#include <gui/widgets/seq_graphic/vcf_histogram.hpp>

Inheritance diagram for CVcfHistogram:

Collaboration diagram for CVcfHistogram:

Public Types
using	THistogramVector = CVCFVariantsBase::svector

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< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	CVcfHistogram (const string &cache_key)
	Copy constructor is invoked by CGraphCache which clones the data for aynchroneous saving operation. More...

	CVcfHistogram (const CVcfHistogram &data)

virtual	~CVcfHistogram ()
	Init is invoked by CGraphCache when a new instance of CWigGraph is initialized. More...

void	Init (TGraphCachePool &icache_pool)
	Save is invoked by CGraphCache when cached data needs to be permanently saved into NetCache. More...

void	Save (TGraphCachePool &icache_pool)
	Initializes the histogram map for a given range. More...

void	GetHistogram (const TSeqRange &range, CHistogramGlyph::TMap &dmap) const
	Sets the histogram data. More...

void	SetData (const THistogramVector &data)

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (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

Static Public Member Functions
static string	GetStorageName ()
	Creates a cache key for the given remote file and seq_id the key value is CCompoundID that parsed by constructor when the class is instantiated. More...

static string	GetCacheKey (const string &annot_name, const size_t bin_width)

static void	InitHistogramGlyph (size_t bin_width, const TSeqRange &range, const THistogramVector &histogram, CHistogramGlyph::TMap &dmap)

static void	EraseCachePerAnnotation (const string &annot_name)

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)

Protected Attributes
string	m_AnnotName

size_t	m_BinWidth

mutex	m_DataMutex
	data access mutex More...

string	m_DataKey

THistogramVector	m_Data

Static Protected Attributes
static mutex	m_KeysMapMutex
	Mutex for the cache keys. More...

static map< string, vector< string > >	m_KeysMap
	Map of cache keys per annotation. More...

Additional Inherited Members
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...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

CVcfHistogram.

Definition at line 45 of file vcf_histogram.hpp.

Member Typedef Documentation

◆ THistogramVector

using CVcfHistogram::THistogramVector = CVCFVariantsBase::svector

Definition at line 48 of file vcf_histogram.hpp.

Constructor & Destructor Documentation

◆ CVcfHistogram() [1/2]

CVcfHistogram::CVcfHistogram ( const string & cache_key )

Copy constructor is invoked by CGraphCache which clones the data for aynchroneous saving operation.

Definition at line 63 of file vcf_histogram.cpp.

References _ASSERT, CChecksum::AddLine(), eCIT_String, CChecksum::eMD5, eUnknown, CCompoundIDPool::FromString(), CCompoundID::GetFirst(), CChecksum::GetHexSum(), m_AnnotName, m_BinWidth, m_DataKey, m_KeysMap, m_KeysMapMutex, NCBI_THROW, and NStr::NumericToString().

◆ CVcfHistogram() [2/2]

CVcfHistogram::CVcfHistogram ( const CVcfHistogram & data )

Definition at line 93 of file vcf_histogram.cpp.

◆ ~CVcfHistogram()

virtual CVcfHistogram::~CVcfHistogram ( )

inlinevirtual

Init is invoked by CGraphCache when a new instance of CWigGraph is initialized.

Definition at line 65 of file vcf_histogram.hpp.

Member Function Documentation

◆ EraseCachePerAnnotation()

void CVcfHistogram::EraseCachePerAnnotation ( const string & annot_name )

static

Definition at line 154 of file vcf_histogram.cpp.

References map_checker< Container >::end(), map_checker< Container >::erase(), map_checker< Container >::find(), CGraphCache< TData >::GetInstance(), ncbi::grid::netcache::search::fields::key, m_KeysMap, and m_KeysMapMutex.

Referenced by CColumnarVcfProjectItemExtension::ProjectItemDetached(), and CSGDataSourceContext::RemoveNonAsnData().

◆ GetCacheKey()

string CVcfHistogram::GetCacheKey	(	const string &	annot_name,
		const size_t	bin_width
	)

static

Definition at line 51 of file vcf_histogram.cpp.

References CCompoundID::AppendString(), eCIC_GenericID, and CCompoundIDPool::NewID().

Referenced by CVcfFeatureJob::x_Execute().

◆ GetHistogram()

void CVcfHistogram::GetHistogram	(	const TSeqRange &	range,
		CHistogramGlyph::TMap &	dmap
	)		const

Sets the histogram data.

Definition at line 148 of file vcf_histogram.cpp.

References InitHistogramGlyph(), m_BinWidth, m_Data, m_DataMutex, and compile_time_bits::range().

◆ GetStorageName()

static string CVcfHistogram::GetStorageName ( )

inlinestatic

Creates a cache key for the given remote file and seq_id the key value is CCompoundID that parsed by constructor when the class is instantiated.

Definition at line 50 of file vcf_histogram.hpp.

◆ Init()

void CVcfHistogram::Init ( TGraphCachePool & icache_pool )

Save is invoked by CGraphCache when cached data needs to be permanently saved into NetCache.

Definition at line 102 of file vcf_histogram.cpp.

References buffer, bm::sparse_vector_deserializer< SV >::deserialize(), bm::sparse_vector< Val, BV >::empty(), ERR_POST, Error(), eUnknown, CRWStreambuf::fOwnReader, m_Data, m_DataKey, m_DataMutex, NCBI_THROW, NcbiEmptyString, and val.

◆ InitHistogramGlyph()

static void CVcfHistogram::InitHistogramGlyph	(	size_t	bin_width,
		const TSeqRange &	range,
		const THistogramVector &	histogram,
		CHistogramGlyph::TMap &	dmap
	)

inlinestatic

Definition at line 85 of file vcf_histogram.hpp.

References CDensityMap< CntType >::AddRange(), compile_time_bits::range(), and bm::sparse_vector< Val, BV >::size().

Referenced by GetHistogram(), and CVcfFeatureJob::x_Execute().

◆ Save()

void CVcfHistogram::Save ( TGraphCachePool & icache_pool )

Initializes the histogram map for a given range.

Definition at line 133 of file vcf_histogram.cpp.

References _ASSERT, bm::sparse_vector_serial_layout< SV >::buf(), bm::sparse_vector_serializer< SV >::enable_xor_compression(), eUnknown, CRWStreambuf::fOwnWriter, bm::sparse_vector_serializer< SV >::is_xor_ref(), m_Data, m_DataKey, NCBI_THROW, NcbiEmptyString, bm::sparse_vector< Val, BV >::optimize(), bm::sparse_vector_serializer< SV >::serialize(), and bm::sparse_vector_serial_layout< SV >::size().

◆ SetData()

void CVcfHistogram::SetData ( const THistogramVector & data )

inline

Definition at line 79 of file vcf_histogram.hpp.

References m_Data, and m_DataMutex.

Member Data Documentation

◆ m_AnnotName

string CVcfHistogram::m_AnnotName

protected

Definition at line 100 of file vcf_histogram.hpp.

Referenced by CVcfHistogram().

◆ m_BinWidth

size_t CVcfHistogram::m_BinWidth

protected

Definition at line 101 of file vcf_histogram.hpp.

Referenced by CVcfHistogram(), and GetHistogram().

◆ m_Data

THistogramVector CVcfHistogram::m_Data

protected

Definition at line 106 of file vcf_histogram.hpp.

Referenced by GetHistogram(), Init(), Save(), and SetData().

◆ m_DataKey

string CVcfHistogram::m_DataKey

protected

Definition at line 105 of file vcf_histogram.hpp.

Referenced by CVcfHistogram(), Init(), and Save().

◆ m_DataMutex

mutex CVcfHistogram::m_DataMutex

mutableprotected

data access mutex

Definition at line 103 of file vcf_histogram.hpp.

Referenced by GetHistogram(), Init(), and SetData().

◆ m_KeysMap

map< string, vector< string > > CVcfHistogram::m_KeysMap

staticprotected

Map of cache keys per annotation.

Definition at line 109 of file vcf_histogram.hpp.

Referenced by CVcfHistogram(), and EraseCachePerAnnotation().

◆ m_KeysMapMutex

mutex CVcfHistogram::m_KeysMapMutex

staticprotected

Mutex for the cache keys.

CVcfHistogram.

Definition at line 108 of file vcf_histogram.hpp.

Referenced by CVcfHistogram(), and EraseCachePerAnnotation().

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

include/gui/widgets/seq_graphic/vcf_histogram.hpp
src/gui/widgets/seq_graphic/vcf_histogram.cpp

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Static Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ THistogramVector

Constructor & Destructor Documentation

◆ CVcfHistogram() [1/2]

◆ CVcfHistogram() [2/2]

◆ ~CVcfHistogram()

Member Function Documentation

◆ EraseCachePerAnnotation()

◆ GetCacheKey()

◆ GetHistogram()

◆ GetStorageName()

◆ Init()

◆ InitHistogramGlyph()

◆ Save()

◆ SetData()

Member Data Documentation

◆ m_AnnotName

◆ m_BinWidth

◆ m_Data

◆ m_DataKey

◆ m_DataMutex

◆ m_KeysMap

◆ m_KeysMapMutex