test_reader_pubseq.cpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: test_reader_pubseq.cpp,v $
- * PRODUCTION Revision 1000.1 2004/06/01 19:42:37 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: test_reader_pubseq.cpp,v 1000.1 2004/06/01 19:42:37 gouriano Exp $
- * ===========================================================================
- * PUBLIC DOMAIN NOTICE
- * National Center for Biotechnology Information
- *
- * This software/database is a "United States Government Work" under the
- * terms of the United States Copyright Act. It was written as part of
- * the author's official duties as a United States Government employee and
- * thus cannot be copyrighted. This software/database is freely available
- * to the public for use. The National Library of Medicine and the U.S.
- * Government have not placed any restriction on its use or reproduction.
- *
- * Although all reasonable efforts have been taken to ensure the accuracy
- * and reliability of the software and data, the NLM and the U.S.
- * Government do not and cannot warrant the performance or results that
- * may be obtained by using this software or data. The NLM and the U.S.
- * Government disclaim all warranties, express or implied, including
- * warranties of performance, merchantability or fitness for any particular
- * purpose.
- *
- * Please cite the author in any work or product based on this material.
- * ===========================================================================
- */
- #include <ncbi_pch.hpp>
- #include <iostream>
- #include <serial/serial.hpp>
- #include <objects/seqset/Seq_entry.hpp>
- #include <objects/seqloc/Seq_id.hpp>
- #include <objects/seqloc/Textseq_id.hpp>
- #include <serial/objistrasnb.hpp>
- #include <serial/objostrasn.hpp>
- #include <objtools/data_loaders/genbank/readers/pubseqos/reader_pubseq.hpp>
- #include <objmgr/impl/tse_info.hpp>
- #include <connect/ncbi_util.h>
- #include <connect/ncbi_core_cxx.hpp>
- USING_NCBI_SCOPE;
- USING_SCOPE(objects);
- using namespace std;
- int main()
- {
- for(int k = 0; k < 10; ++k) {
- cout << "K: " << k << endl;
- CPubseqReader reader;
- int gi = 156895+k-1;
- vector< CRef<CSeqref> > sr;
- reader.RetrieveSeqrefs(sr, gi, 0);
- ITERATE ( vector< CRef<CSeqref> >, i, sr ) {
- const CSeqref& seqRef = **i;
- cout << "gi: " << gi << " SatKey=" << seqRef.GetSatKey() << " Flags=" << seqRef.GetFlags() << endl;
-
- CRef<CTSE_Info> info = reader.GetBlob(seqRef, 0);
- if (!info) {
- cout << "blob is not availablen";
- continue;
- }
- cout <<"gi: " << gi << " " << 1 << " blobs" << endl;
- }
- }
- return 0;
- }
- /*
- * $Log: test_reader_pubseq.cpp,v $
- * Revision 1000.1 2004/06/01 19:42:37 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
- *
- * Revision 1.4 2004/05/21 21:42:52 gorelenk
- * Added PCH ncbi_pch.hpp
- *
- * Revision 1.3 2003/12/30 22:14:45 vasilche
- * Updated genbank loader and readers plugins.
- *
- * Revision 1.2 2003/12/23 14:16:57 kuznets
- * Fixed include path
- *
- * Revision 1.1 2003/12/16 17:51:23 kuznets
- * Code reorganization
- *
- * Revision 1.10 2003/11/26 17:56:04 vasilche
- * Implemented ID2 split in ID1 cache.
- * Fixed loading of splitted annotations.
- *
- * Revision 1.9 2003/09/30 16:22:06 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 1.8 2003/08/14 20:05:20 vasilche
- * Simple SNP features are stored as table internally.
- * They are recreated when needed using CFeat_CI.
- *
- * Revision 1.7 2003/07/17 20:06:02 vasilche
- * Added OBJMGR_LIBS definition.
- *
- * Revision 1.6 2003/06/02 16:06:39 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 1.5 2003/04/15 14:23:11 vasilche
- * Added missing includes.
- *
- * Revision 1.4 2002/07/22 22:49:05 kimelman
- * test fixes for confidential data retrieval
- *
- * Revision 1.3 2002/05/06 03:28:52 vakatov
- * OM/OM1 renaming
- *
- * Revision 1.2 2002/04/12 14:52:34 butanaev
- * Typos fixed, code cleanup.
- *
- * Revision 1.1 2002/04/08 21:45:58 butanaev
- * Added test for pubseq reader.
- *
- * Revision 1.7 2002/03/27 20:23:50 butanaev
- * Added connection pool.
- *
- * Revision 1.6 2002/03/26 18:48:59 butanaev
- * Fixed bug not deleting streambuf.
- *
- * Revision 1.5 2002/03/26 17:17:04 kimelman
- * reader stream fixes
- *
- * Revision 1.4 2002/03/25 17:49:13 kimelman
- * ID1 failure handling
- *
- * Revision 1.3 2002/03/21 19:14:55 kimelman
- * GB related bugfixes
- *
- * Revision 1.2 2002/01/23 21:59:34 grichenk
- * Redesigned seq-id handles and mapper
- *
- * Revision 1.1 2002/01/11 19:06:27 gouriano
- * restructured objmgr
- *
- * Revision 1.3 2001/12/10 20:08:02 butanaev
- * Code cleanup.
- *
- * Revision 1.2 2001/12/07 21:25:00 butanaev
- * Interface development, code beautyfication.
- *
- * Revision 1.1 2001/12/07 16:43:35 butanaev
- * Switching to new reader interfaces.
- *
- * Revision 1.6 2001/12/06 20:37:05 butanaev
- * Fixed timeout problem.
- *
- * Revision 1.5 2001/12/06 18:06:22 butanaev
- * Ported to linux.
- *
- * Revision 1.4 2001/12/06 14:35:22 butanaev
- * New streamable interfaces designed, ID1 reimplemented.
- *
- * Revision 1.3 2001/11/29 21:24:03 butanaev
- * Classes working with PUBSEQ transferred to separate lib. Code cleanup.
- * Test app redesigned.
- *
- * Revision 1.2 2001/10/11 15:47:34 butanaev
- * Loader from ID1 implemented.
- *
- * Revision 1.1 2001/09/10 20:03:04 butanaev
- * Initial checkin.
- */