annot_types_ci.hpp

ncbi源码

* Revision 1.62  2004/02/04 18:05:32  grichenk
* Added annotation filtering by set of types/subtypes.
* Renamed *Choice to *Type in SAnnotSelector.
*
* Revision 1.61  2004/01/28 20:54:34  vasilche
* Fixed mapping of annotations.
*
* Revision 1.60  2004/01/23 16:14:45  grichenk
* Implemented alignment mapping
*
* Revision 1.59  2003/11/10 18:11:03  grichenk
* Moved CSeq_loc_Conversion_Set to seq_loc_cvt
*
* Revision 1.58  2003/11/04 21:10:00  grichenk
* Optimized feature mapping through multiple segments.
* Fixed problem with CAnnotTypes_CI not releasing scope
* when exception is thrown from constructor.
*
* Revision 1.57  2003/11/04 16:21:36  grichenk
* Updated CAnnotTypes_CI to map whole features instead of splitting
* them by sequence segments.
*
* Revision 1.56  2003/10/27 20:07:10  vasilche
* Started implementation of full annotations' mapping.
*
* Revision 1.55  2003/10/09 20:20:59  vasilche
* Added possibility to include and exclude Seq-annot names to annot iterator.
* Fixed adaptive search. It looked only on selected set of annot names before.
*
* Revision 1.54  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 1.53  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 1.52  2003/09/12 15:50:09  grichenk
* Updated adaptive-depth triggering
*
* Revision 1.51  2003/09/11 17:45:06  grichenk
* Added adaptive-depth option to annot-iterators.
*
* Revision 1.50  2003/09/03 19:59:00  grichenk
* Initialize m_MappedIndex to 0
*
* Revision 1.49  2003/08/27 21:23:35  vasilche
* Fixed warning.
*
* Revision 1.48  2003/08/27 14:28:50  vasilche
* Reduce amount of object allocations in feature iteration.
*
* Revision 1.47  2003/08/22 14:58:55  grichenk
* Added NoMapping flag (to be used by CAnnot_CI for faster fetching).
* Added GetScope().
*
* Revision 1.46  2003/08/15 19:19:15  vasilche
* Fixed memory leak in string packing hooks.
* Fixed processing of 'partial' flag of features.
* Allow table packing of non-point SNP.
* Allow table packing of SNP with long alleles.
*
* Revision 1.45  2003/08/14 20:05:18  vasilche
* Simple SNP features are stored as table internally.
* They are recreated when needed using CFeat_CI.
*
* Revision 1.44  2003/08/04 17:02:57  grichenk
* Added constructors to iterate all annotations from a
* seq-entry or seq-annot.
*
* Revision 1.43  2003/07/18 19:39:44  vasilche
* Workaround for GCC 3.0.4 bug.
*
* Revision 1.42  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 1.41  2003/06/25 20:56:29  grichenk
* Added max number of annotations to annot-selector, updated demo.
*
* Revision 1.40  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 1.39  2003/04/29 19:51:12  vasilche
* Fixed interaction of Data Loader garbage collector and TSE locking mechanism.
* Made some typedefs more consistent.
*
* Revision 1.38  2003/04/24 16:12:37  vasilche
* Object manager internal structures are splitted more straightforward.
* Removed excessive header dependencies.
*
* Revision 1.37  2003/03/27 19:40:10  vasilche
* Implemented sorting in CGraph_CI.
* Added Rewind() method to feature/graph/align iterators.
*
* Revision 1.36  2003/03/21 19:22:48  grichenk
* Redesigned TSE locking, replaced CTSE_Lock with CRef<CTSE_Info>.
*
* Revision 1.35  2003/03/18 21:48:27  grichenk
* Removed obsolete class CAnnot_CI
*
* Revision 1.34  2003/03/05 20:56:42  vasilche
* SAnnotSelector now holds all parameters of annotation iterators.
*
* Revision 1.33  2003/02/28 19:27:20  vasilche
* Cleaned Seq_loc conversion class.
*
* Revision 1.32  2003/02/27 20:56:51  vasilche
* Use one method for lookup on main sequence and segments.
*
* Revision 1.31  2003/02/27 14:35:32  vasilche
* Splitted PopulateTSESet() by logically independent parts.
*
* Revision 1.30  2003/02/26 17:54:14  vasilche
* Added cached total range of mapped location.
*
* Revision 1.29  2003/02/24 21:35:21  vasilche
* Reduce checks in CAnnotObject_Ref comparison.
* Fixed compilation errors on MS Windows.
* Removed obsolete file src/objects/objmgr/annot_object.hpp.
*
* Revision 1.28  2003/02/24 18:57:20  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 1.27  2003/02/13 14:34:31  grichenk
* Renamed CAnnotObject -> CAnnotObject_Info
* + CSeq_annot_Info and CAnnotObject_Ref
* Moved some members of CAnnotObject to CSeq_annot_Info
* and CAnnotObject_Ref.
* Added feat/align/graph to CAnnotObject_Info map
* to CDataSource.
*
* Revision 1.26  2003/02/04 21:44:10  grichenk
* Convert seq-loc instead of seq-annot to the master coordinates
*
* Revision 1.25  2002/12/26 20:51:35  dicuccio
* Added Win32 export specifier
*
* Revision 1.24  2002/12/26 16:39:21  vasilche
* Object manager class CSeqMap rewritten.
*
* Revision 1.23  2002/12/24 15:42:44  grichenk
* CBioseqHandle argument to annotation iterators made const
*
* Revision 1.22  2002/12/06 15:35:57  grichenk
* Added overlap type for annot-iterators
*
* Revision 1.21  2002/11/04 21:28:58  grichenk
* Fixed usage of const CRef<> and CRef<> constructor
*
* Revision 1.20  2002/11/01 20:46:41  grichenk
* Added sorting to set< CRef<CAnnotObject> >
*
* Revision 1.19  2002/10/08 18:57:27  grichenk
* Added feature sorting to the iterator class.
*
* Revision 1.18  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 1.17  2002/05/31 17:52:58  grichenk
* Optimized for better performance (CTSE_Info uses atomic counter,
* delayed annotations indexing, no location convertions in
* CAnnot_Types_CI if no references resolution is required etc.)
*
* Revision 1.16  2002/05/24 14:58:53  grichenk
* Fixed Empty() for unsigned intervals
* SerialAssign<>() -> CSerialObject::Assign()
* Improved performance for eResolve_None case
*
* Revision 1.15  2002/05/06 03:30:35  vakatov
* OM/OM1 renaming
*
* Revision 1.14  2002/05/03 21:28:01  ucko
* Introduce T(Signed)SeqPos.
*
* Revision 1.13  2002/04/30 14:30:41  grichenk
* Added eResolve_TSE flag in CAnnot_Types_CI, made it default
*
* Revision 1.12  2002/04/22 20:06:15  grichenk
* Minor changes in private interface
*
* Revision 1.11  2002/04/17 21:11:58  grichenk
* Fixed annotations loading
* Set "partial" flag in features if necessary
* Implemented most seq-loc types in reference resolving methods
* Fixed searching for annotations within a signle TSE
*
* Revision 1.10  2002/04/11 12:07:28  grichenk
* Redesigned CAnnotTypes_CI to resolve segmented sequences correctly.
*
* Revision 1.9  2002/04/05 21:26:16  grichenk
* Enabled iteration over annotations defined on segments of a
* delta-sequence.
*
* Revision 1.8  2002/03/07 21:25:31  grichenk
* +GetSeq_annot() in annotation iterators
*
* Revision 1.7  2002/03/05 16:08:12  grichenk
* Moved TSE-restriction to new constructors
*
* Revision 1.6  2002/03/04 15:07:46  grichenk
* Added "bioseq" argument to CAnnotTypes_CI constructor to iterate
* annotations from a single TSE.
*
* Revision 1.5  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 1.4  2002/02/15 20:36:29  gouriano
* changed implementation of HandleRangeMap
*
* Revision 1.3  2002/02/07 21:27:33  grichenk
* Redesigned CDataSource indexing: seq-id handle -> TSE -> seq/annot
*
* Revision 1.2  2002/01/16 16:26:35  gouriano
* restructured objmgr
*
* Revision 1.1  2002/01/11 19:03:59  gouriano
* restructured objmgr
*
*
* ===========================================================================
*/

#endif  // ANNOT_TYPES_CI__HPP