NCBI C++ ToolKit
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#include <ncbi_pch.hpp>
#include <sra/readers/sra/impl/wgsresolver_impl.hpp>
#include <sra/readers/ncbi_traces_path.hpp>
#include <corelib/ncbifile.hpp>
#include <corelib/ncbi_param.hpp>
#include <util/line_reader.hpp>
#include <sra/error_codes.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/general/Dbtag.hpp>
Go to the source code of this file.
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Classes | |
struct | CWGSResolver_VDB::SGiIdxTableCursor |
struct | CWGSResolver_VDB::SAccIdxTableCursor |
Functions | |
NCBI_DEFINE_ERR_SUBCODE_X (36) | |
BEGIN_NAMESPACE (objects) | |
NCBI_PARAM_DECL (bool, WGS, RESOLVER_DIRECT_WGS_INDEX) | |
NCBI_PARAM_DEF (bool, WGS, RESOLVER_DIRECT_WGS_INDEX, true) | |
NCBI_PARAM_DECL (bool, WGS, RESOLVER_WGS_RANGE_INDEX) | |
NCBI_PARAM_DEF (bool, WGS, RESOLVER_WGS_RANGE_INDEX, true) | |
static bool | s_UseWGSRangeIndex (void) |
NCBI_PARAM_DECL (string, WGS, WGS_INDEX) | |
NCBI_PARAM_DEF (string, WGS, WGS_INDEX, "") | |
NCBI_PARAM_DECL (string, WGS, WGS_INDEX2) | |
NCBI_PARAM_DEF (string, WGS, WGS_INDEX2, "") | |
NCBI_PARAM_DECL (string, WGS, WGS_INDEX3) | |
NCBI_PARAM_DEF (string, WGS, WGS_INDEX3, "") | |
NCBI_PARAM_DECL (string, WGS, WGS_INDEX_ACC) | |
NCBI_PARAM_DEF (string, WGS, WGS_INDEX_ACC, "ZZZZ99") | |
NCBI_PARAM_DECL (string, WGS, WGS_INDEX2_ACC) | |
NCBI_PARAM_DEF (string, WGS, WGS_INDEX2_ACC, "ZZZZ98") | |
NCBI_PARAM_DECL (string, WGS, WGS_INDEX3_ACC) | |
NCBI_PARAM_DEF (string, WGS, WGS_INDEX3_ACC, "ZZZZ97") | |
NCBI_PARAM_DECL (string, WGS, WGS_RANGE_INDEX) | |
NCBI_PARAM_DEF (string, WGS, WGS_RANGE_INDEX, "") | |
NCBI_PARAM_DECL (string, WGS, WGS_RANGE_INDEX2) | |
NCBI_PARAM_DEF (string, WGS, WGS_RANGE_INDEX2, "") | |
NCBI_PARAM_DECL (string, WGS, WGS_RANGE_INDEX_ACC) | |
NCBI_PARAM_DEF (string, WGS, WGS_RANGE_INDEX_ACC, "ZZZZ79") | |
NCBI_PARAM_DECL (string, WGS, WGS_RANGE_INDEX2_ACC) | |
NCBI_PARAM_DEF (string, WGS, WGS_RANGE_INDEX2_ACC, "ZZZZ78") | |
static string | GetDirectWGSIndexPath (CWGSResolver_VDB::EIndexType index_type) |
static bool | s_SplitAccIndex (string &uacc, Uint2 &key_num) |
END_NAMESPACE (objects) | |
Variables | |
BEGIN_NCBI_NAMESPACE | |
static const size_t | kTypePrefixLen = 4 |
static const size_t | kNumLettersV1 = 4 |
static const size_t | kNumLettersV2 = 6 |
static const size_t | kVersionDigits = 2 |
static const size_t | kPrefixLenV1 = kNumLettersV1 + kVersionDigits |
static const size_t | kPrefixLenV2 = kNumLettersV2 + kVersionDigits |
static const size_t | kMinRowDigitsV1 = 6 |
static const size_t | kMaxRowDigitsV1 = 8 |
static const size_t | kMinRowDigitsV2 = 7 |
static const size_t | kMaxRowDigitsV2 = 9 |
END_NCBI_NAMESPACE | |
#define DEFAULT_WGS_INDEX2_ACC "ZZZZ98" |
Definition at line 53 of file wgsresolver_impl.cpp.
#define DEFAULT_WGS_INDEX2_PATH1 NCBI_TRACES04_PATH "/wgs03/WGS/ZZ/ZZ/ZZZZ98" |
Definition at line 57 of file wgsresolver_impl.cpp.
#define DEFAULT_WGS_INDEX2_PATH2 NCBI_TRACES04_PATH "/wgs03/WGS/WGS_INDEX_V2" |
Definition at line 58 of file wgsresolver_impl.cpp.
#define DEFAULT_WGS_INDEX3_ACC "ZZZZ97" |
Definition at line 54 of file wgsresolver_impl.cpp.
#define DEFAULT_WGS_INDEX3_PATH1 NCBI_TRACES04_PATH "/wgs03/WGS/ZZ/ZZ/ZZZZ97" |
Definition at line 59 of file wgsresolver_impl.cpp.
#define DEFAULT_WGS_INDEX3_PATH2 NCBI_TRACES04_PATH "/wgs03/WGS/WGS_INDEX_V3" |
Definition at line 60 of file wgsresolver_impl.cpp.
#define DEFAULT_WGS_INDEX_ACC "ZZZZ99" |
Definition at line 52 of file wgsresolver_impl.cpp.
#define DEFAULT_WGS_INDEX_PATH1 NCBI_TRACES04_PATH "/wgs03/WGS/ZZ/ZZ/ZZZZ99" |
Definition at line 55 of file wgsresolver_impl.cpp.
#define DEFAULT_WGS_INDEX_PATH2 NCBI_TRACES04_PATH "/wgs03/WGS/WGS_INDEX" |
Definition at line 56 of file wgsresolver_impl.cpp.
#define DEFAULT_WGS_RANGE_INDEX2_ACC "ZZZZ78" |
Definition at line 63 of file wgsresolver_impl.cpp.
#define DEFAULT_WGS_RANGE_INDEX2_PATH1 NCBI_TRACES04_PATH "/wgs03/WGS/ZZ/ZZ/ZZZZ78" |
Definition at line 66 of file wgsresolver_impl.cpp.
#define DEFAULT_WGS_RANGE_INDEX2_PATH2 NCBI_TRACES04_PATH "/wgs03/WGS/WGS_RANGE_INDEX_2" |
Definition at line 67 of file wgsresolver_impl.cpp.
#define DEFAULT_WGS_RANGE_INDEX_ACC "ZZZZ79" |
Definition at line 62 of file wgsresolver_impl.cpp.
#define DEFAULT_WGS_RANGE_INDEX_PATH1 NCBI_TRACES04_PATH "/wgs03/WGS/ZZ/ZZ/ZZZZ79" |
Definition at line 64 of file wgsresolver_impl.cpp.
#define DEFAULT_WGS_RANGE_INDEX_PATH2 NCBI_TRACES04_PATH "/wgs03/WGS/WGS_RANGE_INDEX_1" |
Definition at line 65 of file wgsresolver_impl.cpp.
#define NCBI_USE_ERRCODE_X WGSResolver |
Definition at line 46 of file wgsresolver_impl.cpp.
#define PROFILE | ( | var | ) |
Definition at line 157 of file wgsresolver_impl.cpp.
BEGIN_NAMESPACE | ( | objects | ) |
END_NAMESPACE | ( | objects | ) |
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static |
Definition at line 257 of file wgsresolver_impl.cpp.
References DEFAULT_WGS_INDEX2_PATH1, DEFAULT_WGS_INDEX2_PATH2, DEFAULT_WGS_INDEX3_PATH1, DEFAULT_WGS_INDEX3_PATH2, DEFAULT_WGS_INDEX_PATH1, DEFAULT_WGS_INDEX_PATH2, DEFAULT_WGS_RANGE_INDEX2_PATH1, DEFAULT_WGS_RANGE_INDEX2_PATH2, DEFAULT_WGS_RANGE_INDEX_PATH1, DEFAULT_WGS_RANGE_INDEX_PATH2, CWGSResolver_VDB::eMainIndex, CWGSResolver_VDB::eSecondIndex, CWGSResolver_VDB::eThirdIndex, NCBI_PARAM_TYPE, and s_UseWGSRangeIndex().
Referenced by CWGSResolver_VDB::CWGSResolver_VDB().
NCBI_DEFINE_ERR_SUBCODE_X | ( | 36 | ) |
NCBI_PARAM_DECL | ( | bool | , |
WGS | , | ||
RESOLVER_DIRECT_WGS_INDEX | |||
) |
NCBI_PARAM_DECL | ( | bool | , |
WGS | , | ||
RESOLVER_WGS_RANGE_INDEX | |||
) |
NCBI_PARAM_DECL | ( | string | , |
WGS | , | ||
WGS_INDEX | |||
) |
NCBI_PARAM_DECL | ( | string | , |
WGS | , | ||
WGS_INDEX2 | |||
) |
NCBI_PARAM_DECL | ( | string | , |
WGS | , | ||
WGS_INDEX2_ACC | |||
) |
NCBI_PARAM_DECL | ( | string | , |
WGS | , | ||
WGS_INDEX3 | |||
) |
NCBI_PARAM_DECL | ( | string | , |
WGS | , | ||
WGS_INDEX3_ACC | |||
) |
NCBI_PARAM_DECL | ( | string | , |
WGS | , | ||
WGS_INDEX_ACC | |||
) |
NCBI_PARAM_DECL | ( | string | , |
WGS | , | ||
WGS_RANGE_INDEX | |||
) |
NCBI_PARAM_DECL | ( | string | , |
WGS | , | ||
WGS_RANGE_INDEX2 | |||
) |
NCBI_PARAM_DECL | ( | string | , |
WGS | , | ||
WGS_RANGE_INDEX2_ACC | |||
) |
NCBI_PARAM_DECL | ( | string | , |
WGS | , | ||
WGS_RANGE_INDEX_ACC | |||
) |
NCBI_PARAM_DEF | ( | string | , |
WGS | , | ||
WGS_INDEX | , | ||
"" | |||
) |
NCBI_PARAM_DEF | ( | string | , |
WGS | , | ||
WGS_INDEX2 | , | ||
"" | |||
) |
NCBI_PARAM_DEF | ( | string | , |
WGS | , | ||
WGS_INDEX2_ACC | , | ||
"ZZZZ98" | |||
) |
NCBI_PARAM_DEF | ( | string | , |
WGS | , | ||
WGS_INDEX3 | , | ||
"" | |||
) |
NCBI_PARAM_DEF | ( | string | , |
WGS | , | ||
WGS_INDEX3_ACC | , | ||
"ZZZZ97" | |||
) |
NCBI_PARAM_DEF | ( | string | , |
WGS | , | ||
WGS_INDEX_ACC | , | ||
"ZZZZ99" | |||
) |
NCBI_PARAM_DEF | ( | string | , |
WGS | , | ||
WGS_RANGE_INDEX | , | ||
"" | |||
) |
NCBI_PARAM_DEF | ( | string | , |
WGS | , | ||
WGS_RANGE_INDEX2 | , | ||
"" | |||
) |
NCBI_PARAM_DEF | ( | string | , |
WGS | , | ||
WGS_RANGE_INDEX2_ACC | , | ||
"ZZZZ78" | |||
) |
NCBI_PARAM_DEF | ( | string | , |
WGS | , | ||
WGS_RANGE_INDEX_ACC | , | ||
"ZZZZ79" | |||
) |
Definition at line 587 of file wgsresolver_impl.cpp.
References i.
Referenced by CWGSResolver_VDB::x_GetAccPrefixes().
Definition at line 76 of file wgsresolver_impl.cpp.
References NCBI_PARAM_TYPE, and rapidjson::value.
Referenced by CWGSResolver_VDB::GetDefaultWGSIndexAcc(), CWGSResolver_VDB::GetDefaultWGSIndexPath(), and GetDirectWGSIndexPath().
BEGIN_NCBI_NAMESPACE |
Definition at line 44 of file wgsresolver_impl.cpp.
END_NCBI_NAMESPACE |
Definition at line 992 of file wgsresolver_impl.cpp.
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Definition at line 716 of file wgsresolver_impl.cpp.
Referenced by CWGSResolver_Ids::ParseWGSAcc().
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Definition at line 718 of file wgsresolver_impl.cpp.
Referenced by CWGSResolver_Ids::ParseWGSAcc().
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Definition at line 715 of file wgsresolver_impl.cpp.
Referenced by CWGSResolver_Ids::ParseWGSAcc().
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Definition at line 717 of file wgsresolver_impl.cpp.
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Definition at line 710 of file wgsresolver_impl.cpp.
Referenced by CWGSResolver_Ids::ParseWGSAcc(), and CWGSResolver_Ids::ParseWGSPrefix().
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Definition at line 711 of file wgsresolver_impl.cpp.
Referenced by CWGSResolver_Ids::ParseWGSAcc(), and CWGSResolver_Ids::ParseWGSPrefix().
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Definition at line 713 of file wgsresolver_impl.cpp.
Referenced by CWGSResolver_Ids::ParseWGSAcc(), and CWGSResolver_Ids::ParseWGSPrefix().
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Definition at line 714 of file wgsresolver_impl.cpp.
Referenced by CWGSResolver_Ids::ParseWGSAcc(), and CWGSResolver_Ids::ParseWGSPrefix().
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Definition at line 709 of file wgsresolver_impl.cpp.
Referenced by CWGSResolver_Ids::ParseWGSPrefix().
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Definition at line 712 of file wgsresolver_impl.cpp.
Referenced by CWGSResolver_Ids::ParseWGSAcc(), and CWGSResolver_Ids::ParseWGSPrefix().