Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/tse__info_8cpp_source.html below:

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

( !slot->

() ) {

(objs.m_AnnotSet.empty());

(objs.m_SNPSet.empty());

: m_InternalBioObjNumber(0),

m_MasterSeqSegmentsLoaded(

)

: m_InternalBioObjNumber(0),

m_MasterSeqSegmentsLoaded(

)

: m_InternalBioObjNumber(0),

m_MasterSeqSegmentsLoaded(

)

: m_InternalBioObjNumber(0),

m_MasterSeqSegmentsLoaded(

)

m_InternalBioObjNumber(0),

m_MasterSeqSegmentsLoaded(

)

);

( !

->GetId().empty() ) {

(!

->GetId().empty())

(

->m_Bioseq_set_Id > 0)

ret = iter->second.m_SNP_annot_Info;

ds.

(obj,

);

( !

.IsGi() ) {

(

.HaveMatchingHandles() ) {

new_id =

;

iter->second.m_Orphan = orphan;

(iter->second.m_Names.insert(name).second);

(iter->second.m_Names.erase(name) == 1);

( iter->second.m_Names.empty() ) {

orphan = iter->second.m_Orphan;

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

ids.erase(unique(ids.begin(), ids.end()), ids.end());

ids.push_back(it->first);

ids.push_back(it2->first);

(

.HaveMatchingHandles() ) {

( *match_it !=

) {

(

& [

,

] : ids ) {

ret[

] = it->second;

(

->IsSeq() ) {

(

<<exc);

(

.HaveMatchingHandles() ) {

( *match_it !=

) {

( !chunk_ids.empty() ) {

pair<TBioseqs::iterator, bool> ins =

<<

<<

<<

<< ins.first->second->IdString() <<

<<

->IdString());

pair<TBioseqs::iterator, bool> ins =

+it->AsString()+

+

+ ins.first->second->IdString()+

+

->IdString());

( iter ==

.

() || iter->first !=

) {

pair<TBioseq_sets::iterator, bool> ins =

.x_UpdateAnnotIndex(*

);

iter->second;

&iter->second;

&iter->second;

pair<SIdAnnotObjs*, bool>

new_id =

;

( it == objs.

() ) {

(it != objs.

() && it->first ==

);

make_pair(&it->second, new_id);

pair<SIdAnnotObjs*, bool>

( it == objs.

() ) {

it && it->first ==

.m_Range; ++it ) {

( it->second.m_AnnotObject_Info == &

) {

rangeMap.

(it);

rangeMap.

();

rangeMap.

();

(

idx = idx_rg->first; idx < idx_rg->second; ++idx) {

(

idx = idx_rg.first; idx < idx_rg.second; ++idx) {

(

idx = idx_rg.first; idx < idx_rg.second; ++idx) {

id_objs.second;

objs.

();

objs.first->m_SNPSet.push_back(

(&snp_info));

TSNPSet::iterator iter = find(objs.

.begin(),

( iter != objs.

.end() ) {

( index.

() ) {

( it->HasSingleKey() ) {

(

= it->GetKeysBegin(); i < it->GetKeysEnd(); ++

) {

( index.

() ) {

*iter->second;

);

*iter->second;

*iter->second;

+

.AsString());

*iter->second;

( xref_tse ==

) {

iter2 != index2.

() && iter2->first ==

; ++iter2 ) {

(

.m_Type == id_type ) {

(

.m_IsChunk ) {

( xref_tse && xref_tse != &

.m_Info->GetSeq_annot_Info().GetXrefTSE() ) {

( xref_tse ==

) {

iter2 != index2.

() && iter2->first ==

; ++iter2 ) {

(

.m_Type == id_type ) {

(

.m_IsChunk ) {

( xref_tse && xref_tse != &

.m_Info->GetSeq_annot_Info().GetXrefTSE() ) {

iter != index.

() && iter->first ==

; ++iter ) {

( iter->second.m_Info == &

&& iter->second.m_Type == id_type ) {

index.

(iter);

(

&& 0);

iter != index.

() && iter->first ==

; ++iter ) {

( iter->second.m_Info == &

&& iter->second.m_Type == id_type ) {

index.

(iter);

(

&& 0);

it->first.first == locus &&

it->first.second ==

;

( it->second == &

) {

(

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

(

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

(

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

(

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

(

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

( xref_tse ==

) {

it->first.first == locus &&

it->first.second ==

;

( xref_tse && xref_tse != &it->second->GetSeq_annot_Info().

() ) {

.push_back(it->second);

range(loc_pos, loc_pos);

( index < objs->x_GetRangeMapCount() &&

*it->second.m_AnnotObject_Info;

( found_feat == &feat ) {

( seen.

(it->second).second ) {

);

);

(

.IsSetSeq_set() && !

.GetSeq_set().

() ) {

submit.

().SetEntrys() =

.GetBioseq_setCore()->GetSeq_set();

(

.IsSetAnnot() && !

.GetAnnot().

() ) {

submit.

().SetAnnots() =

.GetBioseq_setCore()->GetAnnot();

submit.

().SetEntrys().clear();

submit.

().SetAnnots().clear();

User-defined methods of the data storage class.

const string & GetName(void) const

void GetLocsTypes(TTypeIndexSet &idx_set) const

const CSeq_annot_Info & GetSeq_annot_Info(void) const

bool IsRegular(void) const

vector< TIndexRange > TTypeIndexSet

const CSeq_feat * GetFeatFast(void) const

TIndex GetAnnotIndex(void) const

static CSeqFeatData::ESubtype GetSubtypeForIndex(size_t index)

pair< size_t, size_t > TIndexRange

static TIndexRange GetFeatTypeRange(CSeqFeatData::E_Choice type)

static TIndexRange GetTypeIndex(const CAnnotObject_Info &info)

static size_t GetSubtypeIndex(CSeqFeatData::ESubtype subtype)

const CSeq_id_Handle & GetSeqId() const

virtual void Update(CBioseq_Info &seq)=0

vector< CSeq_id_Handle > TId

TClass GetClass(void) const

CConstRef< CSeq_entry_Info > GetFirstEntry(void) const

void Guard(CDataSource &ds)

void x_ResetDirtyAnnotIndex(CTSE_Info &tse)

void x_IndexAnnotTSEs(CTSE_Info *tse_info)

void x_UnindexAnnotTSEs(CTSE_Info *tse_info)

CDataLoader * GetDataLoader(void) const

void x_SetDirtyAnnotIndex(CTSE_Info &tse)

void x_UnindexSeqTSE(const CSeq_id_Handle &ids, CTSE_Info *tse_info)

void x_UnindexAnnotTSE(const CSeq_id_Handle &idh, CTSE_Info *tse_info, bool orphan)

void x_Unmap(const CObject *obj, const CTSE_Info_Object *info)

void x_Map(const CObject *obj, const CTSE_Info_Object *info)

void x_IndexAnnotTSE(const CSeq_id_Handle &idh, CTSE_Info *tse_info, bool orphan)

void x_IndexSeqTSE(const CSeq_id_Handle &idh, CTSE_Info *tse_info)

Base class for all object manager exceptions.

ESubtype GetSubtype(void) const

const CSeq_entry_Info & GetXrefTSE(void) const

void x_DoUpdate(TNeedUpdateFlags flags)

void x_Update(TNeedUpdateFlags flags) const

CConstRef< TObject > GetSeq_entryCore(void) const

vector< CSeq_id_Handle > TSeqIds

void x_SetObject(TObject &obj)

virtual void x_DSDetachContents(CDataSource &ds)

void x_DSMapObject(CConstRef< TObject > obj, CDataSource &ds)

virtual void x_DSAttachContents(CDataSource &ds)

CRef< CBioseq_Base_Info > m_Contents

void x_DetachContents(void)

void x_UpdateAnnotIndexContents(CTSE_Info &tse)

const TSet & GetSet(void) const

void x_DSUnmapObject(CConstRef< TObject > obj, CDataSource &ds)

const CSeq_entry_Info & GetXrefTSE() const

CConstRef< TObject > GetCompleteSeq_entry(void) const

namespace ncbi::objects::

Base class for all serializable objects.

ETopLevelObjectType

Type of top level object added to scope.

@ fNeedUpdate_children_bioseq

@ fNeedUpdate_children_core

@ fNeedUpdate_children_seq_data

void x_TSEAttach(CTSE_Info &tse)

bool x_DirtyAnnotIndex(void) const

vector< TChunkId > TChunkIds

TBioseq_sets m_Bioseq_sets

TBlobVersion GetBlobVersion(void) const

void UpdateAnnotIndex(void) const

TNamedAnnotObjs m_NamedAnnotObjs

CRef< CSeq_annot_SNP_Info > x_GetSNP_Info(const CConstRef< CSeq_annot > &annot)

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

void SetTopLevelObject(ETopLevelObjectType type, CSerialObject *ptr)

CRef< CTSE_Split_Info > m_Split

void x_MapFeatByLocus(const string &locus, bool tag, CAnnotObject_Info &info)

CAtomicCounter_WithAutoInit m_LockCounter

virtual void x_ResetDirtyAnnotIndexNoParent(void)

CSeq_id_Handle m_RequestedId

bool HasNamedAnnot(const string &name) const

CConstRef< CSeq_entry > GetTSECore(void) const

CConstRef< CBioseq_Info > FindBioseq(const CSeq_id_Handle &id) const

virtual void x_SetDirtyAnnotIndexNoParent(void)

SFeatIdIndex::TIndexInt & x_GetFeatIdIndexInt(CSeqFeatData::ESubtype type)

CDataSource & GetDataSource(void) const

void x_MapFeatById(TFeatIdInt id, CAnnotObject_Info &info, EFeatIdType type)

const TAnnotObjs * x_GetAnnotObjs(const CAnnotName &name) const

TBioseqs m_Removed_Bioseqs

bool IsTopLevelSeq_submit() const

void x_LoadChunk(TChunkId chunk_id) const

void x_DSUnmapObject(CConstRef< TObject > obj, CDataSource &ds)

CConstRef< CMasterSeqSegments > GetMasterSeqSegments(void) const

TBlobVersion m_BlobVersion

void x_UnmapSNP_Table(const CAnnotName &name, const CSeq_id_Handle &key, const CSeq_annot_SNP_Info &snp_info)

bool HasUnnamedAnnot(void) const

void AddUsedMemory(size_t size)

CConstRef< CBioseq_Info > FindMatchingBioseq(const CSeq_id_Handle &id) const

void SetTopLevelObjectType(ETopLevelObjectType type)

TAnnotObjects x_GetFeaturesById(CSeqFeatData::E_Choice type, TFeatIdInt id, EFeatIdType id_type, const CSeq_annot_Info *src_annot=0) const

vector< CAnnotObject_Info * > TAnnotObjects

CRef< CSerialObject > m_TopLevelObjectPtr

SSeqMatch_TSE GetSeqMatch(const CSeq_id_Handle &id) const

void x_RemoveAnnotObjs(const CAnnotName &name)

CSeq_id_Handle ContainsMatchingBioseq(const CSeq_id_Handle &id) const

void x_LoadDelayedMainChunk(void) const

void UpdateFeatIdIndex(CSeqFeatData::E_Choice type, EFeatIdType id_type) const

bool x_HasFeaturesWithId(CSeqFeatData::ESubtype subtype) const

CSubmit_block & SetTopLevelSubmit_block() const

void x_DSMapObject(CConstRef< TObject > obj, CDataSource &ds)

void x_UnmapFeatByLocus(const string &locus, bool tag, CAnnotObject_Info &info)

virtual void GetAnnotIds(TSeqIds &ids) const

unique_ptr< SBaseTSE > m_BaseTSE

CSeq_submit & x_GetTopLevelSeq_submit() const

void SetName(const CAnnotName &name)

virtual string GetDescription(void) const

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

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

CBioseq_Handle::TBioseqStateFlags TBlobState

CRef< CBioseqUpdater > m_BioseqUpdater

void SetUsedMemory(size_t size)

void x_UnmapFeatById(TFeatIdInt id, CAnnotObject_Info &info, EFeatIdType type)

CRef< CTSE_SetObjectInfo > m_SetObjectInfo

void x_UpdateAnnotIndexContents(CTSE_Info &tse)

CBioseq_set_Info & x_GetBioseq_set(int id)

const TBlobId & GetBlobId(void) const

bool m_MasterSeqSegmentsLoaded

CBioObjectId x_RegisterBioObject(CTSE_Info_Object &info)

ETopLevelObjectType m_TopLevelObjectType

void x_UnmapAnnotObjects(const SAnnotObjectsIndex &infos)

TSeq_feat_Lock x_FindSeq_feat(const CSeq_id_Handle &loc_id, TSeqPos loc_pos, const CSeq_feat &feat) const

friend class CTSE_Split_Info

void SetBioseqUpdater(CRef< CBioseqUpdater > updater)

virtual void GetBioseqsIds(TSeqIds &ids) const

void x_DoUpdate(TNeedUpdateFlags flags)

void x_AddAllFeaturesById(TAnnotObjects &objects, TFeatIdInt id, EFeatIdType id_type, const CSeq_annot_Info *src_annot=0) const

bool ContainsBioseq(const CSeq_id_Handle &id) const

TAnnotLock & GetAnnotLock(void) const

void x_DSDetachContents(CDataSource &ds)

bool x_HasIdObjects(const CSeq_id_Handle &id) const

void x_IndexSeqTSE(const CSeq_id_Handle &id)

SFeatIdIndex::TIndexStr & x_GetFeatIdIndexStr(CSeqFeatData::ESubtype type)

const CSerialObject * GetTopLevelObjectPtr() const

void x_UnindexSeqTSE(const CSeq_id_Handle &id)

atomic< ELoadState > m_LoadState

bool HasDataSource(void) const

TBioseq_sets m_Removed_Bioseq_sets

CBioObjectId x_IndexBioseq(CBioseq_Info *)

ETopLevelObjectType GetTopLevelObjectType() const

const SIdAnnotObjs * x_GetIdObjects(const TAnnotObjs &objs, const CSeq_id_Handle &idh) const

TFeatIdIndex m_FeatIdIndex

int m_InternalBioObjNumber

vector< CSeq_id_Handle > TSeqIds

const CAnnotName & GetName(void) const

void x_DSAttachContents(CDataSource &ds)

TIdAnnotInfoMap m_IdAnnotInfoMap

const TAnnotObjs * x_GetUnnamedAnnotObjs(void) const

void x_ResetBioseqId(const CSeq_id_Handle &id, CBioseq_Info *info)

const SIdAnnotObjs * x_GetUnnamedIdObjects(const CSeq_id_Handle &id) const

CFastMutex m_BioseqsMutex

void x_SetBioseq_setId(int key, CBioseq_set_Info *info)

CRef< IEditSaver > m_EditSaver

CConstRef< CSeq_entry > GetCompleteTSE(void) const

void x_AddFeaturesById(TAnnotObjects &objects, const SFeatIdIndex &index, TFeatIdInt id, EFeatIdType id_type, const CSeq_annot_Info *src_annot=0) const

CDataSource * m_DataSource

bool HasAnnot(const CAnnotName &name) const

bool x_MapSNP_Table(const CAnnotName &name, const CSeq_id_Handle &key, const CSeq_annot_SNP_Info &snp_info)

void x_UnregisterBioObject(CTSE_Info_Object &info)

CTSE_Split_Info & GetSplitInfo(void)

const CSubmit_block & GetTopLevelSubmit_block() const

pair< string, bool > TLocusKey

void x_SetBioseqIds(CBioseq_Info *info)

TAnnotIdsFlags m_AnnotIdsFlags

bool x_NeedsDelayedMainChunk(void) const

pair< TSeq_annot_Lock, int > TSeq_feat_Lock

const CTSE_Info & GetTSE_Info(void) const

void x_UnindexAnnotTSE(const CAnnotName &name, const CSeq_id_Handle &id)

CConstRef< CMasterSeqSegments > m_MasterSeqSegments

pair< SIdAnnotObjs *, bool > x_SetIdObjects(TAnnotObjs &objs, const CAnnotName &name, const CSeq_id_Handle &id)

void x_LoadChunks(const TChunkIds &chunk_ids) const

void x_ResetBioseq_setId(int key, CBioseq_set_Info *info)

bool x_IndexAnnotTSE(const CAnnotName &name, const CSeq_id_Handle &id)

CBioseq_Info & x_GetBioseq(const CSeq_id_Handle &id)

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

bool HasSplitInfo(void) const

void x_MapAnnotObject(TRangeMap &rangeMap, const SAnnotObject_Key &key, const SAnnotObject_Index &index)

CTSE_Info & Assign(const CTSE_Lock &tse)

CConstRef< CBioseq_Info > GetSegSetMaster(void) const

TAnnotObjects x_GetFeaturesByLocus(const string &locus, bool tag, const CSeq_annot_Info *src_annot=0) const

bool x_UnmapAnnotObject(TRangeMap &rangeMap, const CAnnotObject_Info &info, const SAnnotObject_Key &key)

CBioObjectId x_IndexBioseq_set(CBioseq_set_Info *)

map< size_t, CConstRef< CBioseq_Info > > FindBioseqBulk(const map< size_t, CSeq_id_Handle > &ids) const

void SetBlobVersion(TBlobVersion version)

const CSeq_submit & GetTopLevelSeq_submit() const

TAnnotObjs & x_SetAnnotObjs(const CAnnotName &name)

CTSE_Info_Object * x_FindBioObject(const CBioObjectId &uniq_id) const

map< CSeq_id_Handle, SIdAnnotObjs > TAnnotObjs

void x_SetBioseqId(const CSeq_id_Handle &id, CBioseq_Info *info)

~CTSE_SetObjectInfo(void)

TSeq_annot_InfoMap m_Seq_annot_InfoMap

void x_LoadChunks(const TChunkIds &chunk_ids) const

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

bool ContainsBioseq(const CSeq_id_Handle &id) const

void x_DSDetach(CDataSource &ds)

void x_TSEDetach(CTSE_Info &tse_info)

void x_LoadDelayedMainChunk(void) const

void GetBioseqsIds(TSeqIds &ids) const

void x_UpdateAnnotIndex(void)

void x_LoadChunk(TChunkId chunk_id) const

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

void x_DSAttach(CDataSource &ds)

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

CRef< ITSE_Assigner > GetAssigner(const CTSE_Info &tse)

bool x_NeedsDelayedMainChunk(void) const

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

const_iterator lower_bound(const key_type &key) const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

container_type::const_iterator const_iterator

const_iterator find(const key_type &key) const

const_iterator lower_bound(const key_type &key) const

const_iterator end() const

iterator insert(const value_type &val)

container_type::iterator iterator

container_type::value_type value_type

iterator_bool insert(const value_type &val)

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

TValue Get(void) const THROWS_NONE

Get atomic counter value.

#define ERR_POST(message)

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

#define NCBI_THROW(exception_class, err_code, message)

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

#define NCBI_THROW_FMT(exception_class, err_code, message)

The same as NCBI_THROW but with message processed as output to ostream.

void Reset(void)

Reset the handle (remove seq-id reference)

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

string ToString(void) const

virtual TEditSaver GetEditSaver() const

TObjectType * GetNCPointerOrNull(void) const THROWS_NONE

Get pointer value.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

void Reset(void)

Reset reference object.

TObjectType * GetPointerOrNull(void) THROWS_NONE

Get pointer value.

TObjectType & GetNCObject(void) const

Get object.

TParent::value_type value_type

iterator insert(const value_type &value)

const_iterator begin(void) const

void erase(iterator iter)

const_iterator find(const key_type &key) const

#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.

static void PtrToString(string &out_str, const void *ptr)

Convert pointer to string.

E_Choice

Choice variants.

const TData & GetData(void) const

Get the Data member data.

@ e_not_set

No variant selected.

@ eClass_segset

segmented sequence + parts

@ e_not_set

No variant selected.

void SetSub(TSub &value)

Assign a value to Sub data member.

E_Choice Which(void) const

Which variant is currently selected.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TSub & GetSub(void) const

Get the Sub member data.

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

constexpr auto sort(_Init &&init)

const string version

version string

double value_type

The numeric datatype used by the parser.

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

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

const GenericPointer< typename T::ValueType > T2 value

AutoPtr< TIndexInt > m_IndexInt

AutoPtr< TIndexStr > m_IndexStr

CAnnotObject_Info * m_AnnotObject_Info

bool IsIndexed(void) const

TObjectInfos & GetInfos(void)

const SAnnotObject_Key & GetKey(size_t i) const

const CAnnotName & GetName(void) const

deque< CAnnotObject_Info > TObjectInfos

const TRangeMap & x_GetRangeMap(size_t index) const

vector< TRangeMap * > TAnnotSet

bool x_RangeMapIsEmpty(size_t index) const

CRangeMultimap< SAnnotObject_Index, TSeqPos > TRangeMap

size_t x_GetRangeMapCount(void) const

bool x_CleanRangeMaps(void)

CConstRef< CBioseq_Info > m_Bioseq

NCBI_DEFINE_ERR_SUBCODE_X(3)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4