flatten_asn.cpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: flatten_asn.cpp,v $
- * PRODUCTION Revision 1000.2 2004/06/01 19:43:37 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: flatten_asn.cpp,v 1000.2 2004/06/01 19:43:37 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.
- *
- * ===========================================================================
- *
- * Author: Aaron Ucko, NCBI
- *
- * File Description:
- * new (early 2003) flat-file generator -- sample application
- *
- * ===========================================================================
- */
- #include <ncbi_pch.hpp>
- #include <corelib/ncbiapp.hpp>
- #include <serial/objistr.hpp>
- #include <serial/serial.hpp>
- #include <objects/seqset/Seq_entry.hpp>
- #include <objtools/data_loaders/genbank/gbloader.hpp>
- #include <objmgr/object_manager.hpp>
- #include <objmgr/scope.hpp>
- #include <objtools/flat/flat_gbseq_formatter.hpp>
- #include <objtools/flat/flat_gff_formatter.hpp>
- BEGIN_NCBI_SCOPE
- USING_SCOPE(objects);
- class CFlatteningApp : public CNcbiApplication
- {
- public:
- void Init(void);
- int Run (void);
- };
- void CFlatteningApp::Init(void)
- {
- auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
- arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
- "Convert an ASN.1 Seq-entry into a flat report",
- false);
- arg_desc->AddKey("in", "InputFile", "File to read the Seq-entry from",
- CArgDescriptions::eInputFile);
- arg_desc->AddDefaultKey("format", "Format", "Output format",
- CArgDescriptions::eString, "genbank");
- SetupArgDescriptions(arg_desc.release());
- }
- int CFlatteningApp::Run(void)
- {
- const CArgs& args = GetArgs();
- CObjectManager objmgr;
- CScope scope(objmgr);
- CRef<CSeq_entry> entry(new CSeq_entry);
- {{
- auto_ptr<CObjectIStream> in
- (CObjectIStream::Open(args["in"].AsString(), eSerial_AsnText));
- *in >> *entry;
- }}
- scope.AddTopLevelSeqEntry(*entry);
- // allow external references
- objmgr.RegisterDataLoader(*new CGBDataLoader("ID"),
- CObjectManager::eDefault);
- scope.AddDefaults();
- auto_ptr<CObjectOStream> oos;
- auto_ptr<IFlatFormatter> formatter;
- {{
- const string& format = args["format"].AsString();
- IFlatFormatter::EMode mode = IFlatFormatter::eMode_Dump;
- if ( !NStr::CompareNocase(format, "gbseq") ) {
- oos.reset(CObjectOStream::Open(eSerial_Xml, cout));
- formatter.reset(new CFlatGBSeqFormatter(*oos, scope, mode));
- } else if ( !NStr::CompareNocase(format, "gff") ) {
- formatter.reset(new CFlatGFFFormatter
- (*new CFlatTextOStream(cout), scope, mode,
- CFlatGFFFormatter::fGTFCompat));
- } else {
- IFlatFormatter::EDatabase db;
- if ( !NStr::CompareNocase(format, "genbank") ) {
- db = IFlatFormatter::eDB_NCBI;
- } else if ( !NStr::CompareNocase(format, "embl") ) {
- db = IFlatFormatter::eDB_EMBL;
- } else if ( !NStr::CompareNocase(format, "ddbj") ) {
- db = IFlatFormatter::eDB_DDBJ;
- } else {
- ERR_POST(Fatal << "Bad output format " << format);
- }
- formatter.reset(CFlatTextFormatter::New
- (*new CFlatTextOStream(cout), scope, mode, db));
- }
- }}
- formatter->Format(*entry, *formatter);
- return 0;
- }
- END_NCBI_SCOPE
- USING_NCBI_SCOPE;
- int main(int argc, const char** argv)
- {
- return CFlatteningApp().AppMain(argc, argv);
- }
- /*
- * ===========================================================================
- *
- * $Log: flatten_asn.cpp,v $
- * Revision 1000.2 2004/06/01 19:43:37 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
- *
- * Revision 1.6 2004/05/21 21:42:54 gorelenk
- * Added PCH ncbi_pch.hpp
- *
- * Revision 1.5 2004/01/07 17:37:38 vasilche
- * Fixed include path to genbank loader.
- * Moved split_cache application.
- *
- * Revision 1.4 2003/10/17 20:59:33 ucko
- * Enable the GenBank loader to deal with external references.
- *
- * Revision 1.3 2003/10/08 21:12:04 ucko
- * Support gtf format
- *
- * Revision 1.2 2003/06/02 16:06:42 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 1.1 2003/03/10 16:39:09 ucko
- * Initial check-in of new flat-file generator
- *
- *
- * ===========================================================================
- */