Search Toolkit Book for CSeqFetchQueue

#include <gui/objutils/seqfetch_queue.hpp>

Inheritance diagram for CSeqFetchQueue:

Collaboration diagram for CSeqFetchQueue:

Public Types
enum	ERetrievalFlags { fRetrieveSequence = 0x01 , fRetrieveCoreFeatures = 0x02 , fRetrieveFeatures = 0x04 , fRetrieveAll = fRetrieveSequence \| fRetrieveFeatures , fRetrieveRecursive = 0x08 , fRetrieveProducts = 0x10 , fDefaults = 0x0 }

typedef int	TRetrievalFlags

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
	CSeqFetchQueue (objects::CScope &scope, int threads=4, int max_queue_size=100000)
	CSeqFetchQueue implementation details. More...

void	Add (const objects::CSeq_id &id, TRetrievalFlags flags=fDefaults)
	Enqueue a single ID for retrieval. More...

void	Add (const objects::CSeq_id &id, const TSeqRange &range, TRetrievalFlags flags=fDefaults)

void	Add (objects::CSeq_id_Handle id, TRetrievalFlags flags=fDefaults)
	Enqueue a single ID for retrieval. More...

void	Add (objects::CSeq_id_Handle id, const TSeqRange &range, TRetrievalFlags flags=fDefaults)

void	Add (const vector< objects::CSeq_id_Handle > &ids, TRetrievalFlags flags=fDefaults)
	Enqueue a set of IDs for retrieval. More...

void	Add (const vector< TGi > &ids, TRetrievalFlags flags=fDefaults)
	Enqueue a set of gis for retrieval. More...

bool	IsFull () const
	Ask if the queue is full or empty. More...

bool	IsEmpty () const

void	Clear ()
	Clear all items from the queue. More...

void	Finish ()
	Finish processing of all items in the queue. More...

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

Static Public Member Functions
static CSeqFetchQueue &	GetInstance ()
	static interface to access singleton More...

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)

Protected Member Functions
void	Add (objects::CSeq_id_Handle idh, const TSeqRange &range, TRetrievalFlags flags, int priority)
	internal version of add all of the other APIs feed into this one More...

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

Private Member Functions
	CSeqFetchQueue (const CSeqFetchQueue &)

CSeqFetchQueue &	operator= (const CSeqFetchQueue &)

Private Member Functions inherited from CStdPoolOfThreads
	CStdPoolOfThreads (unsigned int max_threads, unsigned int queue_size, unsigned int spawn_threshold=1, unsigned int max_urgent_threads=kMax_UInt, const string &thread_name=kEmptyStr)
	Constructor. More...

virtual	~CStdPoolOfThreads ()

virtual void	KillAllThreads (TKillFlags flags)
	Causes all threads in the pool to exit cleanly after finishing all pending requests, optionally waiting for them to die. More...

virtual void	KillAllThreads (bool wait)
	Causes all threads in the pool to exit cleanly after finishing all pending requests, optionally waiting for them to die. More...

virtual void	Register (TThread &thread)
	Register a thread. More...

virtual void	UnRegister (TThread &thread)
	Unregister a thread. More...

virtual TThread *	NewThread (TThread::ERunMode mode)
	Create a new thread. More...

Private Member Functions inherited from CPoolOfThreads< CRef< CStdRequest > >
	CPoolOfThreads (unsigned int max_threads, unsigned int queue_size, unsigned int spawn_threshold=1, unsigned int max_urgent_threads=kMax_UInt, const string &thread_name=kEmptyStr)
	Constructor. More...

virtual	~CPoolOfThreads (void)
	Destructor. More...

void	Spawn (unsigned int num_threads)
	Start processing threads. More...

TItemHandle	AcceptRequest (const CRef< CStdRequest > &request, TUserPriority priority=0, unsigned int timeout_sec=0, unsigned int timeout_nsec=0)
	Put a request in the queue with a given priority. More...

TItemHandle	AcceptUrgentRequest (const CRef< CStdRequest > &request, unsigned int timeout_sec=0, unsigned int timeout_nsec=0)
	Puts a request in the queue with the highest priority It will run a new thread even if the maximum of allowed threads has been already reached. More...

void	WaitForRoom (unsigned int timeout_sec=kMax_UInt, unsigned int timeout_nsec=0)
	Wait for the room in the queue up to timeout_sec + timeout_nsec/1E9 seconds. More...

bool	IsFull (void) const
	Check if the queue is full. More...

bool	IsEmpty (void) const
	Check if the queue is empty. More...

bool	HasImmediateRoom (bool urgent=false) const
	Check whether a new request could be immediately processed. More...

void	SetUserPriority (TItemHandle handle, TUserPriority priority)
	Adjust a pending request's priority. More...

void	Withdraw (TItemHandle handle)
	Withdraw a pending request from consideration. More...

size_t	GetQueueSize (void) const
	Get the number of requests in the queue. More...

virtual void	Register (TThread &thread)
	Register a thread. More...

virtual void	UnRegister (TThread &)
	Unregister a thread. More...

Private Attributes
CRef< objects::CScope >	m_Scope

bool	m_IsShuttingDown
	flag: set to true when the class is shutting down this blocks all further acceptances More...

Private Attributes inherited from CPoolOfThreads< CRef< CStdRequest > >
CAtomicCounter_WithAutoInit	m_MaxThreads
	The maximum number of threads the pool can hold. More...

CAtomicCounter_WithAutoInit	m_MaxUrgentThreads
	The maximum number of urgent threads running simultaneously. More...

int	m_Threshold
	for delta More...

CAtomicCounter_WithAutoInit	m_ThreadCount
	The current number of threads in the pool. More...

CAtomicCounter_WithAutoInit	m_UrgentThreadCount
	The current number of urgent threads running now. More...

atomic< int >	m_Delta
	The difference between the number of unfinished requests and the total number of threads in the pool. More...

CMutex	m_Mutex
	The guard for m_MaxThreads, m_MaxUrgentThreads, and m_Delta. More...

TQueue	m_Queue
	The request queue. More...

bool	m_QueuingForbidden

const string	m_ThreadName

Friends
class	CResolveRequest

Additional Inherited Members
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...

Private Types inherited from CStdPoolOfThreads
enum	EKillFlags { fKill_Wait = 0x1 , fKill_Reopen = 0x2 }

typedef CPoolOfThreads< CRef< CStdRequest > >	TParent

typedef int	TKillFlags
	binary OR of EKillFlags More...

Private Types inherited from CPoolOfThreads< CRef< CStdRequest > >
typedef CThreadInPool< CRef< CStdRequest > >	TThread

typedef TThread::ERunMode	ERunMode

typedef CBlockingQueue< CRef< CStdRequest > >	TQueue

typedef TQueue::TUserPriority	TUserPriority

typedef TQueue::TItemHandle	TItemHandle

typedef CAtomicCounter::TValue	TACValue

Detailed Description

Definition at line 49 of file seqfetch_queue.hpp.

Member Typedef Documentation

◆ TRetrievalFlags

typedef int CSeqFetchQueue::TRetrievalFlags

Definition at line 79 of file seqfetch_queue.hpp.

Member Enumeration Documentation

◆ ERetrievalFlags

enum CSeqFetchQueue::ERetrievalFlags

Enumerator
fRetrieveSequence	retrieve the sequence associated with the ID
fRetrieveCoreFeatures	retrieve the "core" features this includes genes, mRNAs, and CDSs only
fRetrieveFeatures	retrieve all features not in external annotations
fRetrieveAll
fRetrieveRecursive	should we enqueue all items recursively? levels below the requested level are retrieved with a lower priority to favor interactive tasks that need immediate attention
fRetrieveProducts	should we enqueue product retrievals as well? this implies retrieval of mRNA and CDS features
fDefaults	default just calls GetBioseqHandle()

Definition at line 53 of file seqfetch_queue.hpp.

Constructor & Destructor Documentation

◆ CSeqFetchQueue() [1/2]

CSeqFetchQueue::CSeqFetchQueue	(	objects::CScope &	scope,
		int	threads = `4`,
		int	max_queue_size = `100000`
	)

CSeqFetchQueue implementation details.

Definition at line 248 of file seqfetch_queue.cpp.

Referenced by GetInstance().

◆ CSeqFetchQueue() [2/2]

CSeqFetchQueue::CSeqFetchQueue ( const CSeqFetchQueue & )

private

Member Function Documentation

◆ Add() [1/7]

void CSeqFetchQueue::Add	(	const objects::CSeq_id &	id,
		const TSeqRange &	range,
		TRetrievalFlags	flags = `fDefaults`
	)

◆ Add() [2/7]

void CSeqFetchQueue::Add	(	const objects::CSeq_id &	id,
		TRetrievalFlags	flags = `fDefaults`
	)

Enqueue a single ID for retrieval.

Referenced by Add(), and CResolveRequest::Process().

◆ Add() [3/7]

void CSeqFetchQueue::Add	(	const vector< objects::CSeq_id_Handle > &	ids,
		TRetrievalFlags	flags = `fDefaults`
	)

Enqueue a set of IDs for retrieval.

◆ Add() [4/7]

void CSeqFetchQueue::Add	(	const vector< TGi > &	ids,
		TRetrievalFlags	flags = `fDefaults`
	)

Enqueue a set of gis for retrieval.

Definition at line 380 of file seqfetch_queue.cpp.

References Add(), flags, CSeq_id_Handle::GetGiHandle(), COpenRange< TSeqPos >::GetWhole(), ITERATE, m_IsShuttingDown, and compile_time_bits::range().

◆ Add() [5/7]

void CSeqFetchQueue::Add	(	objects::CSeq_id_Handle	id,
		const TSeqRange &	range,
		TRetrievalFlags	flags = `fDefaults`
	)

◆ Add() [6/7]

void CSeqFetchQueue::Add	(	objects::CSeq_id_Handle	id,
		TRetrievalFlags	flags = `fDefaults`
	)

Enqueue a single ID for retrieval.

enqueue an ID for retrieval

Definition at line 351 of file seqfetch_queue.cpp.

References Add(), flags, COpenRange< TSeqPos >::GetWhole(), m_IsShuttingDown, and compile_time_bits::range().

◆ Add() [7/7]

void CSeqFetchQueue::Add	(	objects::CSeq_id_Handle	idh,
		const TSeqRange &	range,
		TRetrievalFlags	flags,
		int	priority
	)

protected

internal version of add all of the other APIs feed into this one

◆ Clear()

void CSeqFetchQueue::Clear ( void )

Clear all items from the queue.

Definition at line 287 of file seqfetch_queue.cpp.

References Finish(), CBlockingQueue< TRequest >::GetHandle(), IsEmpty(), m_IsShuttingDown, and CPoolOfThreads< CRef< CStdRequest > >::m_Queue.

◆ Finish()

void CSeqFetchQueue::Finish ( void )

Finish processing of all items in the queue.

Definition at line 297 of file seqfetch_queue.cpp.

References CPoolOfThreads< CRef< CStdRequest > >::AcceptRequest(), IsEmpty(), CStdPoolOfThreads::KillAllThreads(), and m_IsShuttingDown.

Referenced by Clear().

◆ GetInstance()

CSeqFetchQueue & CSeqFetchQueue::GetInstance ( void )

static

static interface to access singleton

Definition at line 257 of file seqfetch_queue.cpp.

References CScope::AddDefaults(), CSeqFetchQueue(), DEFINE_STATIC_MUTEX, CObjectManager::GetInstance(), om, and CRef< C, Locker >::Reset().

◆ IsEmpty()

bool CSeqFetchQueue::IsEmpty ( void ) const

Definition at line 281 of file seqfetch_queue.cpp.

References CBlockingQueue< TRequest >::IsEmpty(), and CPoolOfThreads< CRef< CStdRequest > >::m_Queue.

Referenced by Clear(), and Finish().

◆ IsFull()

bool CSeqFetchQueue::IsFull ( void ) const

Ask if the queue is full or empty.

Definition at line 275 of file seqfetch_queue.cpp.

References CBlockingQueue< TRequest >::IsFull(), and CPoolOfThreads< CRef< CStdRequest > >::m_Queue.

◆ operator=()

CSeqFetchQueue& CSeqFetchQueue::operator= ( const CSeqFetchQueue & )

private

Friends And Related Function Documentation

◆ CResolveRequest

friend class CResolveRequest

friend

Definition at line 123 of file seqfetch_queue.hpp.

Member Data Documentation

◆ m_IsShuttingDown

bool CSeqFetchQueue::m_IsShuttingDown

private

flag: set to true when the class is shutting down this blocks all further acceptances

Definition at line 136 of file seqfetch_queue.hpp.

Referenced by Add(), Clear(), and Finish().

◆ m_Scope

CRef<objects::CScope> CSeqFetchQueue::m_Scope

private

Definition at line 132 of file seqfetch_queue.hpp.

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

include/gui/objutils/seqfetch_queue.hpp
src/gui/objutils/seqfetch_queue.cpp

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TRetrievalFlags

Member Enumeration Documentation

◆ ERetrievalFlags

Constructor & Destructor Documentation

◆ CSeqFetchQueue() [1/2]

◆ CSeqFetchQueue() [2/2]

Member Function Documentation

◆ Add() [1/7]

◆ Add() [2/7]

◆ Add() [3/7]

◆ Add() [4/7]

◆ Add() [5/7]

◆ Add() [6/7]

◆ Add() [7/7]

◆ Clear()

◆ Finish()

◆ GetInstance()

◆ IsEmpty()

◆ IsFull()

◆ operator=()

Friends And Related Function Documentation

◆ CResolveRequest

Member Data Documentation

◆ m_IsShuttingDown

◆ m_Scope