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NCBI C++ ToolKit: src/objtools/data_loaders/lds2/lds2_dataloader.cpp Source File

{

, objects::CLDS2_DataLoader::eLockDatabase},

{

, objects::CLDS2_DataLoader::eDoNotLockDatabase},

{

, objects::CLDS2_DataLoader::eCacheDatabase}

objects::CLDS2_DataLoader::eCacheDatabase,

;

abs_path = db_path;

(db_path !=

) {

+ abs_path;

& db_path,

m_FastaFlags(fasta_flags),

m_LockMode(lock_mode)

m_DbPath(db.GetDbFile()),

m_LockMode(lock_mode)

lock_mode = TLDS2_LockMode::GetDefault();

( lock_mode ) {

(fasta_flags == -1) {

ret = it->second.GetPointerOrNull();

(2,

<<

finfo.

<<

);

unique_ptr<CObjectIStream> obj_in;

( finfo.

) {

( blob.

) {

*obj_in >> entry->SetSeq();

*obj_in >> entry->SetSet();

(annot.

) {

id_it->second.range);

entry->SetSet().SetSeq_set();

back_inserter(entry->SetSet().SetSeq_set()) );

locks.

(load_lock);

( !ret2.

() ) {

( !best_tse || oid > best_oid ) {

oid = int8_blob_id->GetValue();

( chunk_info->

() )

;

(2,

<<

finfo.

<<

);

unique_ptr<CObjectIStream> obj_in;

( finfo.

) {

( blob.

) {

annot->

().SetAlign().push_back(*it);

annot->

().SetAlign().push_back(align);

& db_path =

fasta_flags_str =

lock_mode_str =

( !lock_mode_str.empty() ) {

( !db_path.empty() ) {

User-defined methods of the data storage class.

void SetNamed(const string &name)

vector< CSeq_id_Handle > TId

const TId & GetId(void) const

Blob state exceptions, used by GenBank loader.

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)

Base class for reading FASTA sequences.

@ eBinaryASN

Binary ASN.1.

@ eFasta

FASTA format sequence record, CFastaReader.

virtual ~CLDS2_DataLoaderCF(void)

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

virtual CDataLoader * CreateLoader(void) const

CLDS2_LoaderMaker(const string &db_path, CFastaReader::TFlags fasta_flags, CLDS2_DataLoader::ELockMode lock_mode)

CLDS2_Database::TBlobSet TBlobSet

CRef< CLDS2_Database > m_Db

static string GetLoaderNameFromArgs(void)

virtual TTSE_LockSet GetExternalRecords(const CBioseq_Info &bioseq)

Request from a datasource set of blobs with external annotations.

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

void x_LoadTSE(CTSE_LoadLock &load_lock, const SLDS2_Blob &blob)

virtual ~CLDS2_DataLoader(void)

void RegisterUrlHandler(CLDS2_UrlHandler_Base *handler)

Register URL handler.

CRef< CSeq_entry > x_LoadFastaTSE(CNcbiIstream &in, const SLDS2_Blob &blob)

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh)

virtual void GetChunk(TChunk chunk_info)

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 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.

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

Argument-less loader - for compatibility only, unusable.

virtual bool CanGetBlobById(void) const

virtual CObjectManager::TPriority GetDefaultPriority(void) const

ELockMode

Database lock control.

@ eDoNotLockDatabase

Do not lock the database.

@ eLockDatabase

Lock the database.

@ eCacheDatabase

Clone the database into memory.

@ eDefaultLockMode

Use LDS2_DATALOADER_LOCK parameter, lock by default.

void x_LoadBlobs(const TBlobSet &blobs, TTSE_LockSet &locks)

CFastaReader::TFlags m_FastaFlags

virtual TTSE_LockSet GetExternalAnnotRecords(const CSeq_id_Handle &idh, const SAnnotSelector *sel)

CLDS2_UrlHandler_Base * x_GetUrlHandler(const SLDS2_File &info)

virtual TTSE_Lock GetBlobById(const TBlobId &blob_id)

void GetAnnots(Int8 blob_id, TLDS2Annots &infos)

Get details about all annotations from a blob.

void GetAnnotBlobs(const CSeq_id_Handle &idh, TAnnotChoice choice, TBlobSet &blobs)

Get all blobs, containing annotations for the seq-id.

void GetBioseqBlobs(const CSeq_id_Handle &idh, TBlobSet &blobs)

Get all blobs, containing bioseqs with the seq-id.

void BeginRead(void)

Start reading transaction, lock the db.

void EndRead(void)

End reading transaction, release the lock.

@ fAnnot_External

Annots from blobs not containing the bioseq.

@ fAnnot_Internal

Annots from the blob with the bioseq.

Int8 GetAnnotCountForBlob(Int8 blob_id)

Get number of annotations grouped into a single blob.

SLDS2_Blob GetBlobInfo(const CSeq_id_Handle &idh)

Find blob containing the requested bioseq.

@ eWrite

Read/write access.

@ eRead

Read-only access.

@ eMemory

Copy db to memory and open read-only.

const string & GetDbFile(void) const

Get database file name.

void GetSynonyms(const CSeq_id_Handle &idh, TLdsIdSet &ids)

Get all lds-id synonyms for the seq-id (including lds-id for the seq-id itself).

vector< AutoPtr< SLDS2_Annot > > TLDS2Annots

Int8 GetBioseqId(const CSeq_id_Handle &idh) const

Check if the db contains a bioseq with the given id.

SLDS2_File GetFileInfo(const string &file_name) const

Get complete file info.

Base class for URL handler.

Default handler for local files - registered automatically by LDS2 manager and data loader.

Handler for GZip local files. Not registered by default.

bool IsEntrys(void) const

Simple implementation of ILineReader for i(o)streams.

pair< TBioseqId, TBioseq_setId > TPlace

void x_AddAnnotPlace(const TBioseqId &id)

TBlobId GetBlobId(void) const

void x_LoadAnnot(const TPlace &place, const CSeq_annot &annot)

void SetLoaded(CObject *obj=0)

void x_AddAnnotType(const CAnnotName &annot_name, const SAnnotTypeSelector &annot_type, const TLocationId &location_id)

bool IsLoaded(void) const

const TBlobId & GetBlobId(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

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

void(*)(CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj) handler

Operators to edit gaps in sequences.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

static string CreateAbsolutePath(const string &path, ERelativeToWhat rtw=eRelativeToCwd)

Get an absolute path from some, possibly relative, path.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

virtual CRef< CSeq_entry > ReadOneSeq(ILineErrorListener *pMessageListener=nullptr)

Read a single effective sequence, which may turn out to be a segmented set.

long TFlags

binary OR of EFlags

@ fParseRawID

Try to identify raw accessions.

@ fAssumeNuc

Assume nucs unless accns indicate otherwise.

@ fParseGaps

Make a delta sequence if gaps found.

@ fOneSeq

Just read the first sequence found.

@ fStrictGuess

Assume no typos when guessing sequence type.

TTypeInfo GetTypeInfo(void) const

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

const value_type & GetValue(void) const

TLoader * GetLoader(void) const

Get pointer to the loader.

vector< CSeq_id_Handle > TIds

TRegisterInfo GetRegisterInfo(void)

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.

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.

@ kPriority_Local

Default priority for local data storage.

@ eExtFeatures

external features

@ eExtAnnot

all external annotations

@ eExtAlign

external aligns

@ eAll

all blobs (main and external)

@ eOrphanAnnot

all external annotations if no Bioseq exists

@ eGraph

graph annotations from main blob

@ eCore

?only seq-entry core?

@ eAnnot

all annotations from main blob

@ eBioseq

main blob with complete bioseq

@ eAlign

aligns from main blob

@ eBioseqCore

main blob with bioseq core (no seqdata and annots)

@ eExtGraph

external graph annotations

@ eFeatures

features from main blob

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

@ eParam_NoThread

Do not use per-thread values.

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.

int64_t Int8

8-byte (64-bit) signed 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.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static string Int8ToString(Int8 value, TNumToStringFlags flags=0, int base=10)

Convert Int8 to string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

Tdata & Set(void)

Assign a value to data member.

list< CRef< CSeq_align > > Tdata

void SetData(TData &value)

Assign a value to Data data member.

const TEntrys & GetEntrys(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

void NCBI_EntryPoint_DataLoader_LDS2(CPluginManager< CDataLoader >::TDriverInfoList &info_list, CPluginManager< CDataLoader >::EEntryPointRequest method)

NCBI_PARAM_ENUM_DEF_EX(objects::CLDS2_DataLoader::ELockMode, LDS2, DataLoader_Lock, objects::CLDS2_DataLoader::eCacheDatabase, eParam_NoThread, LDS2_DATALOADER_LOCK)

typedef NCBI_PARAM_TYPE(LDS2, DataLoader_Lock) TLDS2_LockMode

void NCBI_EntryPoint_xloader_lds2(CPluginManager< objects::CDataLoader >::TDriverInfoList &info_list, CPluginManager< objects::CDataLoader >::EEntryPointRequest method)

void DataLoaders_Register_LDS2(void)

CBlobIdFor< Int8 > CBlobIdInt8

NCBI_PARAM_ENUM_ARRAY(objects::CLDS2_DataLoader::ELockMode, LDS2, DataLoader_Lock)

static CLDS2_DataLoader::TBlobId s_Int8ToBlobId(Int8 id)

const string kDataLoader_LDS2_DriverName("lds")

DEFINE_STATIC_FAST_MUTEX(sx_LDS2_Lock)

NCBI_PARAM_ENUM_DECL(objects::CLDS2_DataLoader::ELockMode, LDS2, DataLoader_Lock)

const char * kLDS2_NoLock

#define kCFParam_LDS2_DbPath

#define kCFParam_LDS2_LockMode

#define kCFParam_LDS2_FastaFlags

std::istream & in(std::istream &in_, double &x_)

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

Plugin manager (using class factory paradigm).

Helper classes and templates to implement plugins.

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

CRef< objects::CObjectManager > om

string operator()(Int8 v) const

void SetAnnotType(TAnnotType type)

@ eBioseq_set_element

Used for indexing individual seq-entries from a top-level bioseq-set.

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