genbank_formatter.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: genbank_formatter.hpp,v $
- * PRODUCTION Revision 1000.1 2004/06/01 19:38:52 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
- * PRODUCTION
- * ===========================================================================
- */
- #ifndef OBJTOOLS_FORMAT___GENBANK_FORMATTER__HPP
- #define OBJTOOLS_FORMAT___GENBANK_FORMATTER__HPP
- /* $Id: genbank_formatter.hpp,v 1000.1 2004/06/01 19:38:52 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
- * Mati Shomrat
- *
- * File Description:
- * new (early 2003) flat-file generator -- base class for items
- * (which roughly correspond to blocks/paragraphs in the C version)
- *
- */
- #include <corelib/ncbistd.hpp>
- #include <objtools/format/item_formatter.hpp>
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(objects)
- class CLocusItem;
- class CDeflineItem;
- class CAccessionItem;
- class CVersionItem;
- class CKeywordsItem;
- class CSourceItem;
- class CReferenceItem;
- class CCommentItem;
- class CFeatHeaderItem;
- class CBaseCountItem;
- class CSequenceItem;
- class CPrimaryItem;
- class CSegmentItem;
- class IFlattishFeature;
- class CContigItem;
- class CWGSItem;
- class CGenomeItem;
- class CFlatTextOStream;
- class CDateItem;
- class CDBSourceItem;
- class CBioseqContext;
- class COriginItem;
- class CGenbankFormatter : public CFlatItemFormatter
- {
- public:
- CGenbankFormatter(void);
- virtual SIZE_TYPE GetWidth(void) const { return 79; }
- virtual void EndSection(const CEndSectionItem&, IFlatTextOStream& text_os);
- virtual void FormatLocus(const CLocusItem& locus, IFlatTextOStream& text_os);
- virtual void FormatDefline(const CDeflineItem& defline, IFlatTextOStream& text_os);
- virtual void FormatAccession(const CAccessionItem& acc, IFlatTextOStream& text_os);
- virtual void FormatVersion(const CVersionItem& version, IFlatTextOStream& text_os);
- virtual void FormatKeywords(const CKeywordsItem& keys, IFlatTextOStream& text_os);
- virtual void FormatSource(const CSourceItem& source, IFlatTextOStream& text_os);
- virtual void FormatReference(const CReferenceItem& keys, IFlatTextOStream& text_os);
- virtual void FormatComment(const CCommentItem& keys, IFlatTextOStream& text_os);
- virtual void FormatBasecount(const CBaseCountItem& bc, IFlatTextOStream& text_os);
- virtual void FormatSequence(const CSequenceItem& seq, IFlatTextOStream& text_os);
- virtual void FormatFeatHeader(const CFeatHeaderItem& fh, IFlatTextOStream& text_os);
- virtual void FormatFeature(const CFeatureItemBase& feat, IFlatTextOStream& text_os);
- virtual void FormatSegment(const CSegmentItem& seg, IFlatTextOStream& text_os);
- virtual void FormatDBSource(const CDBSourceItem& dbs, IFlatTextOStream& text_os);
- virtual void FormatPrimary(const CPrimaryItem& prim, IFlatTextOStream& text_os);
- virtual void FormatContig(const CContigItem& contig, IFlatTextOStream& text_os);
- virtual void FormatWGS(const CWGSItem& wgs, IFlatTextOStream& text_os);
- virtual void FormatGenome(const CGenomeItem& genome, IFlatTextOStream& text_os);
- virtual void FormatOrigin(const COriginItem& origin, IFlatTextOStream& text_os);
- private:
- // source
- void x_FormatSourceLine(list<string>& l, const CSourceItem& source) const;
- void x_FormatOrganismLine(list<string>& l, const CSourceItem& source) const;
- // reference
- void x_Reference(list<string>& l, const CReferenceItem& ref, CBioseqContext& ctx) const;
- void x_Authors(list<string>& l, const CReferenceItem& ref, CBioseqContext& ctx) const;
- void x_Consortium(list<string>& l, const CReferenceItem& ref, CBioseqContext& ctx) const;
- void x_Title(list<string>& l, const CReferenceItem& ref, CBioseqContext& ctx) const;
- void x_Journal(list<string>& l, const CReferenceItem& ref, CBioseqContext& ctx) const;
- void x_Medline(list<string>& l, const CReferenceItem& ref, CBioseqContext& ctx) const;
- void x_Pubmed(list<string>& l, const CReferenceItem& ref, CBioseqContext& ctx) const;
- void x_Remark(list<string>& l, const CReferenceItem& ref, CBioseqContext& ctx) const;
- };
- END_SCOPE(objects)
- END_NCBI_SCOPE
- /*
- * ===========================================================================
- *
- * $Log: genbank_formatter.hpp,v $
- * Revision 1000.1 2004/06/01 19:38:52 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
- *
- * Revision 1.4 2004/04/22 15:45:27 shomrat
- * Changes in context
- *
- * Revision 1.3 2004/02/19 17:58:41 shomrat
- * Added method to format Origin item
- *
- * Revision 1.2 2004/01/14 15:54:28 shomrat
- * const removed
- *
- * Revision 1.1 2003/12/17 19:53:06 shomrat
- * Initial revision (adapted from flat lib)
- *
- *
- * ===========================================================================
- */
- #endif /* OBJTOOLS_FORMAT___GENBANK_FORMATTER__HPP */