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CAutoDefParsedtRNAClause * s_tRNAClauseFromNote (CBioseq_Handle bh, const CSeq_feat &cf, const CSeq_loc &mapped_loc, string comment, bool is_first, bool is_last, const CAutoDefOptions &opts) void s_UseCommentBeforeSemicolon (const CSeq_feat &feat, string &label) vector< CRef< CAutoDefFeatureClause > > AddMiscRNAFeatures (const CBioseq_Handle &bh, const CSeq_feat &cf, const CSeq_loc &mapped_loc, const CAutoDefOptions &opts) vector< CRef< CAutoDefFeatureClause > > AddtRNAAndOther (const CBioseq_Handle &bh, const CSeq_feat &cf, const CSeq_loc &mapped_loc, const CAutoDefOptions &opts) vector< CRef< CAutoDefFeatureClause > > FeatureClauseFactory (CBioseq_Handle bh, const CSeq_feat &cf, const CSeq_loc &mapped_loc, const CAutoDefOptions &opts, bool is_single_misc_feat) ◆ AddMiscRNAFeatures()Definition at line 2227 of file autodef_feature_clause.cpp.
References CSeq_feat_Base::CanGetComment(), CSeqFeatData_Base::e_Rna, NStr::Equal(), NStr::Find(), CSeq_feat_Base::GetComment(), CSeq_feat_Base::GetData(), CRNA_ref_Base::GetExt(), CRNA_ref_Base::C_Ext::GetGen(), CAutoDefFeatureClause_Base::GetMiscRNAElements(), CRNA_ref_Base::C_Ext::GetName(), CSeq_feat::GetNamedQual(), CRNA_gen_Base::GetProduct(), CSeqFeatData_Base::GetRna(), CAutoDefFeatureClause_Base::GetTrnaIntergenicSpacerClausePhrases(), NStr::IsBlank(), CRNA_ref_Base::C_Ext::IsGen(), CRNA_ref_Base::C_Ext::IsName(), CSeqFeatData_Base::IsRna(), CSeq_feat_Base::IsSetData(), CRNA_ref_Base::IsSetExt(), CRNA_gen_Base::IsSetProduct(), NPOS, s_tRNAClauseFromNote(), NStr::StartsWith(), NStr::TrimPrefixInPlace(), and CSeqFeatData_Base::Which().
Referenced by FeatureClauseFactory().
◆ AddtRNAAndOther() ◆ FeatureClauseFactory()Definition at line 2342 of file autodef_feature_clause.cpp.
References AddMiscRNAFeatures(), AddtRNAAndOther(), CSeq_feat_Base::CanGetComment(), CAutoDefOptions::eCommentFeat, CAutoDefOptions::eDelete, CAutoDefOptions::eNoncodingProductFeat, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_misc_RNA, CSeqFeatData::eSubtype_mobile_element, CSeqFeatData::eSubtype_ncRNA, CSeqFeatData::eSubtype_otherRNA, CSeqFeatData::eSubtype_rRNA, CSeq_feat_Base::GetComment(), CSeq_feat_Base::GetData(), CAutoDefOptions::GetMiscFeatRule(), CSeqFeatData::GetSubtype(), NStr::IsBlank(), CAutoDefFeatureClause::IsControlRegion(), CAutoDefOptions::IsFeatureSuppressed(), CAutoDefFeatureClause::IsGeneCluster(), CAutoDefFeatureClause::IsPromoter(), CAutoDefPromoterAnd5UTRClause::IsPromoterAnd5UTR(), CAutoDefFeatureClause::IsSatellite(), NULL, and CRef< C, Locker >::Reset().
Referenced by CAutoDef::x_GetFeatureClauses().
◆ s_tRNAClauseFromNote() ◆ s_UseCommentBeforeSemicolon() ◆ kMicrosatellite const char* kMicrosatellite = "microsatellite" ◆ kMinisatellite const char* kMinisatellite = "minisatellite" ◆ kSatellite const char* kSatellite = "satellite" ◆ mobile_element_keywords string mobile_element_keywords[] static Initial value:= {
"insertion sequence",
"retrotransposon",
"non-LTR retrotransposon",
"transposon",
"P-element",
"transposable element",
"integron",
"superintegron",
"SINE",
"MITE",
"LINE"
}
Definition at line 1596 of file autodef_feature_clause.cpp.
Referenced by CAutoDefMobileElementClause::CAutoDefMobileElementClause().
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