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

& srz_acc,

& dir_path,

& bam_name,

& index_name,

;

<<

<< it->m_BamName;

& bam_name,

& index_name)

& dir_path,

vector<SBamFileName>& bam_files)

( !

.m_BamName.empty() ) {

NCBI_PARAM_DECL(string, BAM, DIR_PATH)

const string kDataLoader_Bam_DriverName("bam")

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

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

void DataLoaders_Register_BAM(void)

NCBI_PARAM_DEF_EX(string, BAM, DIR_PATH, "", eParam_NoThread, BAM_DIR_PATH)

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

CDataSource::SGiFound GetGi(const CSeq_id_Handle &idh)

CRef< CBAMBlobId > GetRefSeqBlobId(const CSeq_id_Handle &idh)

CBAMDataLoader::TAnnotNames GetPossibleAnnotNames(void) const

void LoadChunk(const CBAMBlobId &blob_id, CTSE_Chunk_Info &chunk)

double EstimateLoadSeconds(const CBAMBlobId &blob_id, const CTSE_Chunk_Info &chunk, Uint4 bytes)

CDataSource::SAccVerFound GetAccVer(const CSeq_id_Handle &idh)

string GetLabel(const CSeq_id_Handle &idh)

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

TTaxId GetTaxId(const CSeq_id_Handle &idh)

void LoadBAMEntry(const CBAMBlobId &blob_id, CTSE_LoadLock &load_lock)

CRef< CBAMBlobId > GetShortSeqBlobId(const CSeq_id_Handle &idh)

static string GetLoaderNameFromArgs(void)

virtual void GetChunks(const TChunkSet &chunks)

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

virtual TBlobId GetBlobIdFromString(const string &str) const

CRef< CBAMDataLoader_Impl > m_Impl

virtual TTSE_Lock GetBlobById(const TBlobId &blob_id)

virtual double EstimateLoadSeconds(const CTSE_Chunk_Info &chunk, Uint4 bytes) const

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh)

virtual bool CanGetBlobById(void) const

virtual string GetLabel(const CSeq_id_Handle &idh)

Request for a label string of a sequence.

TAnnotNames GetPossibleAnnotNames(void) const

virtual TTaxId GetTaxId(const CSeq_id_Handle &idh)

Request for a taxonomy id of a sequence.

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

virtual unsigned GetDefaultBlobCacheSizeLimit() const

virtual void GetChunk(TChunk chunk)

virtual SAccVerFound GetAccVerFound(const CSeq_id_Handle &idh)

vector< CAnnotName > TAnnotNames

virtual SGiFound GetGiFound(const CSeq_id_Handle &idh)

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

virtual ~CBAM_DataLoaderCF(void)

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:

@ eLifeLevel_AppMain

Destroyed in CNcbiApplication::AppMain, if possible.

TBlobId GetBlobId(void) const

bool IsLoaded(void) const

definition of a Culling tree

iterator_bool insert(const value_type &val)

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.

element_type * get(void) const

Get pointer.

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

@ eOrphanAnnot

all external annotations if no Bioseq exists

void Reset(void)

Reset reference object.

TObjectType & GetNCObject(void) const

Get 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.

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.

Helper classes and templates to implement plugins.

CRef< objects::CObjectManager > om

AutoPtr< IIdMapper > m_IdMapper

vector< SBamFileName > m_BamFiles

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...

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