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

(CSRA_LOADER, QUALITY_GRAPHS)::SetDefault(param);

(CSRA_LOADER, MIN_MAP_QUALITY)::SetDefault(param);

(CSRA_LOADER, MAX_SEPARATE_SPOT_GROUPS)::GetDefault();

(CSRA_LOADER, MAX_SEPARATE_SPOT_GROUPS)::SetDefault(param);

(CSRA_LOADER, SPOT_READ_ALIGN)::SetDefault(param);

m_PileupGraphs != kPileupGraphs_config?

m_QualityGraphs != kQualityGraphs_config?

m_SpotReadAlign != kSpotReadAlign_config?

m_SpotGroups != kSpotGroups_config?

<<

<< m_DirPath;

( !m_CSRAFiles.empty() ) {

( vector<string>, it, m_CSRAFiles ) {

<<

<< m_IdMapper.get();

( !m_AnnotName.empty() ) {

<<

<< m_AnnotName;

( m_MinMapQuality != kMinMapQuality_config ) {

<<

<< m_MinMapQuality;

( m_PileupGraphs != kPileupGraphs_config ) {

<<

<< m_PileupGraphs;

( m_QualityGraphs != kQualityGraphs_config ) {

<<

<< m_QualityGraphs;

( m_SpotGroups != kSpotGroups_config ) {

<<

<< m_SpotGroups;

( m_PathInId != kPathInId_config ) {

<<

<< m_PathInId;

& srz_acc,

& dir_path,

& csra_name,

& dir_path,

vector<string>& csra_files,

;

& csra_name)

& dir_path,

vector<string>& csra_files)

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

CDataSource::SGiFound GetGi(const CSeq_id_Handle &idh)

void SetSpotReadAlign(bool value)

CRef< CCSRABlobId > GetBlobId(const CSeq_id_Handle &idh)

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

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

string GetLabel(const CSeq_id_Handle &idh)

CDataSource::STypeFound GetSequenceType(const CSeq_id_Handle &idh)

TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)

CDataSource::SAccVerFound GetAccVer(const CSeq_id_Handle &idh)

bool GetSpotReadAlign(void) const

TAnnotNames GetPossibleAnnotNames(void) const

TTaxId GetTaxId(const CSeq_id_Handle &idh)

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

static bool GetQualityGraphsParamDefault(void)

virtual bool CanGetBlobById(void) const

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

virtual TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)

Request for a length of a sequence.

CRef< CCSRADataLoader_Impl > m_Impl

virtual void GetChunk(TChunk chunk)

static void SetQualityGraphsParamDefault(bool param)

vector< CAnnotName > TAnnotNames

virtual TTaxId GetTaxId(const CSeq_id_Handle &idh)

Request for a taxonomy id of a sequence.

virtual SAccVerFound GetAccVerFound(const CSeq_id_Handle &idh)

void SetSpotReadAlign(bool value)

static bool GetSpotReadAlignParamDefault(void)

virtual STypeFound GetSequenceTypeFound(const CSeq_id_Handle &idh)

virtual void GetChunks(const TChunkSet &chunks)

static void SetSpotReadAlignParamDefault(bool param)

TAnnotNames GetPossibleAnnotNames(void) const

static bool GetPileupGraphsParamDefault(void)

virtual CObjectManager::TPriority GetDefaultPriority(void) const

virtual TBlobId GetBlobIdFromString(const string &str) const

virtual string GetLabel(const CSeq_id_Handle &idh)

Request for a label string of a sequence.

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

static void SetPileupGraphsParamDefault(bool param)

static string GetLoaderNameFromArgs(void)

virtual unsigned GetDefaultBlobCacheSizeLimit() const

virtual SGiFound GetGiFound(const CSeq_id_Handle &idh)

static int GetMinMapQualityParamDefault(void)

static void SetMinMapQualityParamDefault(int param)

static void SetSpotGroupsParamDefault(int param)

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh)

static int GetSpotGroupsParamDefault(void)

bool GetSpotReadAlign() const

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

virtual ~CCSRA_DataLoaderCF(void)

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

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

NCBI_PARAM_DEF_EX(bool, CSRA_LOADER, PILEUP_GRAPHS, true, eParam_NoThread, CSRA_LOADER_PILEUP_GRAPHS)

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

NCBI_PARAM_DECL(string, CSRA, ACCESSIONS)

void DataLoaders_Register_CSRA(void)

NCBI_PARAM_DEF(string, CSRA, ACCESSIONS, "")

const char kDataLoader_CSRA_DriverName[]

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

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

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

@ kPriority_Replace

Default priority for replacement loaders.

void Reset(void)

Reset reference object.

#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.

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.

CRef< objects::CObjectManager > om

string GetLoaderName(void) const

bool GetEffectiveQualityGraphs(void) const

int GetEffectiveMinMapQuality(void) const

int GetEffectiveSpotGroups(void) const

bool GetEffectiveSpotReadAlign(void) const

bool GetEffectivePileupGraphs(void) const

vector< string > m_CSRAFiles

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

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