#include <ncbi_pch.hpp>
#include <corelib/rwstream.hpp>
#include <objtools/data_loaders/genbank/writer.hpp>
#include <objtools/data_loaders/genbank/impl/processor.hpp>
#include <objtools/data_loaders/genbank/impl/processors.hpp>
#include <objtools/data_loaders/genbank/impl/request_result.hpp>
#include <objtools/data_loaders/genbank/impl/dispatcher.hpp>
#include <objtools/data_loaders/genbank/reader.hpp>
#include <objtools/data_loaders/genbank/impl/statistics.hpp>
#include <objtools/data_loaders/genbank/impl/wgsmaster.hpp>
#include <objtools/data_loaders/genbank/reader_snp.hpp>
#include <objtools/error_codes.hpp>
#include <objmgr/impl/split_parser.hpp>
#include <objmgr/impl/tse_split_info.hpp>
#include <objmgr/impl/bioseq_set_info.hpp>
#include <objmgr/annot_selector.hpp>
#include <objects/id1/id1__.hpp>
#include <objects/id2/ID2_Reply_Data.hpp>
#include <objects/seqsplit/seqsplit__.hpp>
#include <objects/general/general__.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objmgr/objmgr_exception.hpp>
#include <serial/objistr.hpp>
#include <serial/objostr.hpp>
#include <serial/objcopy.hpp>
#include <serial/objistrasnb.hpp>
#include <serial/objostrasnb.hpp>
#include <serial/delaybuf.hpp>
#include <serial/serial.hpp>
#include <serial/iterator.hpp>
#include <util/compress/reader_zlib.hpp>
#include <util/compress/zlib.hpp>
#include <serial/pack_string.hpp>

Include dependency graph for processors.cpp:

Go to the SVN repository for this file.

Macros
#define	NCBI_USE_ERRCODE_X Objtools_Rd_Process

#define	GB_STATS_STOP(action, stat, size) LogStat(action, blob_id, stat, r, size, result)

Functions
	NCBI_PARAM_DEF_EX (bool, GENBANK, SNP_PACK_STRINGS, true, eParam_NoThread, GENBANK_SNP_PACK_STRINGS)

	NCBI_PARAM_DEF_EX (bool, GENBANK, SNP_SPLIT, true, eParam_NoThread, GENBANK_SNP_SPLIT)

	NCBI_PARAM_DEF_EX (bool, GENBANK, SNP_TABLE, true, eParam_NoThread, GENBANK_SNP_TABLE)

	NCBI_PARAM_DEF_EX (bool, GENBANK, USE_MEMORY_POOL, true, eParam_NoThread, GENBANK_USE_MEMORY_POOL)

	NCBI_PARAM_DEF_EX (int, GENBANK, READER_STATS, 0, eParam_NoThread, GENBANK_READER_STATS)

	NCBI_PARAM_DEF_EX (bool, GENBANK, CACHE_RECOMPRESS, true, eParam_NoThread, GENBANK_CACHE_RECOMPRESS)

static bool	s_UseMemoryPool (void)

static bool	s_CacheRecompress (void)

	NCBI_PARAM_DEF_EX (Int8, GENBANK, GI_OFFSET, 0, eParam_NoThread, GENBANK_GI_OFFSET)

static bool	s_CanBeWGSBlob (const CBlob_id &blob_id)

Variables
	BEGIN_LOCAL_NAMESPACE

	END_LOCAL_NAMESPACE

Macro Definition Documentation

◆ GB_STATS_STOP

#define GB_STATS_STOP	(	action,
		stat,
		size
	)	LogStat(action, blob_id, stat, r, size, result)

Definition at line 214 of file processors.cpp.

◆ NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X Objtools_Rd_Process

Definition at line 77 of file processors.cpp.

Function Documentation

◆ NCBI_PARAM_DEF_EX() [1/7]

NCBI_PARAM_DEF_EX	(	bool	,
		GENBANK	,
		CACHE_RECOMPRESS	,
		true	,
		eParam_NoThread	,
		GENBANK_CACHE_RECOMPRESS
	)

References buffer, COSSWriter::COSSWriter(), count, data, eRW_Eof, eRW_Success, COSSWriter::Flush(), i, in(), COSSWriter::m_Output, min(), out(), IReader::PendingCount(), IReader::Read(), ncbi::grid::netcache::search::fields::size, and COSSWriter::Write().

◆ NCBI_PARAM_DEF_EX() [2/7]

NCBI_PARAM_DEF_EX	(	bool	,
		GENBANK	,
		SNP_PACK_STRINGS	,
		true	,
		eParam_NoThread	,
		GENBANK_SNP_PACK_STRINGS
	)

◆ NCBI_PARAM_DEF_EX() [3/7]

NCBI_PARAM_DEF_EX	(	bool	,
		GENBANK	,
		SNP_SPLIT	,
		true	,
		eParam_NoThread	,
		GENBANK_SNP_SPLIT
	)

◆ NCBI_PARAM_DEF_EX() [4/7]

NCBI_PARAM_DEF_EX	(	bool	,
		GENBANK	,
		SNP_TABLE	,
		true	,
		eParam_NoThread	,
		GENBANK_SNP_TABLE
	)

◆ NCBI_PARAM_DEF_EX() [5/7]

NCBI_PARAM_DEF_EX	(	bool	,
		GENBANK	,
		USE_MEMORY_POOL	,
		true	,
		eParam_NoThread	,
		GENBANK_USE_MEMORY_POOL
	)

◆ NCBI_PARAM_DEF_EX() [6/7]

NCBI_PARAM_DEF_EX	(	int	,
		GENBANK	,
		READER_STATS	,
		0	,
		eParam_NoThread	,
		GENBANK_READER_STATS
	)

◆ NCBI_PARAM_DEF_EX() [7/7]

NCBI_PARAM_DEF_EX	(	Int8	,
		GENBANK	,
		GI_OFFSET	,
		0	,
		eParam_NoThread	,
		GENBANK_GI_OFFSET
	)

◆ s_CacheRecompress()

static bool s_CacheRecompress ( void )

static

Definition at line 349 of file processors.cpp.

References NCBI_PARAM_TYPE, and ncbi::grid::netcache::search::s_Value().

Referenced by CProcessor_ID2::ProcessData(), CProcessor_ID2::SaveData(), CProcessor_ID2AndSkel::SaveDataAndSkel(), and CProcessor_ID2_Split::SaveSplitData().

◆ s_CanBeWGSBlob()

static bool s_CanBeWGSBlob ( const CBlob_id & blob_id )

inlinestatic

Definition at line 605 of file processors.cpp.

References CProcessor_ExtAnnot::IsExtAnnot().

Referenced by CProcessor_ID2::ProcessData(), and CProcessor_SE::ProcessObjStream().

◆ s_UseMemoryPool()

static bool s_UseMemoryPool ( void )

static

Definition at line 342 of file processors.cpp.

References NCBI_PARAM_TYPE, and ncbi::grid::netcache::search::s_Value().

Referenced by CProcessor::SetSeqEntryReadHooks().

Variable Documentation

◆ BEGIN_LOCAL_NAMESPACE

BEGIN_LOCAL_NAMESPACE

Definition at line 601 of file processors.cpp.

◆ END_LOCAL_NAMESPACE

END_LOCAL_NAMESPACE

Definition at line 611 of file processors.cpp.

Macros

Functions

Variables