src/objtools/data_loaders/genbank/id1/reader_id1.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbi_param.hpp>
#include <objtools/data_loaders/genbank/id1/reader_id1.hpp>
#include <objtools/data_loaders/genbank/id1/reader_id1_entry.hpp>
#include <objtools/data_loaders/genbank/id1/reader_id1_params.h>
#include <objtools/data_loaders/genbank/readers.hpp>
#include <objtools/data_loaders/genbank/dispatcher.hpp>
#include <objtools/data_loaders/genbank/request_result.hpp>
#include <objtools/error_codes.hpp>
#include <objmgr/objmgr_exception.hpp>
#include <objmgr/impl/tse_info.hpp>
#include <objmgr/impl/tse_chunk_info.hpp>
#include <objmgr/annot_selector.hpp>
#include <corelib/ncbimtx.hpp>
#include <corelib/plugin_manager_impl.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/id1/id1__.hpp>
#include <serial/objistrasnb.hpp>
#include <serial/objostrasnb.hpp>
#include <serial/serial.hpp>
#include <connect/ncbi_conn_stream.hpp>
#include <util/static_map.hpp>
#include <corelib/plugin_manager_store.hpp>
#include <iomanip>

Include dependency graph for reader_id1.cpp:

Go to the source code of this file.

Classes

class  CId1ReaderCF
 Class factory for ID1 reader. More...

Defines

#define NCBI_USE_ERRCODE_X   Objtools_Reader_Id1
#define DEFAULT_SERVICE   "ID1"
#define DEFAULT_NUM_CONN   3
#define DEFAULT_RETRY_COUNT   5
#define DEFAULT_TIMEOUT   20
#define DEFAULT_OPEN_TIMEOUT   5
#define MAX_MT_CONN   5
#define GENBANK_ID1_RANDOM_FAILS_FREQUENCY   20
#define GENBANK_ID1_RANDOM_FAILS_RECOVER   0
#define SetRandomFail(stream)

Typedefs

typedef CId1ReaderBase TRDR
typedef pair< TRDR::ESat,
TRDR::ESubSat > 		TSK
typedef pair< const char *,
TSK > 		TSI
typedef CStaticArrayMap< const
char *, TSK, PNocase_CStr > 		TSatMap

Enumerations

enum  EDebugLevel {
  eTraceError = 1, eTraceOpen = 2, eTraceConn = 4, eTraceASN = 5,
  eTraceASNData = 8
}

Functions

 NCBI_PARAM_DECL (int, GENBANK, ID1_DEBUG)
 NCBI_PARAM_DECL (string, GENBANK, ID1_SERVICE_NAME)
 NCBI_PARAM_DECL (string, NCBI, SERVICE_NAME_ID1)
 NCBI_PARAM_DEF_EX (int, GENBANK, ID1_DEBUG, 0, eParam_NoThread, GENBANK_ID1_DEBUG)
 NCBI_PARAM_DEF_EX (string, GENBANK, ID1_SERVICE_NAME, kEmptyStr, eParam_NoThread, GENBANK_ID1_SERVICE_NAME)
 NCBI_PARAM_DEF_EX (string, NCBI, SERVICE_NAME_ID1,"ID1", eParam_NoThread, GENBANK_SERVICE_NAME_ID1)
static int GetDebugLevel (void)
 DEFINE_STATIC_ARRAY_MAP (TSatMap, sc_SatMap, sc_SatIndex)
void GenBankReaders_Register_Id1 (void)
void NCBI_EntryPoint_Id1Reader (CPluginManager< objects::CReader >::TDriverInfoList &info_list, CPluginManager< objects::CReader >::EEntryPointRequest method)
void NCBI_EntryPoint_xreader_id1 (CPluginManager< objects::CReader >::TDriverInfoList &info_list, CPluginManager< objects::CReader >::EEntryPointRequest method)

Variables

static const TSI sc_SatIndex []
const int kSat_BlobError = -1

Define Documentation

#define DEFAULT_NUM_CONN   3
 

Definition at line 74 of file reader_id1.cpp.

Referenced by CId1Reader::CId1Reader(), and CId2Reader::CId2Reader().

#define DEFAULT_OPEN_TIMEOUT   5
 

Definition at line 77 of file reader_id1.cpp.

#define DEFAULT_RETRY_COUNT   5
 

Definition at line 75 of file reader_id1.cpp.

#define DEFAULT_SERVICE   "ID1"
 

Definition at line 73 of file reader_id1.cpp.

#define DEFAULT_TIMEOUT   20
 

Definition at line 76 of file reader_id1.cpp.

#define GENBANK_ID1_RANDOM_FAILS_FREQUENCY   20
 

Definition at line 81 of file reader_id1.cpp.

#define GENBANK_ID1_RANDOM_FAILS_RECOVER   0
 

Definition at line 82 of file reader_id1.cpp.

#define MAX_MT_CONN   5
 

Definition at line 78 of file reader_id1.cpp.

Referenced by CId2Reader::GetMaximumConnectionsLimit(), and CId1Reader::GetMaximumConnectionsLimit().

#define NCBI_USE_ERRCODE_X   Objtools_Reader_Id1
 

Definition at line 68 of file reader_id1.cpp.

#define SetRandomFail (  stream   ) 
 

Definition at line 122 of file reader_id1.cpp.

Referenced by CId2Reader::x_NewConnection(), CId1Reader::x_NewConnection(), CId2Reader::x_ReceiveReply(), CId1Reader::x_ReceiveReply(), and CId1Reader::x_SendRequest().

Typedef Documentation

typedef CId1ReaderBase TRDR
 

Definition at line 308 of file reader_id1.cpp.

typedef CStaticArrayMap<const char*, TSK, PNocase_CStr> TSatMap
 

Definition at line 324 of file reader_id1.cpp.

typedef pair<const char*, TSK> TSI
 

Definition at line 310 of file reader_id1.cpp.

typedef pair<TRDR::ESat, TRDR::ESubSat> TSK
 

Definition at line 309 of file reader_id1.cpp.

Enumeration Type Documentation

enum EDebugLevel
 

Enumerator:
eTraceError 
eTraceOpen 
eTraceConn 
eTraceASN 
eTraceASNData 

Definition at line 145 of file reader_id1.cpp.

Function Documentation

DEFINE_STATIC_ARRAY_MAP (  TSatMap  ,
sc_SatMap  ,
sc_SatIndex 
) 
 

void GenBankReaders_Register_Id1 (  void   ) 
 

Definition at line 830 of file reader_id1.cpp.

References NCBI_EntryPoint_Id1Reader().

Referenced by CGBDataLoader::x_GetReaderManager().

static int GetDebugLevel (  void   )  [static]
 

Definition at line 138 of file reader_id1.cpp.

References NCBI_PARAM_TYPE.

Referenced by CId1Reader::x_ReceiveReply(), and CId1Reader::x_SendRequest().

void NCBI_EntryPoint_Id1Reader (  CPluginManager< objects::CReader >::TDriverInfoList &  info_list,
CPluginManager< objects::CReader >::EEntryPointRequest  method
) 
 

Definition at line 870 of file reader_id1.cpp.

References CHostEntryPointImpl< TClassFactory >::NCBI_EntryPointImpl().

Referenced by GenBankReaders_Register_Id1(), and NCBI_EntryPoint_xreader_id1().

void NCBI_EntryPoint_xreader_id1 (  CPluginManager< objects::CReader >::TDriverInfoList &  info_list,
CPluginManager< objects::CReader >::EEntryPointRequest  method
) 
 

Definition at line 878 of file reader_id1.cpp.

References NCBI_EntryPoint_Id1Reader().

NCBI_PARAM_DECL (  string  ,
NCBI  ,
SERVICE_NAME_ID1 
) 
 

NCBI_PARAM_DECL (  string  ,
GENBANK  ,
ID1_SERVICE_NAME 
) 
 

NCBI_PARAM_DECL (  int  ,
GENBANK  ,
ID1_DEBUG 
) 
 

NCBI_PARAM_DEF_EX (  string  ,
NCBI  ,
SERVICE_NAME_ID1  ,
"ID1"  ,
eParam_NoThread  ,
GENBANK_SERVICE_NAME_ID1 
) 
 

NCBI_PARAM_DEF_EX (  string  ,
GENBANK  ,
ID1_SERVICE_NAME  ,
kEmptyStr  ,
eParam_NoThread  ,
GENBANK_ID1_SERVICE_NAME 
) 
 

NCBI_PARAM_DEF_EX (  int  ,
GENBANK  ,
ID1_DEBUG  ,
0  ,
eParam_NoThread  ,
GENBANK_ID1_DEBUG 
) 
 

Variable Documentation

const int kSat_BlobError = -1
 

Definition at line 500 of file reader_id1.cpp.

const TSI sc_SatIndex[] [static]
 

Initial value:

 {
    TSI("ANNOT:CDD",  TSK(TRDR::eSat_ANNOT_CDD,  TRDR::eSubSat_CDD)),
    TSI("ANNOT:EXON", TSK(TRDR::eSat_ANNOT,      TRDR::eSubSat_Exon)),
    TSI("ANNOT:MGC",  TSK(TRDR::eSat_ANNOT,      TRDR::eSubSat_MGC)),
    TSI("ANNOT:SNP",  TSK(TRDR::eSat_ANNOT,      TRDR::eSubSat_SNP)),
    TSI("ANNOT:SNP GRAPH",TSK(TRDR::eSat_ANNOT,  TRDR::eSubSat_SNP_graph)),
    TSI("ANNOT:STS",  TSK(TRDR::eSat_ANNOT,      TRDR::eSubSat_STS)),
    TSI("ANNOT:TRNA", TSK(TRDR::eSat_ANNOT,      TRDR::eSubSat_tRNA)),
    TSI("ti",         TSK(TRDR::eSat_TRACE,      TRDR::eSubSat_main)),
    TSI("TR_ASSM_CH", TSK(TRDR::eSat_TR_ASSM_CH, TRDR::eSubSat_main)),
    TSI("TRACE_ASSM", TSK(TRDR::eSat_TRACE_ASSM, TRDR::eSubSat_main)),
    TSI("TRACE_CHGR", TSK(TRDR::eSat_TRACE_CHGR, TRDR::eSubSat_main))
}

Definition at line 311 of file reader_id1.cpp.

Generated on Mon Dec 7 09:27:36 2009 for NCBI C++ ToolKit by  doxygen 1.4.6
Modified on Mon Dec 07 16:22:07 2009 by modify_doxy.py rev. 173732