objmgr_demo.cpp

ncbi源码

        }

        // Region set to interval 0..9 on the bioseq. Any feature
        // intersecting with the region should be selected.
        loc.SetInt().SetId(*id);
        loc.SetInt().SetFrom(0);
        loc.SetInt().SetTo(9);
        count = 0;
        // Iterate features. No feature type restrictions.
        for (CFeat_CI it(scope, loc, base_sel); it;  ++it) {
            count++;
        }
        NcbiCout << "Feat count (int. 0..9, any):   " << count << NcbiEndl;

        // Search features only in the TSE containing the target bioseq.
        // Since only one seq-id may be used as the target bioseq, the
        // iterator is constructed not from a seq-loc, but from a bioseq handle
        // and start/stop points on the bioseq. If both start and stop are 0 the
        // whole bioseq is used. The last parameter may be used for type filtering.
        count = 0;
        for ( CFeat_CI it(handle, 0, 999, base_sel); it;  ++it ) {
            count++;
            if ( print_features ) {
                NcbiCout << MSerial_AsnText <<
                    it->GetMappedFeature() << it->GetLocation();
            }
        }
        NcbiCout << "Feat count (bh, 0..999, any):  " << count << NcbiEndl;

        // The same way may be used to iterate aligns and graphs,
        // except that there is no type filter for both of them.
        // No region restrictions -- the whole bioseq is used:
        loc.SetWhole(*id);
        count = 0;
        for (CGraph_CI it(scope, loc, base_sel); it;  ++it) {
            count++;
            // Get seq-annot containing the feature
            if ( get_mapped_location )
                it->GetLoc();
            if ( get_original_feature )
                it->GetOriginalGraph();
            if ( get_mapped_feature )
                it->GetMappedGraph();
            if ( print_features ) {
                NcbiCout << MSerial_AsnText <<
                    it->GetMappedGraph() << it->GetLoc();
            }
            CSeq_annot_Handle annot = it.GetAnnot();
        }
        NcbiCout << "Graph count (whole, any):       " << count << NcbiEndl;

        if ( !skip_alignments ) {
            count = 0;
            // Create CAlign_CI using the current scope and location.
            for (CAlign_CI it(scope, loc, base_sel); it;  ++it) {
                count++;
                if ( get_mapped_alignments ) {
                    *it;
                }
                if ( print_alignments ) {
                    NcbiCout << MSerial_AsnText << *it;
                }
            }
            NcbiCout << "Align count (whole, any):       " << count << NcbiEndl;
        }
    }

    NcbiCout << "Done" << NcbiEndl;
    return 0;
}


END_NCBI_SCOPE



/////////////////////////////////////////////////////////////////////////////
//  MAIN


USING_NCBI_SCOPE;

int main(int argc, const char* argv[])
{
    return CDemoApp().AppMain(argc, argv);
}

/*
* ---------------------------------------------------------------------------
* $Log: objmgr_demo.cpp,v $
* Revision 1000.2  2004/06/01 18:30:37  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.68
*
* Revision 1.68  2004/05/21 21:41:40  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.67  2004/05/13 19:50:48  vasilche
* Added options to skip and get mapped alignments.
*
* Revision 1.66  2004/05/13 19:33:15  vasilche
* Added option for printing descriptors.
*
* Revision 1.65  2004/04/27 19:00:08  kuznets
* Commented out old cache modes
*
* Revision 1.64  2004/04/09 20:37:48  vasilche
* Added optional test to get mapped location and object for graphs.
*
* Revision 1.63  2004/04/08 14:11:57  vasilche
* Added option to dump loaded Seq-entry.
*
* Revision 1.62  2004/04/05 15:56:13  grichenk
* Redesigned CAnnotTypes_CI: moved all data and data collecting
* functions to CAnnotDataCollector. CAnnotTypes_CI is no more
* inherited from SAnnotSelector.
*
* Revision 1.61  2004/03/18 16:30:24  grichenk
* Changed type of seq-align containers from list to vector.
*
* Revision 1.60  2004/02/09 19:18:50  grichenk
* Renamed CDesc_CI to CSeq_descr_CI. Redesigned CSeq_descr_CI
* and CSeqdesc_CI to avoid using data directly.
*
* Revision 1.59  2004/02/09 14:54:22  vasilche
* Dump synonyms of the sequence.
*
* Revision 1.58  2004/02/05 14:53:53  vasilche
* Used "new" cache interface by default.
*
* Revision 1.57  2004/02/04 18:05:34  grichenk
* Added annotation filtering by set of types/subtypes.
* Renamed *Choice to *Type in SAnnotSelector.
*
* Revision 1.56  2004/01/30 19:18:49  vasilche
* Added -seq_map flag.
*
* Revision 1.55  2004/01/29 20:38:47  vasilche
* Removed loading of whole sequence by CSeqMap_CI.
*
* Revision 1.54  2004/01/26 18:06:35  vasilche
* Add option for printing Seq-align.
* Use MSerial_Asn* manipulators.
* Removed unused includes.
*
* Revision 1.53  2004/01/07 17:38:02  vasilche
* Fixed include path to genbank loader.
*
* Revision 1.52  2004/01/05 18:14:03  vasilche
* Fixed name of project and path to header.
*
* Revision 1.51  2003/12/30 20:00:41  vasilche
* Added test for CGBDataLoader::GetSatSatKey().
*
* Revision 1.50  2003/12/30 19:51:54  vasilche
* Test CGBDataLoader::GetSatSatkey() method.
*
* Revision 1.49  2003/12/30 16:01:41  vasilche
* Added possibility to specify type of cache to use: -cache_mode (old|newid|new).
*
* Revision 1.48  2003/12/19 19:50:22  vasilche
* Removed obsolete split code.
* Do not use intemediate gi.
*
* Revision 1.47  2003/12/02 23:20:22  vasilche
* Allow to specify any Seq-id via ASN.1 text.
*
* Revision 1.46  2003/11/26 17:56:01  vasilche
* Implemented ID2 split in ID1 cache.
* Fixed loading of splitted annotations.
*
* Revision 1.45  2003/10/27 15:06:31  vasilche
* Added option to set ID1 cache keep time.
*
* Revision 1.44  2003/10/21 14:27:35  vasilche
* Added caching of gi -> sat,satkey,version resolution.
* SNP blobs are stored in cache in preprocessed format (platform dependent).
* Limit number of connections to GenBank servers.
* Added collection of ID1 loader statistics.
*
* Revision 1.43  2003/10/14 18:29:05  vasilche
* Added -exclude_named option.
*
* Revision 1.42  2003/10/09 20:20:58  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 1.41  2003/10/08 17:55:32  vasilche
* Print sequence gi when -id option is used.
*
* Revision 1.40  2003/10/07 13:43:23  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 1.39  2003/09/30 20:13:38  vasilche
* Print original feature location if requested.
*
* Revision 1.38  2003/09/30 16:22:05  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 1.37  2003/08/27 14:22:01  vasilche
* Added options get_mapped_location, get_mapped_feature and get_original_feature
* to test feature iterator speed.
*
* Revision 1.36  2003/08/15 19:19:16  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 1.35  2003/08/14 20:05:20  vasilche
* Simple SNP features are stored as table internally.
* They are recreated when needed using CFeat_CI.
*
* Revision 1.34  2003/07/25 21:41:32  grichenk
* Implemented non-recursive mode for CSeq_annot_CI,
* fixed friend declaration in CSeq_entry_Info.
*
* Revision 1.33  2003/07/25 15:25:27  grichenk
* Added CSeq_annot_CI class
*
* Revision 1.32  2003/07/24 20:36:17  vasilche
* Added arguemnt to choose ID1<->PUBSEQOS on Windows easier.
*
* Revision 1.31  2003/07/17 20:06:18  vasilche
* Added OBJMGR_LIBS definition.
*
* Revision 1.30  2003/07/17 19:10:30  grichenk
* Added methods for seq-map and seq-vector validation,
* updated demo.
*
* Revision 1.29  2003/07/08 15:09:44  vasilche
* Added argument to test depth of segment resolution.
*
* Revision 1.28  2003/06/25 20:56:32  grichenk
* Added max number of annotations to annot-selector, updated demo.
*
* Revision 1.27  2003/06/02 16:06:38  dicuccio
* Rearranged src/objects/ subtree.  This includes the following shifts:
*     - src/objects/asn2asn --> arc/app/asn2asn
*     - src/objects/testmedline --> src/objects/ncbimime/test
*     - src/objects/objmgr --> src/objmgr
*     - src/objects/util --> src/objmgr/util
*     - src/objects/alnmgr --> src/objtools/alnmgr
*     - src/objects/flat --> src/objtools/flat
*     - src/objects/validator --> src/objtools/validator
*     - src/objects/cddalignview --> src/objtools/cddalignview
* In addition, libseq now includes six of the objects/seq... libs, and libmmdb
* replaces the three libmmdb? libs.
*
* Revision 1.26  2003/05/27 20:54:52  grichenk
* Fixed CRef<> to bool convertion
*
* Revision 1.25  2003/05/06 16:52:54  vasilche
* Added 'pause' argument.
*
* Revision 1.24  2003/04/29 19:51:14  vasilche
* Fixed interaction of Data Loader garbage collector and TSE locking mechanism.
* Made some typedefs more consistent.
*
* Revision 1.23  2003/04/24 16:12:38  vasilche
* Object manager internal structures are splitted more straightforward.
* Removed excessive header dependencies.
*
* Revision 1.22  2003/04/15 14:24:08  vasilche
* Changed CReader interface to not to use fake streams.
*
* Revision 1.21  2003/04/03 14:17:43  vasilche
* Allow using data loaded from file.
*
* Revision 1.20  2003/03/27 19:40:11  vasilche
* Implemented sorting in CGraph_CI.
* Added Rewind() method to feature/graph/align iterators.
*
* Revision 1.19  2003/03/26 17:27:04  vasilche
* Added optinal reverse feature traversal.
*
* Revision 1.18  2003/03/21 14:51:41  vasilche
* Added debug printing of features collected.
*
* Revision 1.17  2003/03/18 21:48:31  grichenk
* Removed obsolete class CAnnot_CI
*
* Revision 1.16  2003/03/10 16:33:44  vasilche
* Added dump of features if errors were detected.
*
* Revision 1.15  2003/02/27 20:57:36  vasilche
* Addef some options for better performance testing.
*
* Revision 1.14  2003/02/24 19:02:01  vasilche
* Reverted testing shortcut.
*
* Revision 1.13  2003/02/24 18:57:22  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 1.12  2002/12/06 15:36:01  grichenk
* Added overlap type for annot-iterators
*
* Revision 1.11  2002/12/05 19:28:33  grichenk
* Prohibited postfix operator ++()
*
* Revision 1.10  2002/11/08 19:43:36  grichenk
* CConstRef<> constructor made explicit
*
* Revision 1.9  2002/11/04 21:29:13  grichenk
* Fixed usage of const CRef<> and CRef<> constructor
*
* Revision 1.8  2002/10/02 17:58:41  grichenk
* Added CBioseq_CI sample code
*
* Revision 1.7  2002/09/03 21:27:03  grichenk
* Replaced bool arguments in CSeqVector constructor and getters
* with enums.
*
* Revision 1.6  2002/06/12 14:39:03  grichenk
* Renamed enumerators
*
* Revision 1.5  2002/05/06 03:28:49  vakatov
* OM/OM1 renaming
*
* Revision 1.4  2002/05/03 21:28:11  ucko
* Introduce T(Signed)SeqPos.
*
* Revision 1.3  2002/05/03 18:37:34  grichenk
* Added more examples of using CFeat_CI and GetSequenceView()
*
* Revision 1.2  2002/03/28 14:32:58  grichenk
* Minor fixes
*
* Revision 1.1  2002/03/28 14:07:25  grichenk
* Initial revision
*
*
* ===========================================================================
*/