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

(

& acc,

spot_id);

: m_Accession(acc), m_SpotId(spot_id)

& rep_path,

& vol_path,

& rep_path,

& vol_path,

ret =

;

& vol_path)

& vol_path,

pair<CRef<CSRABlobId>,

>

;

( dot1 ==

) {

dot2 = with_chunk? sra.find(

, dot1+1): sra.size();

( dot2 ==

|| dot1+1 >= dot2 || sra[dot1+1] ==

||

(with_chunk && (dot2+2 != sra.size() ||

(sra[dot2+1] !=

&& sra[dot2+1] !=

) )) ) {

ret.first =

(sra.substr(0, dot1), spot_id);

ret.second = sra[dot2+1] -

;

& general =

->GetGeneral();

( general.

() !=

) {

( read_id.first ) {

( read_id.first ) {

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

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

bool ValidParams(const TPluginManagerParamTree *params) const

CTSE_LoadLock GetTSE_LoadLock(const TBlobId &blob_id)

bool IsDataLoaderMatches(CDataLoader &loader) const

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

bool operator==(const CBlobId &id) const

CSRABlobId(const string &acc, unsigned spot_id)

string ToString(void) const

Get string representation of blob id.

bool operator<(const CBlobId &id) const

~CSRADataLoader_Impl(void)

CRef< CSeq_entry > LoadSRAEntry(const string &accession, unsigned spot_id)

TSeqPos GetSequenceLength(const string &accession, unsigned spot_id, unsigned read_id)

CSRADataLoader_Impl(CSraMgr::ETrim trim)

CSeq_inst::TMol GetSequenceType(const string &accession, unsigned spot_id, unsigned read_id)

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

virtual TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)

Request for a length of a sequence.

virtual STypeFound GetSequenceTypeFound(const CSeq_id_Handle &idh)

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh)

virtual bool CanGetBlobById(void) const

virtual TTSE_Lock GetBlobById(const TBlobId &blob_id)

static string GetLoaderNameFromArgs(void)

virtual TBlobId GetBlobIdFromString(const string &str) const

CRef< CSRADataLoader_Impl > m_Impl

virtual CObjectManager::TPriority GetDefaultPriority(void) const

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 ~CSRA_DataLoaderCF(void)

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

@ eLifeLevel_AppMain

Destroyed in CNcbiApplication::AppMain, if possible.

void Init(CSraMgr &mgr, const string &acc)

const string & GetAccession(void) const

TSeqPos GetSequenceLength(spotid_t spot_id, uint8_t read_id) const

CSeq_inst::TMol GetSequenceType(spotid_t spot_id, uint8_t read_id) const

CRef< CSeq_entry > GetSpotEntry(spotid_t spot_id) const

void SetSeq_entry(CSeq_entry &entry, CTSE_SetObjectInfo *set_info=0)

bool IsLoaded(void) const

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

definition of a Culling tree

iterator_bool insert(const value_type &val)

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

std::ofstream out("events_result.xml")

main entry point for tests

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

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

unsigned int TSeqPos

Type for sequence locations and lengths.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

CConstRef< CSeq_id > GetSeqId(void) const

CSeq_id::E_Choice Which(void) const

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.

@ kPriority_Replace

Default priority for replacement loaders.

#define NCBI_PARAM_TYPE(section, name)

Generate typename for a parameter from its {section, name} attributes.

@ 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.

NCBI_NS_STD::string::size_type SIZE_TYPE

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

const TTag & GetTag(void) const

Get the Tag member data.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

@ e_General

for other databases

EMol

molecule class in living organism

string s_Value(TValue value)

Helper classes and templates to implement plugins.

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

const string kDataLoader_Sra_DriverName("sra")

NCBI_PARAM_DEF_EX(bool, SRA_LOADER, TRIM, false, eParam_NoThread, SRA_LOADER_TRIM)

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

pair< CRef< CSRABlobId >, unsigned > TReadId

static bool GetTrimParam(void)

void DataLoaders_Register_SRA(void)

static TReadId sx_GetReadId(const string &sra, bool with_chunk)

NCBI_PARAM_DECL(bool, SRA_LOADER, TRIM)

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

CRef< objects::CObjectManager > om

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

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