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CRemoteBlastDbDataLoader Class Reference

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#include <objtools/data_loaders/blastdb/bdbloader_rmt.hpp>

+ Inheritance diagram for CRemoteBlastDbDataLoader:
+ Collaboration diagram for CRemoteBlastDbDataLoader:

Public Types

typedef SRegisterLoaderInfo< CRemoteBlastDbDataLoaderTRegisterLoaderInfo
 
- Public Types inherited from CBlastDbDataLoader
enum  EDbType { eNucleotide = 0 , eProtein = 1 , eUnknown = 2 }
 Describes the type of blast database to use. More...
 
typedef SRegisterLoaderInfo< CBlastDbDataLoaderTRegisterLoaderInfo
 
typedef limited_size_map< CSeq_id_Handle, intTIdMap
 A mapping from sequence identifier to blob ids. More...
 
- Public Types inherited from CDataLoader
enum  EChoice {
  eBlob , eBioseq , eCore , eBioseqCore ,
  eSequence , eFeatures , eGraph , eAlign ,
  eAnnot , eExtFeatures , eExtGraph , eExtAlign ,
  eExtAnnot , eOrphanAnnot , eAll
}
 main blob is blob with sequence all other blobs are external and contain external annotations More...
 
typedef CTSE_Lock TTSE_Lock
 
typedef set< TTSE_LockTTSE_LockSet
 
typedef CRef< CTSE_Chunk_InfoTChunk
 
typedef vector< TChunkTChunkSet
 
typedef set< stringTProcessedNAs
 
typedef set< CSeq_id_HandleTSeq_idSet
 
typedef vector< CSeq_id_HandleTIds
 
typedef vector< boolTLoaded
 Bulk loading interface for a small pieces of information per id. More...
 
typedef vector< TIdsTBulkIds
 
typedef vector< TGiTGis
 
typedef vector< stringTLabels
 
typedef vector< TTaxIdTTaxIds
 
typedef vector< TSeqPosTSequenceLengths
 
typedef vector< CSeq_inst::TMolTSequenceTypes
 
typedef vector< intTSequenceStates
 
typedef vector< intTSequenceHashes
 
typedef vector< boolTHashKnown
 
typedef map< CSeq_id_Handle, TTSE_LockSetTTSE_LockSets
 
typedef vector< vector< CSeq_id_Handle > > TSeqIdSets
 
typedef vector< CTSE_LockTCDD_Locks
 
typedef CBlobIdKey TBlobId
 
typedef int TBlobVersion
 
typedef CRef< IEditSaverTEditSaver
 
- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void GetBlobs (TTSE_LockSets &tse_sets)
 Support for fetching the sequence length by batch. More...
 
virtual void GetChunks (const TChunkSet &chunks)
 Support for fetching the sequence chunks by batch. More...
 
virtual TTSE_Lock GetBlobById (const TBlobId &blob_id)
 For a given TBlobId, get the TTSE_Lock. More...
 
- Public Member Functions inherited from CBlastDbDataLoader
virtual ~CBlastDbDataLoader ()
 
virtual TTSE_LockSet GetRecords (const CSeq_id_Handle &idh, EChoice choice)
 Load TSE. More...
 
virtual void GetChunk (TChunk chunk)
 Load a description or data chunk. More...
 
virtual TTaxId GetTaxId (const CSeq_id_Handle &idh)
 Request for a taxonomy id of a sequence. More...
 
virtual void GetTaxIds (const TIds &ids, TLoaded &loaded, TTaxIds &ret)
 
virtual TSeqPos GetSequenceLength (const CSeq_id_Handle &idh)
 Request for a length of a sequence. More...
 
virtual void GetSequenceLengths (const TIds &ids, TLoaded &loaded, TSequenceLengths &ret)
 
virtual CSeq_inst::TMol GetSequenceType (const CSeq_id_Handle &idh)
 Request for a type of a sequence Returns CSeq_inst::eMol_not_set if sequence is not known. More...
 
virtual void GetSequenceTypes (const TIds &ids, TLoaded &loaded, TSequenceTypes &ret)
 
virtual TBlobId GetBlobId (const CSeq_id_Handle &idh)
 Gets the blob id for a given sequence. More...
 
virtual bool CanGetBlobById () const
 Test method for GetBlobById feature. More...
 
- Public Member Functions inherited from CDataLoader
virtual ~CDataLoader (void)
 
TTSE_LockSet GetRecordsNoBlobState (const CSeq_id_Handle &idh, EChoice choice)
 The same as GetRecords() but always returns empty TSE lock set instead of throwing CBlobStateException. More...
 
virtual TTSE_LockSet GetDetailedRecords (const CSeq_id_Handle &idh, const SRequestDetails &details)
 Request from a datasource using handles and ranges instead of seq-loc The TSEs loaded in this call will be added to the tse_set. More...
 
virtual TTSE_LockSet GetExternalRecords (const CBioseq_Info &bioseq)
 Request from a datasource set of blobs with external annotations. More...
 
virtual TTSE_LockSet GetOrphanAnnotRecords (const CSeq_id_Handle &idh, const SAnnotSelector *sel)
 old Get*AnnotRecords() methods More...
 
virtual TTSE_LockSet GetExternalAnnotRecords (const CSeq_id_Handle &idh, const SAnnotSelector *sel)
 
virtual TTSE_LockSet GetExternalAnnotRecords (const CBioseq_Info &bioseq, const SAnnotSelector *sel)
 
virtual TTSE_LockSet GetOrphanAnnotRecordsNA (const CSeq_id_Handle &idh, const SAnnotSelector *sel, TProcessedNAs *processed_nas)
 new Get*AnnotRecords() methods More...
 
virtual TTSE_LockSet GetOrphanAnnotRecordsNA (const TSeq_idSet &ids, const SAnnotSelector *sel, TProcessedNAs *processed_nas)
 
virtual TTSE_LockSet GetExternalAnnotRecordsNA (const CSeq_id_Handle &idh, const SAnnotSelector *sel, TProcessedNAs *processed_nas)
 
virtual TTSE_LockSet GetExternalAnnotRecordsNA (const CBioseq_Info &bioseq, const SAnnotSelector *sel, TProcessedNAs *processed_nas)
 
virtual void GetIds (const CSeq_id_Handle &idh, TIds &ids)
 Request for a list of all Seq-ids of a sequence. More...
 
bool SequenceExists (const CSeq_id_Handle &idh)
 helper function to check if sequence exists, uses GetIds() More...
 
virtual CSeq_id_Handle GetAccVer (const CSeq_id_Handle &idh)
 Request for a accession.version Seq-id of a sequence. More...
 
virtual SAccVerFound GetAccVerFound (const CSeq_id_Handle &idh)
 
virtual TGi GetGi (const CSeq_id_Handle &idh)
 Request for a gi of a sequence. More...
 
virtual SGiFound GetGiFound (const CSeq_id_Handle &idh)
 
virtual string GetLabel (const CSeq_id_Handle &idh)
 Request for a label string of a sequence. More...
 
virtual STypeFound GetSequenceTypeFound (const CSeq_id_Handle &idh)
 
virtual int GetSequenceState (const CSeq_id_Handle &idh)
 Request for a state of a sequence. More...
 
virtual int GetSequenceHash (const CSeq_id_Handle &idh)
 Request for a sequence hash. More...
 
virtual SHashFound GetSequenceHashFound (const CSeq_id_Handle &idh)
 
virtual void GetBulkIds (const TIds &ids, TLoaded &loaded, TBulkIds &ret)
 Bulk request for all Seq-ids of a set of sequences. More...
 
virtual void GetAccVers (const TIds &ids, TLoaded &loaded, TIds &ret)
 Bulk request for accession.version Seq-ids of a set of sequences. More...
 
virtual void GetGis (const TIds &ids, TLoaded &loaded, TGis &ret)
 Bulk request for gis of a set of sequences. More...
 
virtual void GetLabels (const TIds &ids, TLoaded &loaded, TLabels &ret)
 Bulk request for label strings of a set of sequences. More...
 
virtual void GetTaxIds (const TIds &ids, TLoaded &loaded, TTaxIds &ret)
 Bulk request for taxonomy ids of a set of sequences. More...
 
virtual void GetSequenceLengths (const TIds &ids, TLoaded &loaded, TSequenceLengths &ret)
 Bulk request for lengths of a set of sequences. More...
 
virtual void GetSequenceTypes (const TIds &ids, TLoaded &loaded, TSequenceTypes &ret)
 Bulk request for types of a set of sequences. More...
 
virtual void GetSequenceStates (const TIds &ids, TLoaded &loaded, TSequenceStates &ret)
 Bulk request for states of a set of sequences. More...
 
virtual void GetSequenceHashes (const TIds &ids, TLoaded &loaded, TSequenceHashes &ret, THashKnown &known)
 Bulk request for hashes of a set of sequences. More...
 
virtual void GetCDDAnnots (const TSeqIdSets &id_sets, TLoaded &loaded, TCDD_Locks &ret)
 
virtual TBlobId GetBlobIdFromString (const string &str) const
 
virtual TBlobVersion GetBlobVersion (const TBlobId &id)
 
virtual SRequestDetails ChoiceToDetails (EChoice choice) const
 
virtual EChoice DetailsToChoice (const SRequestDetails::TAnnotSet &annots) const
 
virtual EChoice DetailsToChoice (const SRequestDetails &details) const
 
virtual void DropTSE (CRef< CTSE_Info > tse_info)
 
void SetTargetDataSource (CDataSource &data_source)
 Specify datasource to send loaded data to. More...
 
string GetName (void) const
 
virtual TTSE_Lock ResolveConflict (const CSeq_id_Handle &id, const TTSE_LockSet &tse_set)
 Resolve TSE conflict *select the best TSE from the set of dead TSEs. More...
 
virtual void GC (void)
 
virtual TEditSaver GetEditSaver () const
 
virtual CObjectManager::TPriority GetDefaultPriority (void) const
 
virtual Uint4 EstimateLoadBytes (const CTSE_Chunk_Info &chunk) const
 
virtual double EstimateLoadSeconds (const CTSE_Chunk_Info &chunk, Uint4 bytes) const
 
virtual unsigned GetDefaultBlobCacheSizeLimit () const
 
virtual bool GetTrackSplitSeq () const
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 

Static Public Member Functions

static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, const string &dbname="nr", const EDbType dbtype=eUnknown, bool use_fixed_size_slices=true, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)
 
static string GetLoaderNameFromArgs (const SBlastDbParam &param)
 
- Static Public Member Functions inherited from CBlastDbDataLoader
static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, const string &dbname="nr", const EDbType dbtype=eUnknown, bool use_fixed_size_slices=true, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)
 
static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, CRef< CSeqDB > db_handle, bool use_fixed_size_slices=true, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)
 
static string GetLoaderNameFromArgs (CConstRef< CSeqDB > db_handle)
 
static string GetLoaderNameFromArgs (const SBlastDbParam &param)
 
static string GetLoaderNameFromArgs (const string &dbname="nr", const EDbType dbtype=eUnknown)
 
static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, const string &dbname, const EDbType dbtype, CObjectManager::EIsDefault is_default, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)
 
static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, CRef< CSeqDB > db_handle, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)
 
- Static Public Member Functions inherited from CDataLoader
static bool IsRequestedAnyNA (const SAnnotSelector *sel)
 
static bool IsRequestedNA (const string &na, const SAnnotSelector *sel)
 
static bool IsProcessedNA (const string &na, const TProcessedNAs *processed_nas)
 
static void SetProcessedNA (const string &na, TProcessedNAs *processed_nas)
 
- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 

Static Public Attributes

static const string kNamePrefix
 All BLAST DB data loader instances have a name that starts with kNamePrefix. More...
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 

Private Types

typedef CParamLoaderMaker< CRemoteBlastDbDataLoader, SBlastDbParamTMaker
 

Private Member Functions

 CRemoteBlastDbDataLoader (const string &loader_name, const SBlastDbParam &param)
 Parametrized constructor. More...
 
 CRemoteBlastDbDataLoader (const CRemoteBlastDbDataLoader &)
 Prevent automatic copy constructor generation. More...
 
CRemoteBlastDbDataLoaderoperator= (const CRemoteBlastDbDataLoader &)
 Prevent automatic assignment operator generation. More...
 

Friends

class CParamLoaderMaker< CRemoteBlastDbDataLoader, SBlastDbParam >
 

Additional Inherited Members

- Protected Types inherited from CBlastDbDataLoader
typedef int TBioseq_setId
 TPlace is a Seq-id or an integer id, this data loader uses the former. More...
 
typedef CSeq_id_Handle TBioseqId
 
typedef pair< TBioseqId, TBioseq_setIdTPlace
 
typedef CParamLoaderMaker< CBlastDbDataLoader, SBlastDbParamTMaker
 
- Protected Member Functions inherited from CBlastDbDataLoader
 CBlastDbDataLoader ()
 Default (no-op) constructor. More...
 
 CBlastDbDataLoader (const string &loader_name, const SBlastDbParam &param)
 Parametrized constructor. More...
 
 CBlastDbDataLoader (const CBlastDbDataLoader &)
 Prevent automatic copy constructor generation. More...
 
CBlastDbDataLoaderoperator= (const CBlastDbDataLoader &)
 Prevent automatic assignment operator generation. More...
 
int x_GetOid (const CSeq_id_Handle &idh)
 Gets the OID from m_Ids cache or the BLAST databases. More...
 
int x_GetOid (const TBlobId &blob_id) const
 Gets the OID from a TBlobId (see typedef in bdbloader.cpp) More...
 
void x_LoadData (const CSeq_id_Handle &idh, int oid, CTSE_LoadLock &lock, int slice_size)
 Load sequence data from cache or from the database. More...
 
- Protected Member Functions inherited from CDataLoader
 CDataLoader (void)
 
 CDataLoader (const string &loader_name)
 
void SetName (const string &loader_name)
 
CDataSourceGetDataSource (void) const
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 
- Static Protected Member Functions inherited from CDataLoader
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. More...
 
- Protected Attributes inherited from CBlastDbDataLoader
string m_DBName
 Blast database name. More...
 
EDbType m_DBType
 Is this database protein or nucleotide? More...
 
CRef< IBlastDbAdapterm_BlastDb
 The sequence database. More...
 
TIdMap m_Ids
 ID to OID translation. More...
 
bool m_UseFixedSizeSlices
 Configuration value specified to the CCachedSequence. More...
 

Detailed Description

Definition at line 45 of file bdbloader_rmt.hpp.

Member Typedef Documentation

◆ TMaker

Definition at line 82 of file bdbloader_rmt.hpp.

◆ TRegisterLoaderInfo

Definition at line 49 of file bdbloader_rmt.hpp.

Constructor & Destructor Documentation

◆ CRemoteBlastDbDataLoader() [1/2]

CRemoteBlastDbDataLoader::CRemoteBlastDbDataLoader ( const string loader_name,
const SBlastDbParam param 
)
private

◆ CRemoteBlastDbDataLoader() [2/2]

CRemoteBlastDbDataLoader::CRemoteBlastDbDataLoader ( const CRemoteBlastDbDataLoader )
private

Prevent automatic copy constructor generation.

Member Function Documentation

◆ DebugDump()

void CRemoteBlastDbDataLoader::DebugDump ( CDebugDumpContext  ddc,
unsigned int  depth 
) const
virtual

Define method for dumping debug information.

Reimplemented from CBlastDbDataLoader.

Definition at line 256 of file bdbloader_rmt.cpp.

References DebugDumpValue(), CBlastDbDataLoader::m_DBName, CBlastDbDataLoader::m_DBType, CBlastDbDataLoader::m_UseFixedSizeSlices, and CDebugDumpContext::SetFrame().

◆ GetBlobById()

CRemoteBlastDbDataLoader::TTSE_Lock CRemoteBlastDbDataLoader::GetBlobById ( const TBlobId blob_id)
virtual

For a given TBlobId, get the TTSE_Lock.

If the provided TBlobId is known to this code, the corresponding TTSE_Lock data will be fetched and returned. Otherwise, an empty valued TTSE_Lock is returned.

Parameters
blob_idIndicates which data to get.
Returns
The returned data.

Reimplemented from CBlastDbDataLoader.

Definition at line 146 of file bdbloader_rmt.cpp.

References first(), CDataLoader::GetDataSource(), CDataSource::GetTSE_LoadLock(), CBlobIdFor< Value, Converter >::GetValue(), CTSE_LoadLock::IsLoaded(), kRmtSequenceSliceSize, and CBlastDbDataLoader::x_LoadData().

Referenced by GetBlobs().

◆ GetBlobs()

void CRemoteBlastDbDataLoader::GetBlobs ( TTSE_LockSets tse_sets)
virtual

◆ GetChunks()

void CRemoteBlastDbDataLoader::GetChunks ( const TChunkSet chunks)
virtual

◆ GetLoaderNameFromArgs()

string CRemoteBlastDbDataLoader::GetLoaderNameFromArgs ( const SBlastDbParam param)
static

◆ operator=()

CRemoteBlastDbDataLoader& CRemoteBlastDbDataLoader::operator= ( const CRemoteBlastDbDataLoader )
private

Prevent automatic assignment operator generation.

◆ RegisterInObjectManager()

CRemoteBlastDbDataLoader::TRegisterLoaderInfo CRemoteBlastDbDataLoader::RegisterInObjectManager ( CObjectManager om,
const string dbname = "nr",
const EDbType  dbtype = eUnknown,
bool  use_fixed_size_slices = true,
CObjectManager::EIsDefault  is_default = CObjectManager::eNonDefault,
CObjectManager::TPriority  priority = CObjectManager::kPriority_NotSet 
)
static

Friends And Related Function Documentation

◆ CParamLoaderMaker< CRemoteBlastDbDataLoader, SBlastDbParam >

Definition at line 82 of file bdbloader_rmt.hpp.

Member Data Documentation

◆ kNamePrefix

const string CRemoteBlastDbDataLoader::kNamePrefix
static

All BLAST DB data loader instances have a name that starts with kNamePrefix.

Definition at line 62 of file bdbloader_rmt.hpp.

Referenced by GetLoaderNameFromArgs().


The documentation for this class was generated from the following files:
Modified on Mon May 20 04:59:39 2024 by modify_doxy.py rev. 669887