CTraceGraph - trace data renderer. More...

#include <gui/widgets/aln_multiple/trace_graph.hpp>

Inheritance diagram for CTraceGraph:

Collaboration diagram for CTraceGraph:

Public Types
typedef CTraceGraphProperties::ESingnalStyle	ESingnalStyle

typedef CTraceGraphProperties::EGraphState	EGraphState

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
	CTraceGraph (const objects::CBioseq_Handle &handle, bool b_neg_strand)

void	SetConfGraphState (EGraphState state)

void	SetSignalGraphState (EGraphState state)

IRenderable implementation
virtual void	Render (CGlPane &pane)

virtual TVPPoint	PreferredSize ()

virtual bool	NeedTooltip (CGlPane &pane, int vp_x, int vp_y)

virtual string	GetTooltip ()

IAlnVecRowGraph implementaion
virtual	~CTraceGraph ()

virtual bool	IsCreated () const
	Graph is not considered fully functional until it has been "created" by the call to create function. More...

virtual bool	Create ()

virtual void	Destroy ()

virtual void	Update (double, double)
	No need to update data for track graph. More...

virtual const IAlnRowGraphProperties *	GetProperties () const

virtual void	SetProperties (IAlnRowGraphProperties *props)

virtual void	Render (CGlPane &pane, IAlnSegmentIterator &it)

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

Public Member Functions inherited from CRenderableImpl
	CRenderableImpl ()
	CRenderableImpl. More...

virtual	~CRenderableImpl ()

virtual TVPRect	GetVPRect () const

virtual void	SetVPRect (const TVPRect &rc)

virtual TModelRect	GetModelRect () const

virtual void	SetModelRect (const TModelRect &rc)

virtual bool	IsVisible ()

virtual void	SetVisible (bool set)

virtual void	SetOrder (int order)

virtual int	GetOrder () const

Public Member Functions inherited from IRenderable
virtual	~IRenderable (void)

Public Member Functions inherited from IAlnVecRowGraph
virtual	~IAlnVecRowGraph ()

Protected Member Functions
int	x_GetConfGraphH () const

int	x_GetSignalGraphH () const

void	x_RenderText (CGlPane &pane)

void	x_RenderContour (CGlPane &pane, int y, int conf_h, int total_h, IAlnSegmentIterator &it)

void	x_RenderConfGraph (CGlPane &pane, int y, int h, IAlnSegmentIterator &it)

void	x_RenderSignalGraph (CGlPane &pane, int y, int h, IAlnSegmentIterator &it)

void	x_RenderCurveSegment (CGlPane &pane, const IAlnSegment &seg, const CTraceData::TPositions &positions, const CTraceData::TValues &values, int bottom_y, int h, int amp)

void	x_RenderIntensityGraphs (CGlPane &pane, int y, int h, IAlnSegmentIterator &it)
	Render signals for all channels as gradient-color bands with color intensity proprotional to signal strength. More...

const CRgbaColor &	GetColorByValue (double value, int signal) const

int	x_FindSampleToLeft (double pos) const
	returns index of rightmost sample having m_SeqPos less then "pos". More...

int	x_FindSampleToRight (double pos) const
	returns index of the leftmost sample having m_SeqPos greater than "pos" if "pos" is to the left of the trace range function returns -1, if "pos" is to the right of the trace range functions returns "n_samples" More...

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

Protected Attributes
CTraceDataProxy	m_DataProxy

CTraceData *	m_Data

CTraceGraphProperties	m_Props

vector< CRgbaColor >	m_vSignalColors

CGlTextureFont	m_Font

CRgbaColor	m_TextColor

Protected Attributes inherited from CRenderableImpl
TVPRect	m_VPRect

TModelRect	m_ModelRect

bool	m_Visible

int	m_Order = 0

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...

Detailed Description

CTraceGraph - trace data renderer.

Renders confidence graph and A, C, T, G chromatograms using CTraceData as datasource.

Definition at line 82 of file trace_graph.hpp.

Member Typedef Documentation

◆ EGraphState

typedef CTraceGraphProperties::EGraphState CTraceGraph::EGraphState

Definition at line 89 of file trace_graph.hpp.

◆ ESingnalStyle

typedef CTraceGraphProperties::ESingnalStyle CTraceGraph::ESingnalStyle

Definition at line 88 of file trace_graph.hpp.

Constructor & Destructor Documentation

◆ CTraceGraph()

CTraceGraph::CTraceGraph	(	const objects::CBioseq_Handle &	handle,
		bool	b_neg_strand
	)

Definition at line 74 of file trace_graph.cpp.

◆ ~CTraceGraph()

CTraceGraph::~CTraceGraph ( )

virtual

Definition at line 84 of file trace_graph.cpp.

References Destroy().

Member Function Documentation

◆ Create()

bool CTraceGraph::Create ( void )

virtual

Implements IAlnVecRowGraph.

Definition at line 162 of file trace_graph.cpp.

References CTraceData::CalculateMax(), CTraceGraphProperties::eExpanded, CTraceGraphProperties::eHidden, CTraceData::GetSamplesCount(), kGradColors, CTraceDataProxy::LoadData(), m_Data, m_DataProxy, m_vSignalColors, SetConfGraphState(), and SetSignalGraphState().

◆ Destroy()

void CTraceGraph::Destroy ( void )

virtual

Implements IAlnVecRowGraph.

Definition at line 189 of file trace_graph.cpp.

References m_Data, m_vSignalColors, and NULL.

Referenced by ~CTraceGraph().

◆ GetColorByValue()

const CRgbaColor & CTraceGraph::GetColorByValue	(	double	value,
		int	signal
	)		const

protected

Definition at line 892 of file trace_graph.cpp.

References _ASSERT, i, int, kGradColors, m_vSignalColors, min(), and value.

Referenced by x_RenderIntensityGraphs().

◆ GetProperties()

const IAlnRowGraphProperties * CTraceGraph::GetProperties ( void ) const

virtual

Implements IAlnVecRowGraph.

Definition at line 200 of file trace_graph.cpp.

References m_Props.

◆ GetTooltip()

string CTraceGraph::GetTooltip ( void )

virtual

Reimplemented from CRenderableImpl.

Definition at line 150 of file trace_graph.cpp.

◆ IsCreated()

bool CTraceGraph::IsCreated ( ) const

virtual

Graph is not considered fully functional until it has been "created" by the call to create function.

Only "Created" graph can be rendered. Creating may include loading data and building internal data structures.

Implements IAlnVecRowGraph.

Definition at line 156 of file trace_graph.cpp.

References m_Data, and NULL.

◆ NeedTooltip()

bool CTraceGraph::NeedTooltip	(	CGlPane &	pane,
		int	vp_x,
		int	vp_y
	)

virtual

Reimplemented from CRenderableImpl.

Definition at line 142 of file trace_graph.cpp.

References _VERIFY, CRenderableImpl::m_VPRect, and CGlRect< T >::PtInRect().

◆ PreferredSize()

TVPPoint CTraceGraph::PreferredSize ( )

virtual

Reimplemented from CRenderableImpl.

Definition at line 127 of file trace_graph.cpp.

References m_Data, x_GetConfGraphH(), and x_GetSignalGraphH().

◆ Render() [1/2]

void CTraceGraph::Render ( CGlPane & pane )

virtual

Implements IRenderable.

Definition at line 120 of file trace_graph.cpp.

◆ Render() [2/2]

void CTraceGraph::Render	(	CGlPane &	pane,
		IAlnSegmentIterator &	it
	)

virtual

◆ SetConfGraphState()

void CTraceGraph::SetConfGraphState ( EGraphState state )

Definition at line 216 of file trace_graph.cpp.

References CTraceGraphProperties::m_ConfGraphState, and m_Props.

Referenced by Create().

◆ SetProperties()

void CTraceGraph::SetProperties ( IAlnRowGraphProperties * props )

virtual

Implements IAlnVecRowGraph.

Definition at line 206 of file trace_graph.cpp.

References m_Props.

◆ SetSignalGraphState()

void CTraceGraph::SetSignalGraphState ( EGraphState state )

Definition at line 222 of file trace_graph.cpp.

References m_Props, and CTraceGraphProperties::m_SignalGraphState.

Referenced by Create().

◆ Update()

virtual void CTraceGraph::Update	(	double	,
		double
	)

inlinevirtual

No need to update data for track graph.

Implements IAlnVecRowGraph.

Definition at line 112 of file trace_graph.hpp.

◆ x_FindSampleToLeft()

int CTraceGraph::x_FindSampleToLeft ( double pos ) const

protected

returns index of rightmost sample having m_SeqPos less then "pos".

if "pos" is to the left of the trace range function returns -1, if "pos" is to the right of the trace range functions returns "n_samples"

Definition at line 906 of file trace_graph.cpp.

References CTraceData::GetPositions(), CTraceData::GetSamplesCount(), CTraceData::GetSeqFrom(), CTraceData::GetSeqLength(), CTraceData::GetSeqTo(), i, int, m_Data, max(), and min().

Referenced by x_RenderCurveSegment(), and x_RenderIntensityGraphs().

◆ x_FindSampleToRight()

int CTraceGraph::x_FindSampleToRight ( double pos ) const

protected

returns index of the leftmost sample having m_SeqPos greater than "pos" if "pos" is to the left of the trace range function returns -1, if "pos" is to the right of the trace range functions returns "n_samples"

Definition at line 938 of file trace_graph.cpp.

References CTraceData::GetPositions(), CTraceData::GetSamplesCount(), CTraceData::GetSeqFrom(), CTraceData::GetSeqLength(), CTraceData::GetSeqTo(), i, int, m_Data, max(), and min().

Referenced by x_RenderCurveSegment(), and x_RenderIntensityGraphs().

◆ x_GetConfGraphH()

int CTraceGraph::x_GetConfGraphH ( ) const

protected

Definition at line 98 of file trace_graph.cpp.

References CTraceGraphProperties::eCollapsed, CTraceGraphProperties::eExpanded, CTraceGraphProperties::eHidden, kCollapsedGraphH, kConfGraphPrefH, CTraceGraphProperties::m_ConfGraphState, and m_Props.

Referenced by PreferredSize(), and Render().

◆ x_GetSignalGraphH()

int CTraceGraph::x_GetSignalGraphH ( ) const

protected

Definition at line 109 of file trace_graph.cpp.

References CTraceGraphProperties::eCollapsed, CTraceGraphProperties::eExpanded, CTraceGraphProperties::eHidden, kCollapsedGraphH, kSignalGraphPrefH, m_Props, and CTraceGraphProperties::m_SignalGraphState.

Referenced by PreferredSize(), and Render().

◆ x_RenderConfGraph()

void CTraceGraph::x_RenderConfGraph	(	CGlPane &	pane,
		int	y,
		int	h,
		IAlnSegmentIterator &	it
	)

protected

Definition at line 417 of file trace_graph.cpp.

References _ASSERT, IRender::Begin(), CGlRect< T >::Bottom(), CGlPane::Close(), IRender::Color3d(), IRender::Disable(), IRender::End(), CGlPane::eOrtho, SChunkTranslator::GetAlnPosFromSeqPos(), IAlnSegment::GetAlnRange(), CTraceData::GetConfidence(), CRange_Base::GetFrom(), GetGl(), CTraceData::GetMaxConfidence(), CGlPane::GetOffsetX(), CGlPane::GetProjMode(), IAlnSegment::GetRange(), CGlPane::GetScaleX(), CTraceData::GetSeqFrom(), SChunkTranslator::GetSeqPosFromAlnPos(), CTraceData::GetSeqTo(), CRange_Base::GetTo(), CGlPane::GetViewport(), CGlPane::GetVisibleRect(), SChunkTranslator::Init(), IAlnSegment::IsAligned(), CTraceData::IsNegative(), kGraphOffsetY, CGlRect< T >::Left(), m_Data, max(), min(), NULL, CGlPane::OpenPixels(), IRender::PolygonMode(), IRender::Rectd(), CGlRect< T >::Right(), swap(), and IRender::Vertex2d().

Referenced by Render().

◆ x_RenderContour()

void CTraceGraph::x_RenderContour	(	CGlPane &	pane,
		int	y,
		int	conf_h,
		int	total_h,
		IAlnSegmentIterator &	it
	)

protected

◆ x_RenderCurveSegment()

void CTraceGraph::x_RenderCurveSegment	(	CGlPane &	pane,
		const IAlnSegment &	seg,
		const CTraceData::TPositions &	positions,
		const CTraceData::TValues &	values,
		int	bottom_y,
		int	h,
		int	amp
	)

protected

◆ x_RenderIntensityGraphs()

void CTraceGraph::x_RenderIntensityGraphs	(	CGlPane &	pane,
		int	y,
		int	h,
		IAlnSegmentIterator &	it_seg
	)

protected

Render signals for all channels as gradient-color bands with color intensity proprotional to signal strength.

Definition at line 722 of file trace_graph.cpp.

References _ASSERT, IRender::Begin(), CGlRect< T >::Bottom(), IRender::ColorC(), CTraceData::eA, IRender::End(), SChunkTranslator::GetAlnPosFromSeqPos(), IAlnSegment::GetAlnRange(), GetColorByValue(), CRange_Base::GetFrom(), GetGl(), CTraceData::GetMax(), CTraceData::GetPositions(), IAlnSegment::GetRange(), CTraceData::GetSamplesCount(), CGlPane::GetScaleX(), CTraceData::GetSeqFrom(), SChunkTranslator::GetSeqPosFromAlnPos(), CTraceData::GetSeqTo(), CRange_Base::GetTo(), CTraceData::GetValues(), CGlPane::GetViewport(), CGlPane::GetVisibleRect(), SChunkTranslator::Init(), IAlnSegment::IsAligned(), CTraceData::IsNegative(), kGraphOffsetY, CGlRect< T >::Left(), CTraceGraphProperties::m_bReverseColors, m_Data, m_Props, max(), min(), CGlRect< T >::Right(), swap(), v2, IRender::Vertex2d(), x_FindSampleToLeft(), and x_FindSampleToRight().

Referenced by Render().

◆ x_RenderSignalGraph()

void CTraceGraph::x_RenderSignalGraph	(	CGlPane &	pane,
		int	y,
		int	h,
		IAlnSegmentIterator &	it
	)

protected

Definition at line 585 of file trace_graph.cpp.

References _ASSERT, IAlnSegmentIterator::Clone(), IRender::ColorC(), CTraceData::eA, CTraceGraphProperties::eCurve, CTraceData::eG, GetGl(), CTraceData::GetMax(), CTraceData::GetPositions(), CTraceData::GetValues(), CTraceData::IsNegative(), kGradColors, kGraphOffsetY, CTraceGraphProperties::m_bReverseColors, m_Data, m_Props, CTraceGraphProperties::m_SignalStyle, m_vSignalColors, max(), IRender::PolygonMode(), and x_RenderCurveSegment().

Referenced by Render().

◆ x_RenderText()

void CTraceGraph::x_RenderText ( CGlPane & pane )

protected

Definition at line 294 of file trace_graph.cpp.

References CGlRect< T >::Bottom(), CGlPane::Close(), IRender::ColorC(), IGlFont::eAlign_Left, GetGl(), CGlRect< T >::Inflate(), kTextOff, CGlRect< T >::Left(), m_Font, m_TextColor, CRenderableImpl::m_VPRect, CGlPane::OpenPixels(), CGlRect< T >::Right(), CGlTextureFont::TextOut(), and CGlRect< T >::Top().

Member Data Documentation

◆ m_Data

CTraceData* CTraceGraph::m_Data

protected

Definition at line 153 of file trace_graph.hpp.

Referenced by Create(), Destroy(), IsCreated(), PreferredSize(), Render(), x_FindSampleToLeft(), x_FindSampleToRight(), x_RenderConfGraph(), x_RenderContour(), x_RenderCurveSegment(), x_RenderIntensityGraphs(), and x_RenderSignalGraph().

◆ m_DataProxy

CTraceDataProxy CTraceGraph::m_DataProxy

protected

Definition at line 152 of file trace_graph.hpp.

Referenced by Create().

◆ m_Font

CGlTextureFont CTraceGraph::m_Font

protected

Definition at line 159 of file trace_graph.hpp.

Referenced by x_RenderText().

◆ m_Props

CTraceGraphProperties CTraceGraph::m_Props

protected

Definition at line 155 of file trace_graph.hpp.

Referenced by GetProperties(), Render(), SetConfGraphState(), SetProperties(), SetSignalGraphState(), x_GetConfGraphH(), x_GetSignalGraphH(), x_RenderIntensityGraphs(), and x_RenderSignalGraph().

◆ m_TextColor

CRgbaColor CTraceGraph::m_TextColor

protected

Definition at line 160 of file trace_graph.hpp.

Referenced by x_RenderText().

◆ m_vSignalColors

vector<CRgbaColor> CTraceGraph::m_vSignalColors

protected

Definition at line 157 of file trace_graph.hpp.

Referenced by Create(), Destroy(), GetColorByValue(), and x_RenderSignalGraph().

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

include/gui/widgets/aln_multiple/trace_graph.hpp
src/gui/widgets/aln_multiple/trace_graph.cpp

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ EGraphState

◆ ESingnalStyle

Constructor & Destructor Documentation

◆ CTraceGraph()

◆ ~CTraceGraph()

Member Function Documentation

◆ Create()

◆ Destroy()

◆ GetColorByValue()

◆ GetProperties()

◆ GetTooltip()

◆ IsCreated()

◆ NeedTooltip()

◆ PreferredSize()

◆ Render() [1/2]

◆ Render() [2/2]

◆ SetConfGraphState()

◆ SetProperties()

◆ SetSignalGraphState()

◆ Update()

◆ x_FindSampleToLeft()

◆ x_FindSampleToRight()

◆ x_GetConfGraphH()

◆ x_GetSignalGraphH()

◆ x_RenderConfGraph()

◆ x_RenderContour()

◆ x_RenderCurveSegment()

◆ x_RenderIntensityGraphs()

◆ x_RenderSignalGraph()

◆ x_RenderText()

Member Data Documentation

◆ m_Data

◆ m_DataProxy

◆ m_Font

◆ m_Props

◆ m_TextColor

◆ m_vSignalColors