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seq_annot_info.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：16k
源码类别：

生物技术

开发平台：

C/C++

seq_annot_info.cpp：源码内容
  1. /*
  2.  * ===========================================================================
  3.  * PRODUCTION $Log: seq_annot_info.cpp,v $
  4.  * PRODUCTION Revision 1000.4  2004/06/01 19:23:51  gouriano
  5.  * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.16
  6.  * PRODUCTION
  7.  * ===========================================================================
  8.  */
  10. /*  $Id: seq_annot_info.cpp,v 1000.4 2004/06/01 19:23:51 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: Eugene Vasilchenko
  36. *
  37. * File Description:
  38. *   CSeq_annot_Info info -- entry for data source information about Seq-annot
  39. *
  40. */
  43. #include <ncbi_pch.hpp>
  44. #include <objmgr/impl/seq_annot_info.hpp>
  45. #include <objmgr/impl/seq_entry_info.hpp>
  46. #include <objmgr/impl/bioseq_base_info.hpp>
  47. #include <objmgr/impl/tse_info.hpp>
  48. #include <objmgr/impl/tse_chunk_info.hpp>
  49. #include <objmgr/impl/annot_object.hpp>
  50. #include <objmgr/impl/handle_range_map.hpp>
  51. #include <objmgr/impl/data_source.hpp>
  52. #include <objmgr/impl/snp_annot_info.hpp>
  53. #include <objmgr/objmgr_exception.hpp>
  55. #include <objects/seq/Seq_annot.hpp>
  56. #include <objects/seq/Annotdesc.hpp>
  57. #include <objects/seq/Annot_descr.hpp>
  59. BEGIN_NCBI_SCOPE
  60. BEGIN_SCOPE(objects)
  63. CSeq_annot_Info::CSeq_annot_Info(const CSeq_annot& annot)
  64. {
  65.     x_SetObject(annot);
  66. }
  69. CSeq_annot_Info::CSeq_annot_Info(CSeq_annot_SNP_Info& snp_annot)
  70. {
  71.     x_SetSNP_annot_Info(snp_annot);
  72. }
  75. CSeq_annot_Info::CSeq_annot_Info(const CSeq_annot_Info& info)
  76. {
  77.     x_SetObject(info);
  78. }
  81. CSeq_annot_Info::~CSeq_annot_Info(void)
  82. {
  83. }
  86. const CBioseq_Base_Info& CSeq_annot_Info::GetParentBioseq_Base_Info(void) const
  87. {
  88.     return static_cast<const CBioseq_Base_Info&>(GetBaseParent_Info());
  89. }
  92. CBioseq_Base_Info& CSeq_annot_Info::GetParentBioseq_Base_Info(void)
  93. {
  94.     return static_cast<CBioseq_Base_Info&>(GetBaseParent_Info());
  95. }
  98. const CSeq_entry_Info& CSeq_annot_Info::GetParentSeq_entry_Info(void) const
  99. {
  100.     return GetParentBioseq_Base_Info().GetParentSeq_entry_Info();
  101. }
  104. CSeq_entry_Info& CSeq_annot_Info::GetParentSeq_entry_Info(void)
  105. {
  106.     return GetParentBioseq_Base_Info().GetParentSeq_entry_Info();
  107. }
  110. void CSeq_annot_Info::x_ParentAttach(CBioseq_Base_Info& parent)
  111. {
  112.     x_BaseParentAttach(parent);
  113. }
  116. void CSeq_annot_Info::x_ParentDetach(CBioseq_Base_Info& parent)
  117. {
  118.     x_BaseParentDetach(parent);
  119. }
  122. void CSeq_annot_Info::x_DSAttachContents(CDataSource& ds)
  123. {
  124.     TParent::x_DSAttachContents(ds);
  125.     x_DSMapObject(m_Object, ds);
  126.     if ( m_SNP_Info ) {
  127.         m_SNP_Info->x_DSAttach(ds);
  128.     }
  129. }
  132. void CSeq_annot_Info::x_DSDetachContents(CDataSource& ds)
  133. {
  134.     if ( m_SNP_Info ) {
  135.         m_SNP_Info->x_DSDetach(ds);
  136.     }
  137.     ITERATE ( TDSMappedObjects, it, m_DSMappedObjects ) {
  138.         x_DSUnmapObject(*it, ds);
  139.     }
  140.     m_DSMappedObjects.clear();
  141.     TParent::x_DSDetachContents(ds);
  142. }
  145. void CSeq_annot_Info::x_DSMapObject(CConstRef<TObject> obj, CDataSource& ds)
  146. {
  147.     m_DSMappedObjects.push_back(obj);
  148.     ds.x_Map(obj, this);
  149. }
  152. void CSeq_annot_Info::x_DSUnmapObject(CConstRef<TObject> obj, CDataSource& ds)
  153. {
  154.     ds.x_Unmap(obj, this);
  155. }
  158. void CSeq_annot_Info::x_TSEAttachContents(CTSE_Info& tse)
  159. {
  160.     TParent::x_TSEAttachContents(tse);
  161.     if ( m_SNP_Info ) {
  162.         m_SNP_Info->x_TSEAttach(tse);
  163.     }
  164. }
  167. void CSeq_annot_Info::x_TSEDetachContents(CTSE_Info& tse)
  168. {
  169.     if ( m_SNP_Info ) {
  170.         m_SNP_Info->x_TSEDetach(tse);
  171.     }
  172.     x_UnmapAnnotObjects(tse);
  173.     TParent::x_TSEDetachContents(tse);
  174. }
  177. size_t
  178. CSeq_annot_Info::GetAnnotObjectIndex(const CAnnotObject_Info& info) const
  179. {
  180.     _ASSERT(&info.GetSeq_annot_Info() == this);
  181.     return m_ObjectInfos.GetIndex(info);
  182. }
  185. const CAnnotName& CSeq_annot_Info::GetName(void) const
  186. {
  187.     return m_Name.IsNamed()? m_Name: GetTSE_Info().GetName();
  188. }
  191. void CSeq_annot_Info::x_UpdateName(void)
  192. {
  193.     if ( m_Object->IsSetDesc() ) {
  194.         string name;
  195.         ITERATE( CSeq_annot::TDesc::Tdata, it, m_Object->GetDesc().Get() ) {
  196.             const CAnnotdesc& desc = **it;
  197.             if ( desc.Which() == CAnnotdesc::e_Name ) {
  198.                 name = desc.GetName();
  199.                 break;
  200.             }
  201.         }
  202.         m_Name.SetNamed(name);
  203.     }
  204.     else {
  205.         m_Name.SetUnnamed();
  206.     }
  207. }
  210. CConstRef<CSeq_annot> CSeq_annot_Info::GetCompleteSeq_annot(void) const
  211. {
  212.     return GetSeq_annotCore();
  213. }
  216. CConstRef<CSeq_annot> CSeq_annot_Info::GetSeq_annotCore(void) const
  217. {
  218.     x_UpdateObject();
  219.     return m_Object;
  220. }
  223. void CSeq_annot_Info::x_SetObject(const TObject& obj)
  224. {
  225.     _ASSERT(!m_SNP_Info && !m_Object);
  226.     m_Object.Reset(&obj);
  227.     x_UpdateName();
  228. }
  231. void CSeq_annot_Info::x_SetObject(const CSeq_annot_Info& info)
  232. {
  233.     _ASSERT(!m_SNP_Info && !m_Object);
  234.     m_Object = info.m_Object;
  235.     m_Name = info.m_Name;
  236.     if ( info.m_SNP_Info ) {
  237.         m_SNP_Info.Reset(new CSeq_annot_SNP_Info(*info.m_SNP_Info));
  238.         m_SNP_Info->x_ParentAttach(*this);
  239.         x_AttachObject(*m_SNP_Info);
  240.     }
  241. }
  244. void CSeq_annot_Info::x_SetSNP_annot_Info(CSeq_annot_SNP_Info& snp_info)
  245. {
  246.     _ASSERT(!m_SNP_Info && !m_Object && !snp_info.HasParent_Info());
  247.     x_SetObject(snp_info.GetRemainingSeq_annot());
  248.     m_SNP_Info.Reset(&snp_info);
  249.     snp_info.x_ParentAttach(*this);
  250.     _ASSERT(&snp_info.GetParentSeq_annot_Info() == this);
  251.     x_AttachObject(snp_info);
  252. }
  255. void CSeq_annot_Info::x_DoUpdateObject(void)
  256. {
  257.     NCBI_THROW(CObjMgrException, eNotImplemented,
  258.                "CSeq_annot_Info::x_DoUpdateObject: unimplemented");
  259. }
  262. void CSeq_annot_Info::UpdateAnnotIndex(void) const
  263. {
  264.     if ( x_DirtyAnnotIndex() ) {
  265.         GetTSE_Info().UpdateAnnotIndex(*this);
  266.         _ASSERT(!x_DirtyAnnotIndex());
  267.     }
  268. }
  271. void CSeq_annot_Info::x_UpdateAnnotIndexContents(CTSE_Info& tse)
  272. {
  273.     m_ObjectInfos.SetName(GetName());
  275.     const CSeq_annot::C_Data& data = m_Object->GetData();
  276.     switch ( data.Which() ) {
  277.     case CSeq_annot::C_Data::e_Ftable:
  278.         x_MapAnnotObjects(tse, data.GetFtable());
  279.         break;
  280.     case CSeq_annot::C_Data::e_Align:
  281.         x_MapAnnotObjects(tse, data.GetAlign());
  282.         break;
  283.     case CSeq_annot::C_Data::e_Graph:
  284.         x_MapAnnotObjects(tse, data.GetGraph());
  285.         break;
  286.     default:
  287.         break;
  288.     }
  289.     if ( m_SNP_Info ) {
  290.         m_SNP_Info->x_UpdateAnnotIndex(tse);
  291.     }
  292.     TParent::x_UpdateAnnotIndexContents(tse);
  293. }
  296. void
  297. CSeq_annot_Info::x_MapAnnotObjects(CTSE_Info& tse,
  298.                                    const CSeq_annot::C_Data::TFtable& objs)
  299. {
  300.     m_ObjectInfos.Reserve(objs.size(), 1.1);
  302.     CTSE_Info::TAnnotObjs& index = tse.x_SetAnnotObjs(GetName());
  304.     SAnnotObject_Key key;
  305.     SAnnotObject_Index annotRef;
  306.     vector<CHandleRangeMap> hrmaps;
  307.     ITERATE ( CSeq_annot::C_Data::TFtable, fit, objs ) {
  308.         const CSeq_feat& feat = **fit;
  310.         CAnnotObject_Info* info =
  311.             m_ObjectInfos.AddInfo(CAnnotObject_Info(feat, *this));
  312.         key.m_AnnotObject_Info = annotRef.m_AnnotObject_Info = info;
  314.         info->GetMaps(hrmaps);
  315.         annotRef.m_AnnotLocationIndex = 0;
  316.         ITERATE ( vector<CHandleRangeMap>, hrmit, hrmaps ) {
  317.             ITERATE ( CHandleRangeMap, hrit, *hrmit ) {
  318.                 key.m_Handle = hrit->first;
  319.                 const CHandleRange& hr = hrit->second;
  320.                 key.m_Range = hr.GetOverlappingRange();
  321.                 if ( hr.HasGaps() ) {
  322.                     annotRef.m_HandleRange.Reset(new CObjectFor<CHandleRange>);
  323.                     annotRef.m_HandleRange->GetData() = hr;
  324.                 }
  325.                 else {
  326.                     annotRef.m_HandleRange.Reset();
  327.                 }
  328.                 
  329.                 tse.x_MapAnnotObject(index, key, annotRef, m_ObjectInfos);
  330.             }
  331.             ++annotRef.m_AnnotLocationIndex;
  332.         }
  333.     }
  334. }
  337. void CSeq_annot_Info::x_MapAnnotObjects(CTSE_Info& tse,
  338.                                         const CSeq_annot::C_Data::TGraph& objs)
  339. {
  340.     m_ObjectInfos.Reserve(objs.size());
  342.     CTSE_Info::TAnnotObjs& index = tse.x_SetAnnotObjs(GetName());
  344.     SAnnotObject_Key key;
  345.     SAnnotObject_Index annotRef;
  346.     vector<CHandleRangeMap> hrmaps;
  347.     ITERATE ( CSeq_annot::C_Data::TGraph, git, objs ) {
  348.         const CSeq_graph& graph = **git;
  350.         CAnnotObject_Info* info =
  351.             m_ObjectInfos.AddInfo(CAnnotObject_Info(graph, *this));
  352.         key.m_AnnotObject_Info = annotRef.m_AnnotObject_Info = info;
  354.         info->GetMaps(hrmaps);
  355.         annotRef.m_AnnotLocationIndex = 0;
  356.         ITERATE ( vector<CHandleRangeMap>, hrmit, hrmaps ) {
  357.             ITERATE ( CHandleRangeMap, hrit, *hrmit ) {
  358.                 key.m_Handle = hrit->first;
  359.                 const CHandleRange& hr = hrit->second;
  360.                 key.m_Range = hr.GetOverlappingRange();
  361.                 if ( hr.HasGaps() ) {
  362.                     annotRef.m_HandleRange.Reset(new CObjectFor<CHandleRange>);
  363.                     annotRef.m_HandleRange->GetData() = hr;
  364.                 }
  365.                 else {
  366.                     annotRef.m_HandleRange.Reset();
  367.                 }
  369.                 tse.x_MapAnnotObject(index, key, annotRef, m_ObjectInfos);
  370.             }
  371.             ++annotRef.m_AnnotLocationIndex;
  372.         }
  373.     }
  374. }
  377. void CSeq_annot_Info::x_MapAnnotObjects(CTSE_Info& tse,
  378.                                         const CSeq_annot::C_Data::TAlign& objs)
  379. {
  380.     m_ObjectInfos.Reserve(objs.size());
  382.     CTSE_Info::TAnnotObjs& index = tse.x_SetAnnotObjs(GetName());
  384.     SAnnotObject_Key key;
  385.     SAnnotObject_Index annotRef;
  386.     vector<CHandleRangeMap> hrmaps;
  387.     ITERATE ( CSeq_annot::C_Data::TAlign, ait, objs ) {
  388.         const CSeq_align& align = **ait;
  390.         CAnnotObject_Info* info =
  391.             m_ObjectInfos.AddInfo(CAnnotObject_Info(align, *this));
  392.         key.m_AnnotObject_Info = annotRef.m_AnnotObject_Info = info;
  394.         info->GetMaps(hrmaps);
  395.         annotRef.m_AnnotLocationIndex = 0;
  396.         ITERATE ( vector<CHandleRangeMap>, hrmit, hrmaps ) {
  397.             ITERATE ( CHandleRangeMap, hrit, *hrmit ) {
  398.                 key.m_Handle = hrit->first;
  399.                 const CHandleRange& hr = hrit->second;
  400.                 key.m_Range = hr.GetOverlappingRange();
  401.                 if ( hr.HasGaps() ) {
  402.                     annotRef.m_HandleRange.Reset(new CObjectFor<CHandleRange>);
  403.                     annotRef.m_HandleRange->GetData() = hr;
  404.                 }
  405.                 else {
  406.                     annotRef.m_HandleRange.Reset();
  407.                 }
  409.                 tse.x_MapAnnotObject(index, key, annotRef, m_ObjectInfos);
  410.             }
  411.             ++annotRef.m_AnnotLocationIndex;
  412.         }
  413.     }
  414. }
  417. void CSeq_annot_Info::x_UnmapAnnotObjects(CTSE_Info& tse)
  418. {
  419.     if ( m_SNP_Info ) {
  420.         m_SNP_Info->x_UnmapAnnotObjects(tse);
  421.     }
  422.     tse.x_UnmapAnnotObjects(m_ObjectInfos);
  423. }
  426. void CSeq_annot_Info::x_DropAnnotObjects(CTSE_Info& tse)
  427. {
  428.     if ( m_SNP_Info ) {
  429.         m_SNP_Info->x_DropAnnotObjects(tse);
  430.     }
  431.     m_ObjectInfos.Clear();
  432. }
  435. END_SCOPE(objects)
  436. END_NCBI_SCOPE
  438. /*
  439.  * ===========================================================================
  440.  * $Log: seq_annot_info.cpp,v $
  441.  * Revision 1000.4  2004/06/01 19:23:51  gouriano
  442.  * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.16
  443.  *
  444.  * Revision 1.16  2004/05/21 21:42:13  gorelenk
  445.  * Added PCH ncbi_pch.hpp
  446.  *
  447.  * Revision 1.15  2004/03/26 19:42:04  vasilche
  448.  * Fixed premature deletion of SNP annot info object.
  449.  * Removed obsolete references to chunk info.
  450.  *
  451.  * Revision 1.14  2004/03/24 18:30:30  vasilche
  452.  * Fixed edit API.
  453.  * Every *_Info object has its own shallow copy of original object.
  454.  *
  455.  * Revision 1.13  2004/03/16 15:47:28  vasilche
  456.  * Added CBioseq_set_Handle and set of EditHandles
  457.  *
  458.  * Revision 1.12  2004/01/22 20:10:40  vasilche
  459.  * 1. Splitted ID2 specs to two parts.
  460.  * ID2 now specifies only protocol.
  461.  * Specification of ID2 split data is moved to seqsplit ASN module.
  462.  * For now they are still reside in one resulting library as before - libid2.
  463.  * As the result split specific headers are now in objects/seqsplit.
  464.  * 2. Moved ID2 and ID1 specific code out of object manager.
  465.  * Protocol is processed by corresponding readers.
  466.  * ID2 split parsing is processed by ncbi_xreader library - used by all readers.
  467.  * 3. Updated OBJMGR_LIBS correspondingly.
  468.  *
  469.  * Revision 1.11  2003/11/26 17:56:00  vasilche
  470.  * Implemented ID2 split in ID1 cache.
  471.  * Fixed loading of splitted annotations.
  472.  *
  473.  * Revision 1.10  2003/11/19 22:18:03  grichenk
  474.  * All exceptions are now CException-derived. Catch "exception" rather
  475.  * than "runtime_error".
  476.  *
  477.  * Revision 1.9  2003/10/07 13:43:23  vasilche
  478.  * Added proper handling of named Seq-annots.
  479.  * Added feature search from named Seq-annots.
  480.  * Added configurable adaptive annotation search (default: gene, cds, mrna).
  481.  * Fixed selection of blobs for loading from GenBank.
  482.  * Added debug checks to CSeq_id_Mapper for easier finding lost CSeq_id_Handles.
  483.  * Fixed leaked split chunks annotation stubs.
  484.  * Moved some classes definitions in separate *.cpp files.
  485.  *
  486.  * Revision 1.8  2003/09/30 16:22:03  vasilche
  487.  * Updated internal object manager classes to be able to load ID2 data.
  488.  * SNP blobs are loaded as ID2 split blobs - readers convert them automatically.
  489.  * Scope caches results of requests for data to data loaders.
  490.  * Optimized CSeq_id_Handle for gis.
  491.  * Optimized bioseq lookup in scope.
  492.  * Reduced object allocations in annotation iterators.
  493.  * CScope is allowed to be destroyed before other objects using this scope are
  494.  * deleted (feature iterators, bioseq handles etc).
  495.  * Optimized lookup for matching Seq-ids in CSeq_id_Mapper.
  496.  * Added 'adaptive' option to objmgr_demo application.
  497.  *
  498.  * Revision 1.7  2003/08/27 14:29:52  vasilche
  499.  * Reduce object allocations in feature iterator.
  500.  *
  501.  * Revision 1.6  2003/07/18 19:41:46  vasilche
  502.  * Removed unused variable.
  503.  *
  504.  * Revision 1.5  2003/07/17 22:51:31  vasilche
  505.  * Fixed unused variables warnings.
  506.  *
  507.  * Revision 1.4  2003/07/17 20:07:56  vasilche
  508.  * Reduced memory usage by feature indexes.
  509.  * SNP data is loaded separately through PUBSEQ_OS.
  510.  * String compression for SNP data.
  511.  *
  512.  * Revision 1.3  2003/07/09 17:54:29  dicuccio
  513.  * Fixed uninitialized variables in CDataSource and CSeq_annot_Info
  514.  *
  515.  * Revision 1.2  2003/06/02 16:06:38  dicuccio
  516.  * Rearranged src/objects/ subtree.  This includes the following shifts:
  517.  *     - src/objects/asn2asn --> arc/app/asn2asn
  518.  *     - src/objects/testmedline --> src/objects/ncbimime/test
  519.  *     - src/objects/objmgr --> src/objmgr
  520.  *     - src/objects/util --> src/objmgr/util
  521.  *     - src/objects/alnmgr --> src/objtools/alnmgr
  522.  *     - src/objects/flat --> src/objtools/flat
  523.  *     - src/objects/validator --> src/objtools/validator
  524.  *     - src/objects/cddalignview --> src/objtools/cddalignview
  525.  * In addition, libseq now includes six of the objects/seq... libs, and libmmdb
  526.  * replaces the three libmmdb? libs.
  527.  *
  528.  * Revision 1.1  2003/04/24 16:12:38  vasilche
  529.  * Object manager internal structures are splitted more straightforward.
  530.  * Removed excessive header dependencies.
  531.  *
  532.  *
  533.  * ===========================================================================
  534.  */