genbank.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: genbank.hpp,v $
 * PRODUCTION Revision 1000.1  2003/11/18 15:46:58  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [ORIGINAL] Dev-tree R1.14
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GENBANK__HPP
#define GENBANK__HPP

/*  $Id: genbank.hpp,v 1000.1 2003/11/18 15:46:58 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
*
* File Description:
*   Code to write Genbank/Genpept flat-file records.
*/

#include <objtools/flat/flat_ncbi_formatter.hpp>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)

class NCBI_XOBJUTIL_EXPORT CGenbankWriter
{
public:
    enum EFormat {
        eFormat_Genbank,
        eFormat_Genpept
    };
    enum EVersion {
        // Genbank 127.0, to be released December 2001, will have a new
        // format for the LOCUS line, with more space for most fields.
        eVersion_pre127,
        eVersion_127 = 127
    };
    
    CGenbankWriter(CNcbiOstream& stream, CScope& scope,
                   EFormat format = eFormat_Genbank,
                   EVersion version = eVersion_127) :
        m_Formatter(*new CFlatTextOStream(stream), scope,
                    IFlatFormatter::eMode_Dump),
        m_Format(format)
        { }

    bool Write(const CSeq_entry& entry);

private:
    CFlatNCBIFormatter m_Formatter;
    EFormat            m_Format;
};


bool CGenbankWriter::Write(const CSeq_entry& entry)
{
    m_Formatter.Format
        (entry, m_Formatter,
         m_Format == eFormat_Genpept ? IFlatFormatter::fSkipNucleotides
         : IFlatFormatter::fSkipProteins);
    return true;
}

END_SCOPE(objects)
END_NCBI_SCOPE


/*
* ===========================================================================
* $Log: genbank.hpp,v $
* Revision 1000.1  2003/11/18 15:46:58  gouriano
* PRODUCTION: UPGRADED [ORIGINAL] Dev-tree R1.14
*
* Revision 1.14  2003/11/05 15:32:29  ucko
* Make Write non-const per IFlatFormatter::Format.
*
* Revision 1.13  2003/07/16 19:01:56  ucko
* Add IFlatFormatter:: where needed.
*
* Revision 1.12  2003/07/16 17:10:55  ucko
* Replace with a trivial inline wrapper around the new formatter.
*
* Revision 1.11  2003/06/02 16:01:38  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 1.10  2002/12/26 12:44:39  dicuccio
* Added Win32 export specifiers
*
* Revision 1.9  2002/10/10 17:57:36  ucko
* Make most methods const (and m_Stream consequently mutable) to keep
* WorkShop from complaining when CGenbankWriter is used as a temporary.
*
* Revision 1.8  2002/05/06 16:11:12  ucko
* Merge in Andrei Gourianov's changes to use the new OM (thanks!)
* Move CVS log to end.
*
*
* *** These two entries are from src/app/id1_fetch1/genbank1.hpp ***
* Revision 1.2  2002/05/06 03:31:52  vakatov
* OM/OM1 renaming
*
* Revision 1.1  2002/04/04 16:31:36  gouriano
* id1_fetch1 - modified version of id1_fetch, which uses objmgr1
*
* Revision 1.6  2001/12/07 18:52:02  grichenk
* Updated "#include"-s and forward declarations to work with the
* new datatool version.
*
* Revision 1.5  2001/11/02 20:54:50  ucko
* Make gbqual.hpp private; clean up cruft from genbank.hpp.
*
* Revision 1.4  2001/11/01 16:32:23  ucko
* Rework qualifier handling to support appropriate reordering
*
* Revision 1.3  2001/10/12 15:34:16  ucko
* Edit in-source version of CVS log to avoid end-of-comment marker.  (Oops.)
*
* Revision 1.2  2001/10/12 15:29:04  ucko
* Drop {src,include}/objects/util/asciiseqdata.* in favor of CSeq_vector.
* Rewrite GenBank output code to take fuller advantage of the object manager.
*
* Revision 1.1  2001/09/25 20:12:04  ucko
* More cleanups from Denis.
* Put utility code in the objects namespace.
* Moved utility code to {src,include}/objects/util (to become libxobjutil).
* Moved static members of CGenbankWriter to above their first use.
* ===========================================================================
*/
#endif  /* GENBANK__HPP */