src/objtools/data_loaders/genbank/processors.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/rwstream.hpp>
#include <objtools/data_loaders/genbank/writer.hpp>
#include <objtools/data_loaders/genbank/processor.hpp>
#include <objtools/data_loaders/genbank/processors.hpp>
#include <objtools/data_loaders/genbank/request_result.hpp>
#include <objtools/data_loaders/genbank/dispatcher.hpp>
#include <objtools/data_loaders/genbank/reader.hpp>
#include <objtools/data_loaders/genbank/statistics.hpp>
#include <objtools/data_loaders/genbank/reader_snp.hpp>
#include <objtools/data_loaders/genbank/split_parser.hpp>
#include <objtools/error_codes.hpp>
#include <objmgr/impl/tse_split_info.hpp>
#include <objects/id1/id1__.hpp>
#include <objects/id2/ID2_Reply_Data.hpp>
#include <objects/seqsplit/ID2S_Split_Info.hpp>
#include <objects/seqsplit/ID2S_Chunk.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.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 source code of this file.

Defines

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

Typedefs

typedef vector< char > TOctetString
typedef list< TOctetString * > TOctetStringSequence
typedef vector< char > TOctetString
typedef list< TOctetString * > TOctetStringSequence

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)
CProcessor::TMagic s_GetMagic (const char *s)
static bool s_UseMemoryPool (void)
static bool s_CacheRecompress (void)
CRef< CWriter::CBlobStream > OpenStream (CWriter *writer, CReaderRequestResult &result, const CProcessor::TBlobId &blob_id, CProcessor::TChunkId chunk_id, const CProcessor *processor)

Variables

const TOctetStringSequence & m_Input
TOctetStringSequence::const_iterator m_CurVec
size_t m_CurPos
size_t m_CurSize
TOctetStringSequence & m_Output
CGBRequestStatistics::EStatType m_StatType
const string m_Descr
const CBlob_id & m_Blob_id
int m_ChunkId

Define Documentation

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

Definition at line 213 of file processors.cpp.

#define NCBI_USE_ERRCODE_X   Objtools_Rd_Process
 

Definition at line 76 of file processors.cpp.

Typedef Documentation

typedef vector<char> TOctetString
 

Definition at line 178 of file processors.cpp.

typedef vector<char> TOctetString
 

Definition at line 117 of file processors.cpp.

typedef list<TOctetString*> TOctetStringSequence
 

Definition at line 179 of file processors.cpp.

typedef list<TOctetString*> TOctetStringSequence
 

Definition at line 118 of file processors.cpp.

Function Documentation

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

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

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

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

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

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

CRef<CWriter::CBlobStream> @1::OpenStream (  CWriter *  writer,
CReaderRequestResult &  result,
const CProcessor::TBlobId &  blob_id,
CProcessor::TChunkId  chunk_id,
const CProcessor *  processor
)  [inline, static]
 

Definition at line 464 of file processors.cpp.

References _ASSERT, and CWriter::OpenBlobStream().

Referenced by CProcessor_St_SE::SaveBlob(), CProcessor_ID1::SaveBlob(), CProcessor_ID2::SaveData(), CProcessor_ID2AndSkel::SaveDataAndSkel(), CProcessor_St_SE::SaveNoBlob(), and CProcessor_St_SE_SNPT::SaveSNPBlob().

static bool s_CacheRecompress (  void   )  [static]
 

Definition at line 347 of file processors.cpp.

References NCBI_PARAM_TYPE.

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

CProcessor::TMagic @0::s_GetMagic (  const char *  s  )  [static]
 

Definition at line 100 of file processors.cpp.

Referenced by CProcessor_ExtAnnot::GetMagic(), CProcessor_ID2AndSkel::GetMagic(), CProcessor_ID2::GetMagic(), CProcessor_St_SE_SNPT::GetMagic(), CProcessor_St_SE::GetMagic(), CProcessor_SE_SNP::GetMagic(), CProcessor_SE::GetMagic(), CProcessor_ID1_SNP::GetMagic(), and CProcessor_ID1::GetMagic().

static bool s_UseMemoryPool (  void   )  [static]
 

Definition at line 340 of file processors.cpp.

References NCBI_PARAM_TYPE.

Referenced by CProcessor::SetSeqEntryReadHooks().

Variable Documentation

const CBlob_id& m_Blob_id
 

Definition at line 2017 of file processors.cpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO().

int m_ChunkId
 

Definition at line 2018 of file processors.cpp.

size_t m_CurPos
 

Definition at line 172 of file processors.cpp.

size_t m_CurSize
 

Definition at line 173 of file processors.cpp.

TOctetStringSequence::const_iterator m_CurVec
 

Definition at line 171 of file processors.cpp.

const string m_Descr
 

Definition at line 2016 of file processors.cpp.

const TOctetStringSequence& m_Input
 

Definition at line 170 of file processors.cpp.

TOctetStringSequence& m_Output
 

Definition at line 203 of file processors.cpp.

Referenced by BEGIN_NAMED_CLASS_INFO(), and COStreamBuffer::FlushBuffer().

CGBRequestStatistics::EStatType m_StatType
 

Definition at line 2015 of file processors.cpp.

Generated on Mon Dec 7 09:27:39 2009 for NCBI C++ ToolKit by  doxygen 1.4.6
Modified on Mon Dec 07 16:22:07 2009 by modify_doxy.py rev. 173732