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CSNPSeqInfo Class Reference

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#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< CSNPBlobIdGetAnnotBlobId (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< CSNPBlobIdGetBlobId (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

CSNPFileInfom_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 171 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

◆ 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

◆ GetSeqIterator() [2/2]

objects::CSNPDbSeqIterator CSNPSeqInfo::GetSeqIterator ( void  ) const

◆ IncludeFeat() [1/2]

bool CSNPSeqInfo::IncludeFeat ( void  ) const
inline

Definition at line 203 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 207 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)

◆ LoadAnnotChunk()

void CSNPSeqInfo::LoadAnnotChunk ( CTSE_Chunk_Info chunk_info)

◆ 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 
)

◆ LoadChunk()

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

◆ 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)

◆ 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 213 of file snploader_impl.hpp.

Member Data Documentation

◆ m_File

CSNPFileInfo * CSNPSeqInfo::m_File
protected

Definition at line 215 of file snploader_impl.hpp.

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

◆ m_FilterIndex

size_t CSNPSeqInfo::m_FilterIndex
protected

Definition at line 217 of file snploader_impl.hpp.

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

◆ m_IsPrimaryTrack

bool CSNPSeqInfo::m_IsPrimaryTrack
protected

◆ m_IsPrimaryTrackGraph

bool CSNPSeqInfo::m_IsPrimaryTrackGraph
protected

Definition at line 220 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 218 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 216 of file snploader_impl.hpp.

Referenced by GetBlobId(), and GetSeqIterator().


The documentation for this class was generated from the following files:
Modified on Mon Jul 22 05:08:26 2024 by modify_doxy.py rev. 669887