flat_gbseq_formatter.hpp

ncbi源码

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