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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/tse__chunk__info_8cpp_source.html below:

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

51 #define NCBI_USE_ERRCODE_X ObjMgr_ObjSplitInfo 137

annot_ids.

insert

(lit->first);

302

listener->

Loaded

(*

this

);

401

dst.push_back(

TLocation

(location_id, location_range));

437

dst.

insert

(dst.end(), ids.begin(), ids.end());

446

dst.

insert

(dst.end(), ids.begin(), ids.end());

455

dst.

insert

(dst.end(), ids.begin(), ids.end());

464

dst.

insert

(dst.end(), ids.begin(), ids.end());

500  size_t

keys_begin = infos.

GetKeys

().size();

502  key

.m_Handle = lit->first;

503  key

.m_Range = lit->second;

504  if

(

key

.m_Range.Empty() ) {

506  if

( it->first.IsNamed() ) {

507

name =

" "

+it->first.GetName();

509  ERR_POST_X

(11,

"Empty region in split-info on "

<<

510  key

.m_Handle<<name<<

" "

<<

513  key

.m_Range =

key

.m_Range.GetWhole();

517  size_t

keys_end = infos.

GetKeys

().size();

518  if

( keys_begin+1 == keys_end &&

524  info

.SetKeys(keys_begin, keys_end);

538  return

!

types

.empty();

545  for

(

size_t

index = range.first; index < range.second; ++index ) {

561  return

!

types

.empty();

579  return

!

types

.empty();

586  for

(

size_t

index = range.first; index < range.second; ++index ) {

602  return

!

types

.empty();

672  if

(

info

->HasSingleKey() ) {

673

mapper.

Map

(

info

->GetKey(), index);

676  for

(

size_t i

=

info

->GetKeysBegin();

677  i

<

info

->GetKeysEnd(); ++

i

) {

678

mapper.

Map

(it->GetKey(

i

), index);

746

list< CRef<CBioseq> > bioseqs;

747

bioseqs.push_back(

Ref

(

const_cast<CBioseq

*

>

(&bioseq)));

User-defined methods of the data storage class.

static CSeqFeatData::ESubtype GetSubtypeForIndex(size_t index)

pair< size_t, size_t > TIndexRange

static TIndexRange GetFeatTypeRange(CSeqFeatData::E_Choice type)

void Guard(CDataSource &ds)

static E_Choice GetTypeFromSubtype(ESubtype subtype)

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

bool Map(const SAnnotObject_Key &key, const SAnnotObject_Index &index) const

virtual void Loaded(CTSE_Chunk_Info &chunk)=0

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

void x_InitObjectIndexList(void)

virtual ~CTSE_Chunk_Info(void)

void x_UpdateAnnotIndex(CTSE_Info &tse)

void x_SplitAttach(CTSE_Split_Info &split_info)

CTSE_Chunk_Info(TChunkId id)

void x_AddXref_ids(const SAnnotTypeSelector &type, const TFeatIdIntList &ids)

vector< TDescInfo > TDescInfos

void x_TSEAttach(CTSE_Info &tse, ITSE_Assigner &tse_info)

pair< TBioseqId, TBioseq_setId > TPlace

void x_AddAnnotPlace(const TBioseqId &id)

void x_LoadBioseq(const TPlace &place, const CBioseq &bioseq)

TBlobId GetBlobId(void) const

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

vector< TAssemblyInfo > TAssemblyInfos

CRef< CTSEChunkLoadListener > m_LoadListener

TObjectIndexList m_ObjectIndexList

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

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

list< TFeatIdStr > TFeatIdStrList

void x_AddDescInfo(TDescTypeMask type_mask, const TBioseqId &id)

Uint4 GetLoadBytes() const

list< CRef< CSeq_align > > TAssembly

CInitMutex< CObject > m_LoadLock

CTSE_Split_Info * m_SplitInfo

pair< TDescTypeMask, TPlace > TDescInfo

void x_SetLoadSeconds(double seconds)

void x_AddUsedMemory(size_t size)

vector< TBioseqId > TBioseqIds

void x_UpdateAnnotIndexContents(CTSE_Info &tse)

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

void SetLoaded(CObject *obj=0)

TBioseqPlaces m_BioseqPlaces

vector< TLocation > TLocationSet

void x_DropAnnotObjects(void)

list< TObjectIndex > TObjectIndexList

void x_AddBioseqPlace(TBioseq_setId id)

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

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

TAnnotContents m_AnnotContents

void x_AddAssemblyInfo(const TBioseqId &id)

TChunkId GetChunkId(void) const

double GetLoadSeconds() const

TAssemblyInfos m_AssemblyInfos

void SetLoadListener(CRef< CTSEChunkLoadListener > listener)

vector< TFeatIdInt > TFeatIdIntList

void x_AddAnnotType(const CAnnotName &annot_name, const SAnnotTypeSelector &annot_type, const TLocationId &location_id)

void GetBioseqsIds(TBioseqIds &ids) const

list< CRef< CSeq_literal > > TSequence

void x_SetLoadBytes(Uint4 bytes)

CInitGuard * GetLoadInitGuard(void)

bool x_Attached(void) const

TBlobVersion GetBlobVersion(void) const

void x_AddSeq_data(const TLocationSet &location)

const CTSE_Split_Info & GetSplitInfo(void) const

pair< Uint4, double > GetLoadCost() const

pair< TLocationId, TLocationRange > TLocation

vector< TBioseq_setId > TBioseqPlaces

bool NotLoaded(void) const

SAnnotObjectsIndex TObjectIndex

bool ContainsBioseq(const CSeq_id_Handle &id) const

void x_AddBioseqId(const TBioseqId &id)

bool IsLoaded(void) const

bool x_ContainsFeatIds(CSeqFeatData::E_Choice type, EFeatIdType id_type) const

bool x_ContainsFeatType(CSeqFeatData::E_Choice type) const

void x_MapChunkByFeatType(CSeqFeatData::ESubtype subtype, TChunkId chunk_id)

CDataSource & GetDataSource(void) const

void x_MapChunkByFeatId(TFeatIdInt id, CSeqFeatData::ESubtype subtype, TChunkId chunk_id, EFeatIdType type)

TAnnotLock & GetAnnotLock(void) const

bool HasDataSource(void) const

const CAnnotName & GetName(void) const

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

TBlobId GetBlobId(void) const

void x_AddAssemblyInfo(const TAssemblyInfo &info, TChunkId chunk_id)

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

CInitMutexPool & GetMutexPool(void)

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

TBlobVersion GetBlobVersion(void) const

void x_AddUsedMemory(size_t size)

void x_UpdateAnnotIndex(void)

void x_AddBioseqPlace(TBioseq_setId place_id, TChunkId chunk_id)

CDataLoader & GetDataLoader(void) const

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)

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

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

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 AddAnnotPlace(CTSE_Info &, const TPlace &place, TChunkId chunk_id)=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 AddBioseqPlace(CTSE_Info &, TBioseq_setId place_id, TChunkId chunk_id)=0

iterator_bool insert(const value_type &val)

iterator_bool insert(const value_type &val)

static void DLIST_NAME() init(DLIST_LIST_TYPE *list)

static const struct type types[]

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.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

virtual double EstimateLoadSeconds(const CTSE_Chunk_Info &chunk, Uint4 bytes) const

virtual Uint4 EstimateLoadBytes(const CTSE_Chunk_Info &chunk) const

virtual void GetChunk(TChunk chunk_info)

CRef< C > Ref(C *object)

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

CObject(void)

Constructor.

uint32_t Uint4

4-byte (32-bit) unsigned integer

static TThisType GetWhole(void)

#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.

E_Choice

Choice variants.

@ e_not_set

No variant selected.

Definition of all error codes used in objmgr libraries (xobjmgr.lib, xobjutil.lib and others).

constexpr auto sort(_Init &&init)

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

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

CAnnotObject_Info * m_AnnotObject_Info

bool IsSingle(void) const

void AddInfo(const CAnnotObject_Info &info)

TObjectInfos & GetInfos(void)

const SAnnotObject_Key & GetKey(size_t i) const

const CAnnotName & GetName(void) const

deque< CAnnotObject_Info > TObjectInfos

void AddMap(const SAnnotObject_Key &key, const SAnnotObject_Index &index)

const TObjectKeys & GetKeys(void) const

NCBI_DEFINE_ERR_SUBCODE_X(11)

static bool x_HasFeatType(const CTSE_Chunk_Info::TAnnotTypes &types, CSeqFeatData::E_Choice type)

static bool x_HasFeatIds(const CTSE_Chunk_Info::TFeatIdsMap &types, CSeqFeatData::E_Choice type)

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