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/gbnative_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/data_loaders/genbank/gbnative.cpp Source File

44 #define REGISTER_READER_ENTRY_POINTS 1 45 #ifdef REGISTER_READER_ENTRY_POINTS 72 #define NCBI_USE_ERRCODE_X Objtools_GBLoader 96 #if defined(HAVE_PUBSEQ_OS) 103 #define GBLOADER_NAME "GBLOADER" 104 #define GBLOADER_HUP_NAME "GBLOADER-HUP" 106 #define DEFAULT_ID_GC_SIZE 10000 107 #define DEFAULT_ID_EXPIRATION_TIMEOUT 2*3600 178 return dynamic_cast<const CBlob_id

>

(*blob_id);

184

unique_ptr<TParamTree> app_params;

201 if

( !param.empty() ) {

213 if

( !param.empty() ) {

215 Uint4

timeout = NStr::StringToNumeric<Uint4>(param);

222 "Bad value of parameter " 224 ": \""

<<param<<

"\""

);

232 if

( !param.empty() ) {

238 "Bad value of parameter " 240 ": \""

<<param<<

"\""

);

248 if

( !param.empty() ) {

254 "Bad value of parameter " 256 ": \""

<<param<<

"\""

);

264 if

( !param.empty() ) {

270 "Bad value of parameter " 272 ": \""

<<param<<

"\""

);

280 if

( !param.empty() ) {

292 "Bad value of parameter " 294 ": \""

<<param<<

"\""

);

316 if

( !param.empty() ) {

339 if

( reader_name ==

"cache"

357

pair<string, string> ret;

364 if

( ret.first.empty() ) {

365

ret.first = TGenbankReaderName::GetDefault();

368 if

(ret.second.empty()) {

371 if

( ret.second.empty() ) {

372

ret.second = TGenbankWriterName::GetDefault();

374 if

( ret.first.empty() || ret.second.empty() ) {

376 if

( method.empty() ) {

379 if

( method.empty() ) {

384 if

( ret.first.empty() ) {

388

ret.second =

"cache"

;

402

vector<string> str_list;

404 size_t

reader_count = 0;

405 for

(

size_t i

= 0;

< str_list.size(); ++

) {

418 if

( !reader_count ) {

420 "no reader available from "

str

);

422 return

reader_count > 1 || str_list.size() > 1;

429

vector<string> str_list;

431 for

(

size_t i

= 0;

< str_list.size(); ++

) {

434 "HUP GBLoader cannot have cache"

);

444 #ifdef REGISTER_READER_ENTRY_POINTS 455 #ifdef REGISTER_READER_ENTRY_POINTS 460 # ifdef HAVE_PUBSEQ_OS 475 #ifdef REGISTER_READER_ENTRY_POINTS 487 return

!name.empty() && name[name.size()-1] !=

':'

;

496 CReader

* ret = manager->CreateInstanceFromList(params, name);

501 "no reader available from "

+name);

520 CWriter

* ret = manager->CreateInstanceFromList(params, name);

525 "no writer available from "

+name);

540

blob_id->SetSat(sat);

541

blob_id->SetSatKey(sat_key);

542

blob_id->SetSubSat(sub_sat);

558 return TBlobId

(it->GetBlob_id().GetPointer());

577 if

( !lock.IsLoaded() ) {

617

ret = lock.

GetGi

();

667 return

loaded[0]? states[0]: kNotFound;

673 for

(

size_t i

= 0;

< ids.size(); ++

) {

686 for

(

size_t i

= 0;

< ids.size(); ++

) {

699 for

(

size_t i

= 0;

< ids.size(); ++

) {

712 for

(

size_t i

= 0;

< ids.size(); ++

) {

725 for

(

size_t i

= 0;

< ids.size(); ++

) {

735 for

(

size_t i

= 0;

< ids.size(); ++

) {

737

loaded[

] =

false

;

764 return

lock.IsLoaded()? lock.

GetLength

(): 0;

771 for

(

size_t i

= 0;

< ids.size(); ++

) {

804 for

(

size_t i

= 0;

< ids.size(); ++

) {

822 for

(

size_t i

= 0;

< ids.size(); ++

) {

881 for

(

size_t i

= 0;

< ids.size(); ++

) {

909 bool

conflict=

false

;

927

best = *sit; conflict=

false

;

930

best = *sit; conflict=

false

;

977 if

( !best || conflict ) {

978 _TRACE

(

"CGBDataLoader::ResolveConflict("

<<handle.

AsString

()<<

"): " 988 if

((it->m_Type & cache_type) != 0) {

997

time_t access_timeout)

1000 if

((it->m_Type & cache_type) != 0) {

1001

it->m_Cache->Purge(access_timeout);

1102 mask

|= (annots << 1);

1105 mask

|= (annots << 2);

1153 if

( id1.

IsGi

() ) {

1187 int

score1 = GetScore(id1);

1188 int

score2 = GetScore(id2);

1189 if

( score1 != score2 ) {

1190 return

score1 > score2;

1203 sort

(ids.begin(), ids.end(), SBetterId());

1236 sort

(ids.begin(), ids.end(), SBetterId());

1259 bool

load_namedacc =

1261 if

( load_external || load_namedacc ) {

1263 if

( load_external ) {

1266 if

( load_namedacc ) {

1297 if

( !blobs.IsLoaded() ) {

1311 "blob state error for "

+sih.

AsString

(),

1318 if

(

info

.Matches(

mask

, sel) ) {

1327 "blob state error for "

+blob_id.

ToString

(),

1330 if

( processed_nas ) {

1331 if

(

auto

annot_info =

info

.GetAnnotInfo() ) {

1332 for

(

auto

& acc : annot_info->GetNamedAnnotNames() ) {

1340 result

.SaveLocksTo(locks);

1364 "blob state error for "

+sih.

AsString

(),

1370 if

( !

info

.IsSetAnnotInfo() ) {

1385 const string

& named_acc)

1408 "blob state error for "

+sih.

AsString

(),

1414 if

( !

info

.IsSetAnnotInfo() ) {

1446 for

(

auto

& it : chunks ) {

1447 auto

chunk_id = it->GetChunkId();

1452

chunks_to_load[

GetRealBlobId

(it->GetBlobId())].push_back(chunk_id);

1456

chunks_to_load.

end

());

1472

ids.push_back(

id

);

1520 if

( annot_info->IsSetName() &&

1538 if

( !core->IsSet() ) {

1542 auto

& seqset = core->

GetSet

();

1543 return

seqset.

GetSeq_set

().empty() && seqset.GetAnnot().empty();

1551

vector<CSeq_id_Handle> best_ids;

1554 for

(

auto

& id_set : id_sets) {

1555

SBetterId score_func;

1557 int

best_score = -1;

1558 for

(

auto

id

: id_set ) {

1562 int

score = score_func.GetScore(

id

);

1563 if

( score > best_score ) {

1568

best_ids.push_back(best_id);

1570

ids.push_back(best_id);

1573 if

( ids.empty() ) {

1581 for

(

auto

id

: best_ids ) {

1595

blobs_to_load.push_back(

info

);

1599 if

( !blobs_to_load.empty() ) {

1608 for

(

auto

id

: best_ids ) {

1624

chunks_to_load.push_back(make_pair(blob_id, main_chunk));

1628 if

( !chunks_to_load.empty() ) {

1633 for

(

size_t i

= 0;

< id_sets.size(); ++

) {

1634 auto

id

= best_ids[

];

1651

loaded[

] =

true

;

1665

(&x), calibrating(x.NeedCalibration())

1667 if

( calibrating ) {

1671

~CTimerGuard(

void

)

1673 if

( calibrating ) {

1692

loader->GetDispatcher(),

1693

loader->GetInfoManager()),

1791 if

((it->m_Type & cache_type) == 0) {

1794 if

( it->m_Cache->SameCacheParams(params) ) {

1795 return

it->m_Cache.get();

ncbi::TMaskedQueryRegions mask

const TId & GetId(void) const

Blob state exceptions, used by GenBank loader.

const TAnnotInfo & GetAnnotInfo(void) const

const TNamedAnnotNames & GetNamedAnnotNames(void) const

const CConstRef< CBlob_Annot_Info > & GetAnnotInfo(void) const

bool IsSetAnnotInfo(void) const

bool Matches(TContentsMask mask, const SAnnotSelector *sel) const

static CBlob_id * CreateFromString(const string &str)

string ToString(void) const

Get string representation of blob id.

CTSE_LoadLock GetTSE_LoadLock(const TBlobId &blob_id)

CTSE_LoadLock GetTSE_LoadLockIfLoaded(const TBlobId &blob_id)

vector< TBlobId > TLoadedBlob_ids

void GetLoadedBlob_ids(const CSeq_id_Handle &idh, TLoadedTypes types, TLoadedBlob_ids &blob_ids) const

TState GetState(void) const

TRegisterInfo GetRegisterInfo(void)

virtual void GetChunk(TChunk chunk) override

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

Request from a datasource using handles and ranges instead of seq-loc The TSEs loaded in this call wi...

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

static CRef< TReaderManager > x_GetReaderManager(void)

TBlobContentsMask x_MakeContentMask(EChoice choice) const

CReader * x_CreateReader(const string &names, const CGBLoaderParams &gb_params, const TParamTree *params=0)

CGBDataLoader_Native(const string &loader_name, const CGBLoaderParams &params)

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

virtual TBlobVersion GetBlobVersion(const TBlobId &id) override

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

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

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

virtual void GC(void) override

virtual TTSE_LockSet GetDetailedRecords(const CSeq_id_Handle &idh, const SRequestDetails &details) override

Request from a datasource using handles and ranges instead of seq-loc The TSEs loaded in this call wi...

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

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

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

virtual void DropTSE(CRef< CTSE_Info > tse_info) override

virtual TTSE_Lock ResolveConflict(const CSeq_id_Handle &handle, const TTSE_LockSet &tse_set) override

Resolve TSE conflict *select the best TSE from the set of dead TSEs.

virtual bool CanGetBlobById(void) const override

virtual TSeqPos GetSequenceLength(const CSeq_id_Handle &sih) override

Request for a length of a sequence.

virtual void GetChunks(const TChunkSet &chunks) override

virtual TNamedAnnotNames GetNamedAnnotAccessions(const CSeq_id_Handle &idh) override

CRef< CGBInfoManager > m_InfoManager

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const CGBLoaderParams &params, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

void x_CreateDriver(const CGBLoaderParams &params)

void PurgeCache(TCacheType cache_type, time_t access_timeout=0) override

CInitMutexPool m_MutexPool

CWriter * x_CreateWriter(const string &names, const TParamTree *params=0)

static CRef< TWriterManager > x_GetWriterManager(void)

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

void x_CreateWriters(const string &str, const TParamTree *params)

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

new Get*AnnotRecords() methods

virtual int GetSequenceState(const CSeq_id_Handle &idh) override

Request for a state of a sequence.

CGBReaderCacheManager m_CacheManager

TTSE_LockSet x_GetRecords(const CSeq_id_Handle &idh, TBlobContentsMask sr_mask, const SAnnotSelector *sel, TProcessedNAs *processed_nas=0)

virtual STypeFound GetSequenceTypeFound(const CSeq_id_Handle &sih) override

virtual TTaxId GetTaxId(const CSeq_id_Handle &idh) override

Request for a taxonomy id of a sequence.

CRef< CReadDispatcher > m_Dispatcher

virtual SGiFound GetGiFound(const CSeq_id_Handle &idh) override

virtual TBlobId GetBlobIdFromString(const string &str) const override

void CloseCache(void) override

virtual TTSE_LockSet GetExternalRecords(const CBioseq_Info &bioseq) override

Request from a datasource set of blobs with external annotations.

virtual ~CGBDataLoader_Native(void)

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

virtual string GetLabel(const CSeq_id_Handle &idh) override

Request for a label string of a sequence.

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

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

virtual SHashFound GetSequenceHashFound(const CSeq_id_Handle &idh) override

virtual TBlobId GetBlobIdFromSatSatKey(int sat, int sat_key, int sub_sat) const override

virtual TTSE_Lock GetBlobById(const TBlobId &id) override

bool x_CreateReaders(const string &str, const TParamTree *params, const CGBLoaderParams &gb_params, CGBLoaderParams::EPreopenConnection preopen)

virtual SAccVerFound GetAccVerFound(const CSeq_id_Handle &idh) override

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh) override

virtual void GetBlobs(TTSE_LockSets &tse_sets) override

TRealBlobId x_GetRealBlobId(const TBlobId &blob_id) const override

pair< string, string > GetReaderWriterName(const TParamTree *params, const CGBLoaderParams &loader_params) const

bool HaveCache(TCacheType cache_type=fCache_Any) override

TExpirationTimeout m_IdExpirationTimeout

TRealBlobId GetRealBlobId(const TBlobId &blob_id) const

bool GetAddWGSMasterDescr(void) const

bool m_AlwaysLoadExternal

EGBErrorAction GetPTISErrorAction(void) const

bool HasHUPIncluded(void) const

static string x_GetLoaderMethod(const TParamTree *params)

TExpirationTimeout GetIdExpirationTimeout(void) const

static string GetParam(const TParamTree *params, const string &param_name)

EGBErrorAction m_PTISErrorAction

static TParamTree * GetLoaderParams(TParamTree *params)

bool m_AlwaysLoadNamedAcc

CReaderCacheManager::TCacheType TCacheType

const string & GetLoaderMethod(void) const

CReader * GetReaderPtr(void) const

EPreopenConnection GetPreopenConnection(void) const

const TParamTree * GetParamTree(void) const

CNullable< bool > m_EnableCDD

CNullable< bool > m_EnableSNP

const string & GetWebCookie(void) const

const string & GetWriterName(void) const

CNullable< bool > m_EnableWGS

const string & GetReaderName(void) const

virtual ICache * FindCache(ECacheType cache_type, const TCacheParams *params)

virtual TCaches & GetCaches(void)

virtual void RegisterCache(ICache &cache, ECacheType cache_type)

CReaderRequestResult TParent

CInitMutexPool & GetMutexPool(void)

virtual TExpirationTime GetIdExpirationTimeout(GBL::EExpirationType type) const override

virtual EGBErrorAction GetPTISErrorAction(void) const override

CGBDataLoader_Native & GetLoader(void)

CRef< CGBDataLoader_Native > m_Loader

virtual bool GetAddWGSMasterDescr(void) const override

~CGBReaderRequestResult(void)

virtual CTSE_LoadLock GetTSE_LoadLock(const TKeyBlob &blob_id) override

virtual CGBDataLoader_Native * GetLoaderPtr(void) override

virtual void GetLoadedBlob_ids(const CSeq_id_Handle &idh, TLoadedBlob_ids &blob_ids) const override

CGBReaderRequestResult(CGBDataLoader_Native *loader, const CSeq_id_Handle &requested_id)

virtual CTSE_LoadLock GetTSE_LoadLockIfLoaded(const TKeyBlob &blob_id) override

TData GetAccVer(void) const

bool IsLoadedAccVer(void) const

TData GetBlob_ids(void) const

bool IsLoadedBlobVersion(void) const

TData GetBlobVersion(void) const

bool IsLoadedBlob(void) const

CTSE_LoadLock & GetTSE_LoadLock(void)

bool IsLoadedGi(void) const

static TGi GetGi(const TData &data)

bool IsLoadedHash(void) const

static int GetHash(const TData &data)

bool IsLoadedLabel(void) const

TData GetLabel(void) const

TData GetLength(void) const

bool IsLoadedLength(void) const

TData GetSeq_ids(void) const

bool IsLoadedTaxId(void) const

TData GetTaxId(void) const

static CSeq_inst::TMol GetType(const TData &data)

bool IsLoadedType(void) const

Data loader exceptions, used by GenBank loader.

Base class for all object manager exceptions.

void LoadStates(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TStates &ret)

void LoadBlobSet(CReaderRequestResult &result, const TIds &seq_ids)

void LoadChunks(CReaderRequestResult &result, const TBlobId &blob_id, const TChunkIds &chunk_ids)

void LoadSeq_idLabel(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

void LoadGis(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TGis &ret)

void LoadBlobVersion(CReaderRequestResult &result, const TBlobId &blob_id, const CReader *asking_reader=0)

void InsertReader(TLevel level, CRef< CReader > reader)

void LoadBulkIds(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TBulkIds &ret)

CReader::TChunkIds TChunkIds

void LoadLabels(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TLabels &ret)

void LoadSeq_idGi(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

void InsertWriter(TLevel level, CRef< CWriter > writer)

void LoadSequenceType(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

void LoadAccVers(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TIds &ret)

void LoadSequenceHash(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

void LoadLengths(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TLengths &ret)

vector< pair< CBlob_id, TChunkIds > > TBlobChunkIds

void LoadTaxIds(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TTaxIds &ret)

void LoadHashes(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, THashes &ret, TKnown &known)

bool HasReaderWithHUPIncluded() const

void LoadTypes(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TTypes &ret)

void LoadSeq_idTaxId(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

vector< CBlob_Info > TBlobInfos

void LoadSeq_idSeq_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

vector< CSeq_id_Handle > TIds

void LoadBlobs(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, TContentsMask mask, const SAnnotSelector *sel)

void LoadSeq_idAccVer(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

void LoadSequenceLength(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

void LoadSeq_idBlob_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel)

void LoadChunk(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id)

void LoadBlob(CReaderRequestResult &result, const CBlob_id &blob_id)

static bool CannotProcess(const CSeq_id_Handle &sih)

vector< SReaderCacheInfo > TCaches

void SetEnableCDD(CNullable< bool > enable)

void SetEnableWGS(CNullable< bool > enable)

void SetEnableSNP(CNullable< bool > enable)

virtual TExpirationTime GetIdExpirationTimeout(GBL::EExpirationType type) const

vector< CBlob_id > TLoadedBlob_ids

GBL::CInfo_Base::TExpirationTime TExpirationTime

void OpenInitialConnection(bool force)

virtual void InitializeCache(CReaderCacheManager &cache_manager, const TPluginManagerParamTree *params)

virtual void SetIncludeHUP(bool include_hup=true, const string &web_cookie=NcbiEmptyString)

virtual void SetParams(const CReaderParams &params)

TBlobId GetBlobId(void) const

TChunkId GetChunkId(void) const

CConstRef< CSeq_entry > GetTSECore(void) const

TBlobState GetBlobState(void) const

bool x_NeedsDelayedMainChunk(void) const

definition of a Culling tree

static void LoadWGSMaster(CDataLoader *loader, CRef< CTSE_Chunk_Info > chunk)

virtual void InitializeCache(CReaderCacheManager &cache_manager, const TPluginManagerParamTree *params)

BLOB cache read/write/maintenance interface.

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

static const struct name_t names[]

static const char * str(char *buf, int n)

#define NCBI_GBLOADER_PARAM_PTIS_ERROR_ACTION

#define NCBI_GBLOADER_PARAM_ID_GC_SIZE

#define NCBI_GBLOADER_PARAM_ADD_WGS_MASTER

#define NCBI_GBLOADER_PARAM_PREOPEN

#define NCBI_GBLOADER_PARAM_READER_NAME

#define NCBI_GBLOADER_PARAM_ID_EXPIRATION_TIMEOUT

#define NCBI_GBLOADER_PARAM_WRITER_NAME

#define NCBI_GBLOADER_PARAM_PTIS_ERROR_ACTION_REPORT

#define NCBI_GBLOADER_PARAM_ALWAYS_LOAD_NAMED_ACC

#define NCBI_GBLOADER_PARAM_PTIS_ERROR_ACTION_IGNORE

#define NCBI_GBLOADER_PARAM_ALWAYS_LOAD_EXTERNAL

#define NCBI_GBLOADER_PARAM_PTIS_ERROR_ACTION_THROW

static bool x_IsCDDBlob(const CBlob_Info &blob_info)

static bool s_ForceDriver(const string &name)

static const char *const DEFAULT_HUP_DRV_ORDER

static const bool s_LoadBulkBlobs

static const char *const DEFAULT_DRV_ORDER

NCBI_PARAM_DECL(string, GENBANK, READER_NAME)

static bool x_IsEmptyCDD(const CTSE_Info &tse)

NCBI_PARAM_DEF_EX(string, GENBANK, READER_NAME, "", eParam_NoThread, GENBANK_READER_NAME)

#define DEFAULT_ID_GC_SIZE

#define DEFAULT_ID_EXPIRATION_TIMEOUT

typedef NCBI_PARAM_TYPE(GENBANK, READER_NAME) TGenbankReaderName

#define GBLOG_POST_X(err_subcode, x)

static CNcbiApplicationGuard InstanceGuard(void)

Singleton method.

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

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.

#define NCBI_RETHROW_FMT(prev_exception, exception_class, err_code, message)

The same as NCBI_RETHROW but with message processed as output to ostream.

#define NCBI_THROW(exception_class, err_code, message)

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

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

Throw exception with extra parameter.

#define NCBI_THROW_FMT(exception_class, err_code, message)

The same as NCBI_THROW but with message processed as output to ostream.

static TParamTree * ConvertRegToTree(const IRegistry &reg, NStr::ECase use_case=NStr::eNocase)

Reconstruct param tree from the application registry.

CConstRef< CSeq_id > GetSeqId(void) const

string AsString(void) const

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

vector< TSeqPos > TSequenceLengths

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

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

vector< bool > THashKnown

CDataSource * GetDataSource(void) const

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

Bulk request for taxonomy ids of a set of sequences.

EChoice

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

static bool IsRequestedAnyNA(const SAnnotSelector *sel)

vector< CSeq_inst::TMol > TSequenceTypes

vector< vector< CSeq_id_Handle > > TSeqIdSets

virtual TTaxId GetTaxId(const CSeq_id_Handle &idh)

Request for a taxonomy id of a sequence.

EIsDefault

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

vector< bool > TLoaded

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

TAnnotBlobType m_AnnotBlobType

static void RegisterInObjectManager(CObjectManager &om, CLoaderMaker_Base &loader_maker, CObjectManager::EIsDefault is_default, CObjectManager::TPriority priority)

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

Bulk request for states of a set of sequences.

vector< int > TSequenceStates

vector< int > TSequenceHashes

vector< TChunk > TChunkSet

@ 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

string CombineWithZoomLevel(const string &acc, int zoom_level)

Combine accession string and zoom level into a string with separator.

SAnnotSelector & IncludeNamedAnnotAccession(const string &acc, int zoom_level=0)

bool ExtractZoomLevel(const string &full_name, string *acc_ptr, int *zoom_level_ptr)

Extract optional zoom level suffix from named annotation string.

@ eParam_NoThread

Do not use per-thread values.

uint32_t Uint4

4-byte (32-bit) unsigned integer

bool NotEmpty(void) const

#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 bool StringToBool(const CTempString str)

Convert string to bool.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

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

Convert string to unsigned 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.

static string & ToLower(string &str)

Convert string to lower case â string& version.

bool IsSetAccession(void) const

Check if a value has been assigned to Accession data member.

bool IsGeneral(void) const

Check if variant General is selected.

bool IsLocal(void) const

Check if variant Local is selected.

bool IsSetVersion(void) const

Check if a value has been assigned to Version data member.

@ e_Gi

GenInfo Integrated Database.

const TSet & GetSet(void) const

Get the variant data.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

constexpr auto sort(_Init &&init)

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Multi-threading â classes, functions, and features.

Helper classes and templates to implement plugins.

const char kCDDAnnotName[]

void GenBankReaders_Register_Cache(void)

void GenBankWriters_Register_Cache(void)

void GenBankReaders_Register_Id1(void)

void GenBankReaders_Register_Id2(void)

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,...

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