NCBI C++ ToolKit
Macros | Enumerations | Functions | Variables
snploader_impl.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <objects/general/general__.hpp>
#include <objects/seqloc/seqloc__.hpp>
#include <objects/seq/seq__.hpp>
#include <objects/seqres/seqres__.hpp>
#include <objects/seqsplit/ID2S_Split_Info.hpp>
#include <objects/seqsplit/ID2S_Chunk.hpp>
#include <objmgr/annot_selector.hpp>
#include <objmgr/impl/data_source.hpp>
#include <objmgr/impl/tse_loadlock.hpp>
#include <objmgr/impl/tse_chunk_info.hpp>
#include <objmgr/impl/tse_split_info.hpp>
#include <objmgr/impl/split_parser.hpp>
#include <objmgr/data_loader_factory.hpp>
#include <corelib/plugin_manager_impl.hpp>
#include <corelib/plugin_manager_store.hpp>
#include <serial/objistr.hpp>
#include <serial/serial.hpp>
#include <sra/error_codes.hpp>
#include <sra/readers/ncbi_traces_path.hpp>
#include <sra/data_loaders/snp/snploader.hpp>
#include <sra/data_loaders/snp/impl/snploader_impl.hpp>
#include <util/sequtil/sequtil_manip.hpp>
#include <objects/dbsnp/primary_track/snpptis.hpp>
#include <algorithm>
#include <cmath>
+ Include dependency graph for snploader_impl.cpp:

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Macros

#define NCBI_USE_ERRCODE_X   SNPLoader
 

Enumerations

enum  {
  eDebug_open = 1 , eDebug_open_time = 2 , eDebug_load = 3 , eDebug_load_time = 4 ,
  eDebug_resolve = 5 , eDebug_data = 9
}
 

Functions

 NCBI_DEFINE_ERR_SUBCODE_X (16)
 
 NCBI_PARAM_DECL (int, SNP_LOADER, DEBUG)
 
 NCBI_PARAM_DEF_EX (int, SNP_LOADER, DEBUG, 0, eParam_NoThread, SNP_LOADER_DEBUG)
 
static int GetDebugLevel (void)
 
 NCBI_PARAM_DECL (size_t, SNP_LOADER, GC_SIZE)
 
 NCBI_PARAM_DEF_EX (size_t, SNP_LOADER, GC_SIZE, 10, eParam_NoThread, SNP_LOADER_GC_SIZE)
 
static size_t GetGCSize (void)
 
 NCBI_PARAM_DECL (unsigned, SNP_LOADER, RETRY_COUNT)
 
 NCBI_PARAM_DEF (unsigned, SNP_LOADER, RETRY_COUNT, 3)
 
static unsigned GetRetryCountParam (void)
 
 NCBI_PARAM_DECL (unsigned, SNP_LOADER, FILE_REOPEN_TIME)
 
 NCBI_PARAM_DEF (unsigned, SNP_LOADER, FILE_REOPEN_TIME, 60 *60)
 
static unsigned GetFileReopenTimeParam (void)
 
 NCBI_PARAM_DECL (unsigned, SNP_LOADER, FILE_RECHECK_TIME)
 
 NCBI_PARAM_DEF (unsigned, SNP_LOADER, FILE_RECHECK_TIME, 5 *60)
 
static unsigned GetFileRecheckTimeParam (void)
 
 NCBI_PARAM_DECL (bool, SNP_LOADER, SPLIT)
 
 NCBI_PARAM_DEF_EX (bool, SNP_LOADER, SPLIT, true, eParam_NoThread, SNP_LOADER_SPLIT)
 
static bool IsSplitEnabled (void)
 
static size_t sx_ExtractFilterIndex (string &s)
 
static string sx_AddFilterIndex (const string &s, size_t filter_index)
 
static string s_GetAccVer (const CSeq_id_Handle &id)
 

Variables

const int kSNPSatBase = 2000
 
const int kSNPSatPrimary = 3000
 
const int kSNPSubSatGraph = 1000000000
 
const int kNAVersionMin = 1
 
const int kNAVersionMax = 99
 
const int kSeqIndexCount = 1000000
 
const int kFilterIndexCount = 2000
 
const int kFilterIndexMaxLength = 4
 
static const char kFileEnd [] = "|||"
 
static const char kFilterPrefixChar = '#'
 

Macro Definition Documentation

◆ NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X   SNPLoader

Definition at line 69 of file snploader_impl.cpp.

Enumeration Type Documentation

◆ anonymous enum

anonymous enum
Enumerator
eDebug_open 
eDebug_open_time 
eDebug_load 
eDebug_load_time 
eDebug_resolve 
eDebug_data 

Definition at line 80 of file snploader_impl.cpp.

Function Documentation

◆ GetDebugLevel()

static int GetDebugLevel ( void  )
static

◆ GetFileRecheckTimeParam()

static unsigned GetFileRecheckTimeParam ( void  )
static

Definition at line 133 of file snploader_impl.cpp.

References NCBI_PARAM_TYPE, and rapidjson::value.

◆ GetFileReopenTimeParam()

static unsigned GetFileReopenTimeParam ( void  )
static

Definition at line 121 of file snploader_impl.cpp.

References NCBI_PARAM_TYPE, and rapidjson::value.

◆ GetGCSize()

static size_t GetGCSize ( void  )
static

◆ GetRetryCountParam()

static unsigned GetRetryCountParam ( void  )
static

Definition at line 110 of file snploader_impl.cpp.

References NCBI_PARAM_TYPE, and rapidjson::value.

◆ IsSplitEnabled()

static bool IsSplitEnabled ( void  )
static

◆ NCBI_DEFINE_ERR_SUBCODE_X()

NCBI_DEFINE_ERR_SUBCODE_X ( 16  )

◆ NCBI_PARAM_DECL() [1/6]

NCBI_PARAM_DECL ( bool  ,
SNP_LOADER  ,
SPLIT   
)

◆ NCBI_PARAM_DECL() [2/6]

NCBI_PARAM_DECL ( int  ,
SNP_LOADER  ,
DEBUG   
)

◆ NCBI_PARAM_DECL() [3/6]

NCBI_PARAM_DECL ( size_t  ,
SNP_LOADER  ,
GC_SIZE   
)

◆ NCBI_PARAM_DECL() [4/6]

NCBI_PARAM_DECL ( unsigned  ,
SNP_LOADER  ,
FILE_RECHECK_TIME   
)

◆ NCBI_PARAM_DECL() [5/6]

NCBI_PARAM_DECL ( unsigned  ,
SNP_LOADER  ,
FILE_REOPEN_TIME   
)

◆ NCBI_PARAM_DECL() [6/6]

NCBI_PARAM_DECL ( unsigned  ,
SNP_LOADER  ,
RETRY_COUNT   
)

◆ NCBI_PARAM_DEF() [1/3]

NCBI_PARAM_DEF ( unsigned  ,
SNP_LOADER  ,
FILE_RECHECK_TIME  ,
5 *  60 
)

◆ NCBI_PARAM_DEF() [2/3]

NCBI_PARAM_DEF ( unsigned  ,
SNP_LOADER  ,
FILE_REOPEN_TIME  ,
60 *  60 
)

◆ NCBI_PARAM_DEF() [3/3]

NCBI_PARAM_DEF ( unsigned  ,
SNP_LOADER  ,
RETRY_COUNT  ,
 
)

◆ NCBI_PARAM_DEF_EX() [1/3]

NCBI_PARAM_DEF_EX ( bool  ,
SNP_LOADER  ,
SPLIT  ,
true  ,
eParam_NoThread  ,
SNP_LOADER_SPLIT   
)

◆ NCBI_PARAM_DEF_EX() [2/3]

NCBI_PARAM_DEF_EX ( int  ,
SNP_LOADER  ,
DEBUG  ,
,
eParam_NoThread  ,
SNP_LOADER_DEBUG   
)

◆ NCBI_PARAM_DEF_EX() [3/3]

NCBI_PARAM_DEF_EX ( size_t  ,
SNP_LOADER  ,
GC_SIZE  ,
10  ,
eParam_NoThread  ,
SNP_LOADER_GC_SIZE   
)

◆ s_GetAccVer()

static string s_GetAccVer ( const CSeq_id_Handle id)
static

◆ sx_AddFilterIndex()

static string sx_AddFilterIndex ( const string s,
size_t  filter_index 
)
static

Definition at line 456 of file snploader_impl.cpp.

References kFilterPrefixChar, and str().

◆ sx_ExtractFilterIndex()

static size_t sx_ExtractFilterIndex ( string s)
static

Variable Documentation

◆ kFileEnd

const char kFileEnd[] = "|||"
static

Definition at line 426 of file snploader_impl.cpp.

◆ kFilterIndexCount

const int kFilterIndexCount = 2000

Definition at line 185 of file snploader_impl.cpp.

◆ kFilterIndexMaxLength

const int kFilterIndexMaxLength = 4

Definition at line 186 of file snploader_impl.cpp.

Referenced by sx_ExtractFilterIndex().

◆ kFilterPrefixChar

const char kFilterPrefixChar = '#'
static

Definition at line 427 of file snploader_impl.cpp.

Referenced by sx_AddFilterIndex(), and sx_ExtractFilterIndex().

◆ kNAVersionMax

const int kNAVersionMax = 99

Definition at line 183 of file snploader_impl.cpp.

◆ kNAVersionMin

const int kNAVersionMin = 1

Definition at line 182 of file snploader_impl.cpp.

◆ kSeqIndexCount

const int kSeqIndexCount = 1000000

Definition at line 184 of file snploader_impl.cpp.

◆ kSNPSatBase

const int kSNPSatBase = 2000

Definition at line 179 of file snploader_impl.cpp.

◆ kSNPSatPrimary

const int kSNPSatPrimary = 3000

Definition at line 180 of file snploader_impl.cpp.

◆ kSNPSubSatGraph

const int kSNPSubSatGraph = 1000000000

Definition at line 181 of file snploader_impl.cpp.

Modified on Thu May 23 12:29:38 2024 by modify_doxy.py rev. 669887