#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 }

enum	EDbxrefValid { eValid = 0 , eDbHasSgml = 1 , eTagHasSgml = 2 , eContainsSpace = 4 , eNotForSource = 8 , eOnlyForSource = 16 , eOnlyForRefSeq = 32 , eRefSeqNotForSource = 64 , eBadCapitalization = 128 , eUnrecognized = 256 }

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)

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

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

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

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

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

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

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

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

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 265 of file validator.hpp.

◆ TEntryInfo

using CValidator::TEntryInfo = CValidatorEntryInfo

Definition at line 270 of file validator.hpp.

◆ TProgressCallback

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

Definition at line 248 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 253 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