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

Inheritance diagram for CSGTraceData:

Collaboration diagram for CSGTraceData:

Public Types
enum	EChannel { eA , eC , eT , eG }

typedef float	TConfidence

typedef double	TFloatSeqPos

typedef float	TSignalValue

typedef vector< TFloatSeqPos >	TPositions

typedef vector< TSignalValue >	TValues

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
	CSGTraceData ()

void	Init (TSignedSeqPos from, TSignedSeqPos to, int samples)
	CSGTraceData. More...

TSignedSeqPos	GetSeqFrom () const
	Sequence related information. More...

TSignedSeqPos	GetSeqTo () const

TSignedSeqPos	GetSeqLength () const

bool	IsNegative () const

TConfidence	GetConfidence (TSignedSeqPos pos) const

void	SetConfidence (TSignedSeqPos pos, TConfidence conf)

int	GetSamplesCount () const

TPositions &	GetPositions ()

TValues &	GetA ()

TValues &	GetC ()

TValues &	GetT ()

TValues &	GetG ()

TValues &	GetValues (EChannel signal)

const TPositions &	GetPositions () const

const TValues &	GetA () const

const TValues &	GetC () const

const TValues &	GetT () const

const TValues &	GetG () const

const TValues &	GetValues (EChannel signal) const

void	CalculateMax ()

TConfidence	GetMaxConfidence () const

TSignalValue	GetMax (EChannel signal) const

void	SetTitle (const string &title)

const string &	GetTitle () const

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

Protected Attributes
TSignedSeqPos	m_From

TSignedSeqPos	m_To

bool	m_bNegative

vector< TConfidence >	m_Confs

TPositions	m_Positions

TValues	m_ASig

TValues	m_CSig

TValues	m_TSig

TValues	m_GSig

TConfidence	m_MaxConfidence

TSignalValue	m_MaxA

TSignalValue	m_MaxC

TSignalValue	m_MaxT

TSignalValue	m_MaxG

string	m_Title = "Trace chromatograms"

Additional Inherited Members
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...

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

Detailed Description

CSGTraceData.

Definition at line 93 of file trace_graph_ds.hpp.

Member Typedef Documentation

◆ TConfidence

typedef float CSGTraceData::TConfidence

Definition at line 96 of file trace_graph_ds.hpp.

◆ TFloatSeqPos

typedef double CSGTraceData::TFloatSeqPos

Definition at line 97 of file trace_graph_ds.hpp.

◆ TPositions

typedef vector<TFloatSeqPos> CSGTraceData::TPositions

Definition at line 100 of file trace_graph_ds.hpp.

◆ TSignalValue

typedef float CSGTraceData::TSignalValue

Definition at line 98 of file trace_graph_ds.hpp.

◆ TValues

typedef vector<TSignalValue> CSGTraceData::TValues

Definition at line 101 of file trace_graph_ds.hpp.

Member Enumeration Documentation

◆ EChannel

enum CSGTraceData::EChannel

Enumerator
eA
eC
eT
eG

Definition at line 103 of file trace_graph_ds.hpp.

Constructor & Destructor Documentation

◆ CSGTraceData()

CSGTraceData::CSGTraceData ( )

inline

Definition at line 111 of file trace_graph_ds.hpp.

Member Function Documentation

◆ CalculateMax()

void CSGTraceData::CalculateMax ( )

Definition at line 305 of file trace_graph_ds.cpp.

References m_ASig, m_Confs, m_CSig, m_GSig, m_MaxA, m_MaxC, m_MaxConfidence, m_MaxG, m_MaxT, and m_TSig.

Referenced by CTraceGlyph::CTraceGlyph().

◆ GetA() [1/2]

CSGTraceData::TValues & CSGTraceData::GetA ( void )

inline

Definition at line 231 of file trace_graph_ds.hpp.

References m_ASig.

◆ GetA() [2/2]

const CSGTraceData::TValues & CSGTraceData::GetA ( void ) const

inline

Definition at line 261 of file trace_graph_ds.hpp.

References m_ASig.

◆ GetC() [1/2]

CSGTraceData::TValues & CSGTraceData::GetC ( )

inline

Definition at line 237 of file trace_graph_ds.hpp.

References m_CSig.

◆ GetC() [2/2]

const CSGTraceData::TValues & CSGTraceData::GetC ( ) const

inline

Definition at line 267 of file trace_graph_ds.hpp.

References m_CSig.

◆ GetConfidence()

CSGTraceData::TConfidence CSGTraceData::GetConfidence ( TSignedSeqPos pos ) const

inline

Definition at line 205 of file trace_graph_ds.hpp.

References m_Confs, and m_From.

Referenced by CTraceGlyph::x_RenderConfGraph().

◆ GetG() [1/2]

CSGTraceData::TValues & CSGTraceData::GetG ( )

inline

Definition at line 249 of file trace_graph_ds.hpp.

References m_GSig.

◆ GetG() [2/2]

const CSGTraceData::TValues & CSGTraceData::GetG ( ) const

inline

Definition at line 279 of file trace_graph_ds.hpp.

References m_GSig.

◆ GetMax()

CSGTraceData::TSignalValue CSGTraceData::GetMax ( EChannel signal ) const

Definition at line 327 of file trace_graph_ds.cpp.

References _ASSERT, eA, eC, eG, eT, eUnknown, m_MaxA, m_MaxC, m_MaxG, m_MaxT, and NCBI_THROW.

Referenced by CTraceGlyph::x_RenderIntensityGraphs(), and CTraceGlyph::x_RenderSignalGraph().

◆ GetMaxConfidence()

CSGTraceData::TConfidence CSGTraceData::GetMaxConfidence ( ) const

Definition at line 322 of file trace_graph_ds.cpp.

References m_MaxConfidence.

Referenced by CTraceGlyph::x_RenderConfGraph().

◆ GetPositions() [1/2]

CSGTraceData::TPositions & CSGTraceData::GetPositions ( )

inline

Definition at line 225 of file trace_graph_ds.hpp.

References m_Positions.

Referenced by CSGTraceGraphDS::LoadData(), CTraceGlyph::x_FindSampleToLeft(), CTraceGlyph::x_FindSampleToRight(), CTraceGlyph::x_RenderIntensityGraphs(), and CTraceGlyph::x_RenderSignalGraph().

◆ GetPositions() [2/2]

const CSGTraceData::TPositions & CSGTraceData::GetPositions ( ) const

inline

Definition at line 255 of file trace_graph_ds.hpp.

References m_Positions.

◆ GetSamplesCount()

int CSGTraceData::GetSamplesCount ( ) const

inline

Definition at line 219 of file trace_graph_ds.hpp.

References m_Positions.

Referenced by CTraceGlyph::CTraceGlyph(), CTraceGlyph::x_FindSampleToLeft(), CTraceGlyph::x_FindSampleToRight(), CTraceGlyph::x_RenderCurveSegment(), and CTraceGlyph::x_RenderIntensityGraphs().

◆ GetSeqFrom()

TSignedSeqPos CSGTraceData::GetSeqFrom ( ) const

inline

Sequence related information.

Definition at line 182 of file trace_graph_ds.hpp.

References m_From.

Referenced by CTraceGlyph::x_FindSampleToLeft(), CTraceGlyph::x_FindSampleToRight(), CTraceGlyph::x_RenderConfGraph(), CTraceGlyph::x_RenderCurveSegment(), and CTraceGlyph::x_RenderIntensityGraphs().

◆ GetSeqLength()

TSignedSeqPos CSGTraceData::GetSeqLength ( void ) const

inline

Definition at line 194 of file trace_graph_ds.hpp.

References m_From, and m_To.

Referenced by Init(), CTraceGlyph::x_FindSampleToLeft(), and CTraceGlyph::x_FindSampleToRight().

◆ GetSeqTo()

TSignedSeqPos CSGTraceData::GetSeqTo ( ) const

inline

Definition at line 188 of file trace_graph_ds.hpp.

References m_To.

Referenced by CTraceGlyph::x_FindSampleToLeft(), CTraceGlyph::x_FindSampleToRight(), CTraceGlyph::x_RenderConfGraph(), CTraceGlyph::x_RenderCurveSegment(), and CTraceGlyph::x_RenderIntensityGraphs().

◆ GetT() [1/2]

CSGTraceData::TValues & CSGTraceData::GetT ( )

inline

Definition at line 243 of file trace_graph_ds.hpp.

References m_TSig.

◆ GetT() [2/2]

const CSGTraceData::TValues & CSGTraceData::GetT ( ) const

inline

Definition at line 273 of file trace_graph_ds.hpp.

References m_TSig.

◆ GetTitle()

const string & CSGTraceData::GetTitle ( void ) const

inline

Definition at line 291 of file trace_graph_ds.hpp.

References m_Title.

Referenced by CTraceGraphTrack::x_UpdateData().

◆ GetValues() [1/2]

CSGTraceData::TValues & CSGTraceData::GetValues ( EChannel signal )

Definition at line 293 of file trace_graph_ds.cpp.

References _ASSERT, eA, eC, eG, eT, eUnknown, m_ASig, m_CSig, m_GSig, m_TSig, and NCBI_THROW.

Referenced by CSGTraceGraphDS::LoadData(), CTraceGlyph::x_RenderIntensityGraphs(), and CTraceGlyph::x_RenderSignalGraph().

◆ GetValues() [2/2]

const CSGTraceData::TValues & CSGTraceData::GetValues ( EChannel signal ) const

Definition at line 281 of file trace_graph_ds.cpp.

References _ASSERT, eA, eC, eG, eT, eUnknown, m_ASig, m_CSig, m_GSig, m_TSig, and NCBI_THROW.

◆ Init()

void CSGTraceData::Init	(	TSignedSeqPos	from,
		TSignedSeqPos	to,
		int	samples
	)

CSGTraceData.

Definition at line 265 of file trace_graph_ds.cpp.

References _ASSERT, GetSeqLength(), m_ASig, m_bNegative, m_Confs, m_CSig, m_From, m_GSig, m_Positions, m_To, and m_TSig.

Referenced by CSGTraceGraphDS::LoadData().

◆ IsNegative()

bool CSGTraceData::IsNegative ( ) const

inline

Definition at line 199 of file trace_graph_ds.hpp.

References m_bNegative.

◆ SetConfidence()

void CSGTraceData::SetConfidence	(	TSignedSeqPos	pos,
		TConfidence	conf
	)

inline

Definition at line 211 of file trace_graph_ds.hpp.

References m_Confs, and m_From.

Referenced by CSGTraceGraphDS::LoadData().

◆ SetTitle()

void CSGTraceData::SetTitle ( const string & title )

inline

Definition at line 285 of file trace_graph_ds.hpp.

References m_Title.

Referenced by CSGTraceGraphDS::LoadData().

Member Data Documentation

◆ m_ASig

TValues CSGTraceData::m_ASig

protected

Definition at line 158 of file trace_graph_ds.hpp.

Referenced by CalculateMax(), GetA(), GetValues(), and Init().

◆ m_bNegative

bool CSGTraceData::m_bNegative

protected

Definition at line 154 of file trace_graph_ds.hpp.

Referenced by Init(), and IsNegative().

◆ m_Confs

vector<TConfidence> CSGTraceData::m_Confs

protected

Definition at line 156 of file trace_graph_ds.hpp.

Referenced by CalculateMax(), GetConfidence(), Init(), and SetConfidence().

◆ m_CSig

TValues CSGTraceData::m_CSig

protected

Definition at line 159 of file trace_graph_ds.hpp.

Referenced by CalculateMax(), GetC(), GetValues(), and Init().

◆ m_From

TSignedSeqPos CSGTraceData::m_From

protected

Definition at line 152 of file trace_graph_ds.hpp.

Referenced by GetConfidence(), GetSeqFrom(), GetSeqLength(), Init(), and SetConfidence().

◆ m_GSig

TValues CSGTraceData::m_GSig

protected

Definition at line 161 of file trace_graph_ds.hpp.

Referenced by CalculateMax(), GetG(), GetValues(), and Init().

◆ m_MaxA

TSignalValue CSGTraceData::m_MaxA

protected

Definition at line 164 of file trace_graph_ds.hpp.

Referenced by CalculateMax(), and GetMax().

◆ m_MaxC

TSignalValue CSGTraceData::m_MaxC

protected

Definition at line 165 of file trace_graph_ds.hpp.

Referenced by CalculateMax(), and GetMax().

◆ m_MaxConfidence

TConfidence CSGTraceData::m_MaxConfidence

protected

Definition at line 163 of file trace_graph_ds.hpp.

Referenced by CalculateMax(), and GetMaxConfidence().

◆ m_MaxG

TSignalValue CSGTraceData::m_MaxG

protected

Definition at line 167 of file trace_graph_ds.hpp.

Referenced by CalculateMax(), and GetMax().

◆ m_MaxT

TSignalValue CSGTraceData::m_MaxT

protected

Definition at line 166 of file trace_graph_ds.hpp.

Referenced by CalculateMax(), and GetMax().

◆ m_Positions

TPositions CSGTraceData::m_Positions

protected

Definition at line 157 of file trace_graph_ds.hpp.

Referenced by GetPositions(), GetSamplesCount(), and Init().

◆ m_Title

string CSGTraceData::m_Title = "Trace chromatograms"

protected

Definition at line 169 of file trace_graph_ds.hpp.

Referenced by GetTitle(), and SetTitle().

◆ m_To

TSignedSeqPos CSGTraceData::m_To

protected

Definition at line 153 of file trace_graph_ds.hpp.

Referenced by GetSeqLength(), GetSeqTo(), and Init().

◆ m_TSig

TValues CSGTraceData::m_TSig

protected

Definition at line 160 of file trace_graph_ds.hpp.

Referenced by CalculateMax(), GetT(), GetValues(), and Init().

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

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

Public Types

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TConfidence

◆ TFloatSeqPos

◆ TPositions

◆ TSignalValue

◆ TValues

Member Enumeration Documentation

◆ EChannel

Constructor & Destructor Documentation

◆ CSGTraceData()

Member Function Documentation

◆ CalculateMax()

◆ GetA() [1/2]

◆ GetA() [2/2]

◆ GetC() [1/2]

◆ GetC() [2/2]

◆ GetConfidence()

◆ GetG() [1/2]

◆ GetG() [2/2]

◆ GetMax()

◆ GetMaxConfidence()

◆ GetPositions() [1/2]

◆ GetPositions() [2/2]

◆ GetSamplesCount()

◆ GetSeqFrom()

◆ GetSeqLength()

◆ GetSeqTo()

◆ GetT() [1/2]

◆ GetT() [2/2]

◆ GetTitle()

◆ GetValues() [1/2]

◆ GetValues() [2/2]

◆ Init()

◆ IsNegative()

◆ SetConfidence()

◆ SetTitle()

Member Data Documentation

◆ m_ASig

◆ m_bNegative

◆ m_Confs

◆ m_CSig

◆ m_From

◆ m_GSig

◆ m_MaxA

◆ m_MaxC

◆ m_MaxConfidence

◆ m_MaxG

◆ m_MaxT

◆ m_Positions

◆ m_Title

◆ m_To

◆ m_TSig