CCreateGeneModelTask Class Reference

Search Toolkit Book for CCreateGeneModelTask

CCreateGeneModelTask. More...

#include <gui/packages/pkg_alignment/create_gene_model_tool_manager.hpp>

Inheritance diagram for CCreateGeneModelTask:

Collaboration diagram for CCreateGeneModelTask:

Public Types
typedef CRef< objects::CLoaderDescriptor >	TLoaderRef
typedef CRef< objects::CProjectItem >	TItemRef
typedef list< SGeneCdsmRnaFeats >	TGeneCDSmRNAList
	a loader might be tied with a specific project item. More...
typedef map< objects::CSeq_id_Handle, TGeneCDSmRNAList >	TGeneModelMap
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 IAppTask
enum	ETaskState {   eInvalid = -1 , eInitial , eRunning , eBackgrounded ,   eCompleted , eFailed , eCanceled , eLastState }
	List of task states defining the task management FSM. More...

Public Member Functions
	CCreateGeneModelTask (const string &descr, CProjectService *service, CSelectProjectOptions &options, const SCreateGeneModelParams &params)
virtual	~CCreateGeneModelTask ()
Public Member Functions inherited from CAppTask
	CAppTask (const string &descr=kEmptyStr, bool visible=true, int display_delay=0)
	CAppTask. More...
virtual ETaskState	Run ()
	execute the task, this function is called on the main UI thread if a task needs to execute in background it should launch a job that will execute asynchronously; then the function shall return eBackgrounded More...
virtual ETaskState	GetState ()
	returns the current task state More...
virtual void	CancelBackgrounded ()
	make a request to cancel backgrounded task (not called for foreground tasks) More...
virtual void	OnCancel ()
	this will be called on pending tasks that will be removed from the queue and won't get a chance to run the purpose is to implement any cleanup procedures for the canceled task More...
virtual bool	IsVisible ()
	returns true if the task should be visible in UI visible task shall represent operations understood by users and usually correspond to menu commands. More...
int	GetStatusDisplayDelay ()
	returns delay in seconds used for certain fast (and not very important tasks) to only show its status when it is running/pending for long enough More...
virtual string	GetDescr () const
	returns a human-readable description of the Task (optional) More...
virtual string	GetStatusText () const
	returns human-readable text describing the current task state More...
virtual void	SetListener (CEventHandler *handler)
	set a Listener; this allows a taks running in background to notify the Listener (usually Task Manager) about changes in Status More...
virtual IEventLogAction *	CreateEventLogAction ()
	returns an action for activating task results (optional, can return NULL) More...
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 IAppTask
virtual	~IAppTask ()

Static Public Member Functions
static objects::CObject_id::TId	s_GetGeneID (const objects::CSeq_feat &feat)
static objects::CObject_id::TId	s_FindHighestFeatId (const objects::CSeq_entry_Handle seh)
static bool	s_FeaturesHaveIDs (const objects::CSeq_annot &annot)
static bool	s_FeaturesHaveXrefs (const objects::CSeq_annot &annot)
static void	s_AssignFeatureIds (objects::CSeq_annot &annot, objects::CObject_id::TId &max_id)
Static Public Member Functions inherited from CAppTask
static string	StateToString (ETaskState state)
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
static const string	sGeneDbName
	CCreateGeneModelTask. 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...

Protected Member Functions
virtual ETaskState	x_Run ()
	override this function in derived classes More...
Protected Member Functions inherited from CAppTask
virtual bool	x_IsFiniteState ()
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...

Private Member Functions
CRef< CCmdComposite >	x_GetCommand ()
void	x_StoreGeneratedFeats (const objects::CSeq_annot &annot, TGeneCDSmRNAList &gene_cds_rna) const
void	x_Group_By_GeneID (objects::CSeq_annot &annot, const objects::CSeq_id_Handle &idh)
void	x_GroupGenes (const objects::CSeq_id_Handle &idh, CRef< objects::CSeq_feat > gene)
void	x_AssignIDsAndCrossLinkFeats (objects::CSeq_annot &annot, const objects::CSeq_id_Handle &idh, objects::CObject_id::TId max_id)
CRef< CCmdComposite >	x_AssignIDsAndUpdateGenes (objects::CSeq_annot &annot, const objects::CSeq_id_Handle &idh, objects::CSeq_entry_Handle seh)
void	x_GetUpdatedGeneCommand (objects::CSeq_entry_Handle seh, const objects::CSeq_id_Handle &idh, CCmdComposite *cmd)
bool	x_UpdateGeneOnSequence (TGeneCDSmRNAList &gene_cds_rna, CRef< objects::CSeq_feat > gene)

Private Attributes
CIRef< CProjectService >	m_Service
CSelectProjectOptions	m_Options
SCreateGeneModelParams	m_Params
TGeneModelMap	m_GeneModelMap
CSelectProjectOptions::TItems	m_Items
CRef< objects::CScope >	m_Scope

Additional Inherited Members
Protected Attributes inherited from CAppTask
CEventHandler *	m_Listener
ETaskState	m_State
const bool	m_Visible
	indicates whether the task is visible More...
string	m_Descr
	task description More...
int	m_DisplayDelay
	tasks display delay More...

Detailed Description

CCreateGeneModelTask.

Definition at line 121 of file create_gene_model_tool_manager.hpp.

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

• include/gui/packages/pkg_alignment/create_gene_model_tool_manager.hpp
• src/gui/packages/pkg_alignment/create_gene_model_tool_manager.cpp