reader_id1.cpp

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    out << id1_request;
    out.Flush();
}


void CId1Reader::x_ReadTSEBlob(CID1server_back& id1_reply,
                               const CSeqref& /*seqref*/,
                               CNcbiIstream& stream)
{
    CObjectIStreamAsnBinary obj_stream(stream);
    
    x_ReadTSEBlob(id1_reply, obj_stream);
}


void CId1Reader::x_ReadTSEBlob(CID1server_back& id1_reply,
                               CObjectIStream& stream)
{
    CReader::SetSeqEntryReadHooks(stream);

    stream >> id1_reply;

#ifdef ID1_COLLECT_STATS
    last_object_bytes = stream.GetStreamOffset();
#endif
}


void CId1Reader::x_ReadSNPAnnot(CSeq_annot_SNP_Info& snp_info,
                                const CSeqref& /*seqref*/,
                                CByteSourceReader& reader)
{
    CObjectIStreamAsnBinary in(reader);

    CSeq_annot_SNP_Info_Reader::Parse(in, snp_info);

#ifdef ID1_COLLECT_STATS
    last_object_bytes = in.GetStreamOffset();
#endif
}


END_SCOPE(objects)

const string kId1ReaderDriverName("id1_reader");


/// Class factory for ID1 reader
///
/// @internal
///
class CId1ReaderCF : 
    public CSimpleClassFactoryImpl<objects::CReader, objects::CId1Reader>
{
public:
    typedef 
      CSimpleClassFactoryImpl<objects::CReader, objects::CId1Reader> TParent;
public:
    CId1ReaderCF() : TParent(kId1ReaderDriverName, 0)
    {
    }
    ~CId1ReaderCF()
    {
    }
};

void NCBI_EntryPoint_Id1Reader(
     CPluginManager<objects::CReader>::TDriverInfoList&   info_list,
     CPluginManager<objects::CReader>::EEntryPointRequest method)
{
    CHostEntryPointImpl<CId1ReaderCF>::NCBI_EntryPointImpl(info_list, method);
}



END_NCBI_SCOPE


/*
 * $Log: reader_id1.cpp,v $
 * Revision 1000.1  2004/06/01 19:41:56  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.81
 *
 * Revision 1.81  2004/05/21 21:42:52  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.80  2004/03/16 17:49:18  vasilche
 * Use enum constant for TRACE_CHGR entries
 *
 * Revision 1.79  2004/03/16 15:47:29  vasilche
 * Added CBioseq_set_Handle and set of EditHandles
 *
 * Revision 1.78  2004/03/05 17:43:52  dicuccio
 * Added support for satellite 31: TRACE_CHGR
 *
 * Revision 1.77  2004/03/03 22:59:47  ucko
 * Gracefully handle CNcbiApplication::Instance returning NULL, as it
 * *is* possible to use other frameworks.
 *
 * Revision 1.76  2004/02/19 19:24:09  vasilche
 * Added conditional compilation of statistics collection code.
 *
 * Revision 1.75  2004/02/19 17:06:57  dicuccio
 * Use sat, sat-key in seq-ref, not sat-key, sat
 *
 * Revision 1.74  2004/02/18 14:01:25  dicuccio
 * Added new satellites for TRACE_ASSM, TR_ASSM_CH.  Added support for overloading
 * the ID1 named service
 *
 * Revision 1.73  2004/02/04 17:47:41  kuznets
 * Fixed naming of entry points
 *
 * Revision 1.72  2004/01/28 20:53:43  vasilche
 * Added CSplitParser::Attach().
 *
 * Revision 1.71  2004/01/22 20:53:30  vasilche
 * Fixed include path.
 *
 * Revision 1.70  2004/01/22 20:10:36  vasilche
 * 1. Splitted ID2 specs to two parts.
 * ID2 now specifies only protocol.
 * Specification of ID2 split data is moved to seqsplit ASN module.
 * For now they are still reside in one resulting library as before - libid2.
 * As the result split specific headers are now in objects/seqsplit.
 * 2. Moved ID2 and ID1 specific code out of object manager.
 * Protocol is processed by corresponding readers.
 * ID2 split parsing is processed by ncbi_xreader library - used by all readers.
 * 3. Updated OBJMGR_LIBS correspondingly.
 *
 * Revision 1.69  2004/01/13 21:54:49  vasilche
 * Requrrected new version
 *
 * Revision 1.5  2004/01/13 16:55:56  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 1.4  2003/12/30 22:14:42  vasilche
 * Updated genbank loader and readers plugins.
 *
 * Revision 1.67  2003/12/30 16:00:24  vasilche
 * Added support for new ICache (CBDB_Cache) interface.
 *
 * Revision 1.66  2003/12/19 19:47:44  vasilche
 * Added support for TRACE data, Seq-id ::= general { db "ti", tag id NNN }.
 *
 * Revision 1.65  2003/12/03 14:30:02  kuznets
 * Code clean up.
 * Made use of driver name constant instead of immediate in-place string.
 *
 * Revision 1.64  2003/12/02 16:18:16  kuznets
 * Added plugin manager support for CReader interface and implementaions
 * (id1 reader, pubseq reader)
 *
 * Revision 1.63  2003/11/26 17:55:59  vasilche
 * Implemented ID2 split in ID1 cache.
 * Fixed loading of splitted annotations.
 *
 * Revision 1.62  2003/11/21 16:32:52  vasilche
 * Cleaned code avoiding ERROR 0 packets.
 *
 * Revision 1.61  2003/11/19 15:43:03  vasilche
 * Temporary fix for extra ERROR 0 packed from ID1 server.
 *  CVS: ----------------------------------------------------------------------
 *
 * Revision 1.60  2003/11/07 16:59:01  vasilche
 * Fixed stats message.
 *
 * Revision 1.59  2003/11/04 21:53:32  vasilche
 * Check only SNP bit in extfeat field in ID1 response.
 *
 * Revision 1.58  2003/10/27 18:50:49  vasilche
 * Detect 'private' blobs in ID1 reader.
 * Avoid reconnecting after ID1 server replied with error packet.
 *
 * Revision 1.57  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 1.56  2003/10/24 13:27:40  vasilche
 * Cached ID1 reader made more safe. Process errors and exceptions correctly.
 * Cleaned statistics printing methods.
 *
 * Revision 1.55  2003/10/22 16:36:25  vasilche
 * Fixed typo.
 *
 * Revision 1.54  2003/10/22 16:32:42  vasilche
 * MSVC forces to use stream::bad() method.
 *
 * Revision 1.53  2003/10/22 16:12:38  vasilche
 * Added CLoaderException::eNoConnection.
 * Added check for 'fail' state of ID1 connection stream.
 * CLoaderException::eNoConnection will be rethrown from CGBLoader.
 *
 * Revision 1.52  2003/10/21 16:32:50  vasilche
 * Cleaned ID1 statistics messages.
 * Now by setting GENBANK_ID1_STATS=1 CId1Reader collects and displays stats.
 * And by setting GENBANK_ID1_STATS=2 CId1Reader logs all activities.
 *
 * Revision 1.51  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 1.50  2003/10/14 21:06:25  vasilche
 * Fixed compression statistics.
 * Disabled caching of SNP blobs.
 *
 * Revision 1.49  2003/10/14 18:59:55  vasilche
 * Temporarily remove collection of compression statistics.
 *
 * Revision 1.48  2003/10/14 18:31:54  vasilche
 * Added caching support for SNP blobs.
 * Added statistics collection of ID1 connection.
 *
 * Revision 1.47  2003/10/08 14:16:13  vasilche
 * Added version of blobs loaded from ID1.
 *
 * Revision 1.46  2003/10/01 18:08:14  kuznets
 * s_SkipBytes renamed to Id1ReaderSkipBytes (made non static)
 *
 * Revision 1.45  2003/09/30 19:38:26  vasilche
 * Added support for cached id1 reader.
 *
 * Revision 1.44  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 1.43  2003/08/27 14:25:22  vasilche
 * Simplified CCmpTSE class.
 *
 * Revision 1.42  2003/08/19 18:34:40  vasilche
 * Fixed warning about enum conversion.
 *
 * Revision 1.41  2003/08/14 20:05:19  vasilche
 * Simple SNP features are stored as table internally.
 * They are recreated when needed using CFeat_CI.
 *
 * Revision 1.40  2003/07/24 19:28:09  vasilche
 * Implemented SNP split for ID1 loader.
 *
 * Revision 1.39  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 1.38  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 1.37  2003/05/13 20:14:40  vasilche
 * Catching exceptions and reconnection were moved from readers to genbank loader.
 *
 * Revision 1.36  2003/04/24 16:12:38  vasilche
 * Object manager internal structures are splitted more straightforward.
 * Removed excessive header dependencies.
 *
 * Revision 1.35  2003/04/15 15:30:15  vasilche
 * Added include <memory> when needed.
 * Removed buggy buffer in printing methods.
 * Removed unnecessary include of stream_util.hpp.
 *
 * Revision 1.34  2003/04/15 14:24:08  vasilche
 * Changed CReader interface to not to use fake streams.
 *
 * Revision 1.33  2003/04/07 16:56:57  vasilche
 * Fixed unassigned member in ID1 request.
 *
 * Revision 1.32  2003/03/31 17:02:03  lavr
 * Some code reformatting to [more closely] meet coding requirements
 *
 * Revision 1.31  2003/03/30 07:00:29  lavr
 * MIPS-specific workaround for lame-designed stream read ops
 *
 * Revision 1.30  2003/03/28 03:28:14  lavr
 * CId1Reader::xsgetn() added; code heavily reformatted
 *
 * Revision 1.29  2003/03/27 19:38:13  vasilche
 * Use safe NStr::IntToString() instead of sprintf().
 *
 * Revision 1.28  2003/03/03 20:34:51  vasilche
 * Added NCBI_THREADS macro - it's opposite to NCBI_NO_THREADS.
 * Avoid using _REENTRANT macro - use NCBI_THREADS instead.
 *
 * Revision 1.27  2003/03/01 22:26:56  kimelman
 * performance fixes
 *
 * Revision 1.26  2003/02/04 18:53:36  dicuccio
 * Include file clean-up
 *
 * Revision 1.25  2002/12/26 20:53:25  dicuccio
 * Minor tweaks to relieve compiler warnings in MSVC
 *
 * Revision 1.24  2002/12/26 16:39:24  vasilche
 * Object manager class CSeqMap rewritten.
 *
 * Revision 1.23  2002/11/18 19:48:43  grichenk
 * Removed "const" from datatool-generated setters
 *
 * Revision 1.22  2002/07/25 15:01:51  grichenk
 * Replaced non-const GetXXX() with SetXXX()
 *
 * Revision 1.21  2002/05/09 21:40:59  kimelman
 * MT tuning
 *
 * Revision 1.20  2002/05/06 03:28:47  vakatov
 * OM/OM1 renaming
 *
 * Revision 1.19  2002/05/03 21:28:10  ucko
 * Introduce T(Signed)SeqPos.
 *
 * Revision 1.18  2002/04/17 19:52:02  kimelman
 * fix: no gi found
 *
 * Revision 1.17  2002/04/09 16:10:56  ucko
 * Split CStrStreamBuf out into a common location.
 *
 * Revision 1.16  2002/04/08 20:52:26  butanaev
 * Added PUBSEQ reader.
 *
 * Revision 1.15  2002/03/29 02:47:05  kimelman
 * gbloader: MT scalability fixes
 *
 * Revision 1.14  2002/03/27 20:23:50  butanaev
 * Added connection pool.
 *
 * Revision 1.13  2002/03/26 23:31:08  gouriano
 * memory leaks and garbage collector fix
 *
 * Revision 1.12  2002/03/26 18:48:58  butanaev
 * Fixed bug not deleting streambuf.
 *
 * Revision 1.11  2002/03/26 17:17:02  kimelman
 * reader stream fixes
 *
 * Revision 1.10  2002/03/26 15:39:25  kimelman
 * GC fixes
 *
 * Revision 1.9  2002/03/25 18:12:48  grichenk
 * Fixed bool convertion
 *
 * Revision 1.8  2002/03/25 17:49:13  kimelman
 * ID1 failure handling
 *
 * Revision 1.7  2002/03/25 15:44:47  kimelman
 * proper logging and exception handling
 *
 * Revision 1.6  2002/03/22 21:50:21  kimelman
 * bugfix: avoid history rtequest for nonexistent sequence
 *
 * Revision 1.5  2002/03/21 19:14:54  kimelman
 * GB related bugfixes
 *
 * Revision 1.4  2002/03/21 01:34:55  kimelman
 * gbloader related bugfixes
 *
 * Revision 1.3  2002/03/20 04:50:13  kimelman
 * GB loader added
 *
 * Revision 1.2  2002/01/16 18:56:28  grichenk
 * Removed CRef<> argument from choice variant setter, updated sources to
 * use references instead of CRef<>s
 *
 * Revision 1.1  2002/01/11 19:06:22  gouriano
 * restructured objmgr
 *
 * Revision 1.7  2001/12/17 21:38:24  butanaev
 * Code cleanup.
 *
 * 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 20:08:02  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 16:10:23  butanaev
 * Switching to new reader interfaces.
 *
 * Revision 1.3  2001/12/06 20:37:05  butanaev
 * Fixed timeout problem.
 *
 * Revision 1.2  2001/12/06 18:06:22  butanaev
 * Ported to linux.
 *
 * Revision 1.1  2001/12/06 14:35:23  butanaev
 * New streamable interfaces designed, ID1 reimplemented.
 *
 */