Search Toolkit Book for CPolyASignalValidator

#include <objtools/validator/single_feat_validator.hpp>

Inheritance diagram for CPolyASignalValidator:

Collaboration diagram for CPolyASignalValidator:

Public Member Functions
void	x_ValidateSeqFeatLoc () override

	CSingleFeatValidator (const CSeq_feat &feat, CScope &scope, CValidError_imp &imp)

Public Member Functions inherited from CSingleFeatValidator
	CSingleFeatValidator (const CSeq_feat &feat, CScope &scope, CValidError_imp &imp)

virtual	~CSingleFeatValidator ()

virtual void	Validate ()

Additional Inherited Members
Static Public Member Functions inherited from CSingleFeatValidator
static bool	x_HasSeqLocBond (const CSeq_feat &feat)

static bool	s_IsPseudo (const CSeq_feat &feat)

static bool	s_IsPseudo (const CGene_ref &ref)

static bool	s_BioseqHasRefSeqThatStartsWithPrefix (CBioseq_Handle bsh, string prefix)

static bool	s_GeneRefsAreEquivalent (const CGene_ref &g1, const CGene_ref &g2, string &label)

static void	s_RemoveDuplicateGoTerms (CUser_object::TData &field_list)

static void	s_RemoveDuplicateGoTerms (CSeq_feat &feat)

Protected Types inherited from CSingleFeatValidator
enum	ELocationGap { eLocationGapNoProblems = 0 , eLocationGapFeatureMatchesGap = 1 , eLocationGapContainedInGap = 4 , eLocationGapContainedInGapOfNs = 8 , eLocationGapInternalIntervalEndpointInGap = 16 , eLocationGapCrossesUnknownGap = 32 , eLocationGapMostlyNs = 64 }

Protected Member Functions inherited from CSingleFeatValidator
void	PostErr (EDiagSev sv, EErrType et, const string &msg)

CBioseq_Handle	x_GetBioseqByLocation (const CSeq_loc &loc)

void	x_ValidateSeqFeatProduct ()

void	x_ValidateBothStrands ()

void	x_ValidateGeneId ()

void	x_ValidateFeatCit ()

virtual void	x_ValidateFeatComment ()

void	x_ValidateGbQual (const CGb_qual &qual)

void	x_ReportECNumFileStatus ()

void	x_ValidateExtUserObject ()

bool	x_HasNamedQual (const string &qual_name)

void	x_ValidateFeatPartialness ()

bool	x_AllowFeatureToMatchGapExactly ()

void	x_ValidateExcept ()

virtual void	x_ValidateExceptText (const string &text)

void	x_ValidateGbquals ()

virtual bool	x_ReportOrigProteinId ()

void	x_ValidateRptUnitVal (const string &val, const string &key)

void	x_ValidateRptUnitSeqVal (const string &val, const string &key)

void	x_ValidateRptUnitRangeVal (const string &val)

void	x_ValidateLabelVal (const string &val)

void	x_ValidateCompareVal (const string &val)

void	x_ValidateReplaceQual (const string &key, const string &qual_str, const string &val)

CBioseq_Handle	x_GetFeatureProduct (bool look_far, bool &is_far)

CBioseq_Handle	x_GetFeatureProduct (bool &is_far)

void	ValidateCharactersInField (string value, string field_name)

void	ValidateSplice (bool gene_pseudo, bool check_all)

EDiagSev	x_SeverityForConsensusSplice ()

void	x_ReportSpliceProblems (const CSpliceProblems &problems, const string &label)

void	x_ReportDonorSpliceSiteReadErrors (const CSpliceProblems::TSpliceProblem &problem, const string &label)

void	x_ReportAcceptorSpliceSiteReadErrors (const CSpliceProblems::TSpliceProblem &problem, const string &label)

void	x_ValidateNonImpFeat ()

void	x_ValidateGeneXRef ()

void	x_ValidateGeneFeaturePair (const CSeq_feat &gene)

void	x_ValidateNonGene ()

void	x_ValidateOldLocusTag (const string &old_locus_tag)

void	x_ValidateImpFeatLoc ()

void	x_ValidateImpFeatQuals ()

void	x_ValidateSeqFeatDataType ()

void	x_ReportPseudogeneConflict (CConstRef< CSeq_feat > gene)

void	x_ValidateLocusTagGeneralMatch (CConstRef< CSeq_feat > gene)

void	x_CheckForNonAsciiCharacters ()

Static Protected Member Functions inherited from CSingleFeatValidator
static void	x_LocHasStrandBoth (const CSeq_loc &feat, bool &both, bool &both_rev)

static size_t	x_CalculateLocationGaps (CBioseq_Handle bsh, const CSeq_loc &loc, vector< TSeqPos > &gap_starts)

static bool	x_IsMostlyNs (const CSeq_loc &loc, CBioseq_Handle bsh)

static TSeqPos	x_FindStartOfGap (CBioseq_Handle bsh, TSeqPos pos, CScope *scope)

static bool	x_BioseqHasNmAccession (CBioseq_Handle bsh)

Protected Attributes inherited from CSingleFeatValidator
const CSeq_feat &	m_Feat

CScope &	m_Scope

CValidError_imp &	m_Imp

CBioseq_Handle	m_LocationBioseq

CBioseq_Handle	m_ProductBioseq

bool	m_ProductIsFar