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NCBI C++ ToolKit: src/objtools/data_loaders/blastdb/bdbloader.cpp Source File

use_fixed_size_slices,

use_fixed_size_slices,

:

;

use_fixed_size_slices)

: m_DbName(db_name), m_DbType(db_type),

m_UseFixedSizeSlices(use_fixed_size_slices), m_BlastDbHandle(0)

use_fixed_size_slices)

m_BlastDbHandle = db_handle;

thread_id + db_handle->GetDBNameList() +

+ db_handle->GetDBNameList() +

cached->RegisterIds(

);

cached->SplitSeqData(chunks);

(ids.size() == loaded.size());

(ids.size() == ret.size());

(CDataLoader::TIds::size_type

= 0;

< ids.size();

++) {

(ids.size() == loaded.size());

(ids.size() == ret.size());

(CDataLoader::TIds::size_type

= 0;

< ids.size();

++) {

(ids.size() == loaded.size());

(ids.size() == ret.size());

ret.assign(ids.size(), retval);

loaded.assign(ids.size(),

);

start = it->second.GetFrom();

end = it->second.GetToOpen();

ddc.

(

);

void(*TArgFuncType)(list<CPluginManager<CDataLoader>

::EEntryPointRequest);

RegisterEntryPoint<CDataLoader>((TArgFuncType)

& dbtype_str =

( !

.empty() ) {

( !dbtype_str.empty() ) {

DEFINE_STATIC_MUTEX(s_Oid_Mutex)

void DataLoaders_Register_BlastDb(void)

string DbTypeToStr(CBlastDbDataLoader::EDbType dbtype)

static const string kPrefixThread

pair< int, CSeq_id_Handle > TBlastDbId

A BLAST DB (blob) ID The first field represents an OID in the BLAST database.

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

static const string kPrefix

CBlobIdFor< TBlastDbId > CBlobIdBlastDb

Type definition consistent with those defined in objmgr/blob_id.hpp.

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

CSeqDB::ESeqType DbTypeToSeqType(CBlastDbDataLoader::EDbType dbtype)

CBlastDbDataLoader::EDbType SeqTypeToDbType(CSeqDB::ESeqType seq_type)

const string kDataLoader_BlastDb_DriverName("blastdb")

Data loader implementation that uses the blast databases.

const string kCFParam_BlastDb_DbName

const string kCFParam_BlastDb_DbType

@ kSequenceSliceSize

If sequence is shorter than this size but greater than kFastSequenceLoadSize, it will be "split" into...

CRef< CSeq_literal > CreateSeqDataChunk(IBlastDbAdapter &blastdb, int oid, TSeqPos begin, TSeqPos end)

Creates a chunk that corresponds to a given OID and its beginning and ending offsets.

Defines the CCachedSequence class.

virtual void GetSequenceLengths(const TIds &ids, TLoaded &loaded, TSequenceLengths &ret)

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.

virtual TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)

Request for a length of a sequence.

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)

CRef< IBlastDbAdapter > m_BlastDb

The sequence database.

TIdMap m_Ids

ID to OID translation.

virtual ~CBlastDbDataLoader()

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh)

Gets the blob id for a given sequence.

virtual bool CanGetBlobById() const

Test method for GetBlobById feature.

string m_DBName

Blast database name.

EDbType m_DBType

Is this database protein or nucleotide?

virtual void GetTaxIds(const TIds &ids, TLoaded &loaded, TTaxIds &ret)

CBlastDbDataLoader()

Default (no-op) constructor.

int x_GetOid(const CSeq_id_Handle &idh)

Gets the OID from m_Ids cache or the BLAST databases.

virtual TTSE_Lock GetBlobById(const TBlobId &blob_id)

For a given TBlobId, get the TTSE_Lock.

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.

EDbType

Describes the type of blast database to use.

@ eNucleotide

nucleotide database

@ eProtein

protein database

@ eUnknown

protein is attempted first, then nucleotide

virtual TTSE_LockSet GetRecords(const CSeq_id_Handle &idh, EChoice choice)

Load TSE.

pair< TBioseqId, TBioseq_setId > TPlace

virtual TTaxId GetTaxId(const CSeq_id_Handle &idh)

Request for a taxonomy id of a sequence.

static string GetLoaderNameFromArgs(CConstRef< CSeqDB > db_handle)

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

Define method for dumping debug information.

virtual void GetSequenceTypes(const TIds &ids, TLoaded &loaded, TSequenceTypes &ret)

virtual void GetChunk(TChunk chunk)

Load a description or data chunk.

bool m_UseFixedSizeSlices

Configuration value specified to the CCachedSequence.

Data Loader Factory for BlastDbDataLoader.

virtual ~CBlastDb_DataLoaderCF(void)

Destructor.

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

Create and register a data loader.

CBlastDb_DataLoaderCF(void)

Constructor.

Manages a TSE and its subordinate chunks for all implementations of the IBlastDbAdapter interface.

vector< CRef< CTSE_Chunk_Info > > TCTSE_Chunk_InfoVector

A list of 'chunk' objects, generic sequence related data elements.

CObjectManager::TPriority GetPriority(const TPluginManagerParamTree *params) const

const string & GetDriverName(void) const

CObjectManager::EIsDefault GetIsDefault(const TPluginManagerParamTree *params) const

bool ValidParams(const TPluginManagerParamTree *params) const

CTSE_LoadLock GetTSE_LoadLock(const TBlobId &blob_id)

void SetFrame(const string &frame)

This class allows retrieval of sequence data from locally installed BLAST databases via CSeqDB.

const string & GetDBNameList() const

Get list of database names.

ESeqType GetSequenceType() const

Returns the type of database opened - protein or nucleotide.

ESeqType

Sequence types (eUnknown tries protein, then nucleotide).

TBlobId GetBlobId(void) const

void x_LoadSequence(const TPlace &place, TSeqPos pos, const TSequence &seq)

void SetLoaded(CObject *obj=0)

vector< TLocation > TLocationSet

const TLocationSet & GetSeq_dataInfos(void) const

list< CRef< CSeq_literal > > TSequence

bool IsLoaded(void) const

CTSE_Split_Info & GetSplitInfo(void)

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

bool IsLoaded(void) const

void AddChunk(CTSE_Chunk_Info &chunk_info)

definition of a Culling tree

virtual TTaxId GetTaxId(const CSeq_id_Handle &)

Retrieve the taxonomy ID for the requested sequence identifier.

virtual bool SeqidToOid(const CSeq_id &id, int &oid)=0

Find a Seq-id in the database and get an OID if found.

virtual list< CRef< CSeq_id > > GetSeqIDs(int oid)=0

Get the list of Seq-ids for the given OID.

list< CRef< CSeq_id > > TSeqIdList

Convenience typedef for a list of CSeq_id-s.

virtual int GetSeqLength(int oid)=0

Get the length of the sequence.

container_type::iterator iterator

iterator_bool insert(const value_type &val)

void DebugDumpValue(CDebugDumpContext &_this, const string &name, const T &value, const string &comment=kEmptyStr)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

SStrictId_Tax::TId TTaxId

Taxon id type.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

iterator find(const key_type &key)

pair< iterator, bool > insert(const value_type &value)

pair< const key_type, mapped_type > value_type

#define NCBI_THROW(exception_class, err_code, message)

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

const string AsFastaString(void) const

CConstRef< CSeq_id > GetSeqId(void) const

E_SIC Compare(const CSeq_id &sid2) const

Compare() - more general.

@ e_YES

SeqIds compared, but are different.

const value_type & GetValue(void) const

TLoader * GetLoader(void) const

Get pointer to the loader.

vector< TSeqPos > TSequenceLengths

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

vector< CSeq_inst::TMol > TSequenceTypes

EIsDefault

Flag defining if the data loader is included in the "default" group.

TRegisterInfo GetRegisterInfo(void)

vector< bool > TLoaded

Bulk loading interface for a small pieces of information per id.

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)

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

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.

#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 int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

EMol

molecule class in living organism

@ eMol_not_set

> cdna = rna

@ eMol_na

just a nucleic acid

char * dbname(DBPROCESS *dbproc)

Get name of current database.

Declaration of the CLocalBlastDbAdapter class.

Helper classes and templates to implement plugins.

CRef< objects::CObjectManager > om

SBlastDbParam(const string &db_name="nr", EDbType dbtype=eUnknown, bool use_fixed_size_slices=true)

CRef< CSeqDB > m_BlastDbHandle

string operator()(const TBlastDbId &v) const

Convert TBlastDbId (blob IDs) to human readable strings.

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