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NCBI C++ ToolKit: src/objtools/data_loaders/asn_cache/asn_cache_loader.cpp Source File

& db_path,

;

(

) + db_path;

& db_path)

time_t timestamp = 0;

time_t timestamp = 0;

sequence_length = 0;

timestamp, sequence_length, tax_id)) {

sequence_length;

vector<CSeq_id_Handle> bioseq_ids;

ids.swap(bioseq_ids);

time_t timestamp = 0;

sequence_length = 0;

timestamp, sequence_length, tax_id)) {

ret.resize(ids.size());

loaded.resize(ids.size());

(

= 0;

< ids.size(); ++

) {

time_t timestamp = 0;

(index.cache->GetIdInfo(ids[

], gi, timestamp)) {

+

);

TIndexMap::iterator iter =

.begin() + id;

( !iter->get() ) {

Contains the class definiton for CAsnCache, the main client class for accessing the ASN cache data.

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

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

void DataLoaders_Register_AsnCache(void)

const string kDataLoader_AsnCache_DriverName("asncache")

virtual ~CAsnCache_DataLoaderCF(void)

CAsnCache_DataLoaderCF(void)

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

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh)

static string GetLoaderNameFromArgs(void)

virtual TTaxId GetTaxId(const CSeq_id_Handle &idh)

Request for a taxonomy id of a sequence.

SCacheInfo & x_GetIndex()

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

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...

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

virtual TGi GetGi(const CSeq_id_Handle &idh)

Request for a gi of a sequence.

virtual TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)

Request for a length of a sequence.

CAsnCache_DataLoader(void)

virtual ~CAsnCache_DataLoader(void)

virtual bool CanGetBlobById() const

CAsnCache is used by clients to access the ASN cache data.

bool GetIdInfo(const objects::CSeq_id_Handle &id, CAsnIndex::TGi &gi, time_t &timestamp)

Return the GI and timestamp for a given seq_id.

bool GetIndexEntry(const objects::CSeq_id_Handle &id, CAsnIndex::SIndexInfo &info)

Get the full ASN cache index entry.

CRef< objects::CSeq_entry > GetEntry(const objects::CSeq_id_Handle &id)

Return a blob as a CSeq_entry object.

bool GetSeqIds(const objects::CSeq_id_Handle &id, vector< objects::CSeq_id_Handle > &all_ids, bool cheap_only=true)

Return the set of seq-ids associated with a given ID.

const string & GetDriverName(void) const

CTSE_LoadLock GetTSE_LoadLock(const TBlobId &blob_id)

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

bool IsLoaded(void) const

definition of a Culling tree

iterator_bool insert(const value_type &val)

#define GI_FROM(T, value)

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define TAX_ID_FROM(T, value)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

string AsString(void) const

const value_type & GetValue(void) const

CBlobIdFor< CSeq_id_Handle > CBlobIdSeq_id

TLoader * GetLoader(void) const

Get pointer to the loader.

vector< CSeq_id_Handle > TIds

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)

virtual void GetGis(const TIds &ids, TLoaded &loaded, TGis &ret)

Bulk request for gis of a set of sequences.

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.

@ eAll

all blobs (main and external)

@ eCore

?only seq-entry core?

@ eBioseq

main blob with complete bioseq

@ eBioseqCore

main blob with bioseq core (no seqdata and annots)

static void NCBI_EntryPointImpl(TDriverInfoList &info_list, EEntryPointRequest method)

Entry point implementation.

string GetParam(const string &driver_name, const TPluginManagerParamTree *params, const string &param_name, bool mandatory, const string &default_value) const

Utility function to get an element of parameter tree Throws an exception when mandatory parameter is ...

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.

Plugin manager (using class factory paradigm).

Helper classes and templates to implement plugins.

CRef< objects::CObjectManager > om

structure for common cache reader&writer implementation

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