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NCBI C++ ToolKit: src/gui/objutils/seqfetch_queue.cpp Source File

, m_Queue(parent_queue)

, m_Priority(priority)

( ; feat_iter; ++feat_iter) {

( ; feat_iter; ++feat_iter) {

( ; seqmap_iter; ++seqmap_iter) {

( ; seqmap_iter; ++seqmap_iter) {

threads,

max_queue_size)

, m_IsShuttingDown(

)

TRetrievalFlags

,

TRetrievalFlags

)

TRetrievalFlags

)

TRetrievalFlags

)

(vector<CSeq_id_Handle>, iter, ids) {

(vector<TGi>, iter, ids) {

static CRef< CScope > m_Scope

Siple fatal request used for terminating processing.

void Process()

Do the actual job Called by whichever thread handles this request.

Wrapper class for a resolution request.

void Process()

Do the actual job Called by whichever thread handles this request.

CSeqFetchQueue::TRetrievalFlags m_Flags

CResolveRequest(CScope &scope, CSeq_id_Handle idh, const TSeqRange &range, CSeqFetchQueue::TRetrievalFlags flags, CSeqFetchQueue &parent_queue, int priority)

friend class CResolveRequest

void Finish()

Finish processing of all items in the queue.

void Clear()

Clear all items from the queue.

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

Enqueue a single ID for retrieval.

bool m_IsShuttingDown

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

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

CSeqFetchQueue implementation details.

CRef< objects::CScope > m_Scope

@ fRetrieveProducts

should we enqueue product retrievals as well? this implies retrieval of mRNA and CDS features

@ fRetrieveRecursive

should we enqueue all items recursively? levels below the requested level are retrieved with a lower ...

@ fRetrieveFeatures

retrieve all features not in external annotations

@ fRetrieveCoreFeatures

retrieve the "core" features this includes genes, mRNAs, and CDSs only

bool IsFull() const

Ask if the queue is full or empty.

static CSeqFetchQueue & GetInstance()

static interface to access singleton

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetGiHandle(TGi gi)

Faster way to create a handle for a gi.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

CSeq_id_Handle GetIdHandle(const CSeq_loc &loc, CScope *scope)

TIds GetIds(const CSeq_id &id, TGetFlags flags=0)

Get "native" bioseq ids without filtering and matching.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

bool IsSetProduct(void) const

TSeqPos GetEndPosition(void) const

return end position of current segment in sequence (exclusive)

SSeqMapSelector & SetResolveCount(size_t res_cnt)

Set max depth of resolving seq-map.

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

SSeqMapSelector & SetFlags(TFlags flags)

Select segment type(s)

SAnnotSelector & SetAdaptiveDepth(bool value=true)

SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower...

SAnnotSelector & SetExcludeExternal(bool exclude=true)

External annotations for the Object Manger are annotations located in top level Seq-entry different f...

const CSeq_loc & GetProduct(void) const

CSeq_id_Handle GetRefSeqid(void) const

The following function makes sense only when the segment is a reference to another seq.

SAnnotSelector & SetResolveNone(void)

SetResolveNone() is equivalent to SetResolveMethod(eResolve_None).

void Reset(void)

Reset reference object.

static TThisType GetWhole(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

virtual void KillAllThreads(TKillFlags flags)

Causes all threads in the pool to exit cleanly after finishing all pending requests,...

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.

bool IsEmpty(void) const

Check if the queue is empty.

TQueue m_Queue

The request queue.

bool IsFull(void) const

Check if the queue is full.

TItemHandle GetHandle(unsigned int timeout_sec=kMax_UInt, unsigned int timeout_nsec=0)

Get the first available request from the queue, and return a handle to it.

static void Exit(void *exit_data)

Cancel current thread.

#define DEFINE_STATIC_MUTEX(id)

Define static mutex and initialize it.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is whole

Multi-threading – mutexes; rw-locks; semaphore.

CRef< objects::CObjectManager > om

Selector used in CSeqMap methods returning iterators.

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