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NCBI C++ ToolKit: src/sra/data_loaders/snp/snploader.cpp Source File

{

, objects::CSeq_id::eSNPScaleLimit_Default},

{

, objects::CSeq_id::eSNPScaleLimit_Unit},

{

, objects::CSeq_id::eSNPScaleLimit_Contig},

{

, objects::CSeq_id::eSNPScaleLimit_Supercontig},

{

, objects::CSeq_id::eSNPScaleLimit_Chromosome},

objects::CSeq_id::eSNPScaleLimit_Default,

0, SNP_LOADER_SCALE_LIMIT);

<<

<< m_DirPath;

( !m_VDBFiles.empty() ) {

(

&

: m_VDBFiles ) {

( !m_AnnotName.empty() ) {

<<

<< m_AnnotName;

vector<string>& files,

SLoaderParams params;

params.m_VDBFiles = files;

maker.GetRegisterInfo();

& dir_path,

&

,

& dir_path,

vector<string>& files,

SLoaderParams params;

params.m_VDBFiles = files;

&

)

vector<string>& files)

SLoaderParams params;

params.m_DirPath = dir_path;

params.m_VDBFiles = files;

&

(*blob_id));

TScale_Limit::GetDefault();

TScale_Limit::SetDefault(

);

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:

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

CObjectManager::TPriority GetDefaultPriority(void) const

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

CDataLoader::TTSE_LockSet GetOrphanAnnotRecords(CDataSource *ds, const CSeq_id_Handle &idh, const SAnnotSelector *sel, CDataLoader::TProcessedNAs *processed_nas)

TAnnotNames GetPossibleAnnotNames(void) const

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

CParamLoaderMaker< CSNPDataLoader, SLoaderParams > TMaker

virtual bool CanGetBlobById(void) const override

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

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

vector< CAnnotName > TAnnotNames

virtual CObjectManager::TPriority GetDefaultPriority(void) const override

static void SetSNP_Scale_Limit(CSeq_id::ESNPScaleLimit value)

virtual TBlobId GetBlobIdFromString(const string &str) const override

virtual void GetChunk(TChunk chunk) override

virtual TTSE_LockSet GetOrphanAnnotRecordsNA(const CSeq_id_Handle &idh, const SAnnotSelector *sel, TProcessedNAs *processed_nas) override

new Get*AnnotRecords() methods

static CSeq_id::ESNPScaleLimit GetSNP_Scale_Limit(void)

virtual TTSE_Lock GetBlobById(const TBlobId &blob_id) override

static bool IsUsingPTIS()

CRef< CSNPDataLoader_Impl > m_Impl

static string GetLoaderNameFromArgs(void)

TAnnotNames GetPossibleAnnotNames(void) const

virtual void GetChunks(const TChunkSet &chunks) override

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

virtual ~CSNP_DataLoaderCF(void)

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

@ eLifeLevel_AppMain

Destroyed in CNcbiApplication::AppMain, if possible.

TBlobId GetBlobId(void) const

definition of a Culling tree

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

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

ESNPScaleLimit

SNP annotation scale limits.

TLoader * GetLoader(void) const

Get pointer to the loader.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

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

void Reset(void)

Reset reference object.

@ eParam_NoThread

Do not use per-thread values.

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.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

const GenericPointer< typename T::ValueType > T2 value

Helper classes and templates to implement plugins.

const char kDataLoader_SNP_DriverName[]

static CSNPDataLoader::SLoaderParams s_GetDefaultParams()

NCBI_PARAM_DECL(string, SNP, ACCESSIONS)

NCBI_PARAM_ENUM_ARRAY(objects::CSeq_id::ESNPScaleLimit, SNP_LOADER, SCALE_LIMIT)

NCBI_PARAM_DEF_EX(string, SNP, ACCESSIONS, "", eParam_NoThread, SNP_ACCESSIONS)

void DataLoaders_Register_SNP(void)

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

NCBI_PARAM_ENUM_DEF_EX(objects::CSeq_id::ESNPScaleLimit, SNP_LOADER, SCALE_LIMIT, objects::CSeq_id::eSNPScaleLimit_Default, 0, SNP_LOADER_SCALE_LIMIT)

NCBI_PARAM_ENUM_DECL(objects::CSeq_id::ESNPScaleLimit, SNP_LOADER, SCALE_LIMIT)

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

typedef NCBI_PARAM_TYPE(SNP_LOADER, SCALE_LIMIT) TScale_Limit

CRef< objects::CObjectManager > om

string GetLoaderName(void) const

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