test_reader_pubseq.cpp

来自「ncbi源码」· C++ 代码 · 共 196 行

/*
 * ===========================================================================
 * 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 available\n";
                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.
*/