Search Toolkit Book for CTable2AsnValidator
#include "table2asn_validator.hpp"
(Private to src/app/table2asn.)
Inheritance diagram for CTable2AsnValidator:
Collaboration diagram for CTable2AsnValidator:
Classes | |
| class | TErrorStats |
Public Member Functions | |
| 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) |
| Public Member Functions inherited from CObject | |
| CObject (void) | |
| Constructor. More... | |
| CObject (const CObject &src) | |
| Copy constructor. More... | |
| virtual | ~CObject (void) |
| Destructor. More... | |
| CObject & | operator= (const CObject &src) THROWS_NONE |
| Assignment operator. More... | |
| bool | CanBeDeleted (void) const THROWS_NONE |
| Check if object can be deleted. More... | |
| bool | IsAllocatedInPool (void) const THROWS_NONE |
| Check if object is allocated in memory pool (not system heap) More... | |
| bool | Referenced (void) const THROWS_NONE |
| Check if object is referenced. More... | |
| bool | ReferencedOnlyOnce (void) const THROWS_NONE |
| Check if object is referenced only once. More... | |
| void | AddReference (void) const |
| Add reference to object. More... | |
| void | RemoveReference (void) const |
| Remove reference to object. More... | |
| void | ReleaseReference (void) const |
| Remove reference without deleting object. More... | |
| virtual void | DoNotDeleteThisObject (void) |
| Mark this object as not allocated in heap – do not delete this object. More... | |
| virtual void | DoDeleteThisObject (void) |
| Mark this object as allocated in heap – object can be deleted. More... | |
| void * | operator new (size_t size) |
| Define new operator for memory allocation. More... | |
| void * | operator new[] (size_t size) |
| Define new[] operator for 'array' memory allocation. More... | |
| void | operator delete (void *ptr) |
| Define delete operator for memory deallocation. More... | |
| void | operator delete[] (void *ptr) |
| Define delete[] operator for memory deallocation. More... | |
| void * | operator new (size_t size, void *place) |
| Define new operator. More... | |
| void | operator delete (void *ptr, void *place) |
| Define delete operator. More... | |
| void * | operator new (size_t size, CObjectMemoryPool *place) |
| Define new operator using memory pool. More... | |
| void | operator delete (void *ptr, CObjectMemoryPool *place) |
| Define delete operator. More... | |
| virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. More... | |
| Public Member Functions inherited from CDebugDumpable | |
| CDebugDumpable (void) | |
| virtual | ~CDebugDumpable (void) |
| void | DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const |
| void | DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const |
| void | DumpToConsole (void) const |
Protected Types | |
| typedef map< int, size_t > | TErrorStatMap |
Protected Member Functions | |
| 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 |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
Protected Attributes | |
| 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 |
| std::mutex | m_mutex |
Additional Inherited Members | |
| Public Types inherited from CObject | |
| enum | EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } |
| Control filling of newly allocated memory. More... | |
| typedef CObjectCounterLocker | TLockerType |
| Default locker type for CRef. More... | |
| typedef atomic< Uint8 > | TCounter |
| Counter type is CAtomiCounter. More... | |
| typedef Uint8 | TCount |
| Alias for value type of counter. More... | |
| Static Public Member Functions inherited from CObject | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (void) |
| Define method to throw null pointer exception. More... | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (const type_info &type) |
| static EAllocFillMode | GetAllocFillMode (void) |
| static void | SetAllocFillMode (EAllocFillMode mode) |
| static void | SetAllocFillMode (const string &value) |
| Set mode from configuration parameter value. More... | |
| Static Public Member Functions inherited from CDebugDumpable | |
| static void | EnableDebugDump (bool on) |
| Static Public Attributes inherited from CObject | |
| static const TCount | eCounterBitsCanBeDeleted = 1 << 0 |
| Define possible object states. More... | |
| static const TCount | eCounterBitsInPlainHeap = 1 << 1 |
| Heap signature was found. More... | |
| static const TCount | eCounterBitsPlaceMask |
| Mask for 'in heap' state flags. More... | |
| static const int | eCounterStep = 1 << 2 |
| Skip over the "in heap" bits. More... | |
| static const TCount | eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2) |
| Minimal value for valid objects (reference counter is zero) Must be a single bit value. More... | |
| static const TCount | eCounterStateMask |
| Valid object, and object in heap. More... | |
Detailed Description
Definition at line 27 of file table2asn_validator.hpp.
Member Typedef Documentation
◆ TErrorStatMap
|
protected |
Definition at line 49 of file table2asn_validator.hpp.
Constructor & Destructor Documentation
◆ CTable2AsnValidator()
| CTable2AsnValidator::CTable2AsnValidator | ( | CTable2AsnContext & | ctx | ) |
Definition at line 48 of file table2asn_validator.cpp.
References m_context, CTable2AsnContext::m_remote_updater, and m_val_context.
◆ ~CTable2AsnValidator()
| CTable2AsnValidator::~CTable2AsnValidator | ( | ) |
Definition at line 56 of file table2asn_validator.cpp.
Member Function Documentation
◆ Cleanup()
| void CTable2AsnValidator::Cleanup | ( | CRef< objects::CSeq_submit > | submit, |
| objects::CSeq_entry_Handle & | entry, | ||
| const string & | flags | ||
| ) | const |
Definition at line 60 of file table2asn_validator.cpp.
References CCleanup::AddLowQualityException(), CCleanup::AddProteinTitle(), cleanup(), CCleanup::CleanupCollectionDates(), CCleanup::eClean_KeepSingleSeqSet, CCleanup::eClean_KeepTopSet, CCleanup::eClean_NoNcbiUserObjects, CCleanup::eClean_SyncGenCodes, CSeq_inst_Base::eMol_na, CCleanup::eScope_UseInPlace, CCleanup::ExtendedCleanup(), ExtendPartialFeatureEnds(), flags, CSeq_entry_Handle::GetScope(), m_context, CTable2AsnContext::m_huge_files_mode, CTable2AsnContext::m_suspect_rules, m_val_context, and CCleanup::WGSCleanup().
◆ Clear()
| void CTable2AsnValidator::Clear | ( | void | ) |
Definition at line 168 of file table2asn_validator.cpp.
References g(), m_mutex, m_val_errors, and m_val_globalInfo.
◆ CollectDiscrepancies()
| void CTable2AsnValidator::CollectDiscrepancies | ( | CRef< objects::CSeq_submit > | submit, |
| objects::CSeq_entry_Handle & | entry | ||
| ) |
Definition at line 260 of file table2asn_validator.cpp.
References dr, g(), CTable2AsnContext::GetOstream(), m_context, m_discr_product, m_discrep_mutex, CTable2AsnContext::m_huge_files_mode, CTable2AsnContext::m_run_discrepancy, CTable2AsnContext::m_split_discrepancy, x_PopulateDiscrepancy(), and x_ReportDiscrepancies().
◆ ReportDiscrepancies() [1/2]
| void CTable2AsnValidator::ReportDiscrepancies | ( | ) |
Definition at line 288 of file table2asn_validator.cpp.
References dr, CTable2AsnContext::GetOstream(), m_context, m_discr_product, and x_ReportDiscrepancies().
◆ ReportDiscrepancies() [2/2]
Definition at line 296 of file table2asn_validator.cpp.
References m_discr_product, and x_ReportDiscrepancies().
◆ UpdateECNumbers()
| void CTable2AsnValidator::UpdateECNumbers | ( | objects::CSeq_entry & | entry | ) |
Definition at line 371 of file table2asn_validator.cpp.
References m_context, and objects::VisitAllFeatures().
◆ ValCollect()
| void CTable2AsnValidator::ValCollect | ( | CRef< objects::CSeq_submit > | submit, |
| CRef< objects::CSeq_entry > | entry, | ||
| const string & | flags | ||
| ) |
Definition at line 120 of file table2asn_validator.cpp.
References CScope::AddDefaults(), CScope::AddTopLevelSeqEntry(), CRef< C, Locker >::Empty(), g(), GetAccessionFromObjects(), CSeq_submit_Base::GetData(), CSeq_submit_Base::C_Data::GetEntrys(), CObjectManager::GetInstance(), CScope::GetObjectManager(), m_context, CTable2AsnContext::m_huge_files_mode, CTable2AsnContext::m_master_genome_flag, m_mutex, m_val_context, m_val_errors, m_val_globalInfo, and CRef< C, Locker >::NotEmpty().
◆ ValReportErrors()
| void CTable2AsnValidator::ValReportErrors | ( | ) |
Definition at line 176 of file table2asn_validator.cpp.
References CValidErrItem::ConvertSeverity(), g(), g_PostprocessErrors(), CValidErrItem::GetErrCode(), CValidErrItem::GetErrGroup(), CValidErrItem_Base::GetErrIndex(), CValidErrItem_Base::GetMsg(), CValidErrItem_Base::GetObjDesc(), CTable2AsnContext::GetOstream(), CValidErrItem_Base::GetSev(), m_context, CTable2AsnContext::m_huge_files_mode, m_mutex, m_val_context, m_val_errors, m_val_globalInfo, m_val_stats, out(), and val.
◆ ValReportErrorStats()
| void CTable2AsnValidator::ValReportErrorStats | ( | CNcbiOstream & | out | ) |
Definition at line 212 of file table2asn_validator.cpp.
References CValidErrItem::ConvertSeverity(), g(), m_mutex, m_val_stats, NStr::NumericToString(), out(), NStr::ToUpper(), and ValTotalErrors().
◆ ValTotalErrors()
| size_t CTable2AsnValidator::ValTotalErrors | ( | ) | const |
Definition at line 200 of file table2asn_validator.cpp.
References g(), m_mutex, m_val_stats, result, and stats.
Referenced by ValReportErrorStats().
◆ x_PopulateDiscrepancy()
|
protected |
Definition at line 237 of file table2asn_validator.cpp.
References asn, CTable2AsnContext::GenerateOutputFilename(), GetDiscrepancyTests(), CDirEntry::GetName(), m_context, CTable2AsnContext::m_disc_lineage, CTable2AsnContext::m_discrepancy_group, and names.
Referenced by CollectDiscrepancies().
◆ x_ReportDiscrepancies()
|
protected |
Definition at line 277 of file table2asn_validator.cpp.
References m_context, CTable2AsnContext::m_master_genome_flag, and CRef< C, Locker >::Reset().
Referenced by CollectDiscrepancies(), and ReportDiscrepancies().
Member Data Documentation
◆ m_context
|
protected |
Definition at line 57 of file table2asn_validator.hpp.
Referenced by Cleanup(), CollectDiscrepancies(), CTable2AsnValidator(), ReportDiscrepancies(), UpdateECNumbers(), ValCollect(), ValReportErrors(), x_PopulateDiscrepancy(), and x_ReportDiscrepancies().
◆ m_discr_product
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protected |
Definition at line 60 of file table2asn_validator.hpp.
Referenced by CollectDiscrepancies(), and ReportDiscrepancies().
◆ m_discrep_mutex
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protected |
Definition at line 59 of file table2asn_validator.hpp.
Referenced by CollectDiscrepancies().
◆ m_mutex
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mutableprotected |
Definition at line 66 of file table2asn_validator.hpp.
Referenced by Clear(), ValCollect(), ValReportErrors(), ValReportErrorStats(), and ValTotalErrors().
◆ m_val_context
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protected |
Definition at line 62 of file table2asn_validator.hpp.
Referenced by Cleanup(), CTable2AsnValidator(), ValCollect(), and ValReportErrors().
◆ m_val_errors
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protected |
Definition at line 64 of file table2asn_validator.hpp.
Referenced by Clear(), ValCollect(), and ValReportErrors().
◆ m_val_globalInfo
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protected |
Definition at line 65 of file table2asn_validator.hpp.
Referenced by Clear(), ValCollect(), and ValReportErrors().
◆ m_val_stats
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protected |
Definition at line 63 of file table2asn_validator.hpp.
Referenced by ValReportErrors(), ValReportErrorStats(), and ValTotalErrors().
The documentation for this class was generated from the following files:
- src/app/table2asn/table2asn_validator.hpp
- src/app/table2asn/table2asn_validator.cpp
