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NCBI C++ ToolKit: src/app/table2asn/table2asn_validator.cpp Source File

pItem->SetErrIndex(ec);

lock_guard<mutex> lock(

);

sev = item.GetSev();

unique_lock<mutex> lock(

);

.wait(lock, [

]() ->

{

* big_separator =

;

(

.empty()) {

(

.find(

) != string::npos) {

(

.find(

) != string::npos) {

}

(

.find(

) != string::npos) {

(

.find(

) != string::npos) {

.ExtendedCleanup(*submit, cleanupflags);

(

.find(

) != string::npos) {

(

.find(

) != string::npos) {

(

.find(

) != string::npos) {

validator::CTaxValidationAndCleanup tval(

->m_taxon_update);

tval.DoTaxonomyUpdate(h_entry,

);

std::lock_guard<std::mutex>

{

};

unneeded_version;

options |= validator::CValidator::eVal_genome_submission;

(pSubmit.

()) {

validator.Validate(top_se, options, msgHandler);

validator.Validate(*pSubmit, &scope, options, msgHandler);

std::lock_guard<std::mutex>

{

};

& entryInfo = validator.GetEntryInfo();

std::lock_guard<std::mutex>

{

};

options |= validator::CValidator::eVal_genome_submission;

(submit.

()) {

errors = validator.Validate(top_se, options);

errors = validator.Validate(*submit, &scope, options);

std::lock_guard<std::mutex>

{

};

& entryInfo = validator.GetEntryInfo();

std::lock_guard<std::mutex>

{

};

std::lock_guard<std::mutex>

{

};

(

& it : errors->GetErrs()) {

std::lock_guard<std::mutex>

(

);

<< big_separator <<

;

(

sev = 0; sev <

.size(); ++sev) {

(

[sev].total > 0) {

(

indivEntry :

[sev].individual) {

<< big_separator <<

;

<< big_separator <<

;

std::lock_guard<std::mutex>

(

);

(

sev = 0; sev <

.size(); sev++) {

out << CValidErrItem::ConvertErrGroup(it.first) <<

<< CValidErrItem::ConvertErrCode(it.first) <<

<< NStr::NumericToString(it.second) <<

;

<< big_separator <<

;

obj = entry.GetCompleteSeq_entry();

product = discrepancy->RunTests(

, *obj, nm.

());

output_flags = NDiscrepancy::CDiscrepancySet::eOutput_Files;

output_flags |= NDiscrepancy::CDiscrepancySet::eOutput_Fatal;

product->Summarize();

product->OutputText(ostr, output_flags);

ostr.exceptions(ios::failbit | ios::badbit);

& EC = feat.

().SetProt().SetEc();

it = EC.begin();

(it != EC.end()) {

xGetLabel(feat,

);

xGetLabel(feat,

);

is_split = newvalue.find(

) != string::npos;

<< *it <<

<< newvalue <<

;

xGetLabel(feat,

);

feat.

().SetProt().ResetEc();

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eErr_SEQ_DESCR_InconsistentBioSources_ConLocation

@ eErr_GENERIC_MissingPubRequirement

@ eErr_SEQ_DESCR_NoOrgFound

@ eErr_SEQ_DESCR_TransgenicProblem

@ eErr_SEQ_DESCR_NoPubFound

@ eErr_SEQ_INST_MitoMetazoanTooLong

@ eErr_SEQ_DESCR_NoSourceDescriptor

User-defined methods of the data storage class.

static bool AddProteinTitle(CBioseq_Handle bsh)

Creates missing protein title descriptor.

static bool WGSCleanup(CSeq_entry_Handle entry, bool instantiate_missing_proteins=true, Uint4 options=0, bool run_extended_cleanup=true, bool also_fix_location=true)

Performs WGS specific cleanup.

static bool AddLowQualityException(CSeq_entry_Handle entry)

For table2asn -c s Adds an exception of "low-quality sequence region" to coding regions and mRNAs tha...

TChanges ExtendedCleanup(CSeq_entry &se, Uint4 options=0)

Cleanup a Seq-entry.

@ eClean_KeepSingleSeqSet

@ eClean_NoNcbiUserObjects

static bool CleanupCollectionDates(CSeq_entry_Handle seh, bool month_first)

static const string & GetECNumberReplacement(const string &old_ecno)

Return a replaced EC number's replacement.

@ eEC_replaced

Obsolete synonym for some other EC number.

@ eEC_unknown

Unrecognized; possibly malformed.

@ eEC_deleted

Withdrawn, with no (single?) replacement.

static EECNumberStatus GetECNumberStatus(const string &ecno)

Determine an EC number's validity and specificity.

namespace ncbi::objects::

Base class for all serializable objects.

unique_ptr< objects::edit::CRemoteUpdater > m_remote_updater

string m_master_genome_flag

NDiscrepancy::EGroup m_discrepancy_group

string GenerateOutputFilename(eFiles kind, string_view basename=kEmptyStr) const

std::ostream & GetOstream(eFiles suffix)

unique_ptr< objects::CFixSuspectProductName > m_suspect_rules

std::list< CRef< objects::CValidError > > m_val_errors

void x_ReportDiscrepancies(TDiscProdRef &discrepancy, std::ostream &ostr) const

void UpdateECNumbers(objects::CSeq_entry &entry)

std::shared_ptr< objects::validator::SValidatorContext > m_val_context

void Cleanup(CRef< objects::CSeq_submit > submit, objects::CSeq_entry_Handle &entry, const string &flags) const

TDiscProdRef m_discr_product

std::mutex m_discrep_mutex

void ValReportErrorStats(CNcbiOstream &out)

void CollectDiscrepancies(CRef< objects::CSeq_submit > submit, objects::CSeq_entry_Handle &entry)

size_t ValTotalErrors() const

CTable2AsnContext * m_context

void ValCollect(CRef< objects::CSeq_submit > submit, CRef< objects::CSeq_entry > entry, const string &flags)

void ReportDiscrepancies()

void Validate(CRef< objects::CSeq_submit > pSubmit, CRef< objects::CSeq_entry > pEntry, CValidMessageHandler &msgHandler)

TGlobalInfo m_val_globalInfo

CTable2AsnValidator(CTable2AsnContext &ctx)

TDiscProdRef x_PopulateDiscrepancy(CRef< objects::CSeq_submit > submit, objects::CSeq_entry_Handle &entry) const

CUpdateECNumbers(CTable2AsnContext &context)

void operator()(CSeq_feat &feat)

CTable2AsnContext & m_Context

static const string & ConvertSeverity(EDiagSev sev)

static const string & ConvertErrCode(unsigned int)

const string GetErrCode() const

const string GetErrGroup() const

static const string & ConvertErrGroup(unsigned int)

const TPostponed & GetPostponed() const

void x_AddItemAsync(CRef< objects::CValidErrItem > pItem)

list< CRef< objects::CValidErrItem > > TPostponed

TPostponed m_PostponedItems

void AddValidErrItem(EDiagSev sev, unsigned int ec, const string &msg, const string &desc, const CSerialObject &obj, const string &acc, const int ver, const string &location=kEmptyStr, const int seq_offset=0) override

void x_LogStats(const objects::CValidErrItem &item)

TValStats m_ProcessedStats

queue< CRef< objects::CValidErrItem > > m_Items

container_type::value_type value_type

TTestNamesSet GetDiscrepancyTests(TGroup group)

std::ofstream out("events_result.xml")

main entry point for tests

static void cleanup(void)

static const struct name_t names[]

static const char location[]

EDiagSev

Severity level for the posted diagnostics.

string GetName(void) const

Get the base entry name with extension (if any).

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

@ eFasta

Tagged ID in NCBI's traditional FASTA style.

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

CObjectManager & GetObjectManager(void)

Get object manager controlling this scope.

CScope & GetScope(void) const

Get scope this handle belongs to.

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 Empty(void) const THROWS_NONE

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

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

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

Check if a string starts with a specified prefix value.

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 & ToUpper(string &str)

Convert string to upper case – string& version.

static const char label[]

bool IsSetEc(void) const

E.C.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

bool IsProt(void) const

Check if variant Prot is selected.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TProt & GetProt(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

@ eMol_na

just a nucleic acid

const TEntrys & GetEntrys(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TObjDesc & GetObjDesc(void) const

Get the ObjDesc member data.

TSev GetSev(void) const

Get the Sev member data.

const TMsg & GetMsg(void) const

Get the Msg member data.

TErrIndex GetErrIndex(void) const

Get the ErrIndex member data.

void g_PostprocessErrors(const CHugeFileValidator::TGlobalInfo &globalInfo, const string &genbankSetId, CRef< CValidError > &pErrors)

bool ExtendPartialFeatureEnds(CBioseq_Handle bsh)

void VisitAllFeatures(objects::CSeq_entry_EditHandle &entry_h, _M m)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static bool s_PostponeItem(const CValidErrItem &item)

void g_FormatErrItem(const CValidErrItem &item, CNcbiOstream &ostr)

void g_FormatValStats(const TValStats &stats, size_t total, CNcbiOstream &ostr)

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

static CS_CONTEXT * context

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