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

Inheritance diagram for CFeatureGraph:

Collaboration diagram for CFeatureGraph:

Public Types
typedef CFeatureGraphProperties::TFeatTypeItem	TFeatTypeItem

typedef CFeatureGraphProperties::TFeatTypeItemSet	TFeatTypeItemSet

typedef objects::CMappingRanges	TMapRanges

typedef vector< SMappedFeatLoc >	TMappedFeatLocs

typedef CAppJobDispatcher::TJobID	TJobID

Public Types inherited from CGraphContainer
enum	ELayoutPolicy { eHorzStack , eVertStack , eWhole }

typedef IRenderable	TGraph

typedef CIRef< IRenderable >	TGraphRef

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 Types inherited from CEventHandler
enum	EDispatch { eDispatch_SelfOnly , eDispatch_AllHandlers , eDispatch_FirstHandler , eDispatch_Default = eDispatch_AllHandlers }
	enum controlling dispatching strategies More...

enum	EPoolName { ePool_Default = 0 , ePool_Parent , ePool_Child , ePool_Sibling , ePool_NextAvailable }
	Identifiers for standard pools. More...

typedef vector< CEventHandler * >	TListeners

typedef map< int, TListeners >	TPools

typedef list< AutoPtr< SPostRequest > >	TPostRequests

typedef std::map< CEventHandler *, int >	THandlerToCount

typedef void(*	FOnPostCallback) ()

Public Member Functions
	CFeatureGraph (const IAlignRowHandle &row_handle, bool isDataReadSync)

void	OnAJNotification (CEvent *evt)

IRenderable implementation
virtual TVPPoint	PreferredSize ()

virtual void	Layout ()

IAlnVecRowGraph implementaion
virtual	~CFeatureGraph ()

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 start, double stop)
	Update data according to the input range. More...

virtual const IAlnRowGraphProperties *	GetProperties () const

virtual void	SetProperties (IAlnRowGraphProperties *props)

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

Public Member Functions inherited from CGraphContainer
	CGraphContainer (ELayoutPolicy policy)
	CGraphContainer. More...

virtual	~CGraphContainer ()

virtual bool	AddGraph (TGraph *graph, bool front=false)

virtual bool	RemoveGraph (TGraph *graph)
	assumes ownership More...

virtual void	RemoveAllGraphs ()

virtual size_t	GetGraphsCount () const

virtual TGraph *	GetGraph (size_t index)

virtual const TGraph *	GetGraph (size_t index) const

virtual void	Clear ()

void	SetHost (IGraphContainerHost *host)

void	OnMouseEvents (wxMouseEvent &event)

void	SetGraphMaxSize (const TVPPoint &size)

virtual void	Render (CGlPane &pane)

virtual void	SetVPRect (const TVPRect &rect)

virtual void	SetModelRect (const TModelRect &rc)

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

virtual string	GetTooltip ()

virtual wxEvtHandler *	GetEvtHandler ()

virtual void	SetPane (CGlPane *pane)

Public Member Functions inherited from CObjectEx
	CObjectEx (void)

virtual	~CObjectEx (void)

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 CWeakObject
	CWeakObject (void)

virtual	~CWeakObject (void)

CPtrToObjectProxy *	GetPtrProxy (void) const
	Get pointer to proxy object containing pointer to this object. More...

Public Member Functions inherited from IGlEventHandler
virtual	~IGlEventHandler ()

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

virtual	~CRenderableImpl ()

virtual TVPRect	GetVPRect () const

virtual TModelRect	GetModelRect () const

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 CEventHandler
	CEventHandler ()
	CEventHandler. More...

virtual	~CEventHandler ()

virtual void	AddListener (CEventHandler *listener, int pool_name=ePool_Default)
	Add a listener. More...

virtual void	RemoveListener (CEventHandler *listener)
	Remove a listener. More...

virtual void	RemoveAllListeners (void)

virtual bool	HasListener (CEventHandler *listener, int pool_name=ePool_Default) const
	returns "true" if the given listener belongs to the specified pool More...

virtual const TListeners *	GetListeners (int pool_name=ePool_Default) const
	returns a set of listeners fro the specified pool More...

virtual bool	OnEvent (CEvent *evt)
	Processes en event. Returns "true" if event has been processed. More...

virtual bool	Dispatch (CEvent *evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)
	Dispatches an event to the listeners (but does not handle it). More...

virtual bool	Send (CEvent *evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)
	Sends an event synchronously. More...

virtual bool	Send (CEvent *evt, int pool_name)

void	Post (CRef< CEvent > evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)
	Handles an event asynchronously (process and/or dispatch). More...

Public Member Functions inherited from IAlnVecRowGraph
virtual	~IAlnVecRowGraph ()

Protected Types
typedef set< objects::CSeqFeatData::ESubtype >	TSubtypeSet

typedef map< TJobID, CRef< CFeatureLoadingJob > >	TJobMap

Protected Types inherited from CGraphContainer
typedef vector< TGraphRef >	TGraphs

Protected Member Functions
	DECLARE_EVENT_MAP ()

void	x_RenderStatusText (CGlPane &pane)

CRef< TMapRanges >	x_CreateMapRanges ()

void	x_StartJob (const TFeatTypeItemSet &feat_set, const TSubtypeSet &filter, bool positive, CRange< TSeqPos > &total_range, TMapRanges &map_ranges, const string &descr, bool separate_types, bool link_genes, int order)

bool	x_StartJob (objects::SAnnotSelector &sel, CRange< TSeqPos > &total_range, TMapRanges &map_ranges, const string &descr, bool separate_types, bool link_genes, int order)

bool	x_CancelJob (TJobID job_id)

void	x_CancelJobs ()
	Cancel all active jobs. More...

void	x_OnJobCompleted (CAppJobNotification &notify)

void	x_OnJobFailed (CAppJobNotification &notify)

void	x_Create (double start, double stop)

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

Protected Member Functions inherited from CWeakObject
void	CleanWeakRefs (void) const
	Method cleaning all CWeakRefs referencing at this moment to the object After calling to this method all existing CWeakRefs referencing to the object will return NULL, so it effectively will be equal to deleting the object. More...

Protected Member Functions inherited from CEventHandler
virtual const SEvtMap *	GetEventMap () const

void	x_DeclareDead ()
	Removes itself unavailable for async event delivery. More...

void	x_AddListenerToPool (CEventHandler *listener, int pool_name)

Protected Attributes
const IAlignRowHandle &	m_RowHandle

bool	m_Created

TJobMap	m_Jobs

string	m_StatusText

CGlTextureFont	m_Font

CFeatureGraphProperties	m_Properties

Protected Attributes inherited from CGraphContainer
wxEvtHandler *	m_Handler

IGraphContainerHost *	m_Host

ELayoutPolicy	m_LayoutPolicy

TGraphs	m_Graphs

TGraph *	m_TooltipGraph

CGlPane *	m_Pane

TVPPoint	m_GraphMaxSize

Protected Attributes inherited from CRenderableImpl
TVPRect	m_VPRect

TModelRect	m_ModelRect

bool	m_Visible

int	m_Order = 0

Protected Attributes inherited from CEventHandler
TPools	m_Pools

Private Attributes
bool	m_isDataReadSync

bool	m_Updated

TGraphs	m_PendingGraphs
	Candidate graphs waiting for replacing the current ones. More...

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 Member Functions inherited from CEventHandler
static bool	HandlePostRequest ()

static void	ClearPostQueue ()
	erases all events from the queue More...

static void	DestroyPostQueue ()

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...

Static Protected Attributes inherited from CEventHandler
static const SEvtMap	sm_EvtMap

Detailed Description

CFeatureGraph.

Definition at line 174 of file feature_graph.hpp.

Member Typedef Documentation

◆ TFeatTypeItem

typedef CFeatureGraphProperties::TFeatTypeItem CFeatureGraph::TFeatTypeItem

Definition at line 179 of file feature_graph.hpp.

◆ TFeatTypeItemSet

typedef CFeatureGraphProperties::TFeatTypeItemSet CFeatureGraph::TFeatTypeItemSet

Definition at line 180 of file feature_graph.hpp.

◆ TJobID

typedef CAppJobDispatcher::TJobID CFeatureGraph::TJobID

Definition at line 183 of file feature_graph.hpp.

◆ TJobMap

typedef map<TJobID, CRef<CFeatureLoadingJob> > CFeatureGraph::TJobMap

protected

Definition at line 246 of file feature_graph.hpp.

◆ TMappedFeatLocs

typedef vector<SMappedFeatLoc> CFeatureGraph::TMappedFeatLocs

Definition at line 182 of file feature_graph.hpp.

◆ TMapRanges

typedef objects::CMappingRanges CFeatureGraph::TMapRanges

Definition at line 181 of file feature_graph.hpp.

◆ TSubtypeSet

typedef set<objects::CSeqFeatData::ESubtype> CFeatureGraph::TSubtypeSet

protected

Definition at line 213 of file feature_graph.hpp.

Constructor & Destructor Documentation

◆ CFeatureGraph()

CFeatureGraph::CFeatureGraph	(	const IAlignRowHandle &	row_handle,
		bool	isDataReadSync
	)

Definition at line 233 of file feature_graph.cpp.

References CSeqFeatData::GetFeatList(), set< Key, Compare >::insert(), ITERATE, CFeatureGraphProperties::m_FeatureTypes, and m_Properties.

◆ ~CFeatureGraph()

CFeatureGraph::~CFeatureGraph ( )

virtual

Definition at line 252 of file feature_graph.cpp.

References Destroy().

Member Function Documentation

◆ Create()

bool CFeatureGraph::Create ( void )

virtual

Implements IAlnVecRowGraph.

Definition at line 265 of file feature_graph.cpp.

References CGlRect< T >::Left(), m_Created, CRenderableImpl::m_ModelRect, CGlRect< T >::Right(), CGlRect< T >::Width(), and x_Create().

◆ DECLARE_EVENT_MAP()

CFeatureGraph::DECLARE_EVENT_MAP ( )

protected

◆ Destroy()

void CFeatureGraph::Destroy ( void )

virtual

Implements IAlnVecRowGraph.

Definition at line 325 of file feature_graph.cpp.

References m_Created, CGraphContainer::RemoveAllGraphs(), and x_CancelJobs().

Referenced by ~CFeatureGraph().

◆ GetProperties()

const IAlnRowGraphProperties * CFeatureGraph::GetProperties ( void ) const

virtual

Implements IAlnVecRowGraph.

Definition at line 349 of file feature_graph.cpp.

References NULL.

◆ IsCreated()

bool CFeatureGraph::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 258 of file feature_graph.cpp.

References m_Created.

◆ Layout()

void CFeatureGraph::Layout ( )

virtual

Reimplemented from CGraphContainer.

Definition at line 443 of file feature_graph.cpp.

References _ASSERT, CGlRect< T >::Bottom(), CGraphContainer::eHorzStack, CGraphContainer::eVertStack, CGraphContainer::Layout(), CGraphContainer::m_Graphs, CGraphContainer::m_LayoutPolicy, CRenderableImpl::m_ModelRect, CRenderableImpl::m_VPRect, NON_CONST_ITERATE, IRenderable::PreferredSize(), IRenderable::SetModelRect(), CGlRect< T >::SetVert(), IRenderable::SetVPRect(), ncbi::grid::netcache::search::fields::size, and CGlPoint< T >::Y().

◆ OnAJNotification()

void CFeatureGraph::OnAJNotification ( CEvent * evt )

◆ PreferredSize()

virtual TVPPoint CFeatureGraph::PreferredSize ( )

virtual

Reimplemented from CGraphContainer.

◆ Render()

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

virtual

Implements IAlnVecRowGraph.

Definition at line 366 of file feature_graph.cpp.

References CGraphContainer::Render(), and x_RenderStatusText().

◆ SetProperties()

void CFeatureGraph::SetProperties ( IAlnRowGraphProperties * props )

virtual

Implements IAlnVecRowGraph.

Definition at line 355 of file feature_graph.cpp.

References _ASSERT, and m_Properties.

◆ Update()

void CFeatureGraph::Update	(	double	start,
		double	stop
	)

virtual

Update data according to the input range.

Parameters

range the current visible range

Implements IAlnVecRowGraph.

Definition at line 334 of file feature_graph.cpp.

References CGlRect< T >::Left(), m_isDataReadSync, CRenderableImpl::m_ModelRect, m_Updated, CGlRect< T >::Right(), x_CancelJobs(), and x_Create().

◆ x_CancelJob()

bool CFeatureGraph::x_CancelJob ( TJobID job_id )

protected

Definition at line 597 of file feature_graph.cpp.

References _ASSERT, CAppJobDispatcher::DeleteJob(), CAppJobException::eEngine_UnknownJob, map_checker< Container >::end(), map_checker< Container >::erase(), ERR_POST, CAppJobException::eUnknownJob, map_checker< Container >::find(), CAppJobDispatcher::GetInstance(), LOG_POST, and m_Jobs.

◆ x_CancelJobs()

void CFeatureGraph::x_CancelJobs ( )

protected

Cancel all active jobs.

Definition at line 583 of file feature_graph.cpp.

References map_checker< Container >::clear(), CAppJobDispatcher::DeleteJob(), CAppJobDispatcher::GetInstance(), m_Jobs, m_PendingGraphs, and NON_CONST_ITERATE.

Referenced by Destroy(), and Update().

◆ x_Create()

void CFeatureGraph::x_Create	(	double	start,
		double	stop
	)

protected

◆ x_CreateMapRanges()

CRef< CMappingRanges > CFeatureGraph::x_CreateMapRanges ( )

protected

◆ x_OnJobCompleted()

void CFeatureGraph::x_OnJobCompleted ( CAppJobNotification & notify )

protected

Definition at line 686 of file feature_graph.cpp.

References copy(), ERR_POST, CAppJobNotification::GetJobID(), CRef< C, Locker >::GetPointer(), CAppJobNotification::GetResult(), m_PendingGraphs, n, and result.

Referenced by OnAJNotification().

◆ x_OnJobFailed()

void CFeatureGraph::x_OnJobFailed ( CAppJobNotification & notify )

protected

Definition at line 707 of file feature_graph.cpp.

References ERR_POST, CAppJobNotification::GetError(), and CAppJobNotification::GetJobID().

Referenced by OnAJNotification().

◆ x_RenderStatusText()

void CFeatureGraph::x_RenderStatusText ( CGlPane & pane )

protected

◆ x_StartJob() [1/2]

void CFeatureGraph::x_StartJob	(	const TFeatTypeItemSet &	feat_set,
		const TSubtypeSet &	filter,
		bool	positive,
		CRange< TSeqPos > &	total_range,
		TMapRanges &	map_ranges,
		const string &	descr,
		bool	separate_types,
		bool	link_genes,
		int	order
	)

protected

Definition at line 276 of file feature_graph.cpp.

References SAnnotSelector::AddNamedAnnots(), set< Key, Compare >::empty(), set< Key, Compare >::end(), CSeqFeatData::eSubtype_any, CSeqFeatData::eSubtype_variation, SAnnotSelector::ExcludeNamedAnnots(), set< Key, Compare >::find(), CSeqUtils::GetAnnotSelector(), SAnnotSelector::IncludeFeatSubtype(), set< Key, Compare >::insert(), ITERATE, and positive().

Referenced by x_Create().

◆ x_StartJob() [2/2]

bool CFeatureGraph::x_StartJob	(	objects::SAnnotSelector &	sel,
		CRange< TSeqPos > &	total_range,
		TMapRanges &	map_ranges,
		const string &	descr,
		bool	separate_types,
		bool	link_genes,
		int	order
	)

protected

Member Data Documentation

◆ m_Created

bool CFeatureGraph::m_Created

protected

Definition at line 249 of file feature_graph.hpp.

Referenced by Create(), Destroy(), and IsCreated().

◆ m_Font

CGlTextureFont CFeatureGraph::m_Font

protected

Definition at line 253 of file feature_graph.hpp.

Referenced by x_RenderStatusText().

◆ m_isDataReadSync

bool CFeatureGraph::m_isDataReadSync

private

Definition at line 258 of file feature_graph.hpp.

Referenced by Update(), and x_Create().

◆ m_Jobs

TJobMap CFeatureGraph::m_Jobs

protected

Definition at line 250 of file feature_graph.hpp.

Referenced by OnAJNotification(), x_CancelJob(), and x_CancelJobs().

◆ m_PendingGraphs

TGraphs CFeatureGraph::m_PendingGraphs

private

Candidate graphs waiting for replacing the current ones.

Definition at line 262 of file feature_graph.hpp.

Referenced by OnAJNotification(), x_CancelJobs(), x_Create(), and x_OnJobCompleted().

◆ m_Properties

CFeatureGraphProperties CFeatureGraph::m_Properties

protected

Definition at line 255 of file feature_graph.hpp.

Referenced by CFeatureGraph(), SetProperties(), and x_Create().

◆ m_RowHandle

const IAlignRowHandle& CFeatureGraph::m_RowHandle

protected

Definition at line 248 of file feature_graph.hpp.

Referenced by x_Create(), and x_CreateMapRanges().

◆ m_StatusText

string CFeatureGraph::m_StatusText

protected

Definition at line 252 of file feature_graph.hpp.

Referenced by OnAJNotification(), x_Create(), and x_RenderStatusText().

◆ m_Updated

bool CFeatureGraph::m_Updated

private

Definition at line 259 of file feature_graph.hpp.

Referenced by Update().

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

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

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TFeatTypeItem

◆ TFeatTypeItemSet

◆ TJobID

◆ TJobMap

◆ TMappedFeatLocs

◆ TMapRanges

◆ TSubtypeSet

Constructor & Destructor Documentation

◆ CFeatureGraph()

◆ ~CFeatureGraph()

Member Function Documentation

◆ Create()

◆ DECLARE_EVENT_MAP()

◆ Destroy()

◆ GetProperties()

◆ IsCreated()

◆ Layout()

◆ OnAJNotification()

◆ PreferredSize()

◆ Render()

◆ SetProperties()

◆ Update()

◆ x_CancelJob()

◆ x_CancelJobs()

◆ x_Create()

◆ x_CreateMapRanges()

◆ x_OnJobCompleted()

◆ x_OnJobFailed()

◆ x_RenderStatusText()

◆ x_StartJob() [1/2]

◆ x_StartJob() [2/2]

Member Data Documentation

◆ m_Created

◆ m_Font

◆ m_isDataReadSync

◆ m_Jobs

◆ m_PendingGraphs

◆ m_Properties

◆ m_RowHandle

◆ m_StatusText

◆ m_Updated