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static bool | x_HasSeqLocBond (const CSeq_feat &feat) |
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static bool | s_IsPseudo (const CSeq_feat &feat) |
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static bool | s_IsPseudo (const CGene_ref &ref) |
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static bool | s_BioseqHasRefSeqThatStartsWithPrefix (CBioseq_Handle bsh, string prefix) |
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static bool | s_GeneRefsAreEquivalent (const CGene_ref &g1, const CGene_ref &g2, string &label) |
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static void | s_RemoveDuplicateGoTerms (CUser_object::TData &field_list) |
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static void | s_RemoveDuplicateGoTerms (CSeq_feat &feat) |
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enum | ELocationGap {
eLocationGapNoProblems = 0
, eLocationGapFeatureMatchesGap = 1
, eLocationGapContainedInGap = 4
, eLocationGapContainedInGapOfNs = 8
,
eLocationGapInternalIntervalEndpointInGap = 16
, eLocationGapCrossesUnknownGap = 32
, eLocationGapMostlyNs = 64
} |
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void | PostErr (EDiagSev sv, EErrType et, const string &msg) |
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CBioseq_Handle | x_GetBioseqByLocation (const CSeq_loc &loc) |
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void | x_ValidateSeqFeatProduct () |
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void | x_ValidateBothStrands () |
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void | x_ValidateGeneId () |
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void | x_ValidateFeatCit () |
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virtual void | x_ValidateFeatComment () |
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void | x_ValidateGbQual (const CGb_qual &qual) |
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void | x_ReportECNumFileStatus () |
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void | x_ValidateExtUserObject () |
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bool | x_HasNamedQual (const string &qual_name) |
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void | x_ValidateFeatPartialness () |
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virtual void | x_ValidateSeqFeatLoc () |
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bool | x_AllowFeatureToMatchGapExactly () |
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void | x_ValidateExcept () |
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virtual void | x_ValidateExceptText (const string &text) |
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void | x_ValidateGbquals () |
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virtual bool | x_ReportOrigProteinId () |
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void | x_ValidateRptUnitVal (const string &val, const string &key) |
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void | x_ValidateRptUnitSeqVal (const string &val, const string &key) |
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void | x_ValidateRptUnitRangeVal (const string &val) |
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void | x_ValidateLabelVal (const string &val) |
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void | x_ValidateCompareVal (const string &val) |
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void | x_ValidateReplaceQual (const string &key, const string &qual_str, const string &val) |
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CBioseq_Handle | x_GetFeatureProduct (bool look_far, bool &is_far) |
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CBioseq_Handle | x_GetFeatureProduct (bool &is_far) |
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void | ValidateCharactersInField (string value, string field_name) |
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void | ValidateSplice (bool gene_pseudo, bool check_all) |
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EDiagSev | x_SeverityForConsensusSplice () |
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void | x_ReportSpliceProblems (const CSpliceProblems &problems, const string &label) |
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void | x_ReportDonorSpliceSiteReadErrors (const CSpliceProblems::TSpliceProblem &problem, const string &label) |
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void | x_ReportAcceptorSpliceSiteReadErrors (const CSpliceProblems::TSpliceProblem &problem, const string &label) |
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void | x_ValidateNonImpFeat () |
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void | x_ValidateGeneXRef () |
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void | x_ValidateGeneFeaturePair (const CSeq_feat &gene) |
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void | x_ValidateNonGene () |
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void | x_ValidateOldLocusTag (const string &old_locus_tag) |
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void | x_ValidateImpFeatLoc () |
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void | x_ValidateImpFeatQuals () |
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void | x_ValidateSeqFeatDataType () |
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void | x_ReportPseudogeneConflict (CConstRef< CSeq_feat > gene) |
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void | x_ValidateLocusTagGeneralMatch (CConstRef< CSeq_feat > gene) |
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void | x_CheckForNonAsciiCharacters () |
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static void | x_LocHasStrandBoth (const CSeq_loc &feat, bool &both, bool &both_rev) |
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static size_t | x_CalculateLocationGaps (CBioseq_Handle bsh, const CSeq_loc &loc, vector< TSeqPos > &gap_starts) |
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static bool | x_IsMostlyNs (const CSeq_loc &loc, CBioseq_Handle bsh) |
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static TSeqPos | x_FindStartOfGap (CBioseq_Handle bsh, TSeqPos pos, CScope *scope) |
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static bool | x_BioseqHasNmAccession (CBioseq_Handle bsh) |
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const CSeq_feat & | m_Feat |
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CScope & | m_Scope |
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CValidError_imp & | m_Imp |
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CBioseq_Handle | m_LocationBioseq |
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CBioseq_Handle | m_ProductBioseq |
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bool | m_ProductIsFar |
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Definition at line 337 of file single_feat_validator.hpp.