seqref.cpp

来自「ncbi源码」· C++ 代码 · 共 246 行

/*
 * ===========================================================================
 * PRODUCTION $Log: seqref.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 19:41:46  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.2
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: seqref.cpp,v 1000.1 2004/06/01 19:41:46 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:  Eugene Vasilchenko
 *
 *  File Description: Base data reader interface
 *
 */

#include <ncbi_pch.hpp>
#include <objtools/data_loaders/genbank/seqref.hpp>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)

CSeqref::CSeqref(void)
    : m_Flags(fHasAllLocal),
      m_Gi(0), m_Sat(0), m_SatKey(0),
      m_Version(0)
{
}


CSeqref::CSeqref(int gi, int sat, int satkey)
    : m_Flags(fHasAllLocal),
      m_Gi(gi), m_Sat(sat), m_SatKey(satkey),
      m_Version(0)
{
}


CSeqref::~CSeqref(void)
{
}


const string CSeqref::print(void) const
{
    CNcbiOstrstream ostr;
    ostr << "SeqRef("<<GetSat()<<','<<GetSatKey()<<','<<GetGi()<<')';
    return CNcbiOstrstreamToString(ostr);
}


const string CSeqref::printTSE(void) const
{
    CNcbiOstrstream ostr;
    ostr << "TSE(" << GetSat() << ',' << GetSatKey() << ')';
    return CNcbiOstrstreamToString(ostr);
}


const string CSeqref::printTSE(const TKeyByTSE& key)
{
    CNcbiOstrstream ostr;
    ostr << "TSE(" << key.first << ',' << key.second << ')';
    return CNcbiOstrstreamToString(ostr);
}


END_SCOPE(objects)
END_NCBI_SCOPE


/*
 * $Log: seqref.cpp,v $
 * Revision 1000.1  2004/06/01 19:41:46  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.2
 *
 * Revision 1.2  2004/05/21 21:42:52  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.1  2004/01/13 16:55:55  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 1.27  2003/11/28 17:53:15  vasilche
 * Avoid calling CStreamUtils::Pushback() when constructing objects from text ASN.
 *
 * Revision 1.26  2003/11/26 17:55:58  vasilche
 * Implemented ID2 split in ID1 cache.
 * Fixed loading of splitted annotations.
 *
 * Revision 1.25  2003/10/27 15:05:41  vasilche
 * Added correct recovery of cached ID1 loader if gi->sat/satkey cache is invalid.
 * Added recognition of ID1 error codes: private, etc.
 * Some formatting of old code.
 *
 * Revision 1.24  2003/10/08 14:16:13  vasilche
 * Added version of blobs loaded from ID1.
 *
 * Revision 1.23  2003/10/07 13:43:23  vasilche
 * Added proper handling of named Seq-annots.
 * Added feature search from named Seq-annots.
 * Added configurable adaptive annotation search (default: gene, cds, mrna).
 * Fixed selection of blobs for loading from GenBank.
 * Added debug checks to CSeq_id_Mapper for easier finding lost CSeq_id_Handles.
 * Fixed leaked split chunks annotation stubs.
 * Moved some classes definitions in separate *.cpp files.
 *
 * Revision 1.22  2003/09/30 16:22:02  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 1.21  2003/08/27 14:25:22  vasilche
 * Simplified CCmpTSE class.
 *
 * Revision 1.20  2003/08/19 18:35:21  vasilche
 * CPackString classes were moved to SERIAL library.
 *
 * Revision 1.19  2003/08/14 20:05:19  vasilche
 * Simple SNP features are stored as table internally.
 * They are recreated when needed using CFeat_CI.
 *
 * Revision 1.18  2003/07/24 19:28:09  vasilche
 * Implemented SNP split for ID1 loader.
 *
 * Revision 1.17  2003/07/17 20:07:56  vasilche
 * Reduced memory usage by feature indexes.
 * SNP data is loaded separately through PUBSEQ_OS.
 * String compression for SNP data.
 *
 * Revision 1.16  2003/06/02 16:06:38  dicuccio
 * Rearranged src/objects/ subtree.  This includes the following shifts:
 *     - src/objects/asn2asn --> arc/app/asn2asn
 *     - src/objects/testmedline --> src/objects/ncbimime/test
 *     - src/objects/objmgr --> src/objmgr
 *     - src/objects/util --> src/objmgr/util
 *     - src/objects/alnmgr --> src/objtools/alnmgr
 *     - src/objects/flat --> src/objtools/flat
 *     - src/objects/validator --> src/objtools/validator
 *     - src/objects/cddalignview --> src/objtools/cddalignview
 * In addition, libseq now includes six of the objects/seq... libs, and libmmdb
 * replaces the three libmmdb? libs.
 *
 * Revision 1.15  2003/04/24 16:12:38  vasilche
 * Object manager internal structures are splitted more straightforward.
 * Removed excessive header dependencies.
 *
 * Revision 1.14  2003/04/15 16:25:39  vasilche
 * Added initialization of int members.
 *
 * Revision 1.13  2003/04/15 14:24:08  vasilche
 * Changed CReader interface to not to use fake streams.
 *
 * Revision 1.12  2003/03/28 03:27:24  lavr
 * CIStream::Eof() conditional compilation removed; code reformatted
 *
 * Revision 1.11  2003/03/26 22:12:11  lavr
 * Revert CIStream::Eof() to destructive test
 *
 * Revision 1.10  2003/03/26 20:42:50  lavr
 * CIStream::Eof() made (temporarily) non-destructive w/o get()
 *
 * Revision 1.9  2003/02/26 18:02:39  vasilche
 * Added istream error check.
 * Avoid use of string::c_str() method.
 *
 * Revision 1.8  2003/02/25 22:03:44  vasilche
 * Fixed identation.
 *
 * Revision 1.7  2002/11/27 21:09:43  lavr
 * Take advantage of CStreamUtils::Readsome() in CIStream::Read()
 * CIStream::Eof() modified to use get() instead of operator>>()
 *
 * Revision 1.6  2002/05/06 03:28:47  vakatov
 * OM/OM1 renaming
 *
 * Revision 1.5  2002/03/27 20:23:50  butanaev
 * Added connection pool.
 *
 * Revision 1.4  2002/03/27 18:06:08  kimelman
 * stream.read/write instead of << >>
 *
 * Revision 1.3  2002/03/21 19:14:54  kimelman
 * GB related bugfixes
 *
 * Revision 1.2  2002/03/20 04:50:13  kimelman
 * GB loader added
 *
 * Revision 1.1  2002/01/11 19:06:21  gouriano
 * restructured objmgr
 *
 * Revision 1.6  2001/12/13 00:19:25  kimelman
 * bugfixes:
 *
 * Revision 1.5  2001/12/12 21:46:40  kimelman
 * Compare interface fix
 *
 * Revision 1.4  2001/12/10 20:08:01  butanaev
 * Code cleanup.
 *
 * Revision 1.3  2001/12/07 21:24:59  butanaev
 * Interface development, code beautyfication.
 *
 * Revision 1.2  2001/12/07 16:43:58  butanaev
 * Fixed includes.
 *
 * Revision 1.1  2001/12/07 16:10:22  butanaev
 * Switching to new reader interfaces.
 *
 * Revision 1.2  2001/12/06 18:06:22  butanaev
 * Ported to linux.
 *
 * Revision 1.1  2001/12/06 14:35:22  butanaev
 * New streamable interfaces designed, ID1 reimplemented.
 *
 */