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NCBI C++ ToolKit: src/objmgr/tse_split_info.cpp Source File

m_SeqIdToChunksSorted(

),

m_ContainsBioseqs(

)

m_BlobVersion(blob_ver),

m_SeqIdToChunksSorted(

),

m_ContainsBioseqs(

)

it->second->x_DropAnnotObjects();

it->second->x_TSEAttach(tse, *lsnr);

vector<CSeq_id_Handle> ids;

chunk.second->GetBioseqsIds(ids);

vector<CSeq_id_Handle> ids;

chunk.second->GetBioseqsIds(ids);

delayed_chunk = iter->second;

( iter != begin ) {

( iter != begin ) {

delayed_chunk = iter->second;

( delayed_chunk ) {

delayed_chunk->

();

*iter->second;

*iter->second;

*iter->second;

.push_back(pair<CSeq_id_Handle, TChunkId>(

, chunk_id));

( seq_ids.empty() && annot_ids.

() ) {

(

&

: seq_ids ) {

.push_back(pair<CSeq_id_Handle, TChunkId>(

, chunk_id));

(

&

: annot_ids ) {

.push_back(pair<CSeq_id_Handle, TChunkId>(

, chunk_id));

( it->first->ContainsBioseq(

) ) {

CTSE_Split_Info::TSeqIdToChunks::const_iterator

pair<CSeq_id_Handle, TChunkId>(

, -1));

vector<TChunkId> chunk_ids;

( TSeqIdToChunks::const_iterator iter =

(

);

chunk_ids.push_back(iter->second);

vector<TChunkId> chunk_ids;

(

& [

,

] : ids ) {

( TSeqIdToChunks::const_iterator iter =

(

);

chunk_ids.push_back(iter->second);

( TSeqIdToChunks::const_iterator iter =

(

);

chunks.push_back(

(&chunk));

it->second->GetBioseqsIds(ids);

( TSeqIdToChunks::const_iterator iter =

(

);

vector< CRef<CTSE_Chunk_Info> > TChunkRefs;

vector< AutoPtr<CInitGuard> > TInitGuards;

(sorted_ids.begin(), sorted_ids.end());

sorted_ids.erase(unique(sorted_ids.begin(), sorted_ids.end()),

limit_chunks_request = 15;

limit_chunks_request = 200;

reserve_size =

(sorted_ids.size(), limit_chunks_request);

chunks.reserve(reserve_size);

guards.reserve(reserve_size);

( !(*guard.

()) ) {

chunks.push_back(chunk);

guards.push_back(guard);

( guards.size() >= limit_chunks_request ) {

( !guards.empty() ) {

vector<CRef<CTSE_Chunk_Info>> sorted_chunks;

sorted_chunks.reserve(src_chunks.size());

(

& chunk : src_chunks ) {

(&chunk->GetSplitInfo().GetDataLoader() == loader);

(sorted_chunks.begin(), sorted_chunks.end(),

auto blob_id_a = a->GetBlobId();

auto blob_id_b = b->GetBlobId();

return ((blob_id_a < blob_id_b) ||

(!(blob_id_b < blob_id_a) && a->GetChunkId() < b->GetChunkId()));

sorted_chunks.erase(unique(sorted_chunks.begin(), sorted_chunks.end(),

return ((&a->GetSplitInfo() == &b->GetSplitInfo()) &&

(a->GetChunkId() == b->GetChunkId()));

sorted_chunks.end());

limit_chunks_request = 15;

limit_chunks_request = 200;

reserve_size =

(sorted_chunks.size(), limit_chunks_request);

chunks.reserve(reserve_size);

vector< AutoPtr<CInitGuard> > guards;

guards.reserve(reserve_size);

(

& chunk : sorted_chunks ) {

( !guard.

() || !*guard.

() ) {

chunks.push_back(chunk);

guards.push_back(guard);

( guards.size() >= limit_chunks_request ) {

( !guards.empty() ) {

listener.

(tse, place, add, chunk_id);

User-defined methods of the data storage class.

bool x_IsTrackingSplitSeq() const

CDataLoader * GetDataLoader(void) const

void x_UnindexSplitInfo(TSeq_id2SplitInfoSet &split_map, const CSeq_id_Handle &id, CTSE_Split_Info *split_info)

void x_IndexSplitInfo(TSeq_id2SplitInfoSet &split_map, const CSeq_id_Handle &id, CTSE_Split_Info *split_info)

Base class for all object manager exceptions.

@Seq_descr.hpp User-defined methods of the data storage class.

void x_UpdateAnnotIndex(CTSE_Info &tse)

void x_SplitAttach(CTSE_Split_Info &split_info)

CInitMutex< CObject > m_LoadLock

TChunkId GetChunkId(void) const

bool NotLoaded(void) const

bool ContainsBioseq(const CSeq_id_Handle &id) const

bool IsLoaded(void) const

void AddUsedMemory(size_t size)

void SetBioseqUpdater(CRef< CBioseqUpdater > updater)

TSeqIdToChunks::const_iterator x_FindChunk(const CSeq_id_Handle &id) const

void LoadChunks(const TChunkIds &ids) const

CTSE_Chunk_Info::TBioseq_setId TBioseq_setId

CTSE_Chunk_Info::TChunkId TChunkId

void x_LoadBioseqs(const TPlace &place, const list< CRef< CBioseq > > &bioseqs, int chunk_id)

CDataSource * m_DataLoader

TBlobId GetBlobId(void) const

CTSE_Chunk_Info & GetChunk(TChunkId chunk_id)

void x_AddAssemblyInfo(const TAssemblyInfo &info, TChunkId chunk_id)

void x_LoadChunks(const TChunkIds &chunk_ids) const

void x_TSEAttach(CTSE_Info &tse_info, CRef< ITSE_Assigner > &assigner)

CTSE_Chunk_Info::TAssembly TAssembly

void x_LoadDescr(const TPlace &place, const CSeq_descr &descr)

TBlobVersion m_BlobVersion

CInitMutexPool & GetMutexPool(void)

CInitMutexPool m_MutexPool

void x_AddSeq_data(const TLocationSet &location, CTSE_Chunk_Info &chunk)

void x_SetBioseqUpdater(CRef< CBioseqUpdater > updater)

void x_SetContainedId(const TBioseqId &id, TChunkId chunk_id, bool bioseq)

TBlobVersion GetBlobVersion(void) const

void AddChunk(CTSE_Chunk_Info &chunk_info)

CTSE_Chunk_Info & GetSkeletonChunk(void)

bool x_HasDelayedMainChunk(void) const

void x_AddUsedMemory(size_t size)

TSeqIdToChunks m_SeqIdToChunks

bool ContainsBioseq(const CSeq_id_Handle &id) const

void x_DSDetach(CDataSource &ds)

TSplitVersion m_SplitVersion

CTSE_Chunk_Info::TDescInfo TDescInfo

void SetSplitVersion(TSplitVersion version)

void x_TSEDetach(CTSE_Info &tse_info)

void x_LoadDelayedMainChunk(void) const

void GetBioseqsIds(TSeqIds &ids) const

CMutex m_SeqIdToChunksMutex

void LoadChunk(TChunkId id) const

TSplitVersion GetSplitVersion(void) const

void x_UpdateAnnotIndex(void)

atomic< bool > m_ContainsBioseqs

CTSE_Chunk_Info::TLocationSet TLocationSet

void x_AddBioseqPlace(TBioseq_setId place_id, TChunkId chunk_id)

void x_AddChunksForGetRecords(vector< CConstRef< CTSE_Chunk_Info >> &chunks, const CSeq_id_Handle &id) const

void x_LoadChunk(TChunkId chunk_id) const

void x_UpdateFeatIdIndex(CSeqFeatData::E_Choice type, EFeatIdType id_type)

CDataLoader & GetDataLoader(void) const

void x_DSAttach(CDataSource &ds)

void x_GetRecords(const CSeq_id_Handle &id, bool bioseq) const

bool ContainsBioseqs() const

vector< TChunkId > TChunkIds

void x_AddAnnotPlace(const TPlace &place, TChunkId chunk_id)

void x_LoadAssembly(const TBioseqId &seq_id, const TAssembly &assembly)

void x_LoadSequence(const TPlace &place, TSeqPos pos, const TSequence &sequence)

CTSE_Chunk_Info::TSequence TSequence

vector< CSeq_id_Handle > TSeqIds

bool x_CanAddBioseq(const TBioseqId &id) const

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

CTSE_Chunk_Info::TPlace TPlace

void x_LoadAnnot(const TPlace &place, const CSeq_annot &annot, int chunk_id)

CRef< ITSE_Assigner > GetAssigner(const CTSE_Info &tse)

vector< pair< CSeq_id_Handle, TChunkId > > TSeqIdToChunks

bool x_NeedsDelayedMainChunk(void) const

bool m_SeqIdToChunksSorted

void x_AddDescInfo(const TDescInfo &info, TChunkId chunk_id)

void x_SetContainedSeqIds(const vector< TBioseqId > &seq_ids, const set< TBioseqId > &annot_ids, TChunkId chunk_id)

virtual void AddDescInfo(CTSE_Info &, const TDescInfo &info, TChunkId chunk_id)=0

virtual void LoadSeq_entry(CTSE_Info &, CSeq_entry &entry, CTSE_SetObjectInfo *set_info)=0

virtual void LoadAssembly(CTSE_Info &, const TBioseqId &seq_id, const TAssembly &assembly)=0

virtual void LoadDescr(CTSE_Info &, const TPlace &place, const CSeq_descr &descr)=0

virtual void AddAnnotPlace(CTSE_Info &, const TPlace &place, TChunkId chunk_id)=0

virtual void LoadSequence(CTSE_Info &, const TPlace &place, TSeqPos pos, const TSequence &sequence)=0

virtual void AddAssemblyInfo(CTSE_Info &, const TAssemblyInfo &info, TChunkId chunk_id)=0

virtual void AddSeq_data(CTSE_Info &, const TLocationSet &location, CTSE_Chunk_Info &chunk)=0

virtual void LoadAnnot(CTSE_Info &, const TPlace &place, CRef< CSeq_annot > annot, int chunk_id)=0

virtual void LoadChunkBioseqs(CTSE_Info &, const TPlace &place, const list< CRef< CBioseq > > &bioseqs, int chunk_id)=0

virtual void AddBioseqPlace(CTSE_Info &, TBioseq_setId place_id, TChunkId chunk_id)=0

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static const char location[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * get(void) const

Get pointer.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

static bool IsActive(void)

virtual void GetChunks(const TChunkSet &chunks)

vector< TChunk > TChunkSet

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

#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.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

E_Choice

Choice variants.

constexpr auto sort(_Init &&init)

const string version

version string

const struct ncbi::grid::netcache::search::fields::SIZE size

Common macro to detect used sanitizers and suppress memory leaks if run under LeakSanitizer.

static const int kTSE_Place_id

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