CValidator Class Reference

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#include <objtools/validator/validator.hpp>

Inheritance diagram for CValidator:

Collaboration diagram for CValidator:

Classes
class	CCache
class	CCacheImpl
	Cache various information for one validation run. More...
class	CProgressInfo

Public Types
enum	EValidOptions {   eVal_non_ascii = 0x1 , eVal_no_context = 0x2 , eVal_val_align = 0x4 , eVal_val_exons = 0x8 ,   eVal_ovl_pep_err = 0x10 , eVal_seqsubmit_parent = 0x20 , eVal_need_isojta = 0x40 , eVal_validate_id_set = 0x80 ,   eVal_remote_fetch = 0x100 , eVal_far_fetch_mrna_products = 0x200 , eVal_far_fetch_cds_products = 0x400 , eVal_locus_tag_general_match = 0x800 ,   eVal_do_rubisco_test = 0x1000 , eVal_indexer_version = 0x2000 , eVal_use_entrez = 0x4000 , eVal_inference_accns = 0x8000 ,   eVal_ignore_exceptions = 0x10000 , eVal_report_splice_as_error = 0x20000 , eVal_latlon_check_state = 0x40000 , eVal_latlon_ignore_water = 0x80000 ,   eVal_genome_submission = 0x100000 , eVal_do_tax_lookup = 0x200000 , eVal_do_barcode_tests = 0x400000 , eVal_refseq_conventions = 0x800000 ,   eVal_collect_locus_tags = 0x1000000 , eVal_generate_golden_file = 0x2000000 , eVal_compare_vdjc_to_cds = 0x4000000 , eVal_ignore_inferences = 0x10000000 }
enum	EDbxrefValid {   eValid = 0 , eDbHasSgml = 1 , eTagHasSgml = 2 , eContainsSpace = 4 ,   eNotForSource = 8 , eOnlyForSource = 16 , eOnlyForRefSeq = 32 , eRefSeqNotForSource = 64 ,   eBadCapitalization = 128 , eUnrecognized = 256 }
using	TSuppressed = set< CValidErrItem::TErrIndex >
typedef bool(*	TProgressCallback) (CProgressInfo *)
typedef int	TDbxrefValidFlags
using	TEntryInfo = CValidatorEntryInfo
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...

Public Member Functions
	CValidator (CObjectManager &objmgr)
	CValidator (CObjectManager &objmgr, shared_ptr< SValidatorContext > pContext)
void	SetTaxon3 (shared_ptr< ITaxon3 > taxon)
	CValidator (const CValidator &)=delete
CValidator &	operator= (const CValidator &)=delete
	~CValidator ()
CRef< CValidError >	Validate (const CSeq_entry &se, CScope *scope=nullptr, Uint4 options=0)
void	Validate (const CSeq_entry &se, CScope *scope, Uint4 options, IValidError &errors, const TSuppressed *pSuppressed=nullptr)
CRef< CValidError >	Validate (const CSeq_entry_Handle &se, Uint4 options=0)
void	Validate (const CSeq_entry_Handle &seh, Uint4 options, IValidError &errors, const TSuppressed *pSuppressed=nullptr)
CRef< CValidError >	Validate (const CSeq_submit &ss, CScope *scope=nullptr, Uint4 options=0)
void	Validate (const CSeq_submit &ss, CScope *scope, Uint4 options, IValidError &errors, const TSuppressed *pSuppressed=nullptr)
CConstRef< CValidError >	Validate (const CSeq_annot_Handle &sa, Uint4 options=0)
void	Validate (const CSeq_annot_Handle &sa, Uint4 options, IValidError &errors)
void	Validate (const CSeq_annot_Handle &sa, Uint4 options, CValidError &errors)
CConstRef< CValidError >	Validate (const CSeq_feat &feat, CScope *scope=nullptr, Uint4 options=0)
void	Validate (const CSeq_feat &feat, CScope *scope, Uint4 options, IValidError &errors)
CConstRef< CValidError >	Validate (const CBioSource &src, CScope *scope=nullptr, Uint4 options=0)
void	Validate (const CBioSource &src, CScope *scope, Uint4 options, IValidError &errors)
CConstRef< CValidError >	Validate (const CPubdesc &pubdesc, CScope *scope=nullptr, Uint4 options=0)
void	Validate (const CPubdesc &desc, CScope *scope, Uint4 options, IValidError &errors)
CConstRef< CValidError >	Validate (const CSeqdesc &desc, const CSeq_entry &ctx, Uint4 options=0)
void	Validate (const CSeqdesc &desc, const CSeq_entry &ctx, Uint4 options, IValidError &errors)
bool	IsValidStructuredComment (const CSeqdesc &desc) const
CConstRef< CValidError >	GetTSANStretchErrors (const CSeq_entry_Handle &se)
CConstRef< CValidError >	GetTSACDSOnMinusStrandErrors (const CSeq_entry_Handle &se)
CConstRef< CValidError >	GetTSAConflictingBiomolTechErrors (const CSeq_entry_Handle &se)
CConstRef< CValidError >	GetTSANStretchErrors (const CBioseq &seq)
CConstRef< CValidError >	GetTSACDSOnMinusStrandErrors (const CSeq_feat &f, const CBioseq &seq)
CConstRef< CValidError >	GetTSAConflictingBiomolTechErrors (const CBioseq &seq)
void	SetProgressCallback (TProgressCallback callback, void *user_data=nullptr)
SValidatorContext &	SetContext ()
bool	IsSetEntryInfo () const
const TEntryInfo &	GetEntryInfo () const
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

Static Public Member Functions
static CRef< CCache >	MakeEmptyCache ()
static bool	BadCharsInAuthorName (const string &str, bool allowcomma, bool allowperiod, bool last)
static bool	BadCharsInAuthorLastName (const string &str)
static bool	BadCharsInAuthorFirstName (const string &str)
static bool	BadCharsInAuthorInitials (const string &str)
static bool	BadCharsInAuthorSuffix (const string &str)
static string	BadCharsInAuthor (const CName_std &author, bool &last_is_bad)
static string	BadCharsInAuthor (const CAuthor &author, bool &last_is_bad)
static bool	IsSeqLocCorrectlyOrdered (const CSeq_loc &loc, CScope &scope)
static bool	DoesSeqLocContainAdjacentIntervals (const CSeq_loc &loc, CScope &scope)
static bool	DoesSeqLocContainDuplicateIntervals (const CSeq_loc &loc, CScope &scope)
static EErrType	ConvertCode (CSubSource::ELatLonCountryErr errcode)
static TDbxrefValidFlags	IsValidDbxref (const CDbtag &xref, bool is_biosource, bool is_refseq_or_gps)
static taxupdate_func_t	MakeTaxUpdateFunction (shared_ptr< ITaxon3 > taxon)
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)

Private Member Functions
void	x_SetEntryInfo (const TEntryInfo &info)

Private Attributes
CRef< CObjectManager >	m_ObjMgr
shared_ptr< ITaxon3 >	m_pOwnTaxon
TProgressCallback	m_PrgCallback =nullptr
void *	m_UserData =nullptr
shared_ptr< SValidatorContext >	m_pContext
unique_ptr< CValidatorEntryInfo >	m_pEntryInfo

Additional Inherited Members
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...
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 73 of file validator.hpp.

Member Typedef Documentation

TDbxrefValidFlags

typedef int CValidator::TDbxrefValidFlags

Definition at line 304 of file validator.hpp.

TEntryInfo

using CValidator::TEntryInfo = CValidatorEntryInfo

Definition at line 309 of file validator.hpp.

TProgressCallback

typedef bool(* CValidator::TProgressCallback) (CProgressInfo *)

Definition at line 287 of file validator.hpp.

TSuppressed

using CValidator::TSuppressed = set<CValidErrItem::TErrIndex>

Definition at line 77 of file validator.hpp.

Member Enumeration Documentation

EDbxrefValid

enum CValidator::EDbxrefValid

Enumerator
eValid
eDbHasSgml
eTagHasSgml
eContainsSpace
eNotForSource
eOnlyForSource
eOnlyForRefSeq
eRefSeqNotForSource
eBadCapitalization
eUnrecognized

Definition at line 292 of file validator.hpp.

EValidOptions

enum CValidator::EValidOptions

Enumerator
eVal_non_ascii
eVal_no_context
eVal_val_align
eVal_val_exons
eVal_ovl_pep_err
eVal_seqsubmit_parent
eVal_need_isojta
eVal_validate_id_set
eVal_remote_fetch
eVal_far_fetch_mrna_products
eVal_far_fetch_cds_products
eVal_locus_tag_general_match
eVal_do_rubisco_test
eVal_indexer_version
eVal_use_entrez
eVal_inference_accns
eVal_ignore_exceptions
eVal_report_splice_as_error
eVal_latlon_check_state
eVal_latlon_ignore_water
eVal_genome_submission
eVal_do_tax_lookup
eVal_do_barcode_tests
eVal_refseq_conventions
eVal_collect_locus_tags
eVal_generate_golden_file
eVal_compare_vdjc_to_cds
eVal_ignore_inferences

Definition at line 79 of file validator.hpp.

Constructor & Destructor Documentation

CValidator() [1/3]

CValidator::CValidator

(

CObjectManager &

objmgr

)

Definition at line 61 of file validator.cpp.

CValidator() [2/3]

CValidator::CValidator	(	CObjectManager &	objmgr,
		shared_ptr< SValidatorContext >	pContext
	)

Definition at line 67 of file validator.cpp.

CValidator() [3/3]

CValidator::CValidator ( const CValidator &  )

delete

~CValidator()

CValidator::~CValidator

(

)

Definition at line 82 of file validator.cpp.

Member Function Documentation

BadCharsInAuthor() [1/2]

string CValidator::BadCharsInAuthor ( const CAuthor &  author, bool &  last_is_bad  )

static

Definition at line 537 of file validator.cpp.

References BadCharsInAuthor(), CAuthor_Base::GetName(), CPerson_id_Base::GetName(), CPerson_id_Base::IsName(), CAuthor_Base::IsSetName(), and kEmptyStr.

BadCharsInAuthor() [2/2]

string CValidator::BadCharsInAuthor ( const CName_std &  author, bool &  last_is_bad  )

static

Definition at line 517 of file validator.cpp.

References BadCharsInAuthorFirstName(), BadCharsInAuthorInitials(), BadCharsInAuthorLastName(), BadCharsInAuthorSuffix(), CName_std_Base::GetFirst(), CName_std_Base::GetInitials(), CName_std_Base::GetLast(), CName_std_Base::GetSuffix(), CName_std_Base::IsSetFirst(), CName_std_Base::IsSetInitials(), CName_std_Base::IsSetLast(), and CName_std_Base::IsSetSuffix().

Referenced by BadCharsInAuthor(), and CValidError_imp::ValidateAuthorList().

BadCharsInAuthorFirstName()

bool CValidator::BadCharsInAuthorFirstName ( const string &  str )

static

Definition at line 499 of file validator.cpp.

References BadCharsInAuthorName(), and str().

Referenced by BadCharsInAuthor().

BadCharsInAuthorInitials()

bool CValidator::BadCharsInAuthorInitials ( const string &  str )

static

Definition at line 505 of file validator.cpp.

References BadCharsInAuthorName(), and str().

Referenced by BadCharsInAuthor().

BadCharsInAuthorLastName()

bool CValidator::BadCharsInAuthorLastName ( const string &  str )

static

Definition at line 489 of file validator.cpp.

References BadCharsInAuthorName(), NStr::EqualNocase(), and str().

Referenced by BadCharsInAuthor().

BadCharsInAuthorName()

bool CValidator::BadCharsInAuthorName ( const string &  str, bool  allowcomma, bool  allowperiod, bool  last  )

static

Definition at line 443 of file validator.cpp.

References NStr::Equal(), isalpha(), NStr::IsBlank(), last(), NStr::StartsWith(), and str().

Referenced by BadCharsInAuthorFirstName(), BadCharsInAuthorInitials(), BadCharsInAuthorLastName(), BadCharsInAuthorSuffix(), and CValidError_imp::ValidateAuthorList().

BadCharsInAuthorSuffix()

bool CValidator::BadCharsInAuthorSuffix ( const string &  str )

static

Definition at line 511 of file validator.cpp.

References BadCharsInAuthorName(), and str().

Referenced by BadCharsInAuthor().

ConvertCode()

EErrType CValidator::ConvertCode ( CSubSource::ELatLonCountryErr  errcode )

static

Definition at line 714 of file validator.cpp.

References eErr_SEQ_DESCR_LatLonCountry, eErr_SEQ_DESCR_LatLonGeoLocName, eErr_SEQ_DESCR_LatLonState, eErr_SEQ_DESCR_LatLonValue, eErr_SEQ_DESCR_LatLonWater, eErr_UNKNOWN, CSubSource::eLatLonCountryErr_Country, CSubSource::eLatLonCountryErr_State, CSubSource::eLatLonCountryErr_Value, CSubSource::eLatLonCountryErr_Water, and CSubSource::NCBI_UseGeoLocNameForCountry().

Referenced by CValidError_imp::ValidateLatLonCountry().

DoesSeqLocContainAdjacentIntervals()

bool CValidator::DoesSeqLocContainAdjacentIntervals ( const CSeq_loc &  loc, CScope &  scope  )

static

Definition at line 680 of file validator.cpp.

References CheckConsecutiveIntervals(), and x_IsNotAdjacent().

Referenced by CValidError_imp::ValidateSeqLoc().

DoesSeqLocContainDuplicateIntervals()

bool CValidator::DoesSeqLocContainDuplicateIntervals ( const CSeq_loc &  loc, CScope &  scope  )

static

Definition at line 708 of file validator.cpp.

References CheckConsecutiveIntervals(), and IsNotDuplicateInterval().

Referenced by CValidError_imp::ValidateSeqLoc().

GetEntryInfo()

const CValidator::TEntryInfo & CValidator::GetEntryInfo

(

)

const

Definition at line 813 of file validator.cpp.

References m_pEntryInfo.

GetTSACDSOnMinusStrandErrors() [1/2]

CConstRef< CValidError > CValidator::GetTSACDSOnMinusStrandErrors

(

const CSeq_entry_Handle &

se

)

Definition at line 199 of file validator.cpp.

References CSeq_entry_Handle::GetCompleteSeq_entry(), CValidError_imp::GetTSACDSOnMinusStrandErrors(), m_ObjMgr, m_pContext, m_PrgCallback, m_UserData, CRef< C, Locker >::Reset(), CValidError_imp::SetProgressCallback(), and CValidErrorFormat::SetSuppressionRules().

GetTSACDSOnMinusStrandErrors() [2/2]

CConstRef< CValidError > CValidator::GetTSACDSOnMinusStrandErrors	(	const CSeq_feat &	f,
		const CBioseq &	seq
	)

Definition at line 239 of file validator.cpp.

References f, CValidError_imp::GetTSACDSOnMinusStrandErrors(), m_ObjMgr, m_pContext, m_PrgCallback, m_UserData, CRef< C, Locker >::Reset(), CValidError_imp::SetProgressCallback(), and CValidErrorFormat::SetSuppressionRules().

GetTSAConflictingBiomolTechErrors() [1/2]

CConstRef< CValidError > CValidator::GetTSAConflictingBiomolTechErrors

(

const CBioseq &

seq

)

Definition at line 252 of file validator.cpp.

References CValidError_imp::GetTSAConflictingBiomolTechErrors(), m_ObjMgr, m_pContext, m_PrgCallback, m_UserData, CRef< C, Locker >::Reset(), CValidError_imp::SetProgressCallback(), and CValidErrorFormat::SetSuppressionRules().

GetTSAConflictingBiomolTechErrors() [2/2]

CConstRef< CValidError > CValidator::GetTSAConflictingBiomolTechErrors

(

const CSeq_entry_Handle &

se

)

Definition at line 212 of file validator.cpp.

References CSeq_entry_Handle::GetCompleteSeq_entry(), CValidError_imp::GetTSAConflictingBiomolTechErrors(), m_ObjMgr, m_pContext, m_PrgCallback, m_UserData, CRef< C, Locker >::Reset(), CValidError_imp::SetProgressCallback(), and CValidErrorFormat::SetSuppressionRules().

GetTSANStretchErrors() [1/2]

CConstRef< CValidError > CValidator::GetTSANStretchErrors

(

const CBioseq &

seq

)

Definition at line 225 of file validator.cpp.

References CValidError_imp::GetTSANStretchErrors(), m_ObjMgr, m_pContext, m_PrgCallback, m_UserData, CRef< C, Locker >::Reset(), CValidError_imp::SetProgressCallback(), and CValidErrorFormat::SetSuppressionRules().

GetTSANStretchErrors() [2/2]

CConstRef< CValidError > CValidator::GetTSANStretchErrors

(

const CSeq_entry_Handle &

se

)

Definition at line 186 of file validator.cpp.

References CSeq_entry_Handle::GetCompleteSeq_entry(), CValidError_imp::GetTSANStretchErrors(), m_ObjMgr, m_pContext, m_PrgCallback, m_UserData, CRef< C, Locker >::Reset(), CValidError_imp::SetProgressCallback(), and CValidErrorFormat::SetSuppressionRules().

IsSeqLocCorrectlyOrdered()

bool CValidator::IsSeqLocCorrectlyOrdered ( const CSeq_loc &  loc, CScope &  scope  )

static

Definition at line 634 of file validator.cpp.

References CheckConsecutiveIntervals(), CSeq_inst_Base::eTopology_circular, CScope::GetBioseqHandle(), CBioseq_Handle::GetInst_Topology(), and x_IsCorrectlyOrdered().

Referenced by CValidError_imp::ValidateSeqLoc().

IsSetEntryInfo()

bool CValidator::IsSetEntryInfo

(

)

const

Definition at line 807 of file validator.cpp.

References m_pEntryInfo.

IsValidDbxref()

CValidator::TDbxrefValidFlags CValidator::IsValidDbxref ( const CDbtag &  xref, bool  is_biosource, bool  is_refseq_or_gps  )

static

Definition at line 744 of file validator.cpp.

References ContainsSgml(), eBadCapitalization, eContainsSpace, eDbHasSgml, eNotForSource, eOnlyForRefSeq, eOnlyForSource, NStr::EqualCase(), NStr::EqualNocase(), eRefSeqNotForSource, eTagHasSgml, eUnrecognized, eValid, flags, CDbtag_Base::GetDb(), CDbtag::GetDBFlags(), CObject_id_Base::GetId(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CObject_id_Base::IsId(), CDbtag_Base::IsSetDb(), CDbtag_Base::IsSetTag(), CObject_id_Base::IsStr(), and NStr::NumericToString().

Referenced by CValidError_imp::ValidateDbxref().

IsValidStructuredComment()

bool CValidator::IsValidStructuredComment

(

const CSeqdesc &

desc

)

const

Definition at line 424 of file validator.cpp.

References CSeqdesc_Base::IsUser(), CValidError_desc::IsValidStructuredComment(), m_ObjMgr, and m_pContext.

MakeEmptyCache()

CRef< CCache > CValidator::MakeEmptyCache ( )

static

Definition at line 832 of file validator.cpp.

References Ref().

MakeTaxUpdateFunction()

taxupdate_func_t CValidator::MakeTaxUpdateFunction ( shared_ptr< ITaxon3 >  taxon )

static

Definition at line 85 of file validator.cpp.

References query.

Referenced by SetTaxon3().

operator=()

CValidator& CValidator::operator= ( const CValidator &  )

delete

SetContext()

SValidatorContext& CValidator::SetContext ( void  )

inline

Definition at line 307 of file validator.hpp.

References m_pContext.

SetProgressCallback()

void CValidator::SetProgressCallback	(	TProgressCallback	callback,
		void *	user_data = nullptr
	)

Definition at line 436 of file validator.cpp.

References m_PrgCallback, and m_UserData.

SetTaxon3()

void CValidator::SetTaxon3

(

shared_ptr< ITaxon3 >

taxon

)

Definition at line 75 of file validator.cpp.

References m_pContext, m_pOwnTaxon, and MakeTaxUpdateFunction().

Validate() [1/17]

void CValidator::Validate	(	const CBioSource &	src,
		CScope *	scope,
		Uint4	options,
		IValidError &	errors
	)

Definition at line 369 of file validator.cpp.

References m_ObjMgr, m_pContext, and CValidError_imp::Validate().

Validate() [2/17]

CConstRef< CValidError > CValidator::Validate	(	const CBioSource &	src,
		CScope *	scope = nullptr,
		Uint4	options = 0
	)

Definition at line 357 of file validator.cpp.

References m_ObjMgr, m_pContext, and CValidError_imp::Validate().

Validate() [3/17]

void CValidator::Validate	(	const CPubdesc &	desc,
		CScope *	scope,
		Uint4	options,
		IValidError &	errors
	)

Definition at line 393 of file validator.cpp.

References m_ObjMgr, m_pContext, and CValidError_imp::Validate().

Validate() [4/17]

CConstRef< CValidError > CValidator::Validate	(	const CPubdesc &	pubdesc,
		CScope *	scope = nullptr,
		Uint4	options = 0
	)

Definition at line 382 of file validator.cpp.

References m_ObjMgr, m_pContext, and CValidError_imp::Validate().

Validate() [5/17]

void CValidator::Validate	(	const CSeq_annot_Handle &	sa,
		Uint4	options,
		CValidError &	errors
	)

Definition at line 313 of file validator.cpp.

References m_ObjMgr, m_pContext, and CValidError_imp::Validate().

Validate() [6/17]

void CValidator::Validate	(	const CSeq_annot_Handle &	sa,
		Uint4	options,
		IValidError &	errors
	)

Definition at line 323 of file validator.cpp.

References m_ObjMgr, m_pContext, and CValidError_imp::Validate().

Validate() [7/17]

CConstRef< CValidError > CValidator::Validate	(	const CSeq_annot_Handle &	sa,
		Uint4	options = 0
	)

Definition at line 303 of file validator.cpp.

References CSeq_annot_Handle::GetCompleteSeq_annot(), Ref(), and Validate().

Validate() [8/17]

void CValidator::Validate	(	const CSeq_entry &	se,
		CScope *	scope,
		Uint4	options,
		IValidError &	errors,
		const TSuppressed *	pSuppressed = nullptr
	)

Definition at line 123 of file validator.cpp.

References CValidError_imp::GetCumulativeInferenceCount(), CValidError_imp::GetEntryInfo(), CValidError_imp::GetGeneCount(), CValidError_imp::GetGeneXrefCount(), m_ObjMgr, m_pContext, m_PrgCallback, m_UserData, CValidError_imp::SetProgressCallback(), CValidError_imp::SetSuppressed(), CValidError_imp::Validate(), and x_SetEntryInfo().

Validate() [9/17]

CRef< CValidError > CValidator::Validate	(	const CSeq_entry &	se,
		CScope *	scope = nullptr,
		Uint4	options = 0
	)

Definition at line 101 of file validator.cpp.

References ctx, CValidError_imp::GetCumulativeInferenceCount(), CValidError_imp::GetEntryInfo(), CValidError_imp::GetGeneCount(), CValidError_imp::GetGeneXrefCount(), m_ObjMgr, m_pContext, m_PrgCallback, m_UserData, CRef< C, Locker >::Reset(), CValidError_imp::SetContext(), CValidError_imp::SetProgressCallback(), CValidErrorFormat::SetSuppressionRules(), CValidError_imp::Validate(), and x_SetEntryInfo().

Referenced by BOOST_AUTO_TEST_CASE(), CAsnvalThreadState::ProcessBioSource(), CAsnvalThreadState::ProcessPubdesc(), CAsnvalThreadState::ProcessSeqAnnot(), CAsnvalThreadState::ProcessSeqDesc(), CAsnvalThreadState::ProcessSeqEntry(), CAsnvalThreadState::ProcessSeqFeat(), CAsnvalThreadState::ProcessSeqSubmit(), CAsnvalThreadState::ReadClassMember(), s_TestOneWrongQual(), CValidateProcess::SeqEntryProcess(), Validate(), and CAsnvalThreadState::ValidateAsync().

Validate() [10/17]

CRef< CValidError > CValidator::Validate	(	const CSeq_entry_Handle &	se,
		Uint4	options = 0
	)

Definition at line 143 of file validator.cpp.

References ctx, CSeq_entry_Handle::GetCompleteSeq_entry(), CValidError_imp::GetCumulativeInferenceCount(), CValidError_imp::GetEntryInfo(), CValidError_imp::GetGeneCount(), CValidError_imp::GetGeneXrefCount(), m_ObjMgr, m_pContext, m_PrgCallback, m_UserData, CRef< C, Locker >::Reset(), CValidError_imp::SetContext(), CValidError_imp::SetProgressCallback(), CValidErrorFormat::SetSuppressionRules(), CValidError_imp::Validate(), and x_SetEntryInfo().

Validate() [11/17]

void CValidator::Validate	(	const CSeq_entry_Handle &	seh,
		Uint4	options,
		IValidError &	errors,
		const TSuppressed *	pSuppressed = nullptr
	)

Definition at line 163 of file validator.cpp.

References ctx, CValidError_imp::GetCumulativeInferenceCount(), CValidError_imp::GetEntryInfo(), CValidError_imp::GetGeneCount(), CValidError_imp::GetGeneXrefCount(), m_ObjMgr, m_pContext, m_PrgCallback, m_UserData, CValidError_imp::SetContext(), CValidError_imp::SetProgressCallback(), CValidError_imp::SetSuppressed(), CValidError_imp::Validate(), and x_SetEntryInfo().

Validate() [12/17]

void CValidator::Validate	(	const CSeq_feat &	feat,
		CScope *	scope,
		Uint4	options,
		IValidError &	errors
	)

Definition at line 345 of file validator.cpp.

References m_ObjMgr, m_pContext, and CValidError_imp::Validate().

Validate() [13/17]

CConstRef< CValidError > CValidator::Validate	(	const CSeq_feat &	feat,
		CScope *	scope = nullptr,
		Uint4	options = 0
	)

Definition at line 333 of file validator.cpp.

References m_ObjMgr, m_pContext, and CValidError_imp::Validate().

Validate() [14/17]

void CValidator::Validate	(	const CSeq_submit &	ss,
		CScope *	scope,
		Uint4	options,
		IValidError &	errors,
		const TSuppressed *	pSuppressed = nullptr
	)

Definition at line 283 of file validator.cpp.

References eVal_seqsubmit_parent, CValidError_imp::GetCumulativeInferenceCount(), CValidError_imp::GetEntryInfo(), CValidError_imp::GetGeneCount(), CValidError_imp::GetGeneXrefCount(), m_ObjMgr, m_pContext, CValidError_imp::SetSuppressed(), CValidError_imp::Validate(), and x_SetEntryInfo().

Validate() [15/17]

CRef< CValidError > CValidator::Validate	(	const CSeq_submit &	ss,
		CScope *	scope = nullptr,
		Uint4	options = 0
	)

Definition at line 266 of file validator.cpp.

References eVal_seqsubmit_parent, CValidError_imp::GetEntryInfo(), m_ObjMgr, m_pContext, CValidErrorFormat::SetSuppressionRules(), CValidError_imp::Validate(), and x_SetEntryInfo().

Validate() [16/17]

void CValidator::Validate	(	const CSeqdesc &	desc,
		const CSeq_entry &	ctx,
		Uint4	options,
		IValidError &	errors
	)

Definition at line 414 of file validator.cpp.

References ctx, m_ObjMgr, m_pContext, and CValidError_imp::Validate().

Validate() [17/17]

CConstRef< CValidError > CValidator::Validate	(	const CSeqdesc &	desc,
		const CSeq_entry &	ctx,
		Uint4	options = 0
	)

Definition at line 403 of file validator.cpp.

References ctx, m_ObjMgr, m_pContext, and CValidError_imp::Validate().

x_SetEntryInfo()

void CValidator::x_SetEntryInfo ( const TEntryInfo &  info )

private

Definition at line 801 of file validator.cpp.

References info, and m_pEntryInfo.

Referenced by Validate().

Member Data Documentation

m_ObjMgr

CRef<CObjectManager> CValidator::m_ObjMgr

private

Definition at line 316 of file validator.hpp.

Referenced by GetTSACDSOnMinusStrandErrors(), GetTSAConflictingBiomolTechErrors(), GetTSANStretchErrors(), IsValidStructuredComment(), and Validate().

m_pContext

shared_ptr<SValidatorContext> CValidator::m_pContext

private

Definition at line 321 of file validator.hpp.

Referenced by GetTSACDSOnMinusStrandErrors(), GetTSAConflictingBiomolTechErrors(), GetTSANStretchErrors(), IsValidStructuredComment(), SetContext(), SetTaxon3(), and Validate().

m_pEntryInfo

unique_ptr<CValidatorEntryInfo> CValidator::m_pEntryInfo

private

Definition at line 322 of file validator.hpp.

Referenced by GetEntryInfo(), IsSetEntryInfo(), and x_SetEntryInfo().

m_pOwnTaxon

shared_ptr<ITaxon3> CValidator::m_pOwnTaxon

private

Definition at line 317 of file validator.hpp.

Referenced by SetTaxon3().

m_PrgCallback

TProgressCallback CValidator::m_PrgCallback =nullptr

private

Definition at line 319 of file validator.hpp.

Referenced by GetTSACDSOnMinusStrandErrors(), GetTSAConflictingBiomolTechErrors(), GetTSANStretchErrors(), SetProgressCallback(), and Validate().

m_UserData

void* CValidator::m_UserData =nullptr

private

Definition at line 320 of file validator.hpp.

Referenced by GetTSACDSOnMinusStrandErrors(), GetTSAConflictingBiomolTechErrors(), GetTSANStretchErrors(), SetProgressCallback(), and Validate().

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The documentation for this class was generated from the following files:

• include/objtools/validator/validator.hpp
• src/objtools/validator/validator.cpp