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NCBI C++ ToolKit: src/objtools/data_loaders/genbank/request_result.cpp Source File

atomic<int> saved_load_trace_level{-1};

load_trace_level = saved_load_trace_level.load(memory_order_acquire);

( load_trace_level < 0 ) {

saved_load_trace_level.store(load_trace_level, memory_order_release);

load_trace_level;

: m_State(kUnknownState),

(ref->GetData(), list);

ref->GetData() = list;

ret.

= it->GetGi();

( !it->IsGi() && it->GetSeqId()->GetTextseq_Id() ) {

* sep =

;

* end =

;

: m_State(kUnknownState),

(ref->GetData(), list);

ref->GetData() = list;

(

& blob_info :

() ) {

infos.push_back(blob_info);

* sep =

;

* end =

;

<< sep << it->GetBlob_id();

: m_Blob_id(blob_id),

( common_mask == 0 ) {

& name = *it;

GetData()->GetSplitInfo().GetChunk(chunk_id).IsLoaded();

( TParent::IsLoaded() ) {

<<

.m_TSE.GetBlobId().ToString();

<<

.m_Chunk.GetSplitInfo().GetBlobId().ToString()<<

<<

.m_Chunk.GetChunkId();

* sep =

;

* end =

;

<< sep << (*it2)->AsFastaString();

: m_AllowIncompleteLoading(

)

: m_AllowIncompleteLoading(

)

m_AllowIncompleteLoading(

)

TParent::operator=(lock);

( tse_name.IsNamed() ) {

*

(blob_id)->SetTSEName(tse_name.GetName());

( TParent::IsLoaded() ) {

: GBL::CInfoRequestor(manager),

m_ReadDispatcher(dispatcher),

m_RequestedId(requested_id),

m_AllocatedConnection(0),

m_InProcessor(in_processor)

.m_RecursiveTime = 0;

++

.m_RecursionLevel;

( rec_time > time ) {

time - rec_time;

: m_CacheAcc(GetMainMutex(), gc_size),

m_CacheSeqIds(GetMainMutex(), gc_size),

m_CacheGi(GetMainMutex(), gc_size),

m_CacheLabel(GetMainMutex(), gc_size),

m_CacheTaxId(GetMainMutex(), gc_size),

m_CacheHash(GetMainMutex(), gc_size),

m_CacheLength(GetMainMutex(), gc_size),

m_CacheType(GetMainMutex(), gc_size),

m_CacheBlobIds(GetMainMutex(), gc_size),

m_CacheBlobState(GetMainMutex(), gc_size),

m_CacheBlobVersion(GetMainMutex(), gc_size),

m_CacheBlob(GetMainMutex(), 0)

TData& blob_ids)

TData& blob_ids,

TExpirationTime expiration)

SetLoaded(*

,

,

, exp_type);

(

<<

<<

<<

<<ids.GetData());

(

<<

<<

<<

<<ids.GetData());

( !lock.IsLoaded() ) {

SetLoaded(*

,

,

, exp_type);

( acc_lock.IsLoaded() ) {

acc_lock.SetLoadedFor(ids_lock.GetData().FindAccVer(),

ids_lock.GetExpirationTime());

(

<<

<<

<<

<<

.acc_ver);

SetLoadedFor(*

,

,

, ids.GetExpirationTime());

(

<<

<<

<<

);

(

<<

<<

<<

);

( gi_lock.IsLoaded() ) {

gi_lock.SetLoadedFor(ids_lock.GetData().FindGi(),

ids_lock.GetExpirationTime());

SetLoadedFor(*

,

,

, ids.GetExpirationTime());

( !lock.IsLoaded() ) {

SetLoaded(*

,

,

, exp_type);

( label_lock.IsLoaded() ) {

label_lock.SetLoadedFor(ids_lock.GetData().FindLabel(),

ids_lock.GetExpirationTime());

SetLoadedFor(*

,

,

, ids.GetExpirationTime());

&

)

SetLoaded(*

,

,

, exp_type);

SetLoaded(*

,

,

, exp_type);

SetLoaded(*

,

,

, exp_type);

SetLoaded(*

,

,

, exp_type);

SetLoaded(*

,

,

, exp_type);

(

<<

<<

<<

<<

.second<<

<<

);

SetLoaded(*

,

,

, exp_type);

.first = seq_id;

.second += it->first;

(

.second ==

) {

.second +=

;

.second +=

;

SetLoaded(*

, blob_id,

, exp_type);

writer->SaveBlobState(*

, blob_id, blob_state);

SetLoaded(*

, blob_id,

, exp_type);

( old_version < 0 ) {

writer->SaveBlobVersion(*

, blob_id,

);

ncbi::TMaskedQueryRegions mask

void AddNamedAnnotName(const string &name)

const TNamedAnnotNames & GetNamedAnnotNames(void) const

TNamedAnnotNames m_NamedAnnotNames

bool Matches(const SAnnotSelector *sel) const

void AddAnnotInfo(const CID2S_Seq_annot_Info &info)

void SetAnnotInfo(CRef< CBlob_Annot_Info > &annot_info)

const TContentsMask & GetContentsMask(void) const

const CConstRef< CBlob_Annot_Info > & GetAnnotInfo(void) const

const CConstRef< CBlob_id > & GetBlob_id(void) const

TBlobContentsMask TContentsMask

bool IsSetAnnotInfo(void) const

bool Matches(TContentsMask mask, const SAnnotSelector *sel) const

CConstRef< CBlob_Annot_Info > m_AnnotInfo

const string & GetTSEName() const

void SetState(TState state)

CFixedBlob_ids Filter(const SAnnotSelector *sel) const

vector< CBlob_Info > TList

const TList & Get(void) const

CConstRef< TObject > m_Ref

CDataLoader::SGiFound FindGi(void) const

vector< CSeq_id_Handle > TList

string FindLabel(void) const

void SetState(TState state)

CDataLoader::SAccVerFound FindAccVer(void) const

CConstRef< TObject > m_Ref

TCacheBlobState m_CacheBlobState

CGBInfoManager(size_t gc_size)

TCacheLength m_CacheLength

TCacheBlobIds m_CacheBlobIds

TCacheSeqIds m_CacheSeqIds

TCacheBlobVersion m_CacheBlobVersion

CID2S_Seq_annot_Info –.

CGBInfoManager::TCacheAcc::TInfoLock TParent

GBL::EExpirationType GetExpType(void) const

CGBInfoManager::TCacheBlobIds::TInfoLock TParent

GBL::EExpirationType GetExpType(void) const

bool SetLoadedBlob_ids(const TData &data, TExpirationTime expiration_time)

CGBInfoManager::TCacheBlobState::TInfoLock TParent

GBL::EExpirationType GetExpType(void) const

CGBInfoManager::TCacheBlobVersion::TInfoLock TParent

GBL::EExpirationType GetExpType(void) const

CLoadLockBlobVersion(void)

CConstRef< CTSE_Chunk_Info > m_Chunk

TChunkId GetSelectedChunkId(void) const

CGBInfoManager::TBlobVersion TBlobVersion

void x_ObtainTSE_LoadLock(CReaderRequestResult &result)

void SelectChunk(TChunkId chunk_id)

CGBInfoManager::TCacheBlob::TInfoLock TParent

bool NeedsDelayedMainChunk(void) const

CLoadLockBlob(CReaderRequestResult &src, const CBlob_id &blob_id, TChunkId chunk_id=kMain_ChunkId)

bool IsLoadedChunk(void) const

CTSE_LoadLock m_TSE_LoadLock

const CTSE_Split_Info & GetSplitInfo(void) const

bool IsLoadedBlob(void) const

CGBInfoManager::TChunkId TChunkId

CTSE_LoadLock & GetTSE_LoadLock(void)

TBlobVersion GetKnownBlobVersion(void) const

bool IsLoadedGi(void) const

TExpirationTime GetExpirationTimeGi(void) const

CGBInfoManager::TCacheGi::TInfoLock TParent

static TGi GetGi(const TData &data)

GBL::EExpirationType GetExpType(void) const

CGBInfoManager::TCacheHash::TInfoLock TParent

GBL::EExpirationType GetExpType(void) const

CGBInfoManager::TCacheLabel::TInfoLock TParent

GBL::EExpirationType GetExpType(void) const

CGBInfoManager::TCacheLength::TInfoLock TParent

GBL::EExpirationType GetExpType(void) const

CGBInfoManager::TCacheSeqIds::TInfoLock TParent

TData GetSeq_ids(void) const

bool SetLoadedSeq_ids(const TData &data)

GBL::EExpirationType GetExpType(void) const

void SetSeq_entry(CSeq_entry &entry, CTSE_SetObjectInfo *set_info=0)

CLoadLockSetter(CLoadLockBlob &blob)

void x_ObtainTSE_LoadLock(CReaderRequestResult &result, const CBlob_id &blob_id)

void x_SelectChunk(TChunkId chunk_id)

bool m_AllowIncompleteLoading

AutoPtr< CInitGuard > m_ChunkLoadLock

CTSE_Split_Info & GetSplitInfo(void)

CTSE_LoadLock m_TSE_LoadLock

bool IsLoaded(void) const

CGBInfoManager::TBlobState TBlobState

void AllowIncompleteLoading()

CRef< CTSE_Chunk_Info > m_Chunk

CGBInfoManager::TChunkId TChunkId

void x_Init(CLoadLockBlob &blob, TChunkId chunk_id)

TBlobState GetBlobState(void) const

CGBInfoManager::TCacheBlob::TInfoLock TParent

GBL::EExpirationType GetExpType(void) const

CGBInfoManager::TCacheTaxId::TInfoLock TParent

CGBInfoManager::TCacheType::TInfoLock TParent

GBL::EExpirationType GetExpType(void) const

static bool IsExtAnnot(const TBlobId &blob_id)

CWriter * GetWriter(const CReaderRequestResult &result, CWriter::EType type) const

~CReaderRequestResultRecursion(void)

CReaderRequestResult & m_Result

double GetCurrentRequestTime(void) const

CReaderRequestResultRecursion(CReaderRequestResult &result, bool in_processor=false)

bool IsLoadedLength(const CSeq_id_Handle &id)

bool SetLoadedBlobIdsFromZeroGi(const CSeq_id_Handle &id, const SAnnotSelector *sel, const CLoadLockGi &gi_lock)

CGBInfoManager::TCacheGi::TInfoLock TInfoLockGi

TTSE_LockSet m_TSE_LockSet

bool MarkLoadingLength(const CSeq_id_Handle &id)

CGBInfoManager::TCacheBlobIds::TInfoLock TInfoLockBlobIds

bool IsLoadedBlobVersion(const TKeyBlob &blob_id)

bool SetLoadedLabel(const CSeq_id_Handle &id, const string &value)

bool IsLoadedBlobState(const TKeyBlob &blob_id)

virtual void GetLoadedBlob_ids(const CSeq_id_Handle &idh, TLoadedBlob_ids &blob_ids) const

virtual TExpirationTime GetIdExpirationTimeout(GBL::EExpirationType type) const

TInfoLockTaxId GetLoadLockTaxId(const CSeq_id_Handle &id)

bool MarkLoadingSeqIds(const CSeq_id_Handle &id)

bool SetLoadedSeqIds(const CSeq_id_Handle &id, const CFixedSeq_ids &value)

TInfoLockHash GetLoadLockHash(const CSeq_id_Handle &id)

void SaveLocksTo(TTSE_LockSet &locks)

CWriter * GetBlobWriter(void) const

CGBInfoManager::TSequenceLength TSequenceLength

TInfoLockType GetLoadedType(const CSeq_id_Handle &id)

bool SetLoadedGiFromSeqIds(const CSeq_id_Handle &id, const CLoadLockSeqIds &ids_lock)

bool MarkLoadingLabel(const CSeq_id_Handle &id)

CGBInfoManager::TCacheLength::TInfoLock TInfoLockLength

bool IsLoadedTaxId(const CSeq_id_Handle &id)

bool MarkLoadingHash(const CSeq_id_Handle &id)

virtual ~CReaderRequestResult(void)

TInfoLockBlobIds GetLoadLockBlobIds(const CSeq_id_Handle &id, const SAnnotSelector *sel)

TInfoLockAcc GetLoadLockAcc(const CSeq_id_Handle &id)

bool SetLoadedBlobState(const TKeyBlob &blob_id, TBlobState state)

CReadDispatcher & m_ReadDispatcher

CGBInfoManager::TTaxId TTaxId

CGBInfoManager & GetGBInfoManager(void)

bool IsLoadedAcc(const CSeq_id_Handle &id)

bool SetLoadedAccFromSeqIds(const CSeq_id_Handle &id, const CLoadLockSeqIds &ids_lock)

CSeq_id_Handle m_RequestedId

bool SetLoadedAcc(const CSeq_id_Handle &id, const TSequenceAcc &value)

bool MarkLoadingGi(const CSeq_id_Handle &id)

CGBInfoManager::TCacheBlobState::TInfoLock TInfoLockBlobState

CGBInfoManager::TBlobState TBlobState

TExpirationTime GetNewIdExpirationTime(GBL::EExpirationType type) const

bool SetLoadedBlobIds(const CSeq_id_Handle &id, const SAnnotSelector *sel, const CLoadLockBlobIds &ids)

TInfoLockBlobIds GetLoadedBlobIds(const CSeq_id_Handle &id, const SAnnotSelector *sel)

CGBInfoManager::TCacheLabel::TInfoLock TInfoLockLabel

void x_AddTSE_LoadLock(const CTSE_LoadLock &lock)

CTSE_LoadLock GetBlobLoadLock(const TKeyBlob &blob_id)

bool SetLoadedHash(const CSeq_id_Handle &id, const TSequenceHash &value)

virtual bool GetAddWGSMasterDescr(void) const

CGBInfoManager::TBlobVersion TBlobVersion

void SetAndSaveBlobVersion(const TKeyBlob &blob_id, TBlobVersion version)

TInfoLockBlob GetLoadLockBlob(const TKeyBlob &blob_id)

TInfoLockLabel GetLoadLockLabel(const CSeq_id_Handle &id)

bool SetLoadedSeqIdsFromZeroGi(const CSeq_id_Handle &id, const CLoadLockGi &gi_lock)

bool IsLoadedSeqIds(const CSeq_id_Handle &id)

TInfoLockLabel GetLoadedLabel(const CSeq_id_Handle &id)

TInfoLockGi GetLoadLockGi(const CSeq_id_Handle &id)

CGBInfoManager::TCacheSeqIds::TInfoLock TInfoLockIds

CGBInfoManager::TCacheType::TInfoLock TInfoLockType

CReaderAllocatedConnection * m_AllocatedConnection

vector< CBlob_id > TLoadedBlob_ids

bool UpdateGiFromSeqIds(TInfoLockGi &gi_lock, const TInfoLockIds &ids_lock)

bool MarkLoadingType(const CSeq_id_Handle &id)

bool UpdateAccFromSeqIds(TInfoLockAcc &acc_lock, const TInfoLockIds &ids_lock)

bool SetLoadedLabelFromSeqIds(const CSeq_id_Handle &id, const CLoadLockSeqIds &ids_lock)

CGBInfoManager::TCacheHash::TInfoLock TInfoLockHash

TInfoLockAcc GetLoadedAcc(const CSeq_id_Handle &id)

TExpirationTime GetRequestTime(void) const

bool UpdateLabelFromSeqIds(TInfoLockLabel &label_lock, const TInfoLockIds &ids_lock)

bool SetLoadedType(const CSeq_id_Handle &id, const TSequenceType &value)

TInfoLockLength GetLoadLockLength(const CSeq_id_Handle &id)

TInfoLockType GetLoadLockType(const CSeq_id_Handle &id)

CGBInfoManager::TCacheTaxId::TInfoLock TInfoLockTaxId

TInfoLockBlobVersion GetLoadedBlobVersion(const TKeyBlob &blob_id)

TInfoLockLength GetLoadedLength(const CSeq_id_Handle &id)

CGBInfoManager::TCacheAcc::TInfoLock TInfoLockAcc

bool SetLoadedTaxId(const CSeq_id_Handle &id, const TTaxId &value)

TInfoLockIds GetLoadLockSeqIds(const CSeq_id_Handle &id)

CReaderRequestResult(const CSeq_id_Handle &requested_id, CReadDispatcher &dispatcher, CGBInfoManager &manager)

bool SetLoadedBlobVersion(const TKeyBlob &blob_id, TBlobVersion version)

bool SetNoBlob(const TKeyBlob &blob_id, TBlobState blob_state)

void SetAndSaveBlobState(const TKeyBlob &blob_id, TBlobState state)

bool MarkLoadingTaxId(const CSeq_id_Handle &id)

TInfoLockGi GetLoadedGi(const CSeq_id_Handle &id)

bool IsLoadedGi(const CSeq_id_Handle &id)

CGBInfoManager::TCacheBlobVersion::TInfoLock TInfoLockBlobVersion

static TKeyBlob_ids s_KeyBlobIds(const CSeq_id_Handle &id, const SAnnotSelector *sel)

void ReleaseNotLoadedBlobs(void)

bool IsLoadedType(const CSeq_id_Handle &id)

CGBInfoManager::TCacheBlob::TInfoLock TInfoLockBlob

TInfoLockHash GetLoadedHash(const CSeq_id_Handle &id)

void SetRequestedId(const CSeq_id_Handle &requested_id)

TExpirationTime GetStartTime(void) const

virtual EGBErrorAction GetPTISErrorAction(void) const

TInfoLockBlob GetLoadedBlob(const TKeyBlob &blob_id)

bool SetLoadedGi(const CSeq_id_Handle &id, const TSequenceGi &value)

GBL::CInfo_Base::TExpirationTime TExpirationTime

bool IsLoadedHash(const CSeq_id_Handle &id)

bool MarkLoadingBlobIds(const CSeq_id_Handle &id, const SAnnotSelector *sel)

pair< CSeq_id_Handle, string > TKeyBlob_ids

TInfoLockBlobState GetLoadLockBlobState(const TKeyBlob &blob_id)

virtual CGBDataLoader * GetLoaderPtr(void)

TInfoLockBlobVersion GetLoadLockBlobVersion(const TKeyBlob &blob_id)

bool SetLoadedLength(const CSeq_id_Handle &id, const TSequenceLength &value)

bool IsLoadedLabel(const CSeq_id_Handle &id)

CWriter * GetIdWriter(void) const

TInfoLockIds GetLoadedSeqIds(const CSeq_id_Handle &id)

TInfoLockTaxId GetLoadedTaxId(const CSeq_id_Handle &id)

TInfoLockBlobState GetLoadedBlobState(const TKeyBlob &blob_id)

TExpirationTime GetNewExpirationTime(GBL::EExpirationType type) const

bool IsLoadedBlobIds(const CSeq_id_Handle &id, const SAnnotSelector *sel)

bool MarkLoadingAcc(const CSeq_id_Handle &id)

void SetLoaded(CObject *obj=0)

void x_LoadSeq_entry(CSeq_entry &entry, CTSE_SetObjectInfo *set_info=0)

TChunkId GetChunkId(void) const

CInitGuard * GetLoadInitGuard(void)

bool IsLoaded(void) const

TBlobVersion GetBlobVersion(void) const

TBlobState GetBlobState(void) const

void SetBlobState(TBlobState state)

void SetName(const CAnnotName &name)

const TBlobId & GetBlobId(void) const

const CAnnotName & GetName(void) const

CTSE_Split_Info & GetSplitInfo(void)

bool x_NeedsDelayedMainChunk(void) const

void SetSeq_entry(CSeq_entry &entry, CTSE_SetObjectInfo *set_info=0)

void SetBlobVersion(TBlobVersion version)

bool IsLoaded(void) const

CTSE_Chunk_Info & GetChunk(TChunkId chunk_id)

Template class for iteration on objects of class C (non-medifiable version)

iterator_bool insert(const value_type &val)

std::ofstream out("events_result.xml")

main entry point for tests

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * get(void) const

Get pointer.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

@ eTakeOwnership

An object can take ownership of another.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Warning(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

static const char * GetSNPScaleLimit_Name(ESNPScaleLimit value)

string GetLabel(const CSeq_id &id)

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

bool IsIncludedAnyNamedAnnotAccession(void) const

check if any named annot accession is included in the search

bool IsIncludedNamedAnnotAccession(const string &acc) const

check if named annot accession is included in the search

TSNPScaleLimit GetSNPScaleLimit(void) const

const TNamedAnnotAccessions & GetNamedAnnotAccessions(void) const

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

#define NCBI_PARAM_TYPE(section, name)

Generate typename for a parameter from its {section, name} attributes.

@ eParam_NoThread

Do not use per-thread values.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

ENcbiOwnership

Ownership relations between objects.

static const char label[]

@ e_Gi

GenInfo Integrated Database.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_id > > TId

constexpr bool empty(list< Ts... >) noexcept

const string version

version string

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

Multi-threading – classes, functions, and features.

static const CReaderRequestResult::TBlobVersion kBlobVersionNotSet

static CReaderRequestResult::TExpirationTime sx_GetCurrentTime(void)

static int s_GetLoadTraceLevel(void)

CNcbiOstream & operator<<(CNcbiOstream &out, const CFixedSeq_ids &ids)

NCBI_PARAM_DECL(int, GENBANK, TRACE_LOAD)

NCBI_PARAM_DEF_EX(int, GENBANK, TRACE_LOAD, 0, eParam_NoThread, GENBANK_TRACE_LOAD)

Better replacement of GetAccVer(), this method should be defined in data loaders, GetAccVer() is left...

Better replacement of GetGi(), this method should be defined in data loaders, GetGi() is left for com...

Better replacement of GetSequenceHash(), this method should be defined in data loaders,...

Better replacement of GetSequenceType(), this method should be defined in data loaders,...

SBlobId(const CTSE_Info &tse)

SChunkId(const CTSE_Chunk_Info &chunk)

const CTSE_Chunk_Info & m_Chunk

const CSeq_entry & m_Entry

SSeqIds(const CSeq_entry &entry)

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