RetroSearch Browse

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCBlastDbDataLoader.html below:

NCBI C++ ToolKit: CBlastDbDataLoader Class Reference

Search Toolkit Book for CBlastDbDataLoader

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

enum EDbType { eNucleotide = 0 , eProtein = 1 , eUnknown = 2 } Describes the type of blast database to use. More...
typedef SRegisterLoaderInfo< CBlastDbDataLoader > TRegisterLoaderInfo typedef limited_size_map< CSeq_id_Handle, int > TIdMap A mapping from sequence identifier to blob ids. More...
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_Lock > TTSE_LockSet typedef CRef< CTSE_Chunk_Info > TChunk typedef vector< TChunk > TChunkSet typedef set< string > TProcessedNAs typedef set< CSeq_id_Handle > TSeq_idSet typedef vector< CSeq_id_Handle > TIds typedef vector< bool > TLoaded Bulk loading interface for a small pieces of information per id. More...
typedef vector< TIds > TBulkIds typedef vector< TGi > TGis typedef vector< string > TLabels typedef vector< TTaxId > TTaxIds typedef vector< TSeqPos > TSequenceLengths typedef vector< CSeq_inst::TMol > TSequenceTypes typedef vector< int > TSequenceStates typedef vector< int > TSequenceHashes typedef vector< bool > THashKnown typedef map< CSeq_id_Handle, TTSE_LockSet > TTSE_LockSets typedef vector< vector< CSeq_id_Handle > > TSeqIdSets typedef vector< CTSE_Lock > TCDD_Locks typedef CBlobIdKey TBlobId typedef int TBlobVersion typedef CRef< IEditSaver > TEditSaver enum EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } Control filling of newly allocated memory. More...
typedef CObjectCounterLocker TLockerType Default locker type for CRef. More...
typedef atomic< Uint8 > TCounter Counter type is CAtomiCounter. More...
typedef Uint8 TCount Alias for value type of counter. More...
virtual ~CBlastDbDataLoader () virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const Define method for dumping debug information. More...
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...
virtual TTSE_Lock GetBlobById (const TBlobId &blob_id) For a given TBlobId, get the TTSE_Lock. More...
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 void GetBlobs (TTSE_LockSets &tse_sets) 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 GetChunks (const TChunkSet &chunks) 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 CObject (void) Constructor. More...
CObject (const CObject &src) Copy constructor. More...
virtual ~CObject (void) Destructor. More...
CObject & operator= (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...
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 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 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 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 void EnableDebugDump (bool on)

Definition at line 53 of file bdbloader.hpp.

◆ TBioseq_setId

TPlace is a Seq-id or an integer id, this data loader uses the former.

Definition at line 176 of file bdbloader.hpp.

◆ TBioseqId ◆ TIdMap

A mapping from sequence identifier to blob ids.

Definition at line 155 of file bdbloader.hpp.

◆ TMaker ◆ TPlace ◆ TRegisterLoaderInfo ◆ EDbType

Describes the type of blast database to use.

Enumerator eNucleotide

nucleotide database

eProtein

protein database

eUnknown

protein is attempted first, then nucleotide

Definition at line 57 of file bdbloader.hpp.

◆ ~CBlastDbDataLoader() CBlastDbDataLoader::~CBlastDbDataLoader ( void ) virtual

Definition at line 203 of file bdbloader.cpp.

◆ CBlastDbDataLoader() [1/3] CBlastDbDataLoader::CBlastDbDataLoader ( ) inlineprotected ◆ CBlastDbDataLoader() [2/3]

Parametrized constructor.

Parameters: loader_name name of this data loader [in] param parameters to initialize this data loader [in]

Definition at line 180 of file bdbloader.cpp.

References _ASSERT, _TRACE, DbTypeToSeqType(), CRef< C, Locker >::Empty(), GetLoaderNameFromArgs(), m_BlastDb, CBlastDbDataLoader::SBlastDbParam::m_BlastDbHandle, m_DBName, m_DBType, NCBI_THROW, CRef< C, Locker >::NotEmpty(), and CRef< C, Locker >::Reset().

◆ CBlastDbDataLoader() [3/3]

Prevent automatic copy constructor generation.

◆ CanGetBlobById() bool CBlastDbDataLoader::CanGetBlobById ( void ) const virtual

Test method for GetBlobById feature.

The caller will use this method to determine whether this data loader allows blobs to be managed by ID.

Returns: Returns true to indicate that GetBlobById() is available.

Reimplemented from CDataLoader.

Definition at line 434 of file bdbloader.cpp.

◆ DebugDump() ◆ GetBlobById()

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_id Indicates which data to get.

Returns: The returned data.

Reimplemented from CDataLoader.

Reimplemented in CRemoteBlastDbDataLoader.

Definition at line 453 of file bdbloader.cpp.

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

Referenced by GetRecords().

◆ GetBlobId()

Gets the blob id for a given sequence.

Given a Seq_id_Handle, this method finds the corresponding top level Seq-entry (TSE) and returns a blob corresponding to it. The BlobId is initialized with a pointer to that CSeq_entry if the sequence is known to this data loader, which will be true if GetRecords() was called for this sequence.

Parameters: idh Indicates the sequence for which to get a blob id.

Returns: A TBlobId corresponding to the provided Seq_id_Handle.

Reimplemented from CDataLoader.

Definition at line 441 of file bdbloader.cpp.

References x_GetOid().

Referenced by GetRecords().

◆ GetChunk() void CBlastDbDataLoader::GetChunk ( TChunk chunk ) virtual ◆ GetLoaderNameFromArgs() [1/3]

Definition at line 164 of file bdbloader.cpp.

References _ASSERT, DbTypeToStr(), CThread::GetSelf(), NStr::IntToString(), kPrefix, kPrefixThread, CConstRef< C, Locker >::NotEmpty(), and SeqTypeToDbType().

Referenced by BOOST_AUTO_TEST_CASE(), CBlastDbDataLoader(), CLBLASTObjectLoader::GetLoaderName(), CDLTestThread::Main(), RegisterOMDataLoader(), s_MTDataLoaderTest2(), and s_RegisterOMDataLoader().

◆ GetLoaderNameFromArgs() [2/3] ◆ GetLoaderNameFromArgs() [3/3] ◆ GetRecords() ◆ GetSequenceLength() ◆ GetSequenceLengths() ◆ GetSequenceType() ◆ GetSequenceTypes() ◆ GetTaxId() ◆ GetTaxIds() ◆ operator=()

Prevent automatic assignment operator generation.

◆ RegisterInObjectManager() [1/4] ◆ RegisterInObjectManager() [2/4]

Definition at line 52 of file bdbloader.cpp.

References dbname(), CParamLoaderMaker< TDataLoader, TParam >::GetRegisterInfo(), om, and CDataLoader::RegisterInObjectManager().

Referenced by CLBLASTObjectLoader::AddDataLoader(), BOOST_AUTO_TEST_CASE(), CAutoRegistrar::CAutoRegistrar(), CBlastDb_DataLoaderCF::CreateAndRegister(), CAlnMrgApp::LoadBlastDb(), CDLTestThread::Main(), RegisterInObjectManager(), RegisterOMDataLoader(), CNgAlignApp::Run(), CSplignApp::Run(), CVectorScreen::Run(), CDemoApp::Run(), s_MTDataLoaderTest2(), s_RegisterOMDataLoader(), TestUtil::CBlastOM::x_InitBlastDatabaseDataLoader(), CBlastScopeSource::x_InitBlastDatabaseDataLoader(), and CDataLoadersUtil::x_SetupBlastDataLoader().

◆ RegisterInObjectManager() [3/4] ◆ RegisterInObjectManager() [4/4] ◆ x_GetOid() [1/2]

Gets the OID from m_Ids cache or the BLAST databases.

Definition at line 379 of file bdbloader.cpp.

References _TRACE, CSeq_id::AsFastaString(), CSeq_id::Compare(), CSeq_id::e_YES, limited_size_map< Key, Value, Less >::end(), limited_size_map< Key, Value, Less >::find(), CSeq_id_Handle::GetSeqId(), IBlastDbAdapter::GetSeqIDs(), limited_size_map< Key, Value, Less >::insert(), ITERATE, m_BlastDb, m_Ids, and IBlastDbAdapter::SeqidToOid().

Referenced by GetBlobId(), GetChunk(), and CRemoteBlastDbDataLoader::GetChunks().

◆ x_GetOid() [2/2] ◆ x_LoadData()

Load sequence data from cache or from the database.

This checks the OID cache and loads the sequence data from there or if not found, from the CSeqDB database. When new data is built, the sequence is also split into chunks. A description of what data is available will be returned in the "lock" parameter.

Parameters: idh A handle to the sequence identifier. oid Object id in BLAST DB lock Information about the sequence data is returned here.

Definition at line 257 of file bdbloader.cpp.

References _ASSERT, CTSE_Split_Info::AddChunk(), CTSE_Info::GetSplitInfo(), CTSE_LoadLock::IsLoaded(), m_BlastDb, m_Ids, m_UseFixedSizeSlices, NON_CONST_ITERATE, CTSE_LoadLock::SetLoaded(), and CTSE_Info::SetSeq_entry().

Referenced by GetBlobById(), and CRemoteBlastDbDataLoader::GetBlobById().

◆ CParamLoaderMaker< CBlastDbDataLoader, SBlastDbParam > ◆ m_BlastDb ◆ m_DBName string CBlastDbDataLoader::m_DBName protected ◆ m_DBType EDbType CBlastDbDataLoader::m_DBType protected ◆ m_Ids TIdMap CBlastDbDataLoader::m_Ids protected ◆ m_UseFixedSizeSlices bool CBlastDbDataLoader::m_UseFixedSizeSlices protected

The documentation for this class was generated from the following files:

include/objtools/data_loaders/blastdb/bdbloader.hpp
src/objtools/data_loaders/blastdb/bdbloader.cpp

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4