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.
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)