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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCPrimeCacheApplication.html below:

NCBI C++ ToolKit: CPrimeCacheApplication Class Reference

Search Toolkit Book for CPrimeCacheApplication

virtual void Init (void) Initialize the application. More...
virtual int Run (void) Run the application. More...
virtual void Exit (void) Cleanup on application exit. More...
void x_Read_Ids (CNcbiIstream &istr, set< CSeq_id_Handle > &ids) void x_Process_Ids (const set< CSeq_id_Handle > &ids, CNcbiOstream &ostr_seqids, unsigned delta_level, size_t count) void x_Process_Fasta (CNcbiIstream &istr, CNcbiOstream &ostr_seqids) void x_Process_SeqEntry (CNcbiIstream &istr, CNcbiOstream &ostr_seqids, ESerialDataFormat serial_fmt, set< CSeq_id_Handle > &delta_ids, size_t &count) void x_ExtractAndIndex (const CSeq_entry &entry, CAsnIndex::TTimestamp timestamp, CAsnIndex::TChunkId chunk_id, CAsnIndex::TOffset offset, CAsnIndex::TSize size) bool x_StripSeqEntry (CScope &scope, CSeq_entry &entry, set< CSeq_id_Handle > &trimmed_bioseqs) void x_CacheSeqEntry (CNcbiIstream &istr, CNcbiOstream &ostr_seqids, ESerialDataFormat serial_fmt, set< CSeq_id_Handle > &delta_ids, size_t &count) void x_SplitAndCacheSeqEntry (CNcbiIstream &istr, CNcbiOstream &ostr_seqids, ESerialDataFormat serial_fmt) void x_ExtractDelta (CBioseq_Handle bsh, set< CSeq_id_Handle > &delta_ids) void x_UpsertDescriptor (list< CRef< CSeqdesc > > &descs, CRef< CSeqdesc > new_desc) enum EAppNameType { eBaseName , eFullName , eRealName } static CNcbiApplication * Instance (void) Singleton method. More...
static CNcbiApplicationAPI * Instance (void) Singleton method. More...
static CNcbiApplicationGuard InstanceGuard (void) Singleton method. More...
static SSystemMutex & GetInstanceMutex (void) Mutex for application singleton object. More...
static string GetAppName (EAppNameType name_type=eBaseName, int argc=0, const char *const *argv=NULL) enum EPreparseArgs { ePreparse_Continue , ePreparse_Exit } Result of PreparseArgs() More...
enum EDisableArgDesc { fDisableStdArgs = 0x01 } Disable argument descriptions. More...
enum EHideStdArgs {
  fHideLogfile = CArgDescriptions::fHideLogfile , fHideConffile = CArgDescriptions::fHideConffile , fHideVersion = CArgDescriptions::fHideVersion , fHideFullVersion = CArgDescriptions::fHideFullVersion ,
  fHideDryRun = CArgDescriptions::fHideDryRun , fHideHelp = CArgDescriptions::fHideHelp , fHideFullHelp = CArgDescriptions::fHideFullHelp , fHideXmlHelp = CArgDescriptions::fHideXmlHelp ,
  fHideAll = CArgDescriptions::fHideAll
} Which standard flag's descriptions should not be displayed in the usage message. More...
enum EStdioSetup {
  fNoSyncWithStdio = 0x01 , fDefault_CinBufferSize = 0x02 , fBinaryCin = 0x04 , fBinaryCout = 0x08 ,
  fDefault_SyncWithStdio = 0x00
} Flags to adjust standard I/O streams' behaviour. More...
enum EExitMode { eNoExits , eExceptionalExits , eAllExits } When to return a user-set exit code. More...
enum EAppFlags { fSkipSafeStaticDestroy = 1 << 0 } typedef int TDisableArgDesc Binary OR of "EDisableArgDesc". More...
typedef int THideStdArgs Binary OR of "EHideStdArgs". More...
typedef int TStdioSetupFlags Binary OR of "EStdioSetup". More...
typedef int TAppFlags virtual EPreparseArgs PreparseArgs (int argc, const char *const *argv) Check the command line arguments before parsing them. More...
void DisableArgDescriptions (TDisableArgDesc disable=fDisableStdArgs) void HideStdArgs (THideStdArgs hide_mask) Set the hide mask for the Hide Std Flags. More...
void SetStdioFlags (TStdioSetupFlags stdio_flags) Adjust the behavior of standard I/O streams. More...
void SetVersion (const CVersionInfo &version) Set the version number for the program. More...
void SetVersion (const CVersionInfo &version, const SBuildInfo &build_info) void SetVersionByBuild (int major) void SetFullVersion (CRef< CVersionAPI > version) Set version data for the program. More...
virtual void SetupArgDescriptions (CArgDescriptions *arg_desc) Setup the command line argument descriptions. More...
const CArgDescriptions * GetArgDescriptions (void) const Get argument descriptions (set by SetupArgDescriptions) More...
bool SetupDiag (EAppDiagStream diag) Setup the application diagnostic stream. More...
virtual bool LoadConfig (CNcbiRegistry &reg, const string *conf, CNcbiRegistry::TFlags reg_flags) Load settings from the configuration file to the registry. More...
virtual bool LoadConfig (CNcbiRegistry &reg, const string *conf) Load settings from the configuration file to the registry. More...
CNcbiRegistry & GetRWConfig (void) Get the application's cached configuration parameters, accessible for read-write for an application's internal use only. More...
void SetProgramDisplayName (const string &app_name) Set program's display name. More...
virtual void AppStart (void) Method to be called before application start. More...
virtual void AppStop (int exit_code) Method to be called before application exit. More...
void SetExitCode (int exit_code, EExitMode when=eExceptionalExits) Force the program to return a specific exit code later, either when it exits due to an exception or unconditionally. More...
void SetAppFlags (TAppFlags flags) void ExecuteOnExitActions () Should only be called from the destructors of classes derived from CNcbiApplicationAPI - if it is necessary to access their data members and virtual methods; or to dynamic_cast<> from the base app class. More...
void SetPhoneHomePolicy (IPhoneHomePolicy *policy, ENcbiOwnership ownership=eNoOwnership) Set Phone Home Policy. More...
IPhoneHomePolicy * GetPhoneHomePolicy () const Return pointer to current Phone Home Policy or NULL. More...
static CRWLock & GetInstanceLock (void) static string FindProgramExecutablePath (int argc, const char *const *argv, string *real_path=0) Find the application's executable file. More...

Definition at line 145 of file prime_cache.cpp.

◆ CPrimeCacheApplication() CPrimeCacheApplication::CPrimeCacheApplication ( ) inline ◆ Exit() void CPrimeCacheApplication::Exit ( void ) privatevirtual

Cleanup on application exit.

Perform cleanup before exiting. The default behavior of this is "do nothing". If you have special cleanup logic that needs to be performed, then you must override this method with your own logic.

Reimplemented from CNcbiApplicationAPI.

Definition at line 1398 of file prime_cache.cpp.

References SetDiagStream().

◆ Init() void CPrimeCacheApplication::Init ( void ) privatevirtual

Initialize the application.

The default behavior of this is "do nothing". If you have special initialization logic that needs to be peformed, then you must override this method with your own logic.

Reimplemented from CNcbiApplicationAPI.

Definition at line 281 of file prime_cache.cpp.

References CLocalTaxon::AddArguments(), CArgAllow_Strings::Allow(), CArgDescriptions::eExcludes, CArgDescriptions::eInputFile, CArgDescriptions::eInteger, CArgDescriptions::eOutputFile, CArgDescriptions::eRequires, CArgDescriptions::eString, CNcbiApplicationAPI::GetArguments(), ITERATE, and CNcbiApplicationAPI::SetupArgDescriptions().

◆ Run() int CPrimeCacheApplication::Run ( void ) privatevirtual

Run the application.

It is defined as a pure virtual method – so you must(!) supply the Run() method to implement the application-specific logic.

Returns: Exit code.

Implements CNcbiApplicationAPI.

Definition at line 1039 of file prime_cache.cpp.

References CSerialObject::Assign(), CSeq_id_Handle::AsString(), CPrimeCacheApplication::SOrgData::biosource, count, CDir::CreatePath(), CSeq_id_Base::e_General, CAsnIndex::e_main, CSeqdesc_Base::e_Molinfo, CAsnIndex::e_seq_id, CSeqdesc_Base::e_Source, eGetId_Best, eGetId_Canonical, set< Key, Compare >::empty(), CBDB_RawFile::eReadWriteCreate, eSerial_AsnBinary, eSerial_AsnText, CSignal::eSignal_HUP, CSignal::eSignal_INT, CSignal::eSignal_QUIT, CSignal::eSignal_TERM, eUnknown, CFile::Exists(), CDir::Exists(), CArgValue::fAppend, CNcbiApplicationAPI::GetArgs(), NASNCacheFileName::GetBDBIndex(), GetDiagContext(), CSeq_id_Handle::GetHandle(), CObjectManager::GetInstance(), CBioSource_Base::GetOrg(), CLocalTaxon::GetOrgRef(), CDirEntry::GetPath(), CDiagContext::GetRequestContext(), CRequestContext::GetRequestTimer(), GetSeqId(), CSeqdesc_Base::GetSource(), i, CInputStreamSource::InitManifest(), CInputStreamSource::InitStream(), set< Key, Compare >::insert(), ncbi::grid::netcache::search::fields::key, m_CachePath, m_ExtractDelta, m_Genome, m_id_type, m_InstMol, m_MainIndex, m_MaxDeltaLevel, m_MolInfo, m_Orgs, m_other_descs, m_PreviousExecutionIds, m_PreviousExecutionRuns, m_SeqIdChunk, m_SeqIdIndex, m_SequenceTaxids, m_SequenceUniprotSources, m_StripInstMol, NCBI_THROW, NcbiGetlineEOL(), NStr::NumericToString(), om, CBDB_File::Open(), CObjectIStream::Open(), CSeqIdChunkFile::OpenForWrite(), CPrimeCacheApplication::SOrgData::orgref, CDiagContext::PrintRequestStart(), CDiagContext::PrintRequestStop(), CRef< C, Locker >::Reset(), CMolInfo_Base::SetBiomol(), CBDB_RawFile::SetCacheSize(), CSeqdesc_Base::SetMolinfo(), CRequestContext::SetRequestStatus(), NStr::Split(), CStopWatch::Start(), NStr::StartsWith(), NStr::StringToInt(), tag, TAX_ID_FROM, CSignal::TrapSignals(), NStr::TruncateSpaces(), NStr::TruncateSpacesInPlace(), CSeqdesc_Base::Which(), x_Process_Fasta(), x_Process_Ids(), x_Process_SeqEntry(), x_Read_Ids(), and ZERO_TAX_ID.

◆ x_CacheSeqEntry()

Definition at line 788 of file prime_cache.cpp.

References CScope::AddTopLevelSeqEntry(), count, CTime::eCurrent, set< Key, Compare >::empty(), Error(), eUnknown, CChunkFile::GetChunkSerialNum(), GetId(), CObjectManager::GetInstance(), CChunkFile::GetOffset(), CTime::GetTimeT(), CSignal::IsSignaled(), LOG_POST, m_CachePath, m_ExtractDelta, m_id_type, m_MainChunk, m_StripInstMol, NCBI_THROW, offset, om, CObjectIStream::Open(), CChunkFile::OpenForWrite(), CCache_blob::Pack(), CSeq_entry::Parentize(), CCache_blob_Base::SetTimestamp(), ncbi::grid::netcache::search::fields::size, CStopWatch::Start(), sw, CChunkFile::Write(), x_ExtractAndIndex(), x_ExtractDelta(), and x_StripSeqEntry().

Referenced by x_Process_SeqEntry().

◆ x_ExtractAndIndex()

Definition at line 451 of file prime_cache.cpp.

References CSeq_id_Handle::GetHandle(), CSeqIdChunkFile::GetOffset(), CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), IndexABioseq(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), ITERATE, m_CachedIds, m_MainIndex, m_SeqIdChunk, m_SeqIdIndex, offset, ncbi::grid::netcache::search::fields::size, and CSeqIdChunkFile::Write().

Referenced by x_CacheSeqEntry(), x_Process_Fasta(), and x_Process_Ids().

◆ x_ExtractDelta()

Definition at line 1374 of file prime_cache.cpp.

References CDelta_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CSeq_id_Handle::GetHandle(), CBioseq_Handle::GetInst(), set< Key, Compare >::insert(), CSeq_ext_Base::IsDelta(), CSeq_inst_Base::IsSetExt(), and ITERATE.

Referenced by x_CacheSeqEntry(), and x_Process_Ids().

◆ x_Process_Fasta()

Definition at line 506 of file prime_cache.cpp.

References CSeq_id_Handle::AsString(), CFastaReader::AtEOF(), CPrimeCacheApplication::SOrgData::biosource, count, CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::e_Source, CTime::eCurrent, CBioSource_Base::eGenome_unknown, CSeq_inst_Base::eMol_aa, Error(), eUnknown, CFastaReader::fAddMods, CFastaReader::fAssumeNuc, CFastaReader::fAssumeProt, CFastaReader::fDisableParseRange, CFastaReader::fForceType, flags, CFastaReader::fNoUserObjs, CFastaReader::fRequireID, CSeq_descr_Base::Get(), CNcbiApplicationAPI::GetArgs(), CMolInfo_Base::GetBiomol(), CChunkFile::GetChunkSerialNum(), CMolInfo_Base::GetCompleteness(), CSeq_entry::GetDescr(), GetId(), CObjectManager::GetInstance(), CSeqdesc_Base::GetMolinfo(), CChunkFile::GetOffset(), CSeq_entry_Base::GetSeq(), CTime::GetTimeT(), CMolInfo_Base::IsSetBiomol(), CMolInfo_Base::IsSetCompleteness(), CSeq_entry::IsSetDescr(), CSignal::IsSignaled(), LOG_POST, m_CachePath, m_Genome, m_id_type, m_InstMol, m_MainChunk, m_MolInfo, m_Orgs, m_other_descs, m_PreviousExecutionIds, m_SequenceTaxids, m_SequenceUniprotSources, NCBI_THROW, NON_CONST_ITERATE, NStr::NumericToString(), offset, om, CChunkFile::OpenForWrite(), CPrimeCacheApplication::SOrgData::orgref, CCache_blob::Pack(), CSeq_entry::Parentize(), CFastaReader::ReadOneSeq(), CBioseq_Base::ResetDescr(), CSeqdesc_Base::SetComment(), CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CFastaReader::SetMaxIDLength(), CSeq_entry_Base::SetSeq(), CCache_blob_Base::SetTimestamp(), ncbi::grid::netcache::search::fields::size, CStopWatch::Start(), sw, CChunkFile::Write(), x_ExtractAndIndex(), x_UpsertDescriptor(), and ZERO_TAX_ID.

Referenced by Run().

◆ x_Process_Ids()

Definition at line 871 of file prime_cache.cpp.

References CScope::AddDefaults(), CSeq_id_Handle::AsString(), count, CTime::eCurrent, set< Key, Compare >::empty(), Error(), eUnknown, CScope::GetBioseqHandle(), CChunkFile::GetChunkSerialNum(), CSeq_entry_Handle::GetCompleteSeq_entry(), GetId(), CObjectManager::GetInstance(), CChunkFile::GetOffset(), CTime::GetTimeT(), CBioseq_Handle::GetTopLevelEntry(), ITERATE, LOG_POST, m_CachedIds, m_CachePath, m_ExtractDelta, m_id_type, m_MainChunk, m_MaxDeltaLevel, m_StripInstMol, NCBI_THROW, offset, CChunkFile::OpenForWrite(), CCache_blob::Pack(), CGBDataLoader::RegisterInObjectManager(), CCache_blob_Base::SetTimestamp(), ncbi::grid::netcache::search::fields::size, CStopWatch::Start(), sw, CChunkFile::Write(), x_ExtractAndIndex(), x_ExtractDelta(), and x_StripSeqEntry().

Referenced by Run().

◆ x_Process_SeqEntry() ◆ x_Read_Ids() ◆ x_SplitAndCacheSeqEntry() ◆ x_StripSeqEntry()

Definition at line 946 of file prime_cache.cpp.

References CBioseq_Base::CanGetInst(), CScope::GetBioseqHandle(), CBioseq::GetFirstId(), GetId(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetMol(), CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), i, set< Key, Compare >::insert(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), m_id_type, m_StripInstMol, CBioseq_Base::ResetAnnot(), CBioseq_set_Base::ResetAnnot(), CBioseq_Base::ResetDescr(), CBioseq_set_Base::ResetDescr(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

Referenced by x_CacheSeqEntry(), and x_Process_Ids().

◆ x_UpsertDescriptor()

Definition at line 475 of file prime_cache.cpp.

References CSeqdesc_Base::e_Create_date, CSeqdesc_Base::e_Embl, CSeqdesc_Base::e_Genbank, CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::e_Name, CSeqdesc_Base::e_Pdb, CSeqdesc_Base::e_Pir, CSeqdesc_Base::e_Prf, CSeqdesc_Base::e_Source, CSeqdesc_Base::e_Sp, CSeqdesc_Base::e_Title, CSeqdesc_Base::e_Update_date, and CSeqdesc_Base::Which().

Referenced by x_Process_Fasta().

◆ CCacheBioseq ◆ m_CachedIds ◆ m_CachePath string CPrimeCacheApplication::m_CachePath private ◆ m_ExtractDelta bool CPrimeCacheApplication::m_ExtractDelta private ◆ m_Genome ◆ m_id_type ◆ m_InstMol ◆ m_MainChunk ◆ m_MainIndex CAsnIndex CPrimeCacheApplication::m_MainIndex private ◆ m_MaxDeltaLevel unsigned CPrimeCacheApplication::m_MaxDeltaLevel private ◆ m_MolInfo ◆ m_Orgs ◆ m_other_descs list< CRef<CSeqdesc> > CPrimeCacheApplication::m_other_descs private ◆ m_PreviousExecutionIds ◆ m_PreviousExecutionRuns set<string> CPrimeCacheApplication::m_PreviousExecutionRuns private ◆ m_SeqIdChunk ◆ m_SeqIdIndex CAsnIndex CPrimeCacheApplication::m_SeqIdIndex private ◆ m_SequenceTaxids ◆ m_SequenceUniprotSources ◆ m_StripInstMol

The documentation for this class was generated from the following file:

src/app/asn_cache/prime_cache.cpp

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