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NCBI C++ ToolKit: include/objmgr/data_loader.hpp Source File

<

TDataLoader>

= TDataLoader::GetLoaderNameFromArgs();

TDataLoader(

);

<

TDataLoader,

TParam>

= TDataLoader::GetLoaderNameFromArgs(param);

IsRequestedNA(

& na,

* sel);

IsProcessedNA(

& na,

* processed_nas);

SetProcessedNA(

& na,

* processed_nas);

vector<CSeq_id_Handle>

;

STypeFound GetSequenceTypeFound(

& idh);

: sequence_found(

),

SHashFound GetSequenceHashFound(

& idh);

GetAccVers(

& ids,

& loaded,

& ret);

GetSequenceLengths(

& ids,

& loaded,

GetSequenceTypes(

& ids,

& loaded,

GetSequenceStates(

& ids,

& loaded,

GetSequenceHashes(

& ids,

& loaded,

GetBlobIdFromString(

&

)

;

CanGetBlobById(

)

;

GetChunk(

chunk_info);

GetChunks(

& chunks);

SetTargetDataSource(

& data_source);

GetName(

)

;

GC(

);

GetDefaultBlobCacheSizeLimit()

;

GetTrackSplitSeq()

;

RegisterInObjectManager(

SetName(

& loader_name);

pair< string, int > GetAccVer(const CAlignModel &a, CScope &scope)

Template function to create dll resolver for interface.

Service class for DLLs resolution.

IEditSaver * GetEditSaver(const Handle &handle)

static const char * str(char *buf, int n)

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

string GetLabel(const CSeq_id &id)

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

virtual CDataLoader * CreateLoader(void) const

SRegisterLoaderInfo< TDataLoader > TRegisterInfo

CParamLoaderMaker(TParam param)

CDataLoader(const CDataLoader &)

TLoader * GetLoader(void) const

Get pointer to the loader.

CRef< IEditSaver > TEditSaver

set< CSeq_id_Handle > TSeq_idSet

set< SAnnotTypeSelector > TAnnotTypesSet

vector< TSeqPos > TSequenceLengths

CDataLoader & operator=(const CDataLoader &)

vector< CTSE_Lock > TCDD_Locks

virtual CDataLoader * CreateLoader(void) const =0

vector< CSeq_id_Handle > TIds

SRegisterLoaderInfo< TDataLoader > TRegisterInfo

virtual ~CParamLoaderMaker(void)

vector< bool > THashKnown

TRegisterInfo GetRegisterInfo(void)

virtual CDataLoader * CreateLoader(void) const

virtual ~CSimpleLoaderMaker(void)

CRef< CTSE_Chunk_Info > TChunk

EChoice

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

NCBI_DECLARE_INTERFACE_VERSION(objects::CDataLoader, "xloader", 9, 0, 0)

CPluginManager_DllResolver * operator()(void)

vector< CSeq_inst::TMol > TSequenceTypes

vector< vector< CSeq_id_Handle > > TSeqIdSets

TRegisterInfo_Base m_RegisterInfo

EIsDefault

Flag defining if the data loader is included in the "default" group.

map< CSeq_id_Handle, TTSE_LockSet > TTSE_LockSets

TRegisterInfo GetRegisterInfo(void)

set< string > TProcessedNAs

vector< bool > TLoaded

Bulk loading interface for a small pieces of information per id.

bool IsCreated(void) const

Return true if the loader was just created, false if already registered or if the operation failed.

TAnnotBlobType m_AnnotBlobType

virtual ~CLoaderMaker_Base(void)

SRegisterLoaderInfo< CDataLoader > TRegisterInfo_Base

map< CAnnotName, TAnnotTypesSet > TAnnotSet

vector< int > TSequenceStates

vector< int > TSequenceHashes

vector< TChunk > TChunkSet

CDataSource * m_DataSource

set< TTSE_Lock > TTSE_LockSet

@ eExtFeatures

external features

@ eExtAnnot

all external annotations

@ eExtAlign

external aligns

@ eOrphanAnnot

all external annotations if no Bioseq exists

@ eGraph

graph annotations from main blob

@ eCore

?only seq-entry core?

@ eAnnot

all annotations from main blob

@ eBioseq

main blob with complete bioseq

@ eAlign

aligns from main blob

@ eBioseqCore

main blob with bioseq core (no seqdata and annots)

@ eExtGraph

external graph annotations

@ eFeatures

features from main blob

virtual void SetDllNamePrefix(const string &prefix)

Set DLL file name prefix.

uint32_t Uint4

4-byte (32-bit) unsigned integer

#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.

#define NCBI_XOBJMGR_EXPORT

EMol

molecule class in living organism

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

Plugin manager (using class factory paradigm).

static bool GetIds(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

Uint4 GetSequenceType(const CBioseq_Handle &bsh)

Return a (corrected) set of flags identifying the sequence type.

CRef< objects::CObjectManager > om

Better replacement of GetAccVer(), this method should be defined in data loaders, GetAccVer() is left...

Better replacement of GetGi(), this method should be defined in data loaders, GetGi() is left for com...

Better replacement of GetSequenceHash(), this method should be defined in data loaders,...

Better replacement of GetSequenceType(), this method should be defined in data loaders,...

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