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

1 #ifndef TABLE2ASN_VALIDATOR_HPP_INCLUDED 2 #define TABLE2ASN_VALIDATOR_HPP_INCLUDED 13 #include <condition_variable> 61 const int

seq_offset = 0)

override

;

71 const int

seq_offset = 0)

override

;

78 const

objects::CSeqdesc& seqdesc,

79 const

objects::CSeq_entry&

ctx

82 const int

seq_offset = 0)

override

;

87 const string

msg

)

override

;

99 void x_LogStats

(

const

objects::CValidErrItem& item);

138 using TGlobalInfo

= objects::validator::CHugeFileValidator::TGlobalInfo;

147

objects::CSeq_entry_Handle& entry)

const

;

User-defined methods of the data storage class.

Base class for all serializable objects.

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

const TGlobalInfo & GetGlobalInfo()

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

objects::validator::SValidatorContext TValidatorContext

std::mutex m_discrep_mutex

objects::validator::CHugeFileValidator::TGlobalInfo TGlobalInfo

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)

shared_ptr< TValidatorContext > GetContextPtr()

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

const TValStats & GetStats()

CValidMessageHandler(CNcbiOstream &ostr, EMode mode=EMode::Asynchronous)

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)

virtual ~CValidMessageHandler()=default

TValStats m_ProcessedStats

void AddValidErrItem(EDiagSev sev, unsigned int ec, const string &msg, const string &desc, const objects::CSeqdesc &seqdesc, const objects::CSeq_entry &ctx, const string &acc, const int ver, const int seq_offset=0) override

void AddValidErrItem(CRef< objects::CValidErrItem > pItem) override

queue< CRef< objects::CValidErrItem > > m_Items

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

main entry point for tests

static const char location[]

EDiagSev

Severity level for the posted diagnostics.

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

map< int, size_t > individual

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

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

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