NCBI C++ ToolKit
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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< SGeneCdsmRnaFeatsTGeneCDSmRNAList
 a loader might be tied with a specific project item. More...
typedef map< objects::CSeq_id_Handle, TGeneCDSmRNAListTGeneModelMap
- 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< Uint8TCounter
 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...
CObjectoperator= (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)
CPtrToObjectProxyGetPtrProxy (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< CCmdCompositex_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< CCmdCompositex_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< CProjectServicem_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
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


Definition at line 121 of file create_gene_model_tool_manager.hpp.

The documentation for this class was generated from the following files:
Modified on Tue Dec 05 02:21:38 2023 by rev. 669887