * Revision 1.22  2003/08/27 14:48:56  vasilche
  579. * Fixed constness of mapped location.
  580. *
  581. * Revision 1.21  2003/08/27 14:29:52  vasilche
  582. * Reduce object allocations in feature iterator.
  583. *
  584. * Revision 1.20  2003/08/15 19:19:16  vasilche
  585. * Fixed memory leak in string packing hooks.
  586. * Fixed processing of 'partial' flag of features.
  587. * Allow table packing of non-point SNP.
  588. * Allow table packing of SNP with long alleles.
  589. *
  590. * Revision 1.19  2003/08/14 20:05:19  vasilche
  591. * Simple SNP features are stored as table internally.
  592. * They are recreated when needed using CFeat_CI.
  593. *
  594. * Revision 1.18  2003/06/02 16:06:37  dicuccio
  595. * Rearranged src/objects/ subtree.  This includes the following shifts:
  596. *     - src/objects/asn2asn --> arc/app/asn2asn
  597. *     - src/objects/testmedline --> src/objects/ncbimime/test
  598. *     - src/objects/objmgr --> src/objmgr
  599. *     - src/objects/util --> src/objmgr/util
  600. *     - src/objects/alnmgr --> src/objtools/alnmgr
  601. *     - src/objects/flat --> src/objtools/flat
  602. *     - src/objects/validator --> src/objtools/validator
  603. *     - src/objects/cddalignview --> src/objtools/cddalignview
  604. * In addition, libseq now includes six of the objects/seq... libs, and libmmdb
  605. * replaces the three libmmdb? libs.
  606. *
  607. * Revision 1.17  2003/04/24 16:12:38  vasilche
  608. * Object manager internal structures are splitted more straightforward.
  609. * Removed excessive header dependencies.
  610. *
  611. * Revision 1.16  2003/02/24 21:35:22  vasilche
  612. * Reduce checks in CAnnotObject_Ref comparison.
  613. * Fixed compilation errors on MS Windows.
  614. * Removed obsolete file src/objects/objmgr/annot_object.hpp.
  615. *
  616. * Revision 1.15  2003/02/24 18:57:22  vasilche
  617. * Make feature gathering in one linear pass using CSeqMap iterator.
  618. * Do not use feture index by sub locations.
  619. * Sort features at the end of gathering in one vector.
  620. * Extracted some internal structures and classes in separate header.
  621. * Delay creation of mapped features.
  622. *
  623. * Revision 1.14  2003/02/13 14:34:34  grichenk
  624. * Renamed CAnnotObject -> CAnnotObject_Info
  625. * + CSeq_annot_Info and CAnnotObject_Ref
  626. * Moved some members of CAnnotObject to CSeq_annot_Info
  627. * and CAnnotObject_Ref.
  628. * Added feat/align/graph to CAnnotObject_Info map
  629. * to CDataSource.
  630. *
  631. * Revision 1.13  2003/02/10 15:50:45  grichenk
  632. * + CMappedFeat, CFeat_CI resolves to CMappedFeat
  633. *
  634. * Revision 1.12  2002/12/20 20:54:24  grichenk
  635. * Added optional location/product switch to CFeat_CI
  636. *
  637. * Revision 1.11  2002/12/06 15:36:00  grichenk
  638. * Added overlap type for annot-iterators
  639. *
  640. * Revision 1.10  2002/11/04 21:29:12  grichenk
  641. * Fixed usage of const CRef<> and CRef<> constructor
  642. *
  643. * Revision 1.9  2002/07/08 20:51:01  grichenk
  644. * Moved log to the end of file
  645. * Replaced static mutex (in CScope, CDataSource) with the mutex
  646. * pool. Redesigned CDataSource data locking.
  647. *
  648. * Revision 1.8  2002/05/06 03:28:47  vakatov
  649. * OM/OM1 renaming
  650. *
  651. * Revision 1.7  2002/05/03 21:28:09  ucko
  652. * Introduce T(Signed)SeqPos.
  653. *
  654. * Revision 1.6  2002/04/05 21:26:19  grichenk
  655. * Enabled iteration over annotations defined on segments of a
  656. * delta-sequence.
  657. *
  658. * Revision 1.5  2002/03/05 16:08:14  grichenk
  659. * Moved TSE-restriction to new constructors
  660. *
  661. * Revision 1.4  2002/03/04 15:07:48  grichenk
  662. * Added "bioseq" argument to CAnnotTypes_CI constructor to iterate
  663. * annotations from a single TSE.
  664. *
  665. * Revision 1.3  2002/02/21 19:27:05  grichenk
  666. * Rearranged includes. Added scope history. Added searching for the
  667. * best seq-id match in data sources and scopes. Updated tests.
  668. *
  669. * Revision 1.2  2002/01/16 16:25:57  gouriano
  670. * restructured objmgr
  671. *
  672. * Revision 1.1  2002/01/11 19:06:18  gouriano
  673. * restructured objmgr
  674. *
  675. *
  676. * ===========================================================================
  677. */