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NCBI C++ ToolKit: src/app/objmgr/split_demo/split_loader.cpp Source File

& data_file,

+ data_file;

& data_file)

m_DataFile(data_file),

chunk->

(annot->m_Place, *annot->m_Annot);

chunk->

(descr->second.m_Place, *descr->second.m_Descr);

sequence.push_back(seq->second.m_Literal);

( blob_id != my_blob_id ) {

.GetSplitInfo().AddChunk(**it);

( (*it)->IsSeq() ) {

.m_Place.first = idh;

.m_Literal->SetSeq_data(bioseq.

().SetSeq_data());

bioseq.

().ResetSeq_data();

loc_set.push_back(loc);

chunks.push_back(chunk);

.m_Place = place;

.m_Descr.Reset(&descr);

chunks.push_back(chunk);

.m_Place = place;

.m_Annot = &annot;

annot_chunks.push_back(

);

chunks.push_back(chunk);

handles.

(loc_it.GetSeq_id_Handle());

handles.

(loc_it.GetSeq_id_Handle());

handles.

(loc_it.GetSeq_id_Handle());

User-defined methods of the data storage class.

const CSeq_id * GetFirstId() const

CTSE_LoadLock GetTSE_LoadLock(const TBlobId &blob_id)

TDim CheckNumRows(void) const

Validatiors.

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

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

namespace ncbi::objects::

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

void x_SplitSet(TChunks &chunks, CBioseq_set &seqset)

void x_SplitAnnot(TChunks &chunks, TPlace place, CBioseq::TAnnot &annots)

TDescrChunks m_DescrChunks

vector< CRef< CTSE_Chunk_Info > > TChunks

virtual void GetChunk(TChunk chunk)

virtual ~CSplitDataLoader(void)

void x_LoadData(CTSE_LoadLock &load_lock)

TAnnotChunks m_AnnotChunks

void x_SplitSeqData(TChunks &chunks, CSeq_id_Handle idh, CBioseq &bioseq)

void x_SplitFeats(CTSE_Chunk_Info &chunk, const CSeq_annot &annot)

void x_SplitSeq(TChunks &chunks, CBioseq &bioseq)

TSequenceChunks m_SeqChunks

virtual bool CanGetBlobById(void) const

void x_SplitAligns(CTSE_Chunk_Info &chunk, const CSeq_annot &annot)

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh)

CSplitDataLoader(const string &loader_name, const string &data_file)

virtual void DropTSE(CRef< CTSE_Info > tse_info)

vector< SAnnotData > TAnnots

CTSE_Chunk_Info::TPlace TPlace

void x_SplitGraphs(CTSE_Chunk_Info &chunk, const CSeq_annot &annot)

virtual TTSE_Lock GetBlobById(const TBlobId &blob_id)

void x_SplitDescr(TChunks &chunks, TPlace place, CSeq_descr &descr)

virtual TTSE_LockSet GetRecords(const CSeq_id_Handle &idh, EChoice choice)

Request from a datasource using handles and ranges instead of seq-loc The TSEs loaded in this call wi...

static string GetLoaderNameFromArgs(const string &data_file)

void x_AddAnnotPlace(const TBioseqId &id)

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

void x_AddDescInfo(TDescTypeMask type_mask, const TBioseqId &id)

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

void SetLoaded(CObject *obj=0)

vector< TLocation > TLocationSet

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

TChunkId GetChunkId(void) const

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

list< CRef< CSeq_literal > > TSequence

void x_AddSeq_data(const TLocationSet &location)

pair< TLocationId, TLocationRange > TLocation

bool IsLoaded(void) const

bool IsLoaded(void) const

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

#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.

@ eSerial_AsnText

ASN.1 text.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

CDataSource * GetDataSource(void) const

EChoice

main blob is blob with sequence all other blobs are external and contain external annotations

TRegisterInfo GetRegisterInfo(void)

CBlobIdFor< string > CBlobIdString

static void RegisterInObjectManager(CObjectManager &om, CLoaderMaker_Base &loader_maker, CObjectManager::EIsDefault is_default, CObjectManager::TPriority priority)

Register the loader only if the name is not yet registered in the object manager.

void Reset(void)

Reset reference object.

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.

TId GetId(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

const TLoc & GetLoc(void) const

Get the Loc member data.

TSet & SetSet(void)

Select the variant.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSetAnnot(void) const

Check if a value has been assigned to Annot data member.

void SetId(TId &value)

Assign a value to Id data member.

bool IsSetDescr(void) const

Check if a value has been assigned to Descr data member.

void ResetDescr(void)

Reset Descr data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

const TId & GetId(void) const

Get the Id member data.

bool IsAlign(void) const

Check if variant Align is selected.

void ResetDescr(void)

Reset Descr data member.

bool IsSetSeq_data(void) const

the sequence Check if a value has been assigned to Seq_data data member.

const TGraph & GetGraph(void) const

Get the variant data.

const TInst & GetInst(void) const

Get the Inst member data.

list< CRef< CSeq_graph > > TGraph

bool IsSetAnnot(void) const

Check if a value has been assigned to Annot data member.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

list< CRef< CSeq_align > > TAlign

TLength GetLength(void) const

Get the Length member data.

const TAlign & GetAlign(void) const

Get the variant data.

void SetInst(TInst &value)

Assign a value to Inst data member.

bool IsSetLength(void) const

length of sequence in residues Check if a value has been assigned to Length data member.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

bool IsGraph(void) const

Check if variant Graph is selected.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

const TFtable & GetFtable(void) const

Get the variant data.

list< CRef< CSeq_feat > > TFtable

bool IsFtable(void) const

Check if variant Ftable is selected.

const TData & GetData(void) const

Get the Data member data.

list< CRef< CSeq_annot > > TAnnot

E_Choice Which(void) const

Which variant is currently selected.

CRef< objects::CObjectManager > om

#define row(bind, expected)

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