CSNPFileInfo Class Reference

Search Toolkit Book for CSNPFileInfo

#include <sra/data_loaders/snp/impl/snploader_impl.hpp>

Inheritance diagram for CSNPFileInfo:

Collaboration diagram for CSNPFileInfo:

Public Types
typedef CSNPDataLoader::TAnnotNames	TAnnotNames

Public Member Functions
	CSNPFileInfo (CSNPDataLoader_Impl &impl, const string &file_name)
bool	IsValidNA (void) const
const string &	GetFileName (void) const
const string &	GetAccession (void) const
const string &	GetBaseAnnotName (void) const
string	GetSNPAnnotName (size_t filter_index) const
CRef< CSNPBlobId >	GetAnnotBlobId (const CSeq_id_Handle &id) const
CRef< CSNPSeqInfo >	GetSeqInfo (const CSeq_id_Handle &seq_id)
CRef< CSNPSeqInfo >	GetSeqInfo (size_t seq_index)
CRef< CSNPSeqInfo >	GetSeqInfo (const CSNPBlobId &blob_id)
CMutex &	GetMutex (void) const
void	InitializeDb (CSNPDataLoader_Impl &impl)
CSNPDb &	GetDb (void)
	operator CSNPDb & (void)
void	AddSeq (const CSeq_id_Handle &id)
void	GetPossibleAnnotNames (TAnnotNames &names) const
	CSNPFileInfo (CSNPClient &client, const string &file_name)
bool	IsValidNA (void) const
const string &	GetFileName (void) const
const string &	GetAccession (void) const
const string &	GetBaseAnnotName (void) const
string	GetSNPAnnotName (size_t filter_index) const
CSNPBlobId	GetAnnotBlobId (const objects::CSeq_id_Handle &id) const
CRef< CSNPSeqInfo >	GetSeqInfo (const objects::CSeq_id_Handle &seq_id)
CRef< CSNPSeqInfo >	GetSeqInfo (size_t seq_index)
CRef< CSNPSeqInfo >	GetSeqInfo (const CSNPBlobId &blob_id)
objects::CSNPDb &	GetDb (void)
	operator objects::CSNPDb & (void)
void	AddSeq (const objects::CSeq_id_Handle &id)

Protected Types
typedef map< CSeq_id_Handle, CRef< CSNPSeqInfo > >	TSeqById
typedef map< size_t, CRef< CSNPSeqInfo > >	TSeqByIdx
typedef map< objects::CSeq_id_Handle, CRef< CSNPSeqInfo > >	TSeqById
typedef map< size_t, CRef< CSNPSeqInfo > >	TSeqByIdx

Protected Member Functions
void	x_Initialize (CSNPDataLoader_Impl &impl, const string &file_name)
void	x_Initialize (CSNPClient &client, const string &file_name)

Protected Attributes
unsigned	m_RemainingOpenRetries
bool	m_IsValidNA
string	m_FileName
string	m_Accession
string	m_AnnotName
CMutex	m_SNPMutex
CSNPDb	m_SNPDb
TSeqById	m_SeqById
TSeqByIdx	m_SeqByIdx
objects::CSNPDb	m_SNPDb

Friends
class	CSNPDataLoader_Impl
class	CSNPClient

Detailed Description

Definition at line 222 of file snploader_impl.hpp.

Member Typedef Documentation

TAnnotNames

typedef CSNPDataLoader::TAnnotNames CSNPFileInfo::TAnnotNames

Definition at line 270 of file snploader_impl.hpp.

TSeqById [1/2]

typedef map<CSeq_id_Handle, CRef<CSNPSeqInfo> > CSNPFileInfo::TSeqById

protected

Definition at line 276 of file snploader_impl.hpp.

TSeqById [2/2]

typedef map<objects::CSeq_id_Handle, CRef<CSNPSeqInfo> > CSNPFileInfo::TSeqById

protected

Definition at line 286 of file snp_client.hpp.

TSeqByIdx [1/2]

typedef map<size_t, CRef<CSNPSeqInfo> > CSNPFileInfo::TSeqByIdx

protected

Definition at line 277 of file snploader_impl.hpp.

TSeqByIdx [2/2]

typedef map<size_t, CRef<CSNPSeqInfo> > CSNPFileInfo::TSeqByIdx

protected

Definition at line 287 of file snp_client.hpp.

Constructor & Destructor Documentation

CSNPFileInfo() [1/2]

CSNPFileInfo::CSNPFileInfo	(	CSNPDataLoader_Impl &	impl,
		const string &	file_name
	)

Definition at line 1010 of file snploader_impl.cpp.

References x_Initialize().

CSNPFileInfo() [2/2]

CSNPFileInfo::CSNPFileInfo	(	CSNPClient &	client,
		const string &	file_name
	)

Definition at line 608 of file snp_client.cpp.

References client, and x_Initialize().

Member Function Documentation

AddSeq() [1/2]

void CSNPFileInfo::AddSeq

(

const CSeq_id_Handle &

id

)

AddSeq() [2/2]

void CSNPFileInfo::AddSeq

(

const objects::CSeq_id_Handle &

id

)

GetAccession() [1/2]

const string& CSNPFileInfo::GetAccession ( void  ) const

inline

Definition at line 236 of file snploader_impl.hpp.

References m_Accession.

GetAccession() [2/2]

const string& CSNPFileInfo::GetAccession ( void  ) const

inline

Definition at line 256 of file snp_client.hpp.

References m_Accession.

GetAnnotBlobId() [1/2]

CRef<CSNPBlobId> CSNPFileInfo::GetAnnotBlobId

(

const CSeq_id_Handle &

id

)

const

GetAnnotBlobId() [2/2]

CSNPBlobId CSNPFileInfo::GetAnnotBlobId

(

const objects::CSeq_id_Handle &

id

)

const

GetBaseAnnotName() [1/2]

const string& CSNPFileInfo::GetBaseAnnotName ( void  ) const

inline

Definition at line 240 of file snploader_impl.hpp.

References m_AnnotName.

Referenced by GetSNPAnnotName().

GetBaseAnnotName() [2/2]

const string& CSNPFileInfo::GetBaseAnnotName ( void  ) const

inline

Definition at line 260 of file snp_client.hpp.

References m_AnnotName.

GetDb() [1/2]

CSNPDb& CSNPFileInfo::GetDb ( void  )

inline

Definition at line 259 of file snploader_impl.hpp.

References m_SNPDb.

Referenced by operator CSNPDb &(), and operator objects::CSNPDb &().

GetDb() [2/2]

objects::CSNPDb& CSNPFileInfo::GetDb ( void  )

inline

Definition at line 272 of file snp_client.hpp.

References m_SNPDb.

GetFileName() [1/2]

const string& CSNPFileInfo::GetFileName ( void  ) const

inline

Definition at line 232 of file snploader_impl.hpp.

References m_FileName.

GetFileName() [2/2]

const string& CSNPFileInfo::GetFileName ( void  ) const

inline

Definition at line 252 of file snp_client.hpp.

References m_FileName.

GetMutex()

CMutex& CSNPFileInfo::GetMutex ( void  ) const

inline

Definition at line 252 of file snploader_impl.hpp.

References m_SNPMutex.

GetPossibleAnnotNames()

void CSNPFileInfo::GetPossibleAnnotNames

(

TAnnotNames &

names

)

const

Definition at line 1064 of file snploader_impl.cpp.

References GetSNPAnnotName(), m_SNPDb, and names.

GetSeqInfo() [1/6]

CRef< CSNPSeqInfo > CSNPFileInfo::GetSeqInfo

(

const CSeq_id_Handle &

seq_id

)

Definition at line 642 of file snp_client.cpp.

References m_SNPDb.

Referenced by GetSeqInfo().

GetSeqInfo() [2/6]

CRef< CSNPSeqInfo > CSNPFileInfo::GetSeqInfo

(

const CSNPBlobId &

blob_id

)

Definition at line 662 of file snp_client.cpp.

References CSNPBlobId::GetSeqId(), CSNPBlobId::GetSeqIndex(), GetSeqInfo(), CSNPBlobId::IsSatId(), and CSNPSeqInfo::SetFromBlobId().

GetSeqInfo() [3/6]

CRef<CSNPSeqInfo> CSNPFileInfo::GetSeqInfo

(

const CSNPBlobId &

blob_id

)

GetSeqInfo() [4/6]

CRef<CSNPSeqInfo> CSNPFileInfo::GetSeqInfo

(

const objects::CSeq_id_Handle &

seq_id

)

GetSeqInfo() [5/6]

CRef< CSNPSeqInfo > CSNPFileInfo::GetSeqInfo

(

size_t

seq_index

)

Definition at line 653 of file snp_client.cpp.

References _ASSERT, and m_SNPDb.

GetSeqInfo() [6/6]

CRef<CSNPSeqInfo> CSNPFileInfo::GetSeqInfo

(

size_t

seq_index

)

GetSNPAnnotName() [1/2]

string CSNPFileInfo::GetSNPAnnotName

(

size_t

filter_index

)

const

Definition at line 636 of file snp_client.cpp.

References GetBaseAnnotName(), and s_AddFilterIndex().

Referenced by CSNPSeqInfo::GetAnnotName(), and GetPossibleAnnotNames().

GetSNPAnnotName() [2/2]

string CSNPFileInfo::GetSNPAnnotName

(

size_t

filter_index

)

const

InitializeDb()

void CSNPFileInfo::InitializeDb

(

CSNPDataLoader_Impl &

impl

)

Definition at line 1039 of file snploader_impl.cpp.

References eDebug_open, eDebug_open_time, CStopWatch::Elapsed(), GetDebugLevel(), Info(), LOG_POST_X, m_FileName, m_RemainingOpenRetries, m_SNPDb, CStopWatch::Start(), and sw.

IsValidNA() [1/2]

bool CSNPFileInfo::IsValidNA ( void  ) const

inline

Definition at line 228 of file snploader_impl.hpp.

References m_IsValidNA.

IsValidNA() [2/2]

bool CSNPFileInfo::IsValidNA ( void  ) const

inline

Definition at line 247 of file snp_client.hpp.

References m_IsValidNA.

operator CSNPDb &()

CSNPFileInfo::operator CSNPDb & ( void  )

inline

Definition at line 263 of file snploader_impl.hpp.

References GetDb().

operator objects::CSNPDb &()

CSNPFileInfo::operator objects::CSNPDb & ( void  )

inline

Definition at line 276 of file snp_client.hpp.

References GetDb().

x_Initialize() [1/2]

void CSNPFileInfo::x_Initialize ( CSNPClient &  client, const string &  file_name  )

protected

Definition at line 616 of file snp_client.cpp.

References client, CSNPBlobId::IsValidNA(), m_Accession, m_AnnotName, m_FileName, m_IsValidNA, NPOS, and s_ExtractFilterIndex().

x_Initialize() [2/2]

void CSNPFileInfo::x_Initialize ( CSNPDataLoader_Impl &  impl, const string &  file_name  )

protected

Definition at line 1017 of file snploader_impl.cpp.

References CSNPBlobId::IsValidNA(), m_Accession, m_AnnotName, m_FileName, m_IsValidNA, m_RemainingOpenRetries, NPOS, and sx_ExtractFilterIndex().

Referenced by CSNPFileInfo().

Friends And Related Function Documentation

CSNPClient

friend class CSNPClient

friend

Definition at line 284 of file snp_client.hpp.

CSNPDataLoader_Impl

friend class CSNPDataLoader_Impl

friend

Definition at line 274 of file snploader_impl.hpp.

Member Data Documentation

m_Accession

string CSNPFileInfo::m_Accession

protected

Definition at line 285 of file snploader_impl.hpp.

Referenced by GetAccession(), and x_Initialize().

m_AnnotName

string CSNPFileInfo::m_AnnotName

protected

Definition at line 286 of file snploader_impl.hpp.

Referenced by GetBaseAnnotName(), and x_Initialize().

m_FileName

string CSNPFileInfo::m_FileName

protected

Definition at line 284 of file snploader_impl.hpp.

Referenced by GetFileName(), InitializeDb(), and x_Initialize().

m_IsValidNA

bool CSNPFileInfo::m_IsValidNA

protected

Definition at line 283 of file snploader_impl.hpp.

Referenced by IsValidNA(), and x_Initialize().

m_RemainingOpenRetries

unsigned CSNPFileInfo::m_RemainingOpenRetries

protected

Definition at line 282 of file snploader_impl.hpp.

Referenced by InitializeDb(), and x_Initialize().

m_SeqById

TSeqById CSNPFileInfo::m_SeqById

protected

Definition at line 289 of file snploader_impl.hpp.

m_SeqByIdx

TSeqByIdx CSNPFileInfo::m_SeqByIdx

protected

Definition at line 290 of file snploader_impl.hpp.

m_SNPDb [1/2]

CSNPDb CSNPFileInfo::m_SNPDb

protected

Definition at line 288 of file snploader_impl.hpp.

Referenced by GetDb(), GetPossibleAnnotNames(), GetSeqInfo(), and InitializeDb().

m_SNPDb [2/2]

objects::CSNPDb CSNPFileInfo::m_SNPDb

protected

Definition at line 296 of file snp_client.hpp.

m_SNPMutex

CMutex CSNPFileInfo::m_SNPMutex

mutableprotected

Definition at line 287 of file snploader_impl.hpp.

Referenced by GetMutex().

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

• include/sra/data_loaders/snp/impl/snploader_impl.hpp
• src/app/pubseq_gateway/server/snp_client.hpp
• src/app/pubseq_gateway/server/snp_client.cpp
• src/sra/data_loaders/snp/snploader_impl.cpp