seqref_pubseq.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: seqref_pubseq.hpp,v $
 * PRODUCTION Revision 1000.0  2004/04/12 17:38:22  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [CATCHUP_003] Dev-tree R1.2
 * PRODUCTION
 * ===========================================================================
 */

#ifndef SEQREF_PUBSEQ__HPP_INCLUDED
#define SEQREF_PUBSEQ__HPP_INCLUDED

/*  $Id: seqref_pubseq.hpp,v 1000.0 2004/04/12 17:38:22 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:  Anton Butanaev, Eugene Vasilchenko
*
*  File Description: support classes for data reader from Pubseq_OS
*
*/

#include <corelib/ncbiobj.hpp>

#include <serial/serial.hpp>
#include <serial/enumvalues.hpp>
#include <serial/objistrasnb.hpp>
#include <serial/objostrasnb.hpp>

#include <util/bytesrc.hpp>

#include <dbapi/driver/public.hpp>

#include <memory>


BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)

class NCBI_XREADER_PUBSEQOS_EXPORT CResultBtSrcRdr : public CByteSourceReader
{
public:
    CResultBtSrcRdr(CDB_Result* result);
    ~CResultBtSrcRdr();

    virtual size_t Read(char* buffer, size_t bufferLength);

private:
    CDB_Result* m_Result;
};


END_SCOPE(objects)
END_NCBI_SCOPE


/*
* $Log: seqref_pubseq.hpp,v $
* Revision 1000.0  2004/04/12 17:38:22  gouriano
* PRODUCTION: IMPORTED [CATCHUP_003] Dev-tree R1.2
*
* Revision 1.2  2004/01/13 16:55:54  vasilche
* CReader, CSeqref and some more classes moved from xobjmgr to separate lib.
* Headers moved from include/objmgr to include/objtools/data_loaders/genbank.
*
* Revision 1.1  2003/12/30 22:14:41  vasilche
* Updated genbank loader and readers plugins.
*
* Revision 1.11  2003/10/21 14:27:35  vasilche
* Added caching of gi -> sat,satkey,version resolution.
* SNP blobs are stored in cache in preprocessed format (platform dependent).
* Limit number of connections to GenBank servers.
* Added collection of ID1 loader statistics.
*
* Revision 1.10  2003/09/30 16:22:01  vasilche
* Updated internal object manager classes to be able to load ID2 data.
* SNP blobs are loaded as ID2 split blobs - readers convert them automatically.
* Scope caches results of requests for data to data loaders.
* Optimized CSeq_id_Handle for gis.
* Optimized bioseq lookup in scope.
* Reduced object allocations in annotation iterators.
* CScope is allowed to be destroyed before other objects using this scope are
* deleted (feature iterators, bioseq handles etc).
* Optimized lookup for matching Seq-ids in CSeq_id_Mapper.
* Added 'adaptive' option to objmgr_demo application.
*
* Revision 1.9  2003/08/27 14:24:43  vasilche
* Simplified CCmpTSE class.
*
* Revision 1.8  2003/08/14 20:05:18  vasilche
* Simple SNP features are stored as table internally.
* They are recreated when needed using CFeat_CI.
*
* Revision 1.7  2003/07/24 20:36:48  vasilche
* Fixed includes.
*
* Revision 1.6  2003/07/24 19:28:08  vasilche
* Implemented SNP split for ID1 loader.
*
* Revision 1.5  2003/07/17 20:07:55  vasilche
* Reduced memory usage by feature indexes.
* SNP data is loaded separately through PUBSEQ_OS.
* String compression for SNP data.
*
* Revision 1.4  2003/06/02 16:01:37  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  2003/04/15 16:31:37  dicuccio
* Placed CResultBtSrcRdr in XOBJMGR Win32 export namespace (was
* erroneously in XUTIL)
*
* Revision 1.2  2003/04/15 15:30:14  vasilche
* Added include <memory> when needed.
* Removed buggy buffer in printing methods.
* Removed unnecessary include of stream_util.hpp.
*
* Revision 1.1  2003/04/15 14:24:08  vasilche
* Changed CReader interface to not to use fake streams.
*
*/

#endif // SEQREF_PUBSEQ__HPP_INCLUDED