NCBI C++ ToolKit
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CPubseqGatewayCacheBioseqInfo Class Reference

Search Toolkit Book for CPubseqGatewayCacheBioseqInfo

#include "psg_cache_bioseq_info.hpp"
(Private to src/objtools/pubseq_gateway/cache.)

+ Inheritance diagram for CPubseqGatewayCacheBioseqInfo:
+ Collaboration diagram for CPubseqGatewayCacheBioseqInfo:

Public Member Functions

 CPubseqGatewayCacheBioseqInfo (const string &file_name)
 
 ~CPubseqGatewayCacheBioseqInfo () override
 
void Open ()
 
vector< CBioseqInfoRecord > Fetch (CBioseqInfoFetchRequest const &request)
 
vector< CBioseqInfoRecord > FetchLast (void)
 
- Public Member Functions inherited from CPubseqGatewayCacheBase
 CPubseqGatewayCacheBase (const string &file_name)
 
virtual ~CPubseqGatewayCacheBase ()=default
 
void Open ()
 
void UseReadAhead (bool value)
 

Static Public Member Functions

static string PackKey (const string &accession, int version)
 
static string PackKey (const string &accession, int version, int seq_id_type)
 
static string PackKey (const string &accession, int version, int seq_id_type, int64_t gi)
 
static bool UnpackKey (const char *key, size_t key_sz, int &version, int &seq_id_type, int64_t &gi)
 
static bool UnpackKey (const char *key, size_t key_sz, string &accession, int &version, int &seq_id_type, int64_t &gi)
 

Private Member Functions

bool x_ExtractRecord (CBioseqInfoRecord &record, lmdb::val const &value) const
 
string x_MakeLookupKey (CBioseqInfoFetchRequest const &request) const
 
bool x_IsMatchingRecord (CBioseqInfoFetchRequest const &request, int version, int seq_id_type, int64_t gi) const
 
void ResetDbi ()
 

Private Attributes

unique_ptr< lmdb::dbi, function< void(lmdb::dbi *)> > m_Dbi
 

Additional Inherited Members

- Protected Member Functions inherited from CPubseqGatewayCacheBase
CLMDBReadOnlyTxn BeginReadTxn ()
 
- Protected Attributes inherited from CPubseqGatewayCacheBase
string m_FileName
 
unique_ptr< lmdb::env > m_Env
 

Detailed Description

Definition at line 47 of file psg_cache_bioseq_info.hpp.

Constructor & Destructor Documentation

◆ CPubseqGatewayCacheBioseqInfo()

BEGIN_IDBLOB_SCOPE CPubseqGatewayCacheBioseqInfo::CPubseqGatewayCacheBioseqInfo ( const string &  file_name)
explicit

Definition at line 82 of file psg_cache_bioseq_info.cpp.

◆ ~CPubseqGatewayCacheBioseqInfo()

CPubseqGatewayCacheBioseqInfo::~CPubseqGatewayCacheBioseqInfo ( )
overridedefault

Member Function Documentation

◆ Fetch()

vector< CBioseqInfoRecord > CPubseqGatewayCacheBioseqInfo::Fetch ( CBioseqInfoFetchRequest const &  request)

Definition at line 167 of file psg_cache_bioseq_info.cpp.

References CPubseqGatewayCacheBase::BeginReadTxn(), CBioseqInfoFetchRequest::eAccession, CBioseqInfoFetchRequest::GetAccession(), CBioseqInfoFetchRequest::HasField(), ncbi::grid::netcache::search::fields::key, m_Dbi, MDB_GET_CURRENT, MDB_NEXT, MDB_SET_RANGE, lmdb::cursor::open(), PackedKeySize(), UnpackKey(), val, dtl::version, x_ExtractRecord(), x_IsMatchingRecord(), and x_MakeLookupKey().

Referenced by ApplyInheritedSeqIds().

◆ FetchLast()

vector< CBioseqInfoRecord > CPubseqGatewayCacheBioseqInfo::FetchLast ( void  )

Definition at line 215 of file psg_cache_bioseq_info.cpp.

References CPubseqGatewayCacheBase::BeginReadTxn(), ncbi::grid::netcache::search::fields::key, m_Dbi, MDB_LAST, MDB_NEXT, lmdb::cursor::open(), UnpackKey(), val, dtl::version, and x_ExtractRecord().

◆ Open()

void CPubseqGatewayCacheBioseqInfo::Open ( void  )

Definition at line 89 of file psg_cache_bioseq_info.cpp.

References CPubseqGatewayCacheBase::BeginReadTxn(), lmdb::dbi::close(), m_Dbi, CPubseqGatewayCacheBase::m_Env, CPubseqGatewayCacheBase::Open(), and lmdb::dbi::open().

◆ PackKey() [1/3]

string CPubseqGatewayCacheBioseqInfo::PackKey ( const string &  accession,
int  version 
)
static

Definition at line 247 of file psg_cache_bioseq_info.cpp.

References kPackedVersionSz, kPackedZeroSz, CPubseqGatewayCachePackBytes::Pack(), and dtl::version.

Referenced by CPubseqGatewayCache::PackBioseqInfoKey(), and x_MakeLookupKey().

◆ PackKey() [2/3]

string CPubseqGatewayCacheBioseqInfo::PackKey ( const string &  accession,
int  version,
int  seq_id_type 
)
static

Definition at line 258 of file psg_cache_bioseq_info.cpp.

References kPackedSeqIdTypeSz, kPackedVersionSz, kPackedZeroSz, CPubseqGatewayCachePackBytes::Pack(), and dtl::version.

◆ PackKey() [3/3]

string CPubseqGatewayCacheBioseqInfo::PackKey ( const string &  accession,
int  version,
int  seq_id_type,
int64_t  gi 
)
static

Definition at line 270 of file psg_cache_bioseq_info.cpp.

References kPackedGISz, kPackedSeqIdTypeSz, kPackedVersionSz, kPackedZeroSz, CPubseqGatewayCachePackBytes::Pack(), and dtl::version.

◆ ResetDbi()

void CPubseqGatewayCacheBioseqInfo::ResetDbi ( )
private

◆ UnpackKey() [1/2]

bool CPubseqGatewayCacheBioseqInfo::UnpackKey ( const char *  key,
size_t  key_sz,
int &  version,
int &  seq_id_type,
int64_t &  gi 
)
static

Definition at line 284 of file psg_cache_bioseq_info.cpp.

References ncbi::grid::netcache::search::fields::key, kPackedGISz, kPackedSeqIdTypeSz, kPackedVersionSz, kPackedZeroSz, CPubseqGatewayCacheUnpackBytes::Unpack(), and dtl::version.

Referenced by Fetch(), FetchLast(), CPubseqGatewayCache::UnpackBioseqInfoKey(), and UnpackKey().

◆ UnpackKey() [2/2]

bool CPubseqGatewayCacheBioseqInfo::UnpackKey ( const char *  key,
size_t  key_sz,
string &  accession,
int &  version,
int &  seq_id_type,
int64_t &  gi 
)
static

Definition at line 302 of file psg_cache_bioseq_info.cpp.

References ncbi::grid::netcache::search::fields::key, kPackedGISz, kPackedSeqIdTypeSz, kPackedVersionSz, kPackedZeroSz, UnpackKey(), and dtl::version.

◆ x_ExtractRecord()

bool CPubseqGatewayCacheBioseqInfo::x_ExtractRecord ( CBioseqInfoRecord &  record,
lmdb::val const &  value 
) const
private

Definition at line 142 of file psg_cache_bioseq_info.cpp.

References info, set< Key, Compare >::insert(), CBioseqInfoRecord::SetDateChanged(), CBioseqInfoRecord::SetHash(), CBioseqInfoRecord::SetLength(), CBioseqInfoRecord::SetMol(), CBioseqInfoRecord::SetName(), CBioseqInfoRecord::SetSat(), CBioseqInfoRecord::SetSatKey(), CBioseqInfoRecord::SetSeqIds(), CBioseqInfoRecord::SetSeqState(), CBioseqInfoRecord::SetState(), CBioseqInfoRecord::SetTaxId(), and rapidjson::value.

Referenced by Fetch(), and FetchLast().

◆ x_IsMatchingRecord()

bool CPubseqGatewayCacheBioseqInfo::x_IsMatchingRecord ( CBioseqInfoFetchRequest const &  request,
int  version,
int  seq_id_type,
int64_t  gi 
) const
private

Definition at line 124 of file psg_cache_bioseq_info.cpp.

References CBioseqInfoFetchRequest::eGI, CBioseqInfoFetchRequest::eSeqIdType, CBioseqInfoFetchRequest::eVersion, CBioseqInfoFetchRequest::GetGI(), CBioseqInfoFetchRequest::GetSeqIdType(), CBioseqInfoFetchRequest::GetVersion(), CBioseqInfoFetchRequest::HasField(), and dtl::version.

Referenced by Fetch().

◆ x_MakeLookupKey()

string CPubseqGatewayCacheBioseqInfo::x_MakeLookupKey ( CBioseqInfoFetchRequest const &  request) const
private

Definition at line 106 of file psg_cache_bioseq_info.cpp.

References CBioseqInfoFetchRequest::eGI, CBioseqInfoFetchRequest::eSeqIdType, CBioseqInfoFetchRequest::eVersion, CBioseqInfoFetchRequest::GetAccession(), CBioseqInfoFetchRequest::GetGI(), CBioseqInfoFetchRequest::GetSeqIdType(), CBioseqInfoFetchRequest::GetVersion(), CBioseqInfoFetchRequest::HasField(), and PackKey().

Referenced by Fetch().

Member Data Documentation

◆ m_Dbi

unique_ptr<lmdb::dbi, function<void(lmdb::dbi*)> > CPubseqGatewayCacheBioseqInfo::m_Dbi
private

Definition at line 70 of file psg_cache_bioseq_info.hpp.

Referenced by Fetch(), FetchLast(), and Open().

The documentation for this class was generated from the following files:
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Modified on Fri Sep 20 14:58:08 2024 by modify_doxy.py rev. 669887