NCBI C++ ToolKit
Classes | Macros | Enumerations | Functions
reader_pubseq.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbi_param.hpp>
#include <objtools/data_loaders/genbank/pubseq/reader_pubseq.hpp>
#include <objtools/data_loaders/genbank/pubseq/reader_pubseq_entry.hpp>
#include <objtools/data_loaders/genbank/pubseq/reader_pubseq_params.h>
#include <objtools/data_loaders/genbank/readers.hpp>
#include <objtools/data_loaders/genbank/impl/request_result.hpp>
#include <objtools/data_loaders/genbank/impl/dispatcher.hpp>
#include <objtools/error_codes.hpp>
#include <objmgr/objmgr_exception.hpp>
#include <objmgr/impl/tse_info.hpp>
#include <objmgr/annot_selector.hpp>
#include <dbapi/driver/types.hpp>
#include <dbapi/driver/exception.hpp>
#include <dbapi/driver/driver_mgr.hpp>
#include <dbapi/driver/drivers.hpp>
#include <dbapi/driver/dbapi_svc_mapper.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqsplit/ID2S_Seq_annot_Info.hpp>
#include <objects/seqsplit/ID2S_Feat_type_Info.hpp>
#include <corelib/ncbicntr.hpp>
#include <corelib/plugin_manager_impl.hpp>
#include <corelib/plugin_manager_store.hpp>
#include <corelib/rwstream.hpp>
#include <serial/objistrasnb.hpp>
#include <serial/objostrasn.hpp>
#include <serial/serial.hpp>
#include <util/compress/zlib.hpp>
#include <corelib/ncbi_cookies.hpp>
+ Include dependency graph for reader_pubseq.cpp:

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Classes

struct  SPubseqReaderReceiveData
 
class  CPubseqReaderCF
 Class factory for Pubseq reader. More...
 

Macros

#define DEFAULT_DB_SERVER   "PUBSEQ_OS_PUBLIC_GI64"
 
#define DEFAULT_DB_USER   "anyone"
 
#define DEFAULT_DB_PASSWORD   "allowed"
 
#define DEFAULT_DB_DRIVER   "ftds;ctlib"
 
#define DEFAULT_NUM_CONN   2
 
#define MAX_MT_CONN   5
 
#define DEFAULT_ALLOW_GZIP   true
 
#define DEFAULT_EXCL_WGS_MASTER   true
 
#define NCBI_USE_ERRCODE_X   Objtools_Rd_Pubseq
 
#define RPC_GET_ASN   "id_get_asn"
 
#define RPC_GET_BLOB_INFO   "id_get_blob_prop"
 

Enumerations

enum  { fZipType_gzipped = 2 }
 

Functions

 NCBI_PARAM_DECL (int, GENBANK, PUBSEQOS_DEBUG)
 
 NCBI_PARAM_DEF_EX (int, GENBANK, PUBSEQOS_DEBUG, 0, eParam_NoThread, GENBANK_PUBSEQOS_DEBUG)
 
static int GetDebugLevel (void)
 
static void sx_SetIntId (CDB_RPCCmd &cmd, const char *param, TIntId id)
 
static TIntId sx_GetIntId (CDB_Result &dbr, int pos)
 
void GenBankReaders_Register_Pubseq (void)
 
void NCBI_EntryPoint_ReaderPubseqos (CPluginManager< objects::CReader >::TDriverInfoList &info_list, CPluginManager< objects::CReader >::EEntryPointRequest method)
 
void NCBI_EntryPoint_xreader_pubseqos (CPluginManager< objects::CReader >::TDriverInfoList &info_list, CPluginManager< objects::CReader >::EEntryPointRequest method)
 

Macro Definition Documentation

◆ DEFAULT_ALLOW_GZIP

#define DEFAULT_ALLOW_GZIP   true

Definition at line 74 of file reader_pubseq.cpp.

◆ DEFAULT_DB_DRIVER

#define DEFAULT_DB_DRIVER   "ftds;ctlib"

Definition at line 71 of file reader_pubseq.cpp.

◆ DEFAULT_DB_PASSWORD

#define DEFAULT_DB_PASSWORD   "allowed"

Definition at line 70 of file reader_pubseq.cpp.

◆ DEFAULT_DB_SERVER

#define DEFAULT_DB_SERVER   "PUBSEQ_OS_PUBLIC_GI64"

Definition at line 68 of file reader_pubseq.cpp.

◆ DEFAULT_DB_USER

#define DEFAULT_DB_USER   "anyone"

Definition at line 69 of file reader_pubseq.cpp.

◆ DEFAULT_EXCL_WGS_MASTER

#define DEFAULT_EXCL_WGS_MASTER   true

Definition at line 75 of file reader_pubseq.cpp.

◆ DEFAULT_NUM_CONN

#define DEFAULT_NUM_CONN   2

Definition at line 72 of file reader_pubseq.cpp.

◆ MAX_MT_CONN

#define MAX_MT_CONN   5

Definition at line 73 of file reader_pubseq.cpp.

◆ NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X   Objtools_Rd_Pubseq

Definition at line 77 of file reader_pubseq.cpp.

◆ RPC_GET_ASN

#define RPC_GET_ASN   "id_get_asn"

Definition at line 92 of file reader_pubseq.cpp.

◆ RPC_GET_BLOB_INFO

#define RPC_GET_BLOB_INFO   "id_get_blob_prop"

Definition at line 93 of file reader_pubseq.cpp.

Enumeration Type Documentation

◆ anonymous enum

anonymous enum
Enumerator
fZipType_gzipped 

Definition at line 95 of file reader_pubseq.cpp.

Function Documentation

◆ GenBankReaders_Register_Pubseq()

void GenBankReaders_Register_Pubseq ( void  )

◆ GetDebugLevel()

static int GetDebugLevel ( void  )
static

◆ NCBI_EntryPoint_ReaderPubseqos()

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

◆ NCBI_EntryPoint_xreader_pubseqos()

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

Definition at line 1377 of file reader_pubseq.cpp.

References NCBI_EntryPoint_ReaderPubseqos().

◆ NCBI_PARAM_DECL()

NCBI_PARAM_DECL ( int  ,
GENBANK  ,
PUBSEQOS_DEBUG   
)

◆ NCBI_PARAM_DEF_EX()

NCBI_PARAM_DEF_EX ( int  ,
GENBANK  ,
PUBSEQOS_DEBUG  ,
,
eParam_NoThread  ,
GENBANK_PUBSEQOS_DEBUG   
)

◆ sx_GetIntId()

static TIntId sx_GetIntId ( CDB_Result dbr,
int  pos 
)
static

◆ sx_SetIntId()

static void sx_SetIntId ( CDB_RPCCmd cmd,
const char *  param,
TIntId  id 
)
static
Modified on Wed May 15 15:09:59 2024 by modify_doxy.py rev. 669887