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CBamRefSeqInfo Class Reference

Search Toolkit Book for CBamRefSeqInfo

#include <sra/data_loaders/bam/impl/bamloader_impl.hpp>

+ Inheritance diagram for CBamRefSeqInfo:
+ Collaboration diagram for CBamRefSeqInfo:

Public Member Functions

 CBamRefSeqInfo (CBamFileInfo *bam_file, const string &refseqid, const CSeq_id_Handle &seq_id)
const stringGetRefSeqId (void) const
const CSeq_id_HandleGetRefSeq_id (void) const
void SetCovFileName (const string &name)
void LoadRanges (void)
CRange< TSeqPosGetChunkGraphRange (size_t range_id)
void LoadMainSplit (CTSE_LoadLock &load_lock)
void LoadMainEntry (CTSE_LoadLock &load_lock)
void CreateChunks (CTSE_Split_Info &split_info)
double EstimateLoadSeconds (const CTSE_Chunk_Info &chunk, Uint4 bytes) const
double EstimatePileupLoadSeconds (const CTSE_Chunk_Info &chunk, Uint4 bytes) const
double EstimateAlignLoadSeconds (const CTSE_Chunk_Info &chunk, Uint4 bytes) const
double EstimateSeqLoadSeconds (const CTSE_Chunk_Info &chunk, Uint4 bytes) const
void LoadChunk (CTSE_Chunk_Info &chunk_info)
void LoadMainChunk (CTSE_Chunk_Info &chunk_info)
void LoadAlignChunk (CTSE_Chunk_Info &chunk_info)
void LoadSeqChunk (CTSE_Chunk_Info &chunk_info)
void LoadPileupChunk (CTSE_Chunk_Info &chunk_info)
void GetShortSeqBlobId (CRef< CBAMBlobId > &ret, const CSeq_id_Handle &idh) const
void SetBlobId (CRef< CBAMBlobId > &ret, const CSeq_id_Handle &idh) const
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 CObject (const CObject &src)
 Copy constructor. More...
virtual ~CObject (void)
 Destructor. More...
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
void AddReference (void) const
 Add reference to object. More...
void RemoveReference (void) const
 Remove reference to object. More...
void ReleaseReference (void) const
 Remove reference without deleting object. More...
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
void * operator new (size_t size)
 Define new operator for memory allocation. More...
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
void * operator new (size_t size, void *place)
 Define new operator. More...
void operator delete (void *ptr, void *place)
 Define delete operator. More...
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
virtual ~CDebugDumpable (void)
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
void DumpToConsole (void) const

Protected Types

typedef CRange< TSeqPosTRange
typedef vector< CBamRefSeqChunkInfoTChunks
typedef map< CSeq_id_Handle, intTSeq2Chunk

Protected Member Functions

void x_LoadRangesScan (void)
void x_LoadRangesStat (void)
bool x_LoadRangesCov (void)
bool x_LoadRangesEstimated (void)
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...

Protected Attributes

string m_RefSeqId
CSeq_id_Handle m_RefSeq_id
string m_CovFileName
CRef< CSeq_entrym_CovEntry
int m_MinMapQuality
TChunks m_Chunks
bool m_LoadedRanges
CIRef< CBamAlignIterator::ISpotIdDetectorm_SpotIdDetector
TSeq2Chunk m_Seq2Chunk
CMutex m_Seq2ChunkMutex

Additional Inherited Members

- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
typedef Uint8 TCount
 Alias for value type of counter. More...
- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
static EAllocFillMode GetAllocFillMode (void)
static void SetAllocFillMode (EAllocFillMode mode)
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
static const TCount eCounterStateMask
 Valid object, and object in heap. More...

Detailed Description

Definition at line 124 of file bamloader_impl.hpp.

Member Typedef Documentation

◆ TChunks

typedef vector<CBamRefSeqChunkInfo> CBamRefSeqInfo::TChunks

Definition at line 172 of file bamloader_impl.hpp.

◆ TRange

Definition at line 171 of file bamloader_impl.hpp.

◆ TSeq2Chunk

Definition at line 173 of file bamloader_impl.hpp.

Constructor & Destructor Documentation

◆ CBamRefSeqInfo()

CBamRefSeqInfo::CBamRefSeqInfo ( CBamFileInfo bam_file,
const string refseqid,
const CSeq_id_Handle seq_id 

Definition at line 762 of file bamloader_impl.cpp.

References m_SpotIdDetector.

Member Function Documentation

◆ CreateChunks()

void CBamRefSeqInfo::CreateChunks ( CTSE_Split_Info split_info)

◆ EstimateAlignLoadSeconds()

double CBamRefSeqInfo::EstimateAlignLoadSeconds ( const CTSE_Chunk_Info chunk,
Uint4  bytes 
) const

◆ EstimateLoadSeconds()

double CBamRefSeqInfo::EstimateLoadSeconds ( const CTSE_Chunk_Info chunk,
Uint4  bytes 
) const

◆ EstimatePileupLoadSeconds()

double CBamRefSeqInfo::EstimatePileupLoadSeconds ( const CTSE_Chunk_Info chunk,
Uint4  bytes 
) const

◆ EstimateSeqLoadSeconds()

double CBamRefSeqInfo::EstimateSeqLoadSeconds ( const CTSE_Chunk_Info chunk,
Uint4  bytes 
) const

◆ GetChunkGraphRange()

CRange< TSeqPos > CBamRefSeqInfo::GetChunkGraphRange ( size_t  range_id)

Definition at line 1346 of file bamloader_impl.cpp.

References m_Chunks, and compile_time_bits::range().

Referenced by CreateChunks(), and LoadPileupChunk().

◆ GetRefSeq_id()

const CSeq_id_Handle& CBamRefSeqInfo::GetRefSeq_id ( void  ) const

◆ GetRefSeqId()

const string& CBamRefSeqInfo::GetRefSeqId ( void  ) const

◆ GetShortSeqBlobId()

void CBamRefSeqInfo::GetShortSeqBlobId ( CRef< CBAMBlobId > &  ret,
const CSeq_id_Handle idh 
) const

◆ LoadAlignChunk()

void CBamRefSeqInfo::LoadAlignChunk ( CTSE_Chunk_Info chunk_info)

◆ LoadChunk()

void CBamRefSeqInfo::LoadChunk ( CTSE_Chunk_Info chunk_info)

◆ LoadMainChunk()

void CBamRefSeqInfo::LoadMainChunk ( CTSE_Chunk_Info chunk_info)

◆ LoadMainEntry()

void CBamRefSeqInfo::LoadMainEntry ( CTSE_LoadLock load_lock)

◆ LoadMainSplit()

void CBamRefSeqInfo::LoadMainSplit ( CTSE_LoadLock load_lock)

◆ LoadPileupChunk()

void CBamRefSeqInfo::LoadPileupChunk ( CTSE_Chunk_Info chunk_info)

Definition at line 2431 of file bamloader_impl.cpp.

References _TRACE, SBaseStats::add_base(), SBaseStats::add_base_raw(), SBaseStats::add_gap(), SBaseStats::add_intron(), SBaseStats::add_match(), SBaseStats::cc, CTempString::data(), CStopWatch::Elapsed(), ERR_POST_X, SBaseStats::finish_add(), SBaseStats::get_max_count(), CBamFileInfo::GetAnnotName(), GetChunkGraphRange(), CTSE_Chunk_Info::GetChunkId(), CBamAlignIterator::GetCIGAR(), CBamAlignIterator::GetCIGARPos(), CBamAlignIterator::GetCIGARRefSize(), GetDebugLevel(), CBamAlignIterator::GetMapQuality(), CRef< C, Locker >::GetNCPointer(), CBamAlignIterator::GetRawIndexIteratorPtr(), GetRefSeq_id(), GetRefSeqId(), CBamFileInfo::GetRefSeqLength(), CBamAlignIterator::GetRefSeqPos(), CBamRefSeqChunkInfo::GetRefSeqRange(), GetSeqId(), CBamAlignIterator::GetShortSequence(), GetSkipEmptyPileupGraphsParam(), CByte_graph_Base::GetValues(), CInt_graph_Base::GetValues(), i, Info(), kChunkIdMul, SBamAlignInfo::kCIGAR_D, SBamAlignInfo::kCIGAR_eq, SBamAlignInfo::kCIGAR_I, SBamAlignInfo::kCIGAR_M, SBamAlignInfo::kCIGAR_N, SBamAlignInfo::kCIGAR_S, SBamAlignInfo::kCIGAR_X, SBaseStats::kNumStat, SBaseStats::kStat_Intron, SBaseStats::kStat_Match, kTSEId, LOG_POST_X, m_Chunks, m_File, m_MinMapQuality, m_SpotIdDetector, max(), PILEUP_NAME_SUFFIX, SerialClone(), CByte_graph_Base::SetAxis(), CInt_graph_Base::SetAxis(), CSeq_annot_Base::SetData(), CSeq_annot_Base::SetDesc(), CSeq_interval_Base::SetFrom(), CSeq_graph_Base::SetGraph(), CSeq_interval_Base::SetId(), CTSE_Chunk_Info::SetLoaded(), CSeq_graph_Base::SetLoc(), CByte_graph_Base::SetMax(), CInt_graph_Base::SetMax(), CByte_graph_Base::SetMin(), CInt_graph_Base::SetMin(), CAnnotdesc_Base::SetName(), CSeq_graph_Base::SetNumval(), CBamAlignIterator::SetSpotIdDetector(), CSeq_graph_Base::SetTitle(), CSeq_interval_Base::SetTo(), CByte_graph_Base::SetValues(), CInt_graph_Base::SetValues(), CTempString::size(), CStopWatch::Start(), sw, sx_GetBaseRaw(), CTSE_Chunk_Info::x_AddUsedMemory(), and CTSE_Chunk_Info::x_LoadAnnot().

Referenced by LoadChunk().

◆ LoadRanges()

void CBamRefSeqInfo::LoadRanges ( void  )

◆ LoadSeqChunk()

void CBamRefSeqInfo::LoadSeqChunk ( CTSE_Chunk_Info chunk_info)

◆ SetBlobId()

void CBamRefSeqInfo::SetBlobId ( CRef< CBAMBlobId > &  ret,
const CSeq_id_Handle idh 
) const

Definition at line 775 of file bamloader_impl.cpp.

References ERR_POST_X, CBamFileInfo::GetBamName(), GetRefSeq_id(), and m_File.

Referenced by GetShortSeqBlobId().

◆ SetCovFileName()

void CBamRefSeqInfo::SetCovFileName ( const string name)

Definition at line 140 of file bamloader_impl.hpp.

References m_CovFileName.

◆ x_LoadRangesCov()

bool CBamRefSeqInfo::x_LoadRangesCov ( void  )

◆ x_LoadRangesEstimated()

bool CBamRefSeqInfo::x_LoadRangesEstimated ( void  )

◆ x_LoadRangesScan()

void CBamRefSeqInfo::x_LoadRangesScan ( void  )

◆ x_LoadRangesStat()

void CBamRefSeqInfo::x_LoadRangesStat ( void  )

Member Data Documentation

◆ m_Chunks

TChunks CBamRefSeqInfo::m_Chunks

◆ m_CovEntry

CRef<CSeq_entry> CBamRefSeqInfo::m_CovEntry

◆ m_CovFileName

string CBamRefSeqInfo::m_CovFileName

Definition at line 183 of file bamloader_impl.hpp.

Referenced by LoadMainSplit(), SetCovFileName(), and x_LoadRangesCov().

◆ m_File

CBamFileInfo* CBamRefSeqInfo::m_File

◆ m_LoadedRanges

bool CBamRefSeqInfo::m_LoadedRanges

Definition at line 187 of file bamloader_impl.hpp.

Referenced by LoadRanges(), and x_LoadRangesStat().

◆ m_MinMapQuality

int CBamRefSeqInfo::m_MinMapQuality

◆ m_RefSeq_id

CSeq_id_Handle CBamRefSeqInfo::m_RefSeq_id

Definition at line 182 of file bamloader_impl.hpp.

Referenced by GetRefSeq_id().

◆ m_RefSeqId

string CBamRefSeqInfo::m_RefSeqId

Definition at line 181 of file bamloader_impl.hpp.

Referenced by GetRefSeqId().

◆ m_Seq2Chunk

TSeq2Chunk CBamRefSeqInfo::m_Seq2Chunk

Definition at line 189 of file bamloader_impl.hpp.

Referenced by CreateChunks(), GetShortSeqBlobId(), LoadAlignChunk(), and LoadSeqChunk().

◆ m_Seq2ChunkMutex

CMutex CBamRefSeqInfo::m_Seq2ChunkMutex

Definition at line 190 of file bamloader_impl.hpp.

Referenced by CreateChunks(), GetShortSeqBlobId(), LoadAlignChunk(), and LoadSeqChunk().

◆ m_SpotIdDetector

CIRef<CBamAlignIterator::ISpotIdDetector> CBamRefSeqInfo::m_SpotIdDetector

Definition at line 188 of file bamloader_impl.hpp.

Referenced by CBamRefSeqInfo(), LoadAlignChunk(), LoadPileupChunk(), and LoadSeqChunk().

The documentation for this class was generated from the following files:
Modified on Wed Dec 06 07:14:12 2023 by rev. 669887