gbnative.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbi_param.hpp>
#include <objtools/data_loaders/genbank/gbnative.hpp>
#include <objtools/data_loaders/genbank/gbloader_params.h>
#include <objtools/data_loaders/genbank/impl/dispatcher.hpp>
#include <objtools/data_loaders/genbank/impl/request_result.hpp>
#include <objtools/data_loaders/genbank/impl/wgsmaster.hpp>
#include <objtools/data_loaders/genbank/reader_interface.hpp>
#include <objtools/data_loaders/genbank/writer_interface.hpp>
#include <objtools/data_loaders/genbank/readers.hpp>
#include <objtools/data_loaders/genbank/seqref.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/impl/bioseq_info.hpp>
#include <objmgr/impl/data_source.hpp>
#include <objmgr/data_loader_factory.hpp>
#include <objmgr/annot_selector.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <corelib/ncbithr.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/plugin_manager_impl.hpp>
#include <corelib/plugin_manager_store.hpp>
#include <algorithm>

Include dependency graph for gbnative.cpp:

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Classes
class	CGBReaderRequestResult

Macros
#define	REGISTER_READER_ENTRY_POINTS   1
#define	NCBI_USE_ERRCODE_X   Objtools_GBLoader
#define	GBLOADER_NAME   "GBLOADER"
#define	GBLOADER_HUP_NAME   "GBLOADER-HUP"
#define	DEFAULT_ID_GC_SIZE   10000
#define	DEFAULT_ID_EXPIRATION_TIMEOUT   2*3600

Functions
	NCBI_PARAM_DECL (string, GENBANK, READER_NAME)
	NCBI_PARAM_DEF_EX (string, GENBANK, READER_NAME, "", eParam_NoThread, GENBANK_READER_NAME)
typedef	NCBI_PARAM_TYPE (GENBANK, READER_NAME) TGenbankReaderName
	NCBI_PARAM_DECL (string, GENBANK, WRITER_NAME)
	NCBI_PARAM_DEF_EX (string, GENBANK, WRITER_NAME, "", eParam_NoThread, GENBANK_WRITER_NAME)
typedef	NCBI_PARAM_TYPE (GENBANK, WRITER_NAME) TGenbankWriterName
	NCBI_PARAM_DECL (bool, GENBANK, REGISTER_READERS)
	NCBI_PARAM_DEF_EX (bool, GENBANK, REGISTER_READERS, true, eParam_NoThread, GENBANK_REGISTER_READERS)
static bool	s_ForceDriver (const string &name)
static bool	x_IsCDDBlob (const CBlob_Info &blob_info)
static bool	x_IsEmptyCDD (const CTSE_Info &tse)
	USING_SCOPE (objects)

Variables
static const char *const	DEFAULT_DRV_ORDER = "id2"
static const char *const	DEFAULT_HUP_DRV_ORDER = "pubseqos2:pubseqos"
static const bool	s_LoadBulkBlobs = true

Macro Definition Documentation

DEFAULT_ID_EXPIRATION_TIMEOUT

#define DEFAULT_ID_EXPIRATION_TIMEOUT   2*3600

Definition at line 107 of file gbnative.cpp.

DEFAULT_ID_GC_SIZE

#define DEFAULT_ID_GC_SIZE   10000

Definition at line 106 of file gbnative.cpp.

GBLOADER_HUP_NAME

#define GBLOADER_HUP_NAME   "GBLOADER-HUP"

Definition at line 104 of file gbnative.cpp.

GBLOADER_NAME

#define GBLOADER_NAME   "GBLOADER"

Definition at line 103 of file gbnative.cpp.

NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X   Objtools_GBLoader

Definition at line 72 of file gbnative.cpp.

REGISTER_READER_ENTRY_POINTS

#define REGISTER_READER_ENTRY_POINTS   1

Definition at line 44 of file gbnative.cpp.

Function Documentation

NCBI_PARAM_DECL() [1/3]

NCBI_PARAM_DECL	(	bool	,
		GENBANK	,
		REGISTER_READERS
	)

NCBI_PARAM_DECL() [2/3]

NCBI_PARAM_DECL	(	string	,
		GENBANK	,
		READER_NAME
	)

NCBI_PARAM_DECL() [3/3]

NCBI_PARAM_DECL	(	string	,
		GENBANK	,
		WRITER_NAME
	)

NCBI_PARAM_DEF_EX() [1/3]

NCBI_PARAM_DEF_EX	(	bool	,
		GENBANK	,
		REGISTER_READERS	,
		true	,
		eParam_NoThread	,
		GENBANK_REGISTER_READERS
	)

NCBI_PARAM_DEF_EX() [2/3]

NCBI_PARAM_DEF_EX	(	string	,
		GENBANK	,
		READER_NAME	,
		""	,
		eParam_NoThread	,
		GENBANK_READER_NAME
	)

NCBI_PARAM_DEF_EX() [3/3]

NCBI_PARAM_DEF_EX	(	string	,
		GENBANK	,
		WRITER_NAME	,
		""	,
		eParam_NoThread	,
		GENBANK_WRITER_NAME
	)

NCBI_PARAM_TYPE() [1/2]

typedef NCBI_PARAM_TYPE	(	GENBANK	,
		READER_NAME
	)

Referenced by CGBDataLoader_Native::x_GetReaderManager(), and CGBDataLoader_Native::x_GetWriterManager().

NCBI_PARAM_TYPE() [2/2]

typedef NCBI_PARAM_TYPE	(	GENBANK	,
		WRITER_NAME
	)

s_ForceDriver()

static bool s_ForceDriver ( const string &  name )

static

Definition at line 485 of file gbnative.cpp.

Referenced by CGBDataLoader_Native::x_CreateReader(), and CGBDataLoader_Native::x_CreateWriter().

USING_SCOPE()

USING_SCOPE

(

objects

)

x_IsCDDBlob()

static bool x_IsCDDBlob ( const CBlob_Info &  blob_info )

static

Definition at line 1503 of file gbnative.cpp.

References NStr::EqualNocase(), fBlobHasExtAnnot, CBlob_Annot_Info::GetAnnotInfo(), CBlob_Info::GetAnnotInfo(), CBlob_Annot_Info::GetNamedAnnotNames(), CBlob_Info::IsSetAnnotInfo(), kCDDAnnotName, and CBlob_Info::Matches().

Referenced by CGBDataLoader_Native::GetCDDAnnots().

x_IsEmptyCDD()

static bool x_IsEmptyCDD ( const CTSE_Info &  tse )

static

Definition at line 1529 of file gbnative.cpp.

References CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), CTSE_Info::GetTSECore(), and CTSE_Info::x_NeedsDelayedMainChunk().

Referenced by CGBDataLoader_Native::GetCDDAnnots().

Variable Documentation

DEFAULT_DRV_ORDER

const char* const DEFAULT_DRV_ORDER = "id2"

static

Definition at line 99 of file gbnative.cpp.

Referenced by CGBDataLoader_Native::GetReaderWriterName().

DEFAULT_HUP_DRV_ORDER

const char* const DEFAULT_HUP_DRV_ORDER = "pubseqos2:pubseqos"

static

Definition at line 101 of file gbnative.cpp.

Referenced by CGBDataLoader_Native::GetReaderWriterName().

s_LoadBulkBlobs

const bool s_LoadBulkBlobs = true

static

Definition at line 751 of file gbnative.cpp.

Referenced by CGBDataLoader_Native::GetSequenceStates().