NCBI C++ ToolKit
Classes | Macros | Functions | Variables
vdbgraphloader_impl.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <objects/general/general__.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seq/seq__.hpp>
#include <objects/seqres/seqres__.hpp>
#include <objmgr/annot_selector.hpp>
#include <objmgr/impl/data_source.hpp>
#include <objmgr/impl/tse_loadlock.hpp>
#include <objmgr/impl/tse_split_info.hpp>
#include <objmgr/impl/tse_chunk_info.hpp>
#include <objmgr/data_loader_factory.hpp>
#include <corelib/plugin_manager_impl.hpp>
#include <corelib/plugin_manager_store.hpp>
#include <sra/readers/sra/graphread.hpp>
#include <sra/data_loaders/vdbgraph/vdbgraphloader.hpp>
#include <sra/data_loaders/vdbgraph/impl/vdbgraphloader_impl.hpp>
#include <sra/error_codes.hpp>
+ Include dependency graph for vdbgraphloader_impl.cpp:

Go to the source code of this file.

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Classes

class  CVDBGraphBlobId
 

Macros

#define NCBI_USE_ERRCODE_X   VDBGraphLoader
 
#define OVERVIEW_NAME_SUFFIX   "@@5000"
 
#define MID_ZOOM_NAME_SUFFIX   "@@100"
 

Functions

 NCBI_DEFINE_ERR_SUBCODE_X (8)
 
 NCBI_PARAM_DECL (int, VDBGRAPH_LOADER, DEBUG)
 
 NCBI_PARAM_DEF_EX (int, VDBGRAPH_LOADER, DEBUG, 0, eParam_NoThread, VDBGRAPH_LOADER_DEBUG)
 
static int GetDebugLevel (void)
 
 NCBI_PARAM_DECL (size_t, VDBGRAPH_LOADER, GC_SIZE)
 
 NCBI_PARAM_DEF_EX (size_t, VDBGRAPH_LOADER, GC_SIZE, 10, eParam_NoThread, VDBGRAPH_LOADER_GC_SIZE)
 
static size_t GetGCSize (void)
 
 NCBI_PARAM_DECL (size_t, VDBGRAPH_LOADER, MISSING_GC_SIZE)
 
 NCBI_PARAM_DEF_EX (size_t, VDBGRAPH_LOADER, MISSING_GC_SIZE, 10000, eParam_NoThread, VDBGRAPH_LOADER_MISSING_GC_SIZE)
 
static size_t GetMissingGCSize (void)
 
 NCBI_PARAM_DECL (int, VDBGRAPH_LOADER, USE_TABLE)
 
 NCBI_PARAM_DEF_EX (int, VDBGRAPH_LOADER, USE_TABLE, 2, eParam_NoThread, VDBGRAPH_LOADER_USE_TABLE)
 
static int GetUseTable (void)
 
 NCBI_PARAM_DECL (bool, VDBGRAPH_LOADER, DISABLE_ZOOM)
 
 NCBI_PARAM_DEF_EX (bool, VDBGRAPH_LOADER, DISABLE_ZOOM, false, eParam_NoThread, VDBGRAPH_LOADER_DISABLE_ZOOM)
 
static bool GetDisabledZoom (void)
 
static bool GetEnabledOverview (void)
 
static bool GetEnabledMidZoom (void)
 
 NCBI_PARAM_DECL (int, VDBGRAPH_LOADER, LOOKUP_TYPE)
 
 NCBI_PARAM_DEF_EX (int, VDBGRAPH_LOADER, LOOKUP_TYPE, CVDBGraphDb_Impl::eLookupDefault, eParam_NoThread, VDBGRAPH_LOADER_LOOKUP_TYPE)
 
static CVDBGraphDb_Impl::ELookupType GetLookupType (void)
 
 NCBI_PARAM_DECL (unsigned, VDBGRAPH_LOADER, RETRY_COUNT)
 
 NCBI_PARAM_DEF (unsigned, VDBGRAPH_LOADER, RETRY_COUNT, 3)
 
static unsigned GetRetryCountParam (void)
 
static bool sx_IsNA (const string &s)
 

Variables

static const TSeqPos kOverviewChunkSize = 20000*5000
 
static const TSeqPos kMidZoomChunkSize = 20000*100
 
static const TSeqPos kMainChunkSize = 100000
 
static const size_t kOverviewChunkIdAdd = 0
 
static const size_t kMidZoomChunkIdAdd = 1
 
static const size_t kMainGraphChunkIdAdd = 2
 
static const size_t kMainTableChunkIdAdd = 3
 
static const size_t kChunkIdMul = 4
 
static const int kTSEId = 1
 

Macro Definition Documentation

◆ MID_ZOOM_NAME_SUFFIX

#define MID_ZOOM_NAME_SUFFIX   "@@100"

Definition at line 67 of file vdbgraphloader_impl.cpp.

◆ NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X   VDBGraphLoader

Definition at line 57 of file vdbgraphloader_impl.cpp.

◆ OVERVIEW_NAME_SUFFIX

#define OVERVIEW_NAME_SUFFIX   "@@5000"

Definition at line 66 of file vdbgraphloader_impl.cpp.

Function Documentation

◆ GetDebugLevel()

static int GetDebugLevel ( void  )
static

◆ GetDisabledZoom()

static bool GetDisabledZoom ( void  )
static

◆ GetEnabledMidZoom()

static bool GetEnabledMidZoom ( void  )
static

◆ GetEnabledOverview()

static bool GetEnabledOverview ( void  )
static

◆ GetGCSize()

static size_t GetGCSize ( void  )
static

◆ GetLookupType()

static CVDBGraphDb_Impl::ELookupType GetLookupType ( void  )
static

◆ GetMissingGCSize()

static size_t GetMissingGCSize ( void  )
static

◆ GetRetryCountParam()

static unsigned GetRetryCountParam ( void  )
static

Definition at line 162 of file vdbgraphloader_impl.cpp.

References NCBI_PARAM_TYPE, and rapidjson::value.

◆ GetUseTable()

static int GetUseTable ( void  )
static

◆ NCBI_DEFINE_ERR_SUBCODE_X()

NCBI_DEFINE_ERR_SUBCODE_X ( )

◆ NCBI_PARAM_DECL() [1/7]

NCBI_PARAM_DECL ( bool  ,
VDBGRAPH_LOADER  ,
DISABLE_ZOOM   
)

◆ NCBI_PARAM_DECL() [2/7]

NCBI_PARAM_DECL ( int  ,
VDBGRAPH_LOADER  ,
DEBUG   
)

◆ NCBI_PARAM_DECL() [3/7]

NCBI_PARAM_DECL ( int  ,
VDBGRAPH_LOADER  ,
LOOKUP_TYPE   
)

◆ NCBI_PARAM_DECL() [4/7]

NCBI_PARAM_DECL ( int  ,
VDBGRAPH_LOADER  ,
USE_TABLE   
)

◆ NCBI_PARAM_DECL() [5/7]

NCBI_PARAM_DECL ( size_t  ,
VDBGRAPH_LOADER  ,
GC_SIZE   
)

◆ NCBI_PARAM_DECL() [6/7]

NCBI_PARAM_DECL ( size_t  ,
VDBGRAPH_LOADER  ,
MISSING_GC_SIZE   
)

◆ NCBI_PARAM_DECL() [7/7]

NCBI_PARAM_DECL ( unsigned  ,
VDBGRAPH_LOADER  ,
RETRY_COUNT   
)

◆ NCBI_PARAM_DEF()

NCBI_PARAM_DEF ( unsigned  ,
VDBGRAPH_LOADER  ,
RETRY_COUNT  ,
 
)

◆ NCBI_PARAM_DEF_EX() [1/6]

NCBI_PARAM_DEF_EX ( bool  ,
VDBGRAPH_LOADER  ,
DISABLE_ZOOM  ,
false  ,
eParam_NoThread  ,
VDBGRAPH_LOADER_DISABLE_ZOOM   
)

◆ NCBI_PARAM_DEF_EX() [2/6]

NCBI_PARAM_DEF_EX ( int  ,
VDBGRAPH_LOADER  ,
DEBUG  ,
,
eParam_NoThread  ,
VDBGRAPH_LOADER_DEBUG   
)

◆ NCBI_PARAM_DEF_EX() [3/6]

NCBI_PARAM_DEF_EX ( int  ,
VDBGRAPH_LOADER  ,
LOOKUP_TYPE  ,
CVDBGraphDb_Impl::eLookupDefault  ,
eParam_NoThread  ,
VDBGRAPH_LOADER_LOOKUP_TYPE   
)

◆ NCBI_PARAM_DEF_EX() [4/6]

NCBI_PARAM_DEF_EX ( int  ,
VDBGRAPH_LOADER  ,
USE_TABLE  ,
,
eParam_NoThread  ,
VDBGRAPH_LOADER_USE_TABLE   
)

◆ NCBI_PARAM_DEF_EX() [5/6]

NCBI_PARAM_DEF_EX ( size_t  ,
VDBGRAPH_LOADER  ,
GC_SIZE  ,
10  ,
eParam_NoThread  ,
VDBGRAPH_LOADER_GC_SIZE   
)

◆ NCBI_PARAM_DEF_EX() [6/6]

NCBI_PARAM_DEF_EX ( size_t  ,
VDBGRAPH_LOADER  ,
MISSING_GC_SIZE  ,
10000  ,
eParam_NoThread  ,
VDBGRAPH_LOADER_MISSING_GC_SIZE   
)

◆ sx_IsNA()

static bool sx_IsNA ( const string s)
static

Variable Documentation

◆ kChunkIdMul

const size_t kChunkIdMul = 4
static

◆ kMainChunkSize

const TSeqPos kMainChunkSize = 100000
static

◆ kMainGraphChunkIdAdd

const size_t kMainGraphChunkIdAdd = 2
static

Definition at line 75 of file vdbgraphloader_impl.cpp.

Referenced by CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ kMainTableChunkIdAdd

const size_t kMainTableChunkIdAdd = 3
static

Definition at line 76 of file vdbgraphloader_impl.cpp.

Referenced by CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ kMidZoomChunkIdAdd

const size_t kMidZoomChunkIdAdd = 1
static

Definition at line 74 of file vdbgraphloader_impl.cpp.

Referenced by CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ kMidZoomChunkSize

const TSeqPos kMidZoomChunkSize = 20000*100
static

◆ kOverviewChunkIdAdd

const size_t kOverviewChunkIdAdd = 0
static

Definition at line 73 of file vdbgraphloader_impl.cpp.

Referenced by CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ kOverviewChunkSize

const TSeqPos kOverviewChunkSize = 20000*5000
static

◆ kTSEId

const int kTSEId = 1
static
Modified on Sat May 25 14:17:52 2024 by modify_doxy.py rev. 669887