CSNPSeqInfo Class Reference

Search Toolkit Book for CSNPSeqInfo

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

Inheritance diagram for CSNPSeqInfo:

Collaboration diagram for CSNPSeqInfo:

Public Member Functions
	CSNPSeqInfo (CSNPFileInfo *file, const CSNPDbSeqIterator &it)
CSNPDbSeqIterator	GetSeqIterator (void) const
CRef< CSNPBlobId >	GetAnnotBlobId (void) const
int	GetAnnotChunkId (TSeqPos ref_pos) const
string	GetAnnotName (void) const
void	LoadRanges (void)
void	LoadAnnotBlob (CTSE_LoadLock &load_lock)
void	LoadAnnotChunk (CTSE_Chunk_Info &chunk_info)
void	LoadAnnotMainSplit (CTSE_LoadLock &load_lock)
void	LoadAnnotMainChunk (CTSE_Chunk_Info &chunk_info)
void	LoadAnnotAlignChunk (CTSE_Chunk_Info &chunk_info)
void	LoadAnnotGraphChunk (CTSE_Chunk_Info &chunk_info)
void	LoadSeqBlob (CTSE_LoadLock &load_lock)
void	LoadSeqChunk (CTSE_Chunk_Info &chunk_info)
void	LoadSeqMainEntry (CTSE_LoadLock &load_lock)
CRef< CSNPBlobId >	GetBlobId (void) const
void	SetFilterIndex (size_t filter_index)
void	SetFromBlobId (const CSNPBlobId &blob_id)
bool	IncludeFeat (void) const
bool	IncludeGraph (void) const
	CSNPSeqInfo (CSNPFileInfo *file, const objects::CSNPDbSeqIterator &it)
objects::CSNPDbSeqIterator	GetSeqIterator (void) const
CSNPBlobId	GetAnnotBlobId (void) const
int	GetAnnotChunkId (TSeqPos ref_pos) const
string	GetAnnotName (void) const
void	LoadRanges (void)
CSNPBlobId	GetBlobId (void) const
void	SetFilterIndex (size_t filter_index)
void	SetFromBlobId (const CSNPBlobId &blob_id)
bool	IncludeFeat (void) const
bool	IncludeGraph (void) const
void	LoadBlob (SSNPData &data, bool split_enabled)
void	LoadChunk (SSNPData &data, int chunk_id)

Protected Attributes
CSNPFileInfo *	m_File
size_t	m_SeqIndex
size_t	m_FilterIndex
CSeq_id_Handle	m_SeqId
bool	m_IsPrimaryTrack
bool	m_IsPrimaryTrackGraph
objects::CSeq_id_Handle	m_SeqId

Friends
class	CSNPDataLoader_Impl
class	CSNPClient

Detailed Description

Definition at line 169 of file snploader_impl.hpp.

Constructor & Destructor Documentation

CSNPSeqInfo() [1/2]

CSNPSeqInfo::CSNPSeqInfo	(	CSNPFileInfo *	file,
		const CSNPDbSeqIterator &	it
	)

Definition at line 500 of file snp_client.cpp.

References file, CSNPDbSeqIterator::GetSeqIdHandle(), and m_SeqId.

CSNPSeqInfo() [2/2]

CSNPSeqInfo::CSNPSeqInfo	(	CSNPFileInfo *	file,
		const objects::CSNPDbSeqIterator &	it
	)

Member Function Documentation

GetAnnotBlobId() [1/2]

CRef<CSNPBlobId> CSNPSeqInfo::GetAnnotBlobId

(

void

)

const

GetAnnotBlobId() [2/2]

CSNPBlobId CSNPSeqInfo::GetAnnotBlobId

(

void

)

const

GetAnnotChunkId() [1/2]

int CSNPSeqInfo::GetAnnotChunkId

(

TSeqPos

ref_pos

)

const

GetAnnotChunkId() [2/2]

int CSNPSeqInfo::GetAnnotChunkId

(

TSeqPos

ref_pos

)

const

GetAnnotName() [1/2]

string CSNPSeqInfo::GetAnnotName

(

void

)

const

Definition at line 556 of file snp_client.cpp.

References CSNPFileInfo::GetSNPAnnotName(), m_File, m_FilterIndex, and m_IsPrimaryTrack.

Referenced by LoadAnnotBlob(), LoadAnnotChunk(), LoadBlob(), and LoadChunk().

GetAnnotName() [2/2]

string CSNPSeqInfo::GetAnnotName

(

void

)

const

GetBlobId() [1/2]

CRef< CSNPBlobId > CSNPSeqInfo::GetBlobId

(

void

)

const

Definition at line 513 of file snp_client.cpp.

References _ASSERT, m_File, m_FilterIndex, m_SeqId, and m_SeqIndex.

Referenced by CSNPClient::GetAnnotInfo(), LoadAnnotBlob(), and LoadAnnotChunk().

GetBlobId() [2/2]

CSNPBlobId CSNPSeqInfo::GetBlobId

(

void

)

const

GetSeqIterator() [1/2]

CSNPDbSeqIterator CSNPSeqInfo::GetSeqIterator

(

void

)

const

Definition at line 540 of file snp_client.cpp.

References m_File, m_FilterIndex, m_SeqId, m_SeqIndex, and CSNPDbSeqIterator::SetTrack().

Referenced by LoadAnnotBlob(), LoadAnnotChunk(), LoadBlob(), and LoadChunk().

GetSeqIterator() [2/2]

objects::CSNPDbSeqIterator CSNPSeqInfo::GetSeqIterator

(

void

)

const

IncludeFeat() [1/2]

bool CSNPSeqInfo::IncludeFeat ( void  ) const

inline

Definition at line 201 of file snploader_impl.hpp.

References m_IsPrimaryTrack, and m_IsPrimaryTrackGraph.

IncludeFeat() [2/2]

bool CSNPSeqInfo::IncludeFeat ( void  ) const

inline

Definition at line 218 of file snp_client.hpp.

References m_IsPrimaryTrack, and m_IsPrimaryTrackGraph.

IncludeGraph() [1/2]

bool CSNPSeqInfo::IncludeGraph ( void  ) const

inline

Definition at line 205 of file snploader_impl.hpp.

References m_IsPrimaryTrack, and m_IsPrimaryTrackGraph.

IncludeGraph() [2/2]

bool CSNPSeqInfo::IncludeGraph ( void  ) const

inline

Definition at line 222 of file snp_client.hpp.

References m_IsPrimaryTrack, and m_IsPrimaryTrackGraph.

LoadAnnotAlignChunk()

void CSNPSeqInfo::LoadAnnotAlignChunk

(

CTSE_Chunk_Info &

chunk_info

)

LoadAnnotBlob()

void CSNPSeqInfo::LoadAnnotBlob

(

CTSE_LoadLock &

load_lock

)

Definition at line 1198 of file snploader_impl.cpp.

References CSplitParser::Attach(), eDebug_data, CSNPDbSeqIterator::fDefaultFlags, flags, CSNPDbSeqIterator::fNoSNPFeat, CSNPDbSeqIterator::fOnlySNPFeat, GetAnnotName(), GetBlobId(), GetDebugLevel(), CSNPDbSeqIterator::GetEntry(), GetSeqIterator(), CTSE_Info::GetSplitInfo(), CSNPDbSeqIterator::GetSplitInfoAndVersion(), Info(), IsSplitEnabled(), LOG_POST_X, m_IsPrimaryTrack, m_IsPrimaryTrackGraph, MSerial_AsnText, CTSE_Info::SetSeq_entry(), CTSE_Split_Info::SetSplitVersion(), and split().

Referenced by CSNPDataLoader_Impl::LoadBlob().

LoadAnnotChunk()

void CSNPSeqInfo::LoadAnnotChunk

(

CTSE_Chunk_Info &

chunk_info

)

Definition at line 1233 of file snploader_impl.cpp.

References eDebug_data, GetAnnotName(), GetBlobId(), CSNPDbSeqIterator::GetChunkForVersion(), CTSE_Chunk_Info::GetChunkId(), GetDebugLevel(), GetSeqIterator(), CTSE_Chunk_Info::GetSplitInfo(), CTSE_Split_Info::GetSplitVersion(), Info(), CSplitParser::Load(), LOG_POST_X, MSerial_AsnText, and CTSE_Chunk_Info::SetLoaded().

Referenced by CSNPDataLoader_Impl::GetChunkOnce().

LoadAnnotGraphChunk()

void CSNPSeqInfo::LoadAnnotGraphChunk

(

CTSE_Chunk_Info &

chunk_info

)

LoadAnnotMainChunk()

void CSNPSeqInfo::LoadAnnotMainChunk

(

CTSE_Chunk_Info &

chunk_info

)

LoadAnnotMainSplit()

void CSNPSeqInfo::LoadAnnotMainSplit

(

CTSE_LoadLock &

load_lock

)

LoadBlob()

void CSNPSeqInfo::LoadBlob	(	SSNPData &	data,
		bool	split_enabled
	)

Definition at line 568 of file snp_client.cpp.

References CSNPDbSeqIterator::fDefaultFlags, flags, CSNPDbSeqIterator::fNoSNPFeat, CSNPDbSeqIterator::fOnlySNPFeat, GetAnnotName(), CSNPDbSeqIterator::GetEntry(), GetSeqIterator(), CSNPDbSeqIterator::GetSplitInfoAndVersion(), m_IsPrimaryTrack, m_IsPrimaryTrackGraph, SSNPData::m_SplitInfo, SSNPData::m_SplitVersion, SSNPData::m_TSE, and split().

Referenced by CSNPClient::GetBlobByBlobId().

LoadChunk()

void CSNPSeqInfo::LoadChunk	(	SSNPData &	data,
		int	chunk_id
	)

Definition at line 595 of file snp_client.cpp.

References GetAnnotName(), CSNPDbSeqIterator::GetChunkForVersion(), GetSeqIterator(), SSNPData::m_Chunk, and SSNPData::m_SplitVersion.

Referenced by CSNPClient::GetChunk().

LoadRanges() [1/2]

void CSNPSeqInfo::LoadRanges

(

void

)

LoadRanges() [2/2]

void CSNPSeqInfo::LoadRanges

(

void

)

LoadSeqBlob()

void CSNPSeqInfo::LoadSeqBlob

(

CTSE_LoadLock &

load_lock

)

LoadSeqChunk()

void CSNPSeqInfo::LoadSeqChunk

(

CTSE_Chunk_Info &

chunk_info

)

LoadSeqMainEntry()

void CSNPSeqInfo::LoadSeqMainEntry

(

CTSE_LoadLock &

load_lock

)

SetFilterIndex() [1/2]

void CSNPSeqInfo::SetFilterIndex

(

size_t

filter_index

)

Definition at line 523 of file snp_client.cpp.

References CSNPBlobId::IsValidFilterIndex(), and m_FilterIndex.

Referenced by CSNPClient::GetAnnotInfo(), and SetFromBlobId().

SetFilterIndex() [2/2]

void CSNPSeqInfo::SetFilterIndex

(

size_t

filter_index

)

SetFromBlobId() [1/2]

void CSNPSeqInfo::SetFromBlobId

(

const CSNPBlobId &

blob_id

)

Definition at line 532 of file snp_client.cpp.

References CSNPBlobId::GetFilterIndex(), CSNPBlobId::IsPrimaryTrack(), CSNPBlobId::IsPrimaryTrackGraph(), m_IsPrimaryTrack, m_IsPrimaryTrackGraph, and SetFilterIndex().

Referenced by CSNPFileInfo::GetSeqInfo().

SetFromBlobId() [2/2]

void CSNPSeqInfo::SetFromBlobId

(

const CSNPBlobId &

blob_id

)

Friends And Related Function Documentation

CSNPClient

friend class CSNPClient

friend

Definition at line 231 of file snp_client.hpp.

CSNPDataLoader_Impl

friend class CSNPDataLoader_Impl

friend

Definition at line 211 of file snploader_impl.hpp.

Member Data Documentation

m_File

CSNPFileInfo * CSNPSeqInfo::m_File

protected

Definition at line 213 of file snploader_impl.hpp.

Referenced by GetAnnotName(), GetBlobId(), and GetSeqIterator().

m_FilterIndex

size_t CSNPSeqInfo::m_FilterIndex

protected

Definition at line 215 of file snploader_impl.hpp.

Referenced by GetAnnotName(), GetBlobId(), GetSeqIterator(), and SetFilterIndex().

m_IsPrimaryTrack

bool CSNPSeqInfo::m_IsPrimaryTrack

protected

Definition at line 217 of file snploader_impl.hpp.

Referenced by GetAnnotName(), IncludeFeat(), IncludeGraph(), LoadAnnotBlob(), LoadBlob(), and SetFromBlobId().

m_IsPrimaryTrackGraph

bool CSNPSeqInfo::m_IsPrimaryTrackGraph

protected

Definition at line 218 of file snploader_impl.hpp.

Referenced by IncludeFeat(), IncludeGraph(), LoadAnnotBlob(), LoadBlob(), and SetFromBlobId().

m_SeqId [1/2]

CSeq_id_Handle CSNPSeqInfo::m_SeqId

protected

Definition at line 216 of file snploader_impl.hpp.

Referenced by CSNPSeqInfo(), GetBlobId(), and GetSeqIterator().

m_SeqId [2/2]

objects::CSeq_id_Handle CSNPSeqInfo::m_SeqId

protected

Definition at line 236 of file snp_client.hpp.

m_SeqIndex

size_t CSNPSeqInfo::m_SeqIndex

protected

Definition at line 214 of file snploader_impl.hpp.

Referenced by GetBlobId(), and GetSeqIterator().

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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