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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/wgsloader_8cpp_source.html below:

NCBI C++ ToolKit: src/sra/data_loaders/wgs/wgsloader.cpp Source File

& dir_path,

vector<string>& wgs_files,

;

& dir_path,

vector<string>& wgs_files)

&

(*blob_id));

CObjectManager::TPriority GetPriority(const TPluginManagerParamTree *params) const

CObjectManager::EIsDefault GetIsDefault(const TPluginManagerParamTree *params) const

bool ValidParams(const TPluginManagerParamTree *params) const

bool IsDataLoaderMatches(CDataLoader &loader) const

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

@ eLifeLevel_AppMain

Destroyed in CNcbiApplication::AppMain, if possible.

TBlobId GetBlobId(void) const

definition of a Culling tree

CDataLoader::SHashFound GetSequenceHash(const CSeq_id_Handle &idh)

CDataLoader::TTSE_LockSet GetRecords(CDataSource *data_source, const CSeq_id_Handle &idh, CDataLoader::EChoice choice)

TTaxId GetTaxId(const CSeq_id_Handle &idh)

CDataLoader::STypeFound GetSequenceType(const CSeq_id_Handle &idh)

CDataLoader::SGiFound GetGi(const CSeq_id_Handle &idh)

CTSE_LoadLock GetBlobById(CDataSource *data_source, const CWGSBlobId &blob_id)

CRef< CWGSBlobId > GetBlobId(const CSeq_id_Handle &idh)

void GetChunk(const CWGSBlobId &blob_id, CTSE_Chunk_Info &chunk)

CDataLoader::SAccVerFound GetAccVer(const CSeq_id_Handle &idh)

void GetIds(const CSeq_id_Handle &idh, TIds &ids)

bool GetAddWGSMasterDescr(void) const

TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)

void SetAddWGSMasterDescr(bool flag)

virtual TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)

Request for a length of a sequence.

virtual TBlobId GetBlobIdFromString(const string &str) const

virtual SHashFound GetSequenceHashFound(const CSeq_id_Handle &idh)

static string GetLoaderNameFromArgs(void)

CRef< CWGSDataLoader_Impl > m_Impl

virtual SAccVerFound GetAccVerFound(const CSeq_id_Handle &idh)

virtual STypeFound GetSequenceTypeFound(const CSeq_id_Handle &idh)

virtual void GetChunk(TChunk chunk)

bool GetAddWGSMasterDescr(void) const

virtual TTaxId GetTaxId(const CSeq_id_Handle &idh)

Request for a taxonomy id of a sequence.

virtual TTSE_Lock GetBlobById(const TBlobId &blob_id)

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...

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const SLoaderParams &params, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

virtual CObjectManager::TPriority GetDefaultPriority(void) const

virtual void GetChunks(const TChunkSet &chunks)

virtual TTSE_LockSet GetOrphanAnnotRecords(const CSeq_id_Handle &idh, const SAnnotSelector *sel)

old Get*AnnotRecords() methods

void SetAddWGSMasterDescr(bool flag)

virtual bool CanGetBlobById(void) const

virtual SGiFound GetGiFound(const CSeq_id_Handle &idh)

virtual TTSE_LockSet GetExternalAnnotRecords(const CSeq_id_Handle &idh, const SAnnotSelector *sel)

virtual TTSE_LockSet GetExternalRecords(const CBioseq_Info &bioseq)

Request from a datasource set of blobs with external annotations.

virtual void GetIds(const CSeq_id_Handle &idh, TIds &ids)

virtual CDataLoader * CreateAndRegister(CObjectManager &om, const TPluginManagerParamTree *params) const

virtual ~CWGS_DataLoaderCF(void)

Include a standard set of the NCBI C++ Toolkit most basic headers.

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

TLoader * GetLoader(void) const

Get pointer to the loader.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

vector< CSeq_id_Handle > TIds

void RevokeDataLoaders(IDataLoaderFilter &filter)

Revoke data loaders by filter, even if they were still used.

CDataSource * GetDataSource(void) const

EChoice

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

EIsDefault

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

TRegisterInfo GetRegisterInfo(void)

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.

vector< TChunk > TChunkSet

set< TTSE_Lock > TTSE_LockSet

@ kPriority_Replace

Default priority for replacement loaders.

void Reset(void)

Reset reference object.

static void NCBI_EntryPointImpl(TDriverInfoList &info_list, EEntryPointRequest method)

Entry point implementation.

list< SDriverInfo > TDriverInfoList

List of driver information.

EEntryPointRequest

Actions performed by the entry point.

#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.

Helper classes and templates to implement plugins.

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,...

vector< string > m_WGSFiles

void NCBI_EntryPoint_DataLoader_WGS(CPluginManager< CDataLoader >::TDriverInfoList &info_list, CPluginManager< CDataLoader >::EEntryPointRequest method)

void NCBI_EntryPoint_xloader_wgs(CPluginManager< objects::CDataLoader >::TDriverInfoList &info_list, CPluginManager< objects::CDataLoader >::EEntryPointRequest method)

const char kDataLoader_WGS_DriverName[]

void DataLoaders_Register_WGS(void)

static CSafeStatic< CRevoker > s_Revoker(CSafeStaticLifeSpan(CSafeStaticLifeSpan::eLifeLevel_AppMain, CSafeStaticLifeSpan::eLifeSpan_Long))

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