table2asn_validator.hpp

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#ifndef TABLE2ASN_VALIDATOR_HPP_INCLUDED
#define TABLE2ASN_VALIDATOR_HPP_INCLUDED
 
#include <objtools/validator/validator_context.hpp>
#include <objtools/validator/huge_file_validator.hpp>
 
#include "utils.hpp"
 
BEGIN_NCBI_SCOPE
 
namespace objects
{
    class CSeq_entry;
    class CBioseq;
    class CSeq_entry_Handle;
    class CValidError;
    class CSeq_submit;
    class CScope;
}
namespace NDiscrepancy
{
    class CDiscrepancySet;
    class CDiscrepancyProduct;
}
 
class CTable2AsnContext;
class CTable2AsnValidator: public CObject
{
public:
    CTable2AsnValidator(CTable2AsnContext& ctx);
    ~CTable2AsnValidator();
 
    void Clear();
    void ValCollect(CRef<objects::CSeq_submit> submit, CRef<objects::CSeq_entry> entry, const string& flags);
    void ValReportErrorStats(CNcbiOstream& out);
    void ValReportErrors();
    size_t ValTotalErrors() const;
 
    void Cleanup(CRef<objects::CSeq_submit> submit, objects::CSeq_entry_Handle& entry, const string& flags) const;
    void UpdateECNumbers(objects::CSeq_entry& entry);
 
    void CollectDiscrepancies(CRef<objects::CSeq_submit> submit, objects::CSeq_entry_Handle& entry);
    void ReportDiscrepancies();
    void ReportDiscrepancies(const string& filename);
 
protected:
    CRef<NDiscrepancy::CDiscrepancyProduct> x_PopulateDiscrepancy(CRef<objects::CSeq_submit> submit, objects::CSeq_entry_Handle& entry) const;
    void x_ReportDiscrepancies(CRef<NDiscrepancy::CDiscrepancyProduct>& discrepancy, std::ostream& ostr) const;
    typedef map<int, size_t> TErrorStatMap;
    class TErrorStats
    {
    public:
        TErrorStats() : m_total(0) {};
        TErrorStatMap m_individual;
        size_t m_total;
    };
    CTable2AsnContext*     m_context;
 
    std::mutex  m_discrep_mutex;
    CRef<NDiscrepancy::CDiscrepancyProduct>                m_discr_product;
 
    std::shared_ptr<objects::validator::SValidatorContext> m_val_context;
    vector<TErrorStats>                                    m_val_stats;
    std::list<CRef<objects::CValidError>>                  m_val_errors;
    objects::validator::CHugeFileValidator::TGlobalInfo    m_val_globalInfo;
    mutable std::mutex m_mutex;
};
 
END_NCBI_SCOPE
 
#endif