test_objmgr_title.cpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: test_objmgr_title.cpp,v $
- * PRODUCTION Revision 1000.1 2004/06/01 19:47:20 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.2
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: test_objmgr_title.cpp,v 1000.1 2004/06/01 19:47:20 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.
- *
- * ===========================================================================
- *
- * Author: Aaron Ucko
- *
- * File Description:
- * test code for CScope::GetTitle
- */
- #include <ncbi_pch.hpp>
- #include <corelib/ncbistd.hpp>
- #include <corelib/ncbiapp.hpp>
- #include <corelib/ncbiargs.hpp>
- #include <corelib/ncbienv.hpp>
- #include <objmgr/object_manager.hpp>
- #include <objmgr/scope.hpp>
- #include <objmgr/bioseq_handle.hpp>
- #include <objtools/data_loaders/genbank/gbloader.hpp>
- #include <objmgr/util/sequence.hpp>
- // (BEGIN_NCBI_SCOPE must be followed by END_NCBI_SCOPE later in this file)
- BEGIN_NCBI_SCOPE
- USING_SCOPE(objects);
- USING_SCOPE(sequence);
- class CTitleTester : public CNcbiApplication
- {
- virtual void Init(void);
- virtual int Run(void);
- };
- void CTitleTester::Init(void)
- {
- auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
- arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
- "Show a sequence's title", false);
- arg_desc->AddKey("gi", "SeqEntryID", "GI id of the Seq-Entry to examine",
- CArgDescriptions::eInteger);
- arg_desc->AddFlag("reconstruct", "Reconstruct title");
- arg_desc->AddFlag("accession", "Prepend accession");
- arg_desc->AddFlag("organism", "Append organism name");
- SetupArgDescriptions(arg_desc.release());
- }
- int CTitleTester::Run(void)
- {
- const CArgs& args = GetArgs();
- CObjectManager objmgr;
- CScope scope(objmgr);
- CSeq_id id;
-
- id.SetGi(args["gi"].AsInteger());
- objmgr.RegisterDataLoader(*(new CGBDataLoader), CObjectManager::eDefault);
- scope.AddDefaults();
- CBioseq_Handle handle = scope.GetBioseqHandle(id);
- TGetTitleFlags flags = 0;
- if (args["reconstruct"]) {
- flags |= fGetTitle_Reconstruct;
- }
- if (args["organism"]) {
- flags |= fGetTitle_Organism;
- }
- NcbiCout << GetTitle(handle, flags) << NcbiEndl;
- return 0;
- }
- // (END_NCBI_SCOPE must be preceded by BEGIN_NCBI_SCOPE)
- END_NCBI_SCOPE
- USING_NCBI_SCOPE;
- int main(int argc, const char** argv)
- {
- return CTitleTester().AppMain(argc, argv);
- }
- /*
- * ===========================================================================
- *
- * $Log: test_objmgr_title.cpp,v $
- * Revision 1000.1 2004/06/01 19:47:20 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.2
- *
- * Revision 1.2 2004/05/21 21:42:56 gorelenk
- * Added PCH ncbi_pch.hpp
- *
- * Revision 1.1 2003/12/16 17:51:22 kuznets
- * Code reorganization
- *
- * Revision 1.12 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 1.11 2002/11/15 17:53:28 ucko
- * Only print the title once.
- * Move CVS log to end.
- *
- * Revision 1.10 2002/06/07 16:13:34 ucko
- * GetTitle() is now in sequence::.
- *
- * Revision 1.9 2002/06/07 14:34:33 ucko
- * More changes for GetTitle(): pull in <objects/util/sequence.hpp>, drop
- * CBioseq_Handle:: from flag-related identifiers.
- *
- * Revision 1.8 2002/06/06 19:47:38 clausen
- * Removed usage of fGetTitle_Accession
- *
- * Revision 1.7 2002/05/06 03:28:53 vakatov
- * OM/OM1 renaming
- *
- * Revision 1.6 2002/03/27 22:08:46 ucko
- * Use high-level GB loader instead of low-level ID1 reader.
- *
- * Revision 1.5 2002/02/21 19:27:08 grichenk
- * Rearranged includes. Added scope history. Added searching for the
- * best seq-id match in data sources and scopes. Updated tests.
- *
- * Revision 1.4 2002/01/29 18:21:07 grichenk
- * CScope::GetTitle() -> CBioseq_Handle::GetTitle()
- *
- * Revision 1.3 2002/01/23 21:59:34 grichenk
- * Redesigned seq-id handles and mapper
- *
- * Revision 1.2 2002/01/15 21:36:41 grichenk
- * Fixed to work with the new OM and scopes
- *
- * Revision 1.1 2002/01/11 19:06:28 gouriano
- * restructured objmgr
- *
- * Revision 1.4 2001/12/07 19:39:19 butanaev
- * Minor code improvements.
- *
- * Revision 1.3 2001/12/07 16:43:35 butanaev
- * Switching to new reader interfaces.
- *
- * Revision 1.2 2001/10/17 20:51:54 ucko
- * Pass flags to GetTitle.
- *
- * Revision 1.1 2001/10/12 21:20:37 ucko
- * Add test for CScope::GetTitle
- *
- * ===========================================================================
- */