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

<<this<<") "<<m_TSE.GetPointer()<<" " type)

( *

== tse ) {

( order1 != order2 ) {

((order1 < order2) || (order2 < order1));

order1 < order2;

);

);

: m_TSE_ScopeInfo(0),

m_TSE_HandleAssigned(

),

m_ObjectInfoAssigned(

)

: m_TSE_ScopeInfo(tse.GetNonNullNCPointer()),

m_ObjectInfo(&

),

m_TSE_HandleAssigned(

),

m_ObjectInfoAssigned(

)

: m_TSE_ScopeInfo(&tse.x_GetScopeInfo()),

m_ObjectInfo(&

),

m_TSE_HandleAssigned(

),

m_ObjectInfoAssigned(

)

handles.reserve(infos.size());

ret.insert(ret.end(), hh.begin(), hh.end());

ret.insert(ret.end(), hh.begin(), hh.end());

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

CDataLoader * GetDataLoader(void) const

Base class for all object manager exceptions.

CConstRef< CObject > m_ObjectInfo

CTSE_ScopeInfo * m_TSE_ScopeInfo

bool IsDetached(void) const

void x_SetTSE_Lock(const CTSE_ScopeUserLock &tse, const CTSE_Info_Object &info)

void x_SetTSE_Handle(const CTSE_Handle &tse)

atomic< bool > m_TSE_HandleAssigned

virtual void x_DetachTSE(CTSE_ScopeInfo *tse)

bool IsAttached(void) const

virtual const TIndexIds * GetIndexIds(void) const

CScope_Impl & x_GetScopeImpl(void) const

CTSE_ScopeInfo & x_GetTSE_ScopeInfo(void) const

atomic< bool > m_ObjectInfoAssigned

vector< TIndexId > TIndexIds

virtual void x_AttachTSE(CTSE_ScopeInfo *tse)

void x_ResetTSE_Lock(void)

const CTSE_Info_Object & GetObjectInfo_Base(void) const

bool HasObject(void) const

atomic< Uint8 > m_LockCounter

CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id_Handle &id, const CTSE_Handle &tse)

CConstRef< TObject > GetSeq_entryCore(void) const

CConstRef< TObject > GetCompleteSeq_entry(void) const

TBlobId GetBlobId(void) const

TSeq_feat_Handles GetGenesWithLocus(const string &locus, bool tag) const

bool OrderedBefore(const CTSE_Handle &tse) const

bool Blob_IsDead(void) const

int TFeatureIdInt

Find features by an integer FeatId.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

bool Blob_IsSuppressedTemp(void) const

ETopLevelObjectType

Type of top level object added to scope.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id) const

Get Bioseq handle from this TSE.

bool Blob_IsSuppressedPerm(void) const

CConstRef< CSeq_entry > GetCompleteTSE(void) const

Complete and get const reference to the seq-entry.

bool Blob_IsSuppressed(void) const

vector< CAnnotObject_Info * > TAnnotObjectList

CSeq_feat_Handle x_MakeHandle(CAnnotObject_Info *info) const

TSeq_feat_Handles GetFeaturesWithId(CSeqFeatData::E_Choice type, TFeatureIdInt id) const

CConstRef< CSeq_entry > GetTSECore(void) const

Get const reference to the seq-entry.

CScope_Impl & x_GetScopeImpl(void) const

void Reset(void)

Reset to null state.

CSubmit_block & SetTopLevelSubmit_block() const

size_t GetUsedMemory(void) const

return estimated memory size occupied by this TSE

vector< CSeq_feat_Handle > TSeq_feat_Handles

CSeq_feat_Handle GetGeneByRef(const CGene_ref &ref) const

string TFeatureIdStr

Find features by a string FeatId.

const CSubmit_block & GetTopLevelSubmit_block() const

More efficient direct access to Seq-submit.sub field.

TSeq_feat_Handles x_MakeHandles(const TAnnotObjectList &infos) const

CSeq_feat_Handle GetFeatureWithId(CSeqFeatData::E_Choice type, TFeatureIdInt id) const

bool IsValid(void) const

State check.

bool AddUsedTSE(const CTSE_Handle &tse) const

Register argument TSE as used by this TSE, so it will be released by scope only after this TSE is rel...

TSeq_feat_Handles GetGenesByRef(const CGene_ref &ref) const

TSeq_feat_Handles GetFeaturesWithXref(CSeqFeatData::E_Choice type, TFeatureIdInt id) const

void Swap(CTSE_Handle &tse)

CSeq_feat_Handle GetGeneWithLocus(const string &locus, bool tag) const

Find genes by locus, locus tag, or Gene-ref.

bool IsTopLevelSeq_submit() const

CDataLoader * GetDataLoader(void) const

CTSE_Handle & operator=(const CTSE_Handle &tse)

const CSeq_submit & GetTopLevelSeq_submit() const

Return reference to top-level Seq-submit object Throw an exception if it's not available.

ETopLevelObjectType GetTopLevelObjectType() const

Get type of top level object added to scope.

bool CanBeEdited(void) const

Return true if this TSE handle is local to scope and can be edited.

TScopeInfo & x_GetScopeInfo(void) const

const CTSE_Info & x_GetTSE_Info(void) const

CTSE_Handle(void)

Default constructor/destructor and assignment.

CScope & GetScope(void) const

Returns scope.

size_t GetUsedMemory(void) const

CDataSource & GetDataSource(void) const

bool IsTopLevelSeq_submit() const

CSubmit_block & SetTopLevelSubmit_block() const

const TBlobId & GetBlobId(void) const

ETopLevelObjectType GetTopLevelObjectType() const

const CSubmit_block & GetTopLevelSubmit_block() const

const CSeq_submit & GetTopLevelSeq_submit() const

pair< int, int > TBlobOrder

bool AddUsedTSE(const CTSE_ScopeUserLock &lock) const

int GetLoadIndex(void) const

TBlobOrder GetBlobOrder(void) const

bool CanBeEdited(void) const

CScope_Impl & GetScopeImpl(void) const

bool IsAttached(void) const

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

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

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

const CSeq_annot_Info & x_GetInfo(void) const

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.

bool IsSetLocus_tag(void) const

systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data mem...

bool IsSetLocus(void) const

Official gene symbol Check if a value has been assigned to Locus data member.

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

const TLocus & GetLocus(void) const

Get the Locus member data.

E_Choice

Choice variants.

#define _TRACE_TSE_LOCK(type)

DEFINE_STATIC_FAST_MUTEX(s_Info_TSE_HandleMutex)

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