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

( place.second ) {

);

);

(bioseq != last_bioseq) {

bioseq->x_AddSeq_dataChunkId(chunk.

());

last_bioseq = bioseq;

it->second.GetFrom(),

it->second.GetLength());

annot_info.

(

(tse, place).AddAnnot(*annot, chunk_id));

( !entry_info->x_GetBaseInfo().GetAnnot().empty() ) {

entry->

(bioseqs.front().GetNCObject());

User-defined methods of the data storage class.

void x_RealLoadDescr(const TDescr &v)

void x_AddDescrChunkId(const TDescTypeMask &types, TChunkId chunk_id)

void x_AddAnnotChunkId(TChunkId chunk_id)

const CSeqMap & GetSeqMap(void) const

void SetInst_Hist_Assembly(const TInst_Hist_Assembly &v)

void x_AddAssemblyChunkId(TChunkId chunk_id)

void x_AddBioseqChunkId(TChunkId chunk_id)

CRef< CSeq_entry_Info > AddEntry(CSeq_entry &entry, int index, bool set_uniqid=false)

void x_SetChunkBioseqs(const list< CRef< CBioseq > > &bioseqs, int chunk_id)

void Guard(CDataSource &ds)

TMainLock & GetMainLock() const

void Guard(resource_type &resource)

Manually force the guard to protect some other resource.

Base class for all object manager exceptions.

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

void x_SetObject(TObject &obj)

const CBioseq_Base_Info & x_GetBaseInfo(void) const

void x_SetBioseqChunkId(TChunkId chunk_id)

void x_UpdateAnnotIndex(CTSE_Info &tse)

TChunkId GetChunkId(void) const

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

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

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

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

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

virtual void UpdateAnnotIndex(CTSE_Info &, CTSE_Chunk_Info &chunk)

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

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

virtual ~CTSE_Default_Assigner()

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

virtual void LoadBioseq(CTSE_Info &, const TPlace &place, CRef< CSeq_entry > entry, int chunk_id)

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

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

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

CDataSource & GetDataSource(void) const

CBioseq_set_Info & x_GetBioseq_set(int id)

TAnnotLock & GetAnnotLock(void) const

bool HasDataSource(void) const

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

static CBioseq_Info & x_GetBioseq(CTSE_Info &tse, const TPlace &place)

CTSE_Chunk_Info::TPlace TPlace

static CBioseq_Base_Info & x_GetBase(CTSE_Info &tse, const TPlace &place)

CTSE_Chunk_Info::TLocationSet TLocationSet

CTSE_Chunk_Info::TChunkId TChunkId

CTSE_Chunk_Info::TSequence TSequence

CTSE_Chunk_Info::TAssembly TAssembly

static CBioseq_set_Info & x_GetBioseq_set(CTSE_Info &tse, const TPlace &place)

CTSE_Chunk_Info::TDescInfo TDescInfo

CTSE_Chunk_Info::TBioseq_setId TBioseq_setId

unsigned int TSeqPos

Type for sequence locations and lengths.

#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.

void SetRegionInChunk(CTSE_Chunk_Info &chunk, TSeqPos pos, TSeqPos length)

void LoadSeq_data(TSeqPos pos, TSeqPos len, const CSeq_data &data)

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.

CTempString literal(const char(&str)[Size])

Templatized initialization from a string literal.

TSeq & SetSeq(void)

Select the variant.

static const int kTSE_Place_id

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