70 else if ( place.second ) {
87 "Bioseq-set id where gi is expected");
97 "Gi where Bioseq-set id is expected");
147 if (bioseq != last_bioseq) {
149 bioseq->x_AddSeq_dataChunkId(chunk.
GetChunkId());
151 last_bioseq = bioseq;
155 it->second.GetFrom(),
156 it->second.GetLength());
196 annot_info.
Reset(
x_GetBase(tse, place).AddAnnot(*annot, chunk_id));
224 if ( !entry_info->x_GetBaseInfo().GetAnnot().empty() ) {
243 entry->
SetSeq(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