flat_gbseq_formatter.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: flat_gbseq_formatter.hpp,v $
- * PRODUCTION Revision 1000.0 2003/10/29 20:59:05 gouriano
- * PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.5
- * PRODUCTION
- * ===========================================================================
- */
- #ifndef OBJECTS_FLAT___FLAT_GBSEQ_FORMATTER__HPP
- #define OBJECTS_FLAT___FLAT_GBSEQ_FORMATTER__HPP
- /* $Id: flat_gbseq_formatter.hpp,v 1000.0 2003/10/29 20:59:05 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 -- GBSeq output
- *
- */
- #include <objtools/flat/flat_formatter.hpp>
- #include <serial/objostr.hpp>
- #include <objects/gbseq/GBSeq.hpp>
- #include <objects/gbseq/GBSet.hpp>
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(objects)
- class NCBI_FLAT_EXPORT CFlatGBSeqFormatter : public IFlatFormatter
- {
- public:
- // populates a GBSet, but does not send it anywhere
- CFlatGBSeqFormatter(CScope& scope, EMode mode,
- EStyle style = eStyle_Normal, TFlags flags = 0)
- : IFlatFormatter(scope, mode, style, flags), m_Set(new CGBSet),
- m_Out(0) { }
- // for automatic seq-by-seq output
- CFlatGBSeqFormatter(CObjectOStream& out, CScope& scope, EMode mode,
- EStyle style = eStyle_Normal, TFlags flags = 0);
- ~CFlatGBSeqFormatter();
- const CGBSet& GetGBSet(void) const { return *m_Set; }
- protected:
- EDatabase GetDatabase(void) const { return eDB_NCBI; }
- void BeginSequence (CFlatContext& context);
- void FormatHead (const CFlatHead& head);
- void FormatKeywords (const CFlatKeywords& keys);
- void FormatSegment (const CFlatSegment& seg);
- void FormatSource (const CFlatSource& source);
- void FormatReference (const CFlatReference& ref);
- void FormatComment (const CFlatComment& comment);
- void FormatPrimary (const CFlatPrimary& prim); // TPAs
- void FormatFeatHeader(const CFlatFeatHeader& /* fh */) { }
- void FormatFeature (const IFlattishFeature& f);
- void FormatDataHeader(const CFlatDataHeader& /* dh */) { }
- void FormatData (const CFlatData& data);
- // alternatives to DataHeader + Data...
- void FormatContig (const CFlatContig& contig);
- // no (current) representation for these two:
- void FormatWGSRange (const CFlatWGSRange& /* range */) { }
- void FormatGenomeInfo(const CFlatGenomeInfo& /* g */) { } // NS_*
- void EndSequence (void);
- private:
- CRef<CGBSet> m_Set;
- CRef<CGBSeq> m_Seq;
- CObjectOStream* m_Out;
- };
- END_SCOPE(objects)
- END_NCBI_SCOPE
- /*
- * ===========================================================================
- *
- * $Log: flat_gbseq_formatter.hpp,v $
- * Revision 1000.0 2003/10/29 20:59:05 gouriano
- * PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.5
- *
- * Revision 1.5 2003/10/09 17:01:48 dicuccio
- * Added export specifiers
- *
- * Revision 1.4 2003/06/02 16:01:39 dicuccio
- * Rearranged include/objects/ subtree. This includes the following shifts:
- * - include/objects/alnmgr --> include/objtools/alnmgr
- * - include/objects/cddalignview --> include/objtools/cddalignview
- * - include/objects/flat --> include/objtools/flat
- * - include/objects/objmgr/ --> include/objmgr/
- * - include/objects/util/ --> include/objmgr/util/
- * - include/objects/validator --> include/objtools/validator
- *
- * Revision 1.3 2003/04/10 20:08:22 ucko
- * Arrange to pass the item as an argument to IFlatTextOStream::AddParagraph
- *
- * Revision 1.2 2003/03/21 18:47:47 ucko
- * Turn most structs into (accessor-requiring) classes; replace some
- * formerly copied fields with pointers to the original data.
- *
- * Revision 1.1 2003/03/10 16:39:08 ucko
- * Initial check-in of new flat-file generator
- *
- *
- * ===========================================================================
- */
- #endif /* OBJECTS_FLAT___FLAT_GBSEQ_FORMATTER__HPP */