genbank_formatter.hpp

ncbi源码

/*
 * ===========================================================================
 * 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 */