scope.hpp

ncbi源码

* assume all not resolved Seq-id as synonym.
* Seq-id conflict messages made clearer.
*
* Revision 1.68  2004/01/27 17:11:13  ucko
* Remove redundant forward declaration of CTSE_Info
*
* Revision 1.67  2003/12/29 20:04:52  grichenk
* CHeapScope can be initialized with null pointer.
*
* Revision 1.66  2003/12/18 16:38:05  grichenk
* Added CScope::RemoveEntry()
*
* Revision 1.65  2003/11/28 15:13:24  grichenk
* Added CSeq_entry_Handle
*
* Revision 1.64  2003/11/21 20:33:03  grichenk
* Added GetBioseqHandleFromTSE(CSeq_id, CSeq_entry)
*
* Revision 1.63  2003/11/12 15:49:48  vasilche
* Added loading annotations on non gi Seq-id.
*
* Revision 1.62  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 1.61  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 1.60  2003/09/05 20:50:24  grichenk
* +AddBioseq(CBioseq&)
*
* Revision 1.59  2003/09/03 19:59:59  grichenk
* Added sequence filtering by level (mains/parts/all)
*
* Revision 1.58  2003/08/12 18:25:39  grichenk
* Fixed default priorities
*
* Revision 1.57  2003/08/06 20:51:14  grichenk
* Removed declarations of non-existent methods
*
* Revision 1.56  2003/08/04 17:02:57  grichenk
* Added constructors to iterate all annotations from a
* seq-entry or seq-annot.
*
* Revision 1.55  2003/07/25 15:25:22  grichenk
* Added CSeq_annot_CI class
*
* Revision 1.54  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 1.53  2003/06/30 18:42:09  vasilche
* CPriority_I made to use less memory allocations/deallocations.
*
* Revision 1.52  2003/06/19 18:34:07  vasilche
* Fixed compilation on Windows.
*
* Revision 1.51  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 1.49  2003/05/27 19:44:04  grichenk
* Added CSeqVector_CI class
*
* Revision 1.48  2003/05/20 15:44:37  vasilche
* Fixed interaction of CDataSource and CDataLoader in multithreaded app.
* Fixed some warnings on WorkShop.
* Added workaround for memory leak on WorkShop.
*
* Revision 1.47  2003/05/14 18:39:25  grichenk
* Simplified TSE caching and filtering in CScope, removed
* some obsolete members and functions.
*
* Revision 1.46  2003/05/12 19:18:28  vasilche
* Fixed locking of object manager classes in multi-threaded application.
*
* Revision 1.45  2003/05/06 18:54:06  grichenk
* Moved TSE filtering from CDataSource to CScope, changed
* some filtering rules (e.g. priority is now more important
* than scope history). Added more caches to CScope.
*
* Revision 1.44  2003/04/29 19:51:12  vasilche
* Fixed interaction of Data Loader garbage collector and TSE locking mechanism.
* Made some typedefs more consistent.
*
* Revision 1.43  2003/04/24 17:24:57  vasilche
* SAnnotSelector is struct.
* Added include required by MS VC.
*
* Revision 1.42  2003/04/24 16:12:37  vasilche
* Object manager internal structures are splitted more straightforward.
* Removed excessive header dependencies.
*
* Revision 1.41  2003/04/09 16:04:29  grichenk
* SDataSourceRec replaced with CPriorityNode
* Added CScope::AddScope(scope, priority) to allow scope nesting
*
* Revision 1.40  2003/04/03 14:18:08  vasilche
* Added public GetSynonyms() method.
*
* Revision 1.39  2003/03/26 21:00:07  grichenk
* Added seq-id -> tse with annotation cache to CScope
*
* Revision 1.38  2003/03/24 21:26:42  grichenk
* Added support for CTSE_CI
*
* Revision 1.37  2003/03/21 19:22:48  grichenk
* Redesigned TSE locking, replaced CTSE_Lock with CRef<CTSE_Info>.
*
* Revision 1.36  2003/03/18 14:46:36  grichenk
* Set limit object type to "none" if the object is null.
*
* Revision 1.35  2003/03/12 20:09:30  grichenk
* Redistributed members between CBioseq_Handle, CBioseq_Info and CTSE_Info
*
* Revision 1.34  2003/03/11 14:15:49  grichenk
* +Data-source priority
*
* Revision 1.33  2003/03/10 16:55:16  vasilche
* Cleaned SAnnotSelector structure.
* Added shortcut when features are limited to one TSE.
*
* Revision 1.32  2003/03/03 20:32:47  vasilche
* Removed obsolete method GetSynonyms().
*
* Revision 1.31  2003/02/28 20:02:35  grichenk
* Added synonyms cache and x_GetSynonyms()
*
* Revision 1.30  2003/02/27 14:35:32  vasilche
* Splitted PopulateTSESet() by logically independent parts.
*
* Revision 1.29  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 1.28  2003/01/22 20:11:53  vasilche
* Merged functionality of CSeqMapResolved_CI to CSeqMap_CI.
* CSeqMap_CI now supports resolution and iteration over sequence range.
* Added several caches to CScope.
* Optimized CSeqVector().
* Added serveral variants of CBioseqHandle::GetSeqVector().
* Tried to optimize annotations iterator (not much success).
* Rewritten CHandleRange and CHandleRangeMap classes to avoid sorting of list.
*
* Revision 1.27  2002/12/26 20:51:36  dicuccio
* Added Win32 export specifier
*
* Revision 1.26  2002/12/26 16:39:21  vasilche
* Object manager class CSeqMap rewritten.
*
* Revision 1.25  2002/11/08 22:15:50  grichenk
* Added methods for removing/replacing annotations
*
* Revision 1.24  2002/11/01 05:34:06  kans
* added GetBioseqHandle taking CBioseq parameter
*
* Revision 1.23  2002/10/31 22:25:09  kans
* added GetBioseqHandle taking CSeq_loc parameter
*
* Revision 1.22  2002/10/18 19:12:39  grichenk
* Removed mutex pools, converted most static mutexes to non-static.
* Protected CSeqMap::x_Resolve() with mutex. Modified code to prevent
* dead-locks.
*
* Revision 1.21  2002/10/02 17:58:21  grichenk
* Added sequence type filter to CBioseq_CI
*
* Revision 1.20  2002/09/30 20:01:17  grichenk
* Added methods to support CBioseq_CI
*
* Revision 1.19  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 1.18  2002/06/04 17:18:32  kimelman
* memory cleanup :  new/delete/Cref rearrangements
*
* Revision 1.17  2002/05/28 18:01:11  gouriano
* DebugDump added
*
* Revision 1.16  2002/05/14 20:06:23  grichenk
* Improved CTSE_Info locking by CDataSource and CDataLoader
*
* Revision 1.15  2002/05/06 03:30:36  vakatov
* OM/OM1 renaming
*
* Revision 1.14  2002/05/03 21:28:02  ucko
* Introduce T(Signed)SeqPos.
*
* Revision 1.13  2002/04/17 21:09:38  grichenk
* Fixed annotations loading
*
* Revision 1.12  2002/04/08 19:14:15  gouriano
* corrected comment to AddDefaults()
*
* Revision 1.11  2002/03/27 18:46:26  gouriano
* three functions made public
*
* Revision 1.10  2002/03/20 21:20:38  grichenk
* +CScope::ResetHistory()
*
* Revision 1.9  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 1.8  2002/02/07 21:27:33  grichenk
* Redesigned CDataSource indexing: seq-id handle -> TSE -> seq/annot
*
* Revision 1.7  2002/02/06 21:46:43  gouriano
* *** empty log message ***
*
* Revision 1.6  2002/02/05 21:47:21  gouriano
* added FindSeqid function, minor tuneup in CSeq_id_mapper
*
* Revision 1.5  2002/01/28 19:45:33  gouriano
* changed the interface of BioseqHandle: two functions moved from Scope
*
* Revision 1.4  2002/01/23 21:59:29  grichenk
* Redesigned seq-id handles and mapper
*
* Revision 1.3  2002/01/18 17:07:12  gouriano
* renamed GetSequence to GetSeqVector
*
* Revision 1.2  2002/01/16 16:26:35  gouriano
* restructured objmgr
*
* Revision 1.1  2002/01/11 19:04:03  gouriano
* restructured objmgr
*
*
* ===========================================================================
*/

#endif//OBJMGR_SCOPE__HPP