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NCBI C++ ToolKit: src/gui/objutils/gencoll_svc.cpp Source File

assm_acc +

+

;

isUseSeqconfigService)

(isUseSeqconfigService) {

perflog.

(

,

);

host =

;

path =

;

url =

+ host + path +

+ params;

(res && res->CanGetAssemblies() && !res->GetAssemblies().empty()) {

gc_assembly = res->GetAssemblies().front();

perflog.

(

,

);

}

(

);

isError(

);

gc_assembly = gencoll_service->GetAssembly(assm_acc,

);

perflog.

(

,

);

(

!= errors)

(

exception& e) {

(

!= errors)

perflog.

(

,

);

(gc_assembly && gc_assembly->

() != assm_acc) {

sGuessTimeout(reg.GetString(

,

,

));

timeout.

= timeout_sec >= 0 ? (unsigned)timeout_sec : (timeout_sec_reg ? timeout_sec_reg : 5);

gencoll_service->SetTimeout(&timeout);

retries = reg.GetInt(

,

, 1);

gencoll_service->SetTryLimit((

)retries);

gencoll_service;

text_id = handle.GetInitialSeqIdOrNull().IsNull() ?

: handle.GetInitialSeqIdOrNull()->GetSeqIdString();

(tmol == CBioseq_Handle::TMol::eMol_rna || tmol == CBioseq_Handle::TMol::eMol_aa) {

perflog.

(

,

);

AssmAccs = iCacheHit->second;

(reply && reply->CanGetAssemblies()) {

(

: reply->GetAssemblies()) {

(

->CanGetAssembly()) {

AssmAccs.push_back(

->GetAssembly().GetAccession());

(

<<

<< seqAcc);

perflog.

(

,

);

(

&iAssmAccs: assm_accs) {

sAssmAcc = iAssmAccs;

(assembly.NotNull()) {

assemblies.push_back(assembly);

(

<<

<< sAssmAcc);

(

<<

<< sAssmAcc <<

<< e.

());

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

string GetAccession() const

Retrieve the accession for this assembly.

static void GetAssmsInfo(const TAssmAccs &assm_accs, const string &mode, TAssemblies &assemblies, IGencollSvcErrors *errors=nullptr)

query GenColl for assembly information, return list of assemblies mode is as described above for GetG...

map< string, CRef< objects::CGC_Assembly > > m_GC_Assembly_cache

mutex to sync our internals

CRef< objects::CGC_Assembly > GetGCAssembly(const string &assm_acc, bool use_caching, const string &mode, IGencollSvcErrors *errors=nullptr, bool isUseSeqconfigService=false)

static bool isGenCollSequence(const objects::CBioseq_Handle &handle)

static CRef< CGencollSvc > GetInstance(void)

static CRef< objects::CGenomicCollectionsService > GetGenCollService(int timeout_sec=-1)

static TSeqAccToAssmAccsCache sm_SeqAccToAssmAccsCache

EGencollSvcStatus GetAssmAccs(const objects::CBioseq_Handle &handle, objects::EGCClient_GetAssemblyBySequenceFilter filter, bool isOne, TAssmAccs &AssmAccs)

get all assembly accessions for a given sequence and filter if isOne == 1, return only the best one a...

list< CRef< objects::CGC_Assembly > > TAssemblies

CNcbiIstream & GetResponseStream()

void AddParameter(const std::string &name, const std::string &value)

void Post(CRequestStatus::ECode status=CRequestStatus::e200_Ok)

static CNcbiApplication * Instance(void)

Singleton method.

CObjectIStreamAsnBinary –.

virtual void ReportError(const string &accession, const string &error)=0

const_iterator end() const

const_iterator find(const key_type &key) const

static string s_MakeCacheKey(const string &assm_acc, const string &mode)

DEFINE_CLASS_STATIC_FAST_MUTEX(CGencollSvc::sm_SeqAccToAssmAccsCacheMutex)

const CNcbiRegistry & GetConfig(void) const

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

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

#define NCBI_CATCH(message)

Catch CExceptions as well This macro is deprecated - use *_X or *_XX variant instead of it.

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

EAccessionInfo

For IdentifyAccession (below)

@ eContent

Untagged human-readable accession or the like.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

bool NotNull(void) const THROWS_NONE

Check if pointer is not null – same effect as NotEmpty().

CRef< C > Ref(C *object)

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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 enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static string URLEncode(const CTempString str, EUrlEncode flag=eUrlEnc_SkipMarkChars)

URL-encode string.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ eNocase

Case insensitive compare.

unsigned int usec

microseconds (modulo 1,000,000)

const TAccession & GetAccession(void) const

Get the Accession member data.

bool CanGetAccession(void) const

Check if it is safe to call GetAccession method.

EGCClient_GetAssemblyBySequenceFilter

This is a bitfield. All values are powers of two.

EMol

molecule class in living organism

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

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