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

Inheritance diagram for CVcfHeatmap:

Collaboration diagram for CVcfHeatmap:

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

	CVcfHeatmap (const CVcfHeatmap &data)

virtual	~CVcfHeatmap ()
	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)

void	GetData (const TSeqRange &range, vector< TSeqRange > &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 (objects::CScope &scope, const objects::CSeq_id &seq_id, const string &bed_id, const string &remote_path, const string &last_modified=NcbiEmptyString)
	CVcfHeatmap. 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)

Protected Member Functions
void	x_CreateDataKey (string &cache_key)

void	x_InitData (ICache &icache)

void	x_SaveData (ICache &icache)

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

Protected Attributes
string	m_SeqId

string	m_RemoteId

size_t	m_SeqLen = 0

string	m_RemotePath
	path to remote data or srz accession More...

string	m_LastModified
	timestamp of the remote data last modified date as reported by www server More...

mutex	m_DataMutex
	data access mutex More...

string	m_DataKey

vector< TSeqRange >	m_Data

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

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

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

CVcfHeatmap.

Definition at line 54 of file vcf_heatmap.hpp.

Constructor & Destructor Documentation

◆ CVcfHeatmap() [1/2]

CVcfHeatmap::CVcfHeatmap ( const string & cache_key )

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

Definition at line 79 of file vcf_heatmap.cpp.

References _ASSERT, CChecksum::AddLine(), eCIT_String, CChecksum::eMD5, eUnknown, CCompoundIDPool::FromString(), CCompoundID::GetFirst(), CChecksum::GetHexSum(), m_DataKey, m_LastModified, m_RemoteId, m_RemotePath, m_SeqId, m_SeqLen, NCBI_THROW, and NStr::NumericToString().

◆ CVcfHeatmap() [2/2]

CVcfHeatmap::CVcfHeatmap ( const CVcfHeatmap & data )

Definition at line 118 of file vcf_heatmap.cpp.

◆ ~CVcfHeatmap()

CVcfHeatmap::~CVcfHeatmap ( )

inlinevirtual

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

Definition at line 109 of file vcf_heatmap.hpp.

Member Function Documentation

◆ GetCacheKey()

string CVcfHeatmap::GetCacheKey	(	objects::CScope &	scope,
		const objects::CSeq_id &	seq_id,
		const string &	bed_id,
		const string &	remote_path,
		const string &	last_modified = `NcbiEmptyString`
	)

static

CVcfHeatmap.

Definition at line 53 of file vcf_heatmap.cpp.

References _ASSERT, eCIC_GenericID, CScope::GetAccVer(), CSeq_id_Handle::GetHandle(), CUrlUtils::GetLastModified(), CSeq_id_Handle::GetSeqId(), CSeq_id::GetSeqIdString(), CScope::GetSequenceLength(), and CCompoundIDPool::NewID().

◆ GetData()

void CVcfHeatmap::GetData	(	const TSeqRange &	range,
		vector< TSeqRange > &	data
	)

Definition at line 236 of file vcf_heatmap.cpp.

References _ASSERT, data, len, m_Data, m_DataMutex, r(), and compile_time_bits::range().

◆ GetStorageName()

static string CVcfHeatmap::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 57 of file vcf_heatmap.hpp.

◆ Init()

void CVcfHeatmap::Init ( TGraphCachePool & icache_pool )

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

Definition at line 130 of file vcf_heatmap.cpp.

References ERR_POST, Error(), CRWStreambuf::fOwnReader, m_Data, m_DataKey, m_DataMutex, NcbiEmptyString, and x_InitData().

◆ Save()

void CVcfHeatmap::Save ( TGraphCachePool & icache_pool )

Definition at line 165 of file vcf_heatmap.cpp.

References x_SaveData().

◆ x_CreateDataKey()

void CVcfHeatmap::x_CreateDataKey ( string & cache_key )

protected

◆ x_InitData()

void CVcfHeatmap::x_InitData ( ICache & icache )

protected

Definition at line 230 of file vcf_heatmap.cpp.

References m_Data, m_RemoteId, m_RemotePath, m_SeqLen, NStr::NumericToString(), and s_GetData().

Referenced by Init().

◆ x_SaveData()

void CVcfHeatmap::x_SaveData ( ICache & icache )

protected

Definition at line 217 of file vcf_heatmap.cpp.

References eUnknown, CRWStreambuf::fOwnWriter, ICache::GetWriteStream(), m_Data, m_DataKey, NCBI_THROW, NcbiEmptyString, and r().

Referenced by Save().

Member Data Documentation

◆ m_Data

vector<TSeqRange> CVcfHeatmap::m_Data

protected

Definition at line 102 of file vcf_heatmap.hpp.

Referenced by GetData(), Init(), x_InitData(), and x_SaveData().

◆ m_DataKey

string CVcfHeatmap::m_DataKey

protected

Definition at line 101 of file vcf_heatmap.hpp.

Referenced by CVcfHeatmap(), Init(), and x_SaveData().

◆ m_DataMutex

mutex CVcfHeatmap::m_DataMutex

protected

data access mutex

Definition at line 99 of file vcf_heatmap.hpp.

Referenced by GetData(), and Init().

◆ m_LastModified

string CVcfHeatmap::m_LastModified

protected

timestamp of the remote data last modified date as reported by www server

Definition at line 97 of file vcf_heatmap.hpp.

Referenced by CVcfHeatmap().

◆ m_RemoteId

string CVcfHeatmap::m_RemoteId

protected

Definition at line 94 of file vcf_heatmap.hpp.

Referenced by CVcfHeatmap(), and x_InitData().

◆ m_RemotePath

string CVcfHeatmap::m_RemotePath

protected

path to remote data or srz accession

Definition at line 96 of file vcf_heatmap.hpp.

Referenced by CVcfHeatmap(), and x_InitData().

◆ m_SeqId

string CVcfHeatmap::m_SeqId

protected

Definition at line 93 of file vcf_heatmap.hpp.

Referenced by CVcfHeatmap().

◆ m_SeqLen

size_t CVcfHeatmap::m_SeqLen = 0

protected

Definition at line 95 of file vcf_heatmap.hpp.

Referenced by CVcfHeatmap(), and x_InitData().

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

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

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CVcfHeatmap() [1/2]

◆ CVcfHeatmap() [2/2]

◆ ~CVcfHeatmap()

Member Function Documentation

◆ GetCacheKey()

◆ GetData()

◆ GetStorageName()

◆ Init()

◆ Save()

◆ x_CreateDataKey()

◆ x_InitData()

◆ x_SaveData()

Member Data Documentation

◆ m_Data

◆ m_DataKey

◆ m_DataMutex

◆ m_LastModified

◆ m_RemoteId

◆ m_RemotePath

◆ m_SeqId

◆ m_SeqLen