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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/data__loader_8cpp_source.html below:

NCBI C++ ToolKit: src/objmgr/data_loader.cpp Source File

59 om

.RegisterDataLoader(loader_maker, is_default, priority);

73 if

(loader_name.empty())

125 "CDataLoader::GetRecords() is not implemented in subclass"

);

191 if

( !ret2.

() ) {

217 return

processed_nas && processed_nas->

(na) == processed_nas->

();

224 if

( processed_nas ) {

225

processed_nas->

(na);

249 if

(!tse_set2.

()) {

250 if

(tse_set.

()) {

251

tse_set.

(tse_set2);

291 "CDataLoader::GetBlobById() is not implemented in subclass"

);

297 "CDataLoader::GetBlobIdFromString(str) is not implemented in subclass"

);

307

ids = bs_info->

();

330 "CDataLoader::GetAccVer() sequence not found"

);

335 "CDataLoader::GetAccVer() sequence doesn't have accession"

);

374 "CDataLoader::GetGi() sequence not found"

);

379 "CDataLoader::GetGi() sequence doesn't have GI"

);

460 "CDataLoader::GetSequenceType() type not set"

);

466 "CDataLoader::GetSequenceType() sequence not found"

);

504 return

(*it)->GetBlobState();

519 "CDataLoader::GetSequenceHash() sequence hash not set"

);

522 "CDataLoader::GetSequenceHash() sequence not found"

);

562 size_t count

= ids.size();

563 _ASSERT

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

564 _ASSERT

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

566 for

(

size_t i

= 0;

i

<

; ++

i

) {

572 if

( !ret[

i

].

() ) {

581 size_t count

= ids.size();

582 _ASSERT

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

583 _ASSERT

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

585 for

(

size_t i

= 0;

i

<

; ++

i

) {

590 if

(

.sequence_found ) {

591

ret[

i

] =

.acc_ver;

600 size_t count

= ids.size();

601 _ASSERT

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

602 _ASSERT

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

604 for

(

size_t i

= 0;

i

<

; ++

i

) {

609 if

(

.sequence_found ) {

619 size_t count

= ids.size();

620 _ASSERT

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

621 _ASSERT

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

622 for

(

size_t i

= 0;

i

<

; ++

i

) {

627 if

( !

.empty() ) {

637 size_t count

= ids.size();

638 _ASSERT

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

639 _ASSERT

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

640 for

(

size_t i

= 0;

i

<

; ++

i

) {

657 size_t count

= ids.size();

658 _ASSERT

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

659 _ASSERT

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

660 for

(

size_t i

= 0;

i

<

; ++

i

) {

677 size_t count

= ids.size();

678 _ASSERT

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

679 _ASSERT

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

680 for

(

size_t i

= 0;

i

<

; ++

i

) {

686 if

(

.sequence_found ) {

687

ret[

i

] =

.type;

700 size_t count

= ids.size();

701 _ASSERT

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

702 _ASSERT

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

703 for

(

size_t i

= 0;

i

<

; ++

i

) {

709 if

(

!= kNotFound ) {

720 size_t count

= ids.size();

721 _ASSERT

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

722 _ASSERT

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

723 for

(

size_t i

= 0;

i

<

; ++

i

) {

729 if

(

.sequence_found ) {

730

ret[

i

] =

.hash;

732

known[

i

] =

.hash_known;

744 for

(

size_t i

= 0;

i

< id_sets.size(); ++

i

) {

745 for

(

auto id

: id_sets[

i

]) {

749

bs_info = (*it)->FindMatchingBioseq(

id

);

750 if

(!bs_info)

continue

;

753 if

(id_locks.empty())

continue

;

754

ret[

i

] = *id_locks.begin();

758 if

(loaded[

i

])

break

;

779 switch

( j->GetAnnotType() ) {

794 if

( cur !=

&& cur != ret ) {

833 if

( ret ==

) {

853 bool

sequence =

false

;

929 "CDataLoader::GetChunk() is not implemented in subclass"

);

980 return

bytes*1e-7+0.001;

1004 return typeid

(*this).before(

typeid

(id2));

1009 return

!(*

this

<

id

||

id

< *

this

);

TInst_Mol GetInst_Mol(void) const

vector< CSeq_id_Handle > TId

TTaxId GetTaxId(void) const

const TId & GetId(void) const

TSeqPos GetBioseqLength(void) const

Blob state exceptions, used by GenBank loader.

Data loader exceptions, used by GenBank loader.

iterator_bool insert(const value_type &val)

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

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.

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

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

string GetLabel(const CSeq_id &id)

virtual int GetSequenceState(const CSeq_id_Handle &idh)

Request for a state of a sequence.

virtual CObjectManager::TPriority GetDefaultPriority(void) const

virtual void GetSequenceHashes(const TIds &ids, TLoaded &loaded, TSequenceHashes &ret, THashKnown &known)

Bulk request for hashes of a set of sequences.

void SetName(const string &loader_name)

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

old Get*AnnotRecords() methods

CRef< IEditSaver > TEditSaver

virtual SRequestDetails ChoiceToDetails(EChoice choice) const

void SetTargetDataSource(CDataSource &data_source)

Specify datasource to send loaded data to.

virtual ~CDataLoader(void)

vector< TSeqPos > TSequenceLengths

virtual int GetSequenceHash(const CSeq_id_Handle &idh)

Request for a sequence hash.

virtual EChoice DetailsToChoice(const SRequestDetails::TAnnotSet &annots) const

vector< CTSE_Lock > TCDD_Locks

vector< CSeq_id_Handle > TIds

virtual TTSE_LockSet GetOrphanAnnotRecordsNA(const CSeq_id_Handle &idh, const SAnnotSelector *sel, TProcessedNAs *processed_nas)

new Get*AnnotRecords() methods

TBlobState GetBlobState(void)

virtual TBlobId GetBlobIdFromString(const string &str) const

static void SetProcessedNA(const string &na, TProcessedNAs *processed_nas)

vector< bool > THashKnown

string GetName(void) const

CDataSource * GetDataSource(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.

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

Bulk request for taxonomy ids of a set of sequences.

virtual void GetBulkIds(const TIds &ids, TLoaded &loaded, TBulkIds &ret)

Bulk request for all Seq-ids of a set of sequences.

virtual bool CanGetBlobById(void) const

virtual TTSE_Lock GetBlobById(const TBlobId &blob_id)

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

Request for a list of all Seq-ids of a sequence.

EChoice

main blob is blob with sequence all other blobs are external and contain external annotations

TTSE_LockSet GetRecordsNoBlobState(const CSeq_id_Handle &idh, EChoice choice)

The same as GetRecords() but always returns empty TSE lock set instead of throwing CBlobStateExceptio...

virtual TGi GetGi(const CSeq_id_Handle &idh)

Request for a gi of a sequence.

static bool IsRequestedAnyNA(const SAnnotSelector *sel)

vector< CSeq_inst::TMol > TSequenceTypes

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_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 wi...

vector< vector< CSeq_id_Handle > > TSeqIdSets

static bool IsRequestedNA(const string &na, const SAnnotSelector *sel)

virtual bool operator==(const CBlobId &id) const

virtual TTaxId GetTaxId(const CSeq_id_Handle &idh)

Request for a taxonomy id of a sequence.

virtual string GetLabel(const CSeq_id_Handle &idh)

Request for a label string of a sequence.

bool SequenceExists(const CSeq_id_Handle &idh)

helper function to check if sequence exists, uses GetIds()

virtual double EstimateLoadSeconds(const CTSE_Chunk_Info &chunk, Uint4 bytes) const

virtual CSeq_id_Handle GetAccVer(const CSeq_id_Handle &idh)

Request for a accession.version Seq-id of a sequence.

static bool IsProcessedNA(const string &na, const TProcessedNAs *processed_nas)

virtual STypeFound GetSequenceTypeFound(const CSeq_id_Handle &idh)

static CSeq_id_Handle x_GetAccVer(const TIds &ids)

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

Bulk request for types of a set of sequences.

virtual void GetCDDAnnots(const TSeqIdSets &id_sets, TLoaded &loaded, TCDD_Locks &ret)

virtual void GetBlobs(TTSE_LockSets &tse_sets)

virtual SAccVerFound GetAccVerFound(const CSeq_id_Handle &idh)

virtual Uint4 EstimateLoadBytes(const CTSE_Chunk_Info &chunk) const

virtual TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)

Request for a length of a sequence.

vector< bool > TLoaded

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

virtual SHashFound GetSequenceHashFound(const CSeq_id_Handle &idh)

virtual SGiFound GetGiFound(const CSeq_id_Handle &idh)

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

Bulk request for lengths of a set of sequences.

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

virtual void DropTSE(CRef< CTSE_Info > tse_info)

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

Bulk request for gis of a set of sequences.

static TGi x_GetGi(const TIds &ids)

TAnnotBlobType m_AnnotBlobType

virtual TTSE_LockSet GetExternalAnnotRecordsNA(const CSeq_id_Handle &idh, const SAnnotSelector *sel, TProcessedNAs *processed_nas)

virtual void GetLabels(const TIds &ids, TLoaded &loaded, TLabels &ret)

Bulk request for label strings of a set of sequences.

virtual TBlobVersion GetBlobVersion(const TBlobId &id)

virtual void GetChunks(const TChunkSet &chunks)

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.

virtual bool GetTrackSplitSeq() const

virtual TEditSaver GetEditSaver() const

virtual unsigned GetDefaultBlobCacheSizeLimit() const

virtual void GetSequenceStates(const TIds &ids, TLoaded &loaded, TSequenceStates &ret)

Bulk request for states of a set of sequences.

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

Bulk request for accession.version Seq-ids of a set of sequences.

virtual TTSE_LockSet GetExternalRecords(const CBioseq_Info &bioseq)

Request from a datasource set of blobs with external annotations.

vector< int > TSequenceStates

vector< int > TSequenceHashes

vector< TChunk > TChunkSet

virtual void GetChunk(TChunk chunk_info)

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh)

CDataSource * m_DataSource

bool LessByTypeId(const CBlobId &id2) const

set< TTSE_Lock > TTSE_LockSet

@ kPriority_Loader

Default priority for main loaders.

@ 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

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

bool IsIncludedAnyNamedAnnotAccession(void) const

check if any named annot accession is included in the search

bool IsIncludedNamedAnnotAccession(const string &acc) const

check if named annot accession is included in the search

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to look for.

uint32_t Uint4

4-byte (32-bit) unsigned integer

static TThisType GetWhole(void)

#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 void PtrToString(string &out_str, const void *ptr)

Convert pointer to string.

static const char label[]

E_Choice

Choice variants.

EMol

molecule class in living organism

@ e_not_set

No variant selected.

@ eMol_not_set

> cdna = rna

constexpr bool empty(list< Ts... >) noexcept

CRef< objects::CObjectManager > om

Better replacement of GetAccVer(), this method should be defined in data loaders, GetAccVer() is left...

Better replacement of GetGi(), this method should be defined in data loaders, GetGi() is left for com...

Better replacement of GetSequenceHash(), this method should be defined in data loaders,...

Better replacement of GetSequenceType(), this method should be defined in data loaders,...

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