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NCBI C++ ToolKit: src/objtools/flatfile/loadfeat.cpp File Reference

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Definition at line 96 of file loadfeat.cpp.

Definition at line 3136 of file loadfeat.cpp.

References Indexblk::bases, Parser::curindx, Parser::DDBJ, Indexblk::drop, Parser::EMBL, Parser::entrylist, ERR_FEATURE_AssemblyGapAndLegacyGap, ERR_FEATURE_ContiguousGaps, ERR_FEATURE_FinishedHTGHasAssemblyGap, ERR_FEATURE_GapSizeEstLengthMissMatch, ERR_FEATURE_IllegalEstimatedLength, ERR_FEATURE_InvalidAssemblyGapLocation, ERR_FEATURE_InvalidGapLocation, ERR_FEATURE_OverlappingGaps, ERR_FEATURE_RequiredQualifierMissing, ERR_FEATURE_UnknownGapNot100, ERR_QUALIFIER_InvalidGapType, ERR_QUALIFIER_InvalidGapTypeForLinkageEvidence, ERR_QUALIFIER_InvalidLinkageEvidence, ERR_QUALIFIER_LinkageShouldBeUnspecified, ERR_QUALIFIER_LinkageShouldNotBeUnspecified, ERR_QUALIFIER_MissingGapType, ERR_QUALIFIER_MissingLinkageEvidence, ERR_QUALIFIER_UnexpectedGapTypeForHTG, CLinkage_evidence_Base::eType_unspecified, NStr::fConvErr_NoThrow, Parser::format, format, FtaErrPost, Indexblk::gaps, GapTypeValues, Parser::GenBank, GetSequenceOfKeywords(), ncbi::grid::netcache::search::fields::key, FeatBlk::key, Indexblk::keywords, LinkageEvidenceValues, FeatBlk::location, location_or(), DataBlk::mBuf, msg(), next(), StrNum::num, ParFlat_COL_DATA, ParFlat_COL_DATA_EMBL, ParFlat_KEYWORDS, ParFlat_KW, DataBlk::ptr, FeatBlk::quals, SEV_ERROR, SEV_REJECT, Parser::source, str(), StrNum::str, StringEqu(), NStr::StringToInt(), Indexblk::xip, Parser::XML, and XMLGetKeywords().

Referenced by LoadFeat().

Definition at line 718 of file loadfeat.cpp.

References buf, DbxrefObsolete, DbxrefTagAny, DbxrefTagInt, DbxrefTagStr, Parser::EMBL, EMBLDbxrefTagStr, NStr::EqualNocase(), ERR_FEATURE_ObsoleteDbXref, ERR_QUALIFIER_DbxrefIncorrect, ERR_QUALIFIER_DbxrefShouldBeNumeric, ERR_QUALIFIER_DbxrefUnknownDBName, ERR_QUALIFIER_DbxrefWrongType, ERR_QUALIFIER_EmptyQual, fta_atoi(), fta_number_is_huge(), FtaErrPost, CGb_qual_Base::GetQual(), CGb_qual_Base::GetVal(), CGb_qual_Base::IsSetQual(), CGb_qual_Base::IsSetVal(), MatchArrayIString(), r(), SEV_ERROR, SEV_WARNING, rapidjson::source, StringEquNI(), tag, and val.

Referenced by FilterDb_xref().

Definition at line 636 of file loadfeat.cpp.

References Parser::accver, Parser::buf, CheckOutsideEntry(), Parser::curindx, Parser::entrylist, ERR_LOCATION_FailedCheck, ERR_LOCATION_NCBIRefersToExternalRecord, ERR_LOCATION_RefersToExternalRecord, Parser::farseq, Parser::ffdb, format, FtaErrPost, CTextseq_id_Base::GetAccession(), CTextseq_id_Base::GetVersion(), Parser::indx, CTextseq_id_Base::IsSetVersion(), len, min(), msg(), Parser::NCBI, Nlm_ErrPostStr(), Nlm_ErrSetContext(), Parser::Refseq, SEV_WARNING, and Parser::source.

Referenced by LoadFeat().

Definition at line 4313 of file loadfeat.cpp.

References ERR_QUALIFIER_InvalidArtificialLoc, format, FtaErrPost, CSeq_feat_Base::GetLocation(), CSeq_feat_Base::IsSetExcept_text(), ncbi::grid::netcache::search::fields::key, location_to_string_or_unknown(), msg(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CSeq_feat_Base::SetQual(), SEV_ERROR, and val.

Referenced by LoadFeat().

Definition at line 2861 of file loadfeat.cpp.

References dummy, CSeq_id_Base::e_not_set, ERR_FEATURE_RequiredQualifierMissing, ERR_QUALIFIER_IllegalCompareQualifier, FtaErrPost, GetNucAccOwner(), FeatBlk::key, FeatBlk::location, FeatBlk::quals, SEV_ERROR, and StringChr.

Referenced by LoadFeat().

Definition at line 2278 of file loadfeat.cpp.

References CSeq_feat_Base::eExp_ev_experimental, CSeq_feat_Base::eExp_ev_not_experimental, NStr::EqualNocase(), ERR_QUALIFIER_Conflict, ERR_QUALIFIER_InvalidEvidence, FtaErrPost, key_or(), location_or(), FeatBlk::quals, CSeq_feat_Base::SetExp_ev(), SEV_ERROR, and SEV_REJECT.

Referenced by ProcFeatBlk().

Definition at line 3759 of file loadfeat.cpp.

References ERR_FEATURE_InvalidQualifierValue, ERR_FEATURE_RequiredQualifierMissing, format, FtaErrPost, i, FeatBlk::location, MatchArrayString(), MobileElementQualValues, FeatBlk::quals, SEV_ERROR, SEV_REJECT, rapidjson::source, StringChr, Parser::USPTO, and Parser::XML.

Referenced by ParseFeatureBlock(), and XMLParseFeatureBlock().

Definition at line 2915 of file loadfeat.cpp.

References Indexblk::drop, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, ERR_LOCATION_AccessionNotTLS, ERR_LOCATION_AccessionNotTPA, ERR_LOCATION_AccessionNotTSA, FtaErrPost, GetNucAccOwner(), i, Indexblk::is_tls, Indexblk::is_tpa, Indexblk::is_tsa, FeatBlk::key, location, FeatBlk::location, MemFree(), r(), SEV_REJECT, StringCat(), StringLen(), and StringSave.

Referenced by LoadFeat().

Definition at line 2728 of file loadfeat.cpp.

References NStr::EqualNocase(), ERR_FEATURE_MatchingOldNewLocusTag, ERR_FEATURE_OldLocusTagWithoutNew, ERR_FEATURE_RedundantOldLocusTag, FtaErrPost, key_or(), location_or(), lt, FeatBlk::quals, SEV_ERROR, and SEV_REJECT.

Referenced by LoadFeat().

Definition at line 2801 of file loadfeat.cpp.

References DeleteQual(), ERR_QUALIFIER_InvalidPseudoGeneValue, ERR_QUALIFIER_MultiplePseudoGeneQuals, ERR_QUALIFIER_OldPseudoWithPseudoGene, FtaErrPost, FeatBlk::key, FeatBlk::location, MatchArrayString(), PseudoGeneValues, FeatBlk::quals, and SEV_ERROR.

Referenced by LoadFeat().

Definition at line 4417 of file loadfeat.cpp.

References b, count, ERR_QUALIFIER_InvalidRegulatoryClass, ERR_QUALIFIER_MissingRegulatoryClass, ERR_QUALIFIER_MultipleRegulatoryClass, ERR_QUALIFIER_NoNoteForOtherRegulatory, fta_convert_to_regulatory(), FtaErrPost, FeatBlk::key, FeatBlk::location, FeatBlk::quals, RegulatoryClassValues, and SEV_REJECT.

Referenced by LoadFeat().

Definition at line 4560 of file loadfeat.cpp.

References Indexblk::acnum, Parser::DDBJ, delta(), Indexblk::drop, Parser::EMBL, ERR_SOURCE_SubmitterSeqidDropped, ERR_SOURCE_SubmitterSeqidIgnored, ERR_SOURCE_SubmitterSeqidNotAllowed, fta_create_wgs_dbtag(), fta_if_wgs_acc(), FtaErrPost, CTextseq_id_Base::GetAccession(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CBioseq_Base::GetInst(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc_CI::GetSeq_id(), i, Indexblk::is_tsa, CSeq_id_Base::IsDdbj(), CSeq_ext_Base::IsDelta(), CSeq_id_Base::IsEmbl(), CSeq_id_Base::IsGenbank(), CSeq_loc_Base::IsInt(), CSeq_id_Base::IsOther(), CTextseq_id_Base::IsSetAccession(), CSeq_inst_Base::IsSetExt(), CSeq_id_Base::IsTpd(), CSeq_id_Base::IsTpe(), CSeq_id_Base::IsTpg(), MemFree(), ok, Indexblk::secaccs, SEV_ERROR, SEV_REJECT, rapidjson::source, StringEquN(), StringSave, and Indexblk::submitter_seqid.

Referenced by LoadFeat().

Definition at line 1785 of file loadfeat.cpp.

References fta_get_aa_from_string(), fta_get_aa_from_symbol(), get_aa_from_trna(), MemFree(), remove(), ShrinkSpaces(), StringChr, StringEqu(), StringEquN(), StringLen(), and StringSave.

Referenced by GetRnaRef().

Definition at line 1617 of file loadfeat.cpp.

References b, first(), fta_get_aa_from_string(), get_aa_from_trna(), CSeq_feat_Base::GetComment(), CSeq_feat_Base::IsSetComment(), MemFree(), remove(), CSeq_feat_Base::SetComment(), ShrinkSpaces(), StringCpy(), StringEqu(), StringEquN(), StringIStr(), StringLen(), StringSave, StringStr, and trna_tags.

Referenced by GetRnaRef().

Definition at line 2208 of file loadfeat.cpp.

References ConvertQualifierValue(), count, ERR_QUALIFIER_ObsoleteRptUnit, first(), FtaErrPost, key_or(), len, location_or(), FeatBlk::quals, SEV_ERROR, and val.

Referenced by ProcFeatBlk().

Definition at line 1435 of file loadfeat.cpp.

References DeleteQual(), CRNA_ref_Base::eType_rRNA, fta_StringCpy(), CSeq_feat_Base::GetComment(), CSeq_feat_Base::GetQual(), GetTheQualValue(), CRNA_ref_Base::GetType(), CSeq_feat_Base::IsSetComment(), len, MemFree(), CSeq_feat_Base::ResetComment(), CSeq_feat_Base::ResetQual(), CRNA_ref_Base::SetExt(), CSeq_feat_Base::SetQual(), StringEquN(), StringEquNI(), StringIStr(), StringLen(), and StringSave.

Referenced by GetRnaRef().

Definition at line 3007 of file loadfeat.cpp.

References Compare(), eContained, ERR_FEATURE_InvalidOperonQual, ERR_FEATURE_MissingOperonQual, ERR_FEATURE_MultipleOperonQuals, ERR_FEATURE_OperonLocationMisMatch, ERR_FEATURE_OperonQualsNotUnique, eSame, fCompareOverlapping, FtaErrPost, CImp_feat_Base::GetKey(), FTAOperon::IsOperon(), CImp_feat_Base::IsSetKey(), location_to_string_or_unknown(), FTAOperon::LocationStr(), FTAOperon::mFeatname, FTAOperon::mOperon, and SEV_REJECT.

Referenced by LoadFeat().

Definition at line 2120 of file loadfeat.cpp.

References CBioSource_Base::CanGetOrg(), COrg_ref_Base::GetDb(), CObject_id_Base::GetId(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CObject_id_Base::GetStr(), COrgName_Base::IsSetMod(), COrg_ref_Base::IsSetOrgname(), CBioSource_Base::IsSetSubtype(), CObject_id_Base::IsStr(), mod(), CBioSource_Base::SetOrg(), and CBioSource_Base::SetSubtype().

Definition at line 1060 of file loadfeat.cpp.

References CSeq_bond_Base::CanGetA(), CTextseq_id_Base::CanGetAccession(), CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, CTextseq_id_Base::GetAccession(), CSeq_loc_Base::GetBond(), CSeq_loc::GetId(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc::GetStrand(), CSeq_id::GetTextseq_Id(), CSeq_id_Base::IsDdbj(), CSeq_id_Base::IsEmbl(), CSeq_id_Base::IsGenbank(), CSeq_id_Base::IsGpipe(), CSeq_id_Base::IsOther(), CSeq_id_Base::IsPir(), CSeq_id_Base::IsPrf(), CSeq_id_Base::IsSwissprot(), CSeq_id_Base::IsTpd(), CSeq_id_Base::IsTpe(), CSeq_id_Base::IsTpg(), PackSeqPntCheckCpp(), SeqIntCheckCpp(), SeqPntCheckCpp(), and CSeq_loc_Base::Which().

Referenced by LoadFeat(), and SeqFeatPub().

Definition at line 5061 of file loadfeat.cpp.

References CheckNA(), CheckNADDBJ(), count, Parser::curindx, Parser::DDBJ, Indexblk::division, Indexblk::drop, CMolInfo_Base::eBiomol_peptide, CMolInfo_Base::eBiomol_unknown, Parser::EMBL, Indexblk::embl_new_ID, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, NStr::eNocase, Parser::entrylist, NStr::EqualNocase(), ERR_DEFINITION_DifferingRnaTokens, ERR_FORMAT_InvalidMolType, ERR_LOCUS_NonViralRNAMoltype, ERR_SOURCE_GenomicViralRnaAssumed, ERR_SOURCE_InvalidMolType, ERR_SOURCE_LineageImpliesGenomicViralRna, ERR_SOURCE_MolTypesDisagree, ERR_SOURCE_MolTypeSeqTypeConflict, ERR_SOURCE_UnclassifiedViralRna, CMolInfo_Base::eTech_est, CMolInfo_Base::eTech_fli_cdna, CMolInfo_Base::eTech_htc, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, CMolInfo_Base::eTech_sts, CMolInfo_Base::eTech_survey, CMolInfo_Base::eTech_targeted, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_wgs, Parser::format, fta_StartsWith(), FtaErrPost, GetBiomolFromToks(), COrgName_Base::GetDiv(), DataBlk::GetEntryData(), COrgName_Base::GetLineage(), COrg_ref_Base::GetOrgname(), DataBlk::GetSubBlocks(), i, Indexblk::is_prot, COrgName_Base::IsSetDiv(), COrgName_Base::IsSetLineage(), COrg_ref_Base::IsSetOrgname(), Parser::LANL, len, Indexblk::moltype, Parser::NCBI, offset, ParFlat_COL_FEATKEY, ParFlat_DE, ParFlat_FH, r(), Seq_descr_GIBB_mol_cRNA, Seq_descr_GIBB_mol_genomic, Seq_descr_GIBB_mol_mRNA, Seq_descr_GIBB_mol_other, Seq_descr_GIBB_mol_other_genetic, Seq_descr_GIBB_mol_preRNA, Seq_descr_GIBB_mol_rRNA, Seq_descr_GIBB_mol_scRNA, Seq_descr_GIBB_mol_snoRNA, Seq_descr_GIBB_mol_snRNA, Seq_descr_GIBB_mol_tRNA, Seq_descr_GIBB_mol_trRNA, Seq_descr_GIBB_mol_unknown, EntryBlk::seq_entry, CBioseq_Base::SetInst(), SEV_ERROR, SEV_FATAL, SEV_REJECT, SEV_WARNING, rapidjson::source, Parser::source, SrchNodeType(), SrchTheStr(), NStr::StartsWith(), StringEqu(), StringEquN(), StringIStr(), TrackNodeType(), Parser::USPTO, and Parser::XML.

Referenced by GetEmblMolInfo(), GetGenBankMolInfo(), and XMLGetMolInfo().

Definition at line 1853 of file loadfeat.cpp.

References CpTheQualValue(), Parser::DDBJ, Parser::EMBL, CSeq_inst_Base::eMol_na, CRef< C, Locker >::Empty(), CRNA_ref_Base::eType_miscRNA, CRNA_ref_Base::eType_mRNA, CRNA_ref_Base::eType_ncRNA, CRNA_ref_Base::eType_premsg, CRNA_ref_Base::eType_rRNA, CRNA_ref_Base::eType_snoRNA, CRNA_ref_Base::eType_tmRNA, CRNA_ref_Base::eType_tRNA, fta_get_trna_from_comment(), fta_get_trna_from_product(), fta_parse_rrna_feat(), get_aa_from_trna(), get_first_codon_from_trna(), CSeq_feat_Base::GetComment(), CSeq_feat_Base::GetData(), CRNA_ref_Base::GetExt(), CBioseq_Base::GetId(), CSeqFeatData_Base::GetImp(), CImp_feat_Base::GetKey(), CSeq_feat_Base::GetQual(), GetQualValueAa(), GetTheQualValue(), CRNA_ref_Base::C_Ext::GetTRNA(), GetTrnaAnticodon(), CSeqFeatData_Base::IsImp(), CTrna_ext_Base::IsSetAnticodon(), CSeq_feat_Base::IsSetComment(), CRNA_ref_Base::IsSetExt(), CRNA_ref_Base::C_Ext::IsTRNA(), MatchArrayString(), CRef< C, Locker >::NotEmpty(), ParFlat_RNA_array, remove(), CRef< C, Locker >::Reset(), CSeq_feat_Base::ResetComment(), CRNA_ref_Base::ResetExt(), CSeq_feat_Base::ResetQual(), CRNA_qual_set_Base::Set(), CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), CRNA_ref_Base::SetExt(), CBioseq_Base::SetInst(), CRNA_qual_Base::SetQual(), CSeq_feat_Base::SetQual(), CRNA_ref_Base::SetType(), CRNA_qual_Base::SetVal(), rapidjson::source, StringIStr(), and type.

Referenced by LoadFeat().

Definition at line 919 of file loadfeat.cpp.

References Parser::accver, CSeq_loc::Assign(), fta_fix_seq_loc_id(), CSeq_loc_mix_Base::Get(), CSeq_loc_mix::GetFirstLoc(), CSeq_feat_Base::GetLocation(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::IsEmpty(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsMix(), location, CRef< C, Locker >::NotEmpty(), Ref(), CSeq_feat_Base::ResetLocation(), CSeq_feat_Base::SetLocation(), and xgbparseint_ver().

Referenced by ParseSourceFeat(), ProcFeatBlk(), SeqFeatPub(), and SpProcFeatBlk().

Definition at line 1357 of file loadfeat.cpp.

References CRef< C, Locker >::Empty(), ERR_FEATURE_BadAnticodonLoc, ERR_FEATURE_FourBaseAntiCodon, ERR_FEATURE_InvalidAnticodonPos, ERR_FEATURE_StrangeAntiCodonSize, fta_fake_gbparse_err_handler(), FtaErrPost, GetLength(), CSeq_feat_Base::GetLocation(), CSeq_loc::GetTotalRange(), COpenRange< Position >::IntersectionWith(), location_to_string_or_unknown(), CRef< C, Locker >::Reset(), SEV_ERROR, SEV_WARNING, StringStr, xgbparseint_ver(), and xinstall_gbparse_error_handler().

Referenced by GetRnaRef().

Definition at line 1284 of file loadfeat.cpp.

References Indexblk::bases, DescrRefs(), CRef< C, Locker >::Empty(), first(), Parser::format, fta_get_seqloc_int_whole(), DataBlk::mBuf, CRef< C, Locker >::NotEmpty(), ParFlat_REF_SITES, DataBlk::ptr, CRef< C, Locker >::Reset(), CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetCit(), CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), CPub_Base::SetEquiv(), CImp_feat_Base::SetKey(), CImp_feat_Base::SetLoc(), CSeq_feat_Base::SetLocation(), TrackNodes(), Indexblk::xip, Parser::XML, and XMLBuildRefDataBlk().

Referenced by LoadFeat().

Definition at line 4732 of file loadfeat.cpp.

References Parser::accver, Indexblk::acnum, Indexblk::bases, Indexblk::biodrop, CheckForeignLoc(), CollectGapFeats(), Parser::curindx, Parser::DDBJ, Parser::debug, Indexblk::drop, CSeq_id_Base::e_Local, Parser::EMBL, CRef< C, Locker >::Empty(), Parser::entrylist, ERR_FEATURE_LocationParsing, ERR_FEATURE_MoreThanOneCAGEFeat, ERR_LOCATION_FailedCheck, ERR_LOCATION_MixedStrand, ERR_LOCATION_TransSpliceMixedStrand, ERR_SOURCE_DescriptorDropped, FilterDb_xref(), flat2asn_range_func(), Parser::format, FreeFeatBlk(), fta_check_artificial_location(), fta_check_compare_qual(), fta_check_multiple_locus_tag(), fta_check_ncrna(), fta_check_non_tpa_tsa_tls_locations(), fta_check_old_locus_tags(), fta_check_pseudogene_qual(), fta_check_replace_regulatory(), fta_check_rpt_unit_range(), fta_create_wgs_seqid(), fta_get_gcode_from_biosource(), fta_perform_operon_checks(), fta_remove_dup_feats(), fta_remove_dup_quals(), fta_sort_quals(), FtaErrPost, FTASeqLocCheck(), Parser::GenBank, CSeq_feat_Base::GetData(), CSeq_feat_Base::GetExcept_text(), CSeqFeatData_Base::GetImp(), CImp_feat_Base::GetKey(), CSeq_feat_Base::GetLocation(), CBioSource_Base::GetOrg(), GetRnaRef(), CSeqdesc_Base::GetSource(), COrg_ref_Base::GetTaxname(), i, ImpFeatPub(), INSDSEQ_SOURCE, Indexblk::is_mga, Indexblk::is_tls, Indexblk::is_tpa, Indexblk::is_tsa, NStr::IsBlank(), CSeqFeatData_Base::IsImp(), CSeq_feat_Base::IsSetExcept_text(), CImp_feat_Base::IsSetKey(), CBioSource_Base::IsSetOrg(), FeatBlk::key, FeatBlk::location, Indexblk::locusname, MakeAccSeqId(), MakeUsptoPatSeqId(), DataBlk::mBuf, Parser::mode, ParFlat_COL_DATA, ParFlat_COL_DATA_EMBL, ParFlat_FEATURES, ParFlat_FH, ParseFeatureBlock(), ParseSourceFeat(), ProcFeatBlk(), DataBlk::ptr, Parser::qamode, Ref(), Parser::Relaxed, remove(), CRef< C, Locker >::Reset(), s_RemoveSourceDescriptors(), SeqFeatPub(), Parser::seqtype, CBioseq_Base::SetAnnot(), CSeq_annot_Base::SetData(), CBioseq_Base::SetDescr(), CSeq_id_Base::SetPatent(), CSeqdesc_Base::SetSource(), SEV_ERROR, SEV_INFO, SEV_REJECT, SEV_WARNING, SortFeaturesByLoc(), SortFeaturesByOrder(), Parser::source, FeatBlk::spindex, SpProcFeatBlk(), Indexblk::submitter_seqid, Parser::taxserver, TrackNodes(), type, Parser::USPTO, Indexblk::vernum, xinstall_gbparse_range_func(), Indexblk::xip, Parser::XML, XML_FEATURES, XMLFindTagValue(), XMLLoadFeatBlk(), and XMLParseFeatureBlock().

Referenced by CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), and CXml2Asn::xGetEntry().

Definition at line 3840 of file loadfeat.cpp.

References Indexblk::bases, compile_time_bits::const_bitset< _MaxBits, T >::begin(), Indexblk::drop, ctll::empty(), ERR_FEATURE_Dropped, ERR_FEATURE_FeatureKeyReplaced, ERR_FEATURE_InvalidQualifier, ERR_FEATURE_LocationParsing, ERR_FEATURE_ObsoleteFeature, ERR_FEATURE_RequiredQualifierMissing, ERR_FEATURE_UnknownFeatKey, CSeqFeatData::eSubtype_bad, Parser::Flybase, format, fta_check_mobile_element(), fta_check_satellite(), fta_convert_to_lower_case(), fta_strip_aa(), FtaDeletePrefix(), FtaErrPost, FtaInstallPrefix(), GB_FEAT_ERR_DROP, GB_FEAT_ERR_NONE, GB_FEAT_ERR_REPAIRABLE, CSeqFeatData::GetMandatoryQualifiers(), CSeqFeatData::GetQualifierAsString(), i, Indexblk::is_mga, Indexblk::is_prot, FeatBlk::key, FeatBlk::location, location_or(), MergeNoteQual(), FeatBlk::num, ParFlat_COL_FEATDAT, ParFlat_COL_FEATKEY, ParseQualifiers(), PREFIX_FEATURE, FeatBlk::quals, SEV_ERROR, SEV_REJECT, SEV_WARNING, ShrinkSpaces(), rapidjson::source, FeatBlk::spindex, str(), string, StringEquN(), CSeqFeatData::SubtypeNameToValue(), Parser::USPTO, XGBFeatKeyQualValid(), and Parser::XML.

Referenced by LoadFeat().

Definition at line 2378 of file loadfeat.cpp.

References b, Parser::buf, Parser::curindx, Parser::debug, DelCharBtwData(), DeleteQual(), Parser::entrylist, ERR_FEATURE_Dropped, ERR_LOCATION_FailedCheck, fta_check_evidence(), fta_parse_rpt_units(), FtaErrPost, GetImpFeat(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetPartial(), GetSeqLocation(), GetTheQualValue(), CSeq_feat_Base::IsSetExcept_text(), CSeq_feat_Base::IsSetPartial(), FeatBlk::key, FeatBlk::location, FeatBlk::quals, CRef< C, Locker >::Reset(), SeqLocHaveFuzz(), CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CSeq_feat_Base::SetPartial(), CSeq_feat_Base::SetPseudo(), CSeq_feat_Base::SetQual(), SEV_ERROR, SEV_WARNING, and TransSplicingFeats.

Referenced by LoadFeat().

Definition at line 1160 of file loadfeat.cpp.

References Indexblk::acnum, Parser::buf, CheckLocStr(), Parser::debug, DescrRefs(), Indexblk::drop, Parser::EMBL, CRef< C, Locker >::Empty(), ERR_LOCATION_FailedCheck, ERR_LOCATION_MixedStrand, ERR_REFERENCE_UnparsableLocation, Parser::format, fta_strip_aa(), FtaErrPost, FTASeqLocCheck(), Parser::GenBank, CSeq_feat_Base::GetLocation(), GetSeqLocation(), i, INSDREFERENCE_POSITION, INSDREFERENCE_REFERENCE, Indexblk::is_prot, isdigit(), location, DataBlk::mBuf, ParFlat_REF_BTW, ParFlat_RP, DataBlk::ptr, CSeq_feat_Base::SetData(), SEV_REJECT, SEV_WARNING, StringChr, TrackNodes(), Indexblk::xip, Parser::XML, XMLBuildRefDataBlk(), and XMLFindTagValue().

Referenced by LoadFeat().

Definition at line 1008 of file loadfeat.cpp.

References CBioseq_Handle::CanGetInst(), CBioseq_Handle::CanGetInst_Length(), CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_interval_Base::GetFrom(), CSeq_loc::GetId(), CSeq_loc_Base::GetInt(), GetScope(), CSeq_interval_Base::GetTo(), len, and max().

Referenced by FTASeqLocCheck().

Definition at line 3316 of file sp_ascii.cpp.

References Parser::buf, CpTheQualValue(), Parser::debug, NStr::EqualNocase(), ERR_FEATURE_Dropped, ERR_FEATURE_ObsoleteFeature, ERR_LOCATION_FailedCheck, FtaErrPost, CSeq_feat_Base::GetLocation(), GetSeqLocation(), GetSPSitesMod(), FeatBlk::key, FeatBlk::location, ParFlat_SPFeat, ParFlatSPBonds, ParFlatSPImports, ParFlatSPInitMet, ParFlatSPNonCons, ParFlatSPNonTer, ParFlatSPRegions, ParFlatSPSites, ParFlatSPSitesModB, FeatBlk::quals, CSeq_feat_Base::Reset(), SeqLocHaveFuzz(), CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetPartial(), SEV_ERROR, SEV_WARNING, FeatBlk::spindex, type, and SPFeatType::type.

Referenced by LoadFeat().

Definition at line 4038 of file loadfeat.cpp.

References b, CheckLegalQual(), DelCharBtwData(), ctll::empty(), EmptyQuals, ERR_FEATURE_EmptyOldLocusTag, ERR_QUALIFIER_EmbeddedQual, ERR_QUALIFIER_EmptyQual, ERR_QUALIFIER_ShouldNotHaveValue, fta_convert_to_lower_case(), fta_process_cons_splice(), FtaErrPost, key_or(), location_or(), FeatBlk::quals, SEV_ERROR, SEV_WARNING, rapidjson::source, Parser::USPTO, and val.

Referenced by XMLParseFeatureBlock().

Definition at line 3502 of file loadfeat.cpp.

References INSDFEATURE_KEY, INSDFEATURE_LOCATION, INSDFEATURE_QUALS, INSDSEQ_FEATURE_TABLE, FeatBlk::key, FeatBlk::location, FeatBlk::quals, FeatBlk::spindex, XML_FEATURES, XMLGetQuals(), and XMLGetTagValue().

Referenced by LoadFeat().

Definition at line 4138 of file loadfeat.cpp.

References compile_time_bits::const_bitset< _MaxBits, T >::begin(), Indexblk::drop, ctll::empty(), ERR_FEATURE_Dropped, ERR_FEATURE_FeatureKeyReplaced, ERR_FEATURE_ObsoleteFeature, ERR_FEATURE_RequiredQualifierMissing, ERR_FEATURE_UnknownFeatKey, CSeqFeatData::eSubtype_bad, CSeqFeatData::eSubtype_conflict, CSeqFeatData::eSubtype_region, CSeqFeatData::eSubtype_site, CSeqFeatData::eSubtype_unsure, Parser::Flybase, fta_check_mobile_element(), fta_convert_to_lower_case(), FtaDeletePrefix(), FtaErrPost, FtaInstallPrefix(), GB_FEAT_ERR_DROP, GB_FEAT_ERR_NONE, GB_FEAT_ERR_REPAIRABLE, CSeqFeatData::GetMandatoryQualifiers(), CSeqFeatData::GetQualifierAsString(), FeatBlk::key, FeatBlk::location, MergeNoteQual(), FeatBlk::num, PREFIX_FEATURE, FeatBlk::quals, SEV_ERROR, SEV_WARNING, ShrinkSpaces(), rapidjson::source, SpFeatKeyNameValid(), FeatBlk::spindex, str(), CSeqFeatData::SubtypeNameToValue(), Parser::USPTO, XGBFeatKeyQualValid(), Parser::XML, and XMLCheckQualifiers().

Referenced by LoadFeat().

= {

"BHB",

"BIOHEALTHBASE",

"GENEW",

"IFO",

"SWISS-PROT",

"SPTREMBL",

"TREMBL",

nullptr

}

Definition at line 291 of file loadfeat.cpp.

Referenced by DbxrefQualToDbtag().

= {

"ATCC",

"ATCC(DNA)",

"ATCC(IN HOST)",

"BDGP_EST",

"BDGP_INS",

"ESTLIB",

"GENEID",

"GI",

"GO",

"GREENGENES",

"INTREPIDBIO",

"JCM",

"LOCUSID",

"MIM",

"MYCOBANK",

"NBRC",

"PBMICE",

"RATMAP",

"RGD",

"UNILIB",

"UNISTS",

nullptr

}

Definition at line 404 of file loadfeat.cpp.

Referenced by DbxrefQualToDbtag().

= {

"BIOMUTA",

"DEPOD",

"ENSEMBLGENOMES-GN",

"ENSEMBLGENOMES-TR",

"ESTHER",

"GENEVISIBLE",

"MOONPROT",

"PROTEOMES",

"UNITE",

"WBPARASITE",

nullptr

}

Definition at line 302 of file loadfeat.cpp.

Referenced by DbxrefQualToDbtag().

= {

"artificial_location",

"chloroplast",

"chromoplast",

"cyanelle",

"environmental_sample",

"focus",

"germline",

"kinetoplast",

"macronuclear",

"metagenomic",

"mitochondrion",

"partial",

"proviral",

"pseudo",

"rearranged",

"ribosomal_slippage",

"trans_splicing",

"transgenic",

"virion",

nullptr

}

Definition at line 429 of file loadfeat.cpp.

Referenced by XMLCheckQualifiers().

= {

"transposon",

"retrotransposon",

"integron",

"insertion sequence",

"non-LTR retrotransposon",

"SINE",

"MITE",

"LINE",

"other",

}

Definition at line 534 of file loadfeat.cpp.

Referenced by fta_check_mobile_element().

= {

"antisense_RNA",

"autocatalytically_spliced_intron",

"hammerhead_ribozyme",

"lncRNA",

"RNase_P_RNA",

"RNase_MRP_RNA",

"telomerase_RNA",

"guide_RNA",

"rasiRNA",

"ribozyme",

"scRNA",

"siRNA",

"miRNA",

"piRNA",

"pre_miRNA",

"snoRNA",

"snRNA",

"SRP_RNA",

"vault_RNA",

"Y_RNA",

"other",

nullptr

}

Definition at line 465 of file loadfeat.cpp.

Referenced by fta_check_ncrna().

= {

"EST",

"expressed sequence tag",

"partial cDNA sequence",

"transcribed sequence fragment",

"TSR",

"putatively transcribed partial sequence",

"UK putts",

"Plastid",

nullptr

}

Definition at line 254 of file loadfeat.cpp.

= {

"precursor_RNA",

"mRNA",

"tRNA",

"rRNA",

"snRNA",

"scRNA",

"snoRNA",

"ncRNA",

"tmRNA",

"misc_RNA",

nullptr

}

Definition at line 266 of file loadfeat.cpp.

Referenced by GetRnaRef().

= {

"attenuator",

"CAAT_signal",

"DNase_I_hypersensitive_site",

"enhancer",

"enhancer_blocking_element",

"GC_signal",

"imprinting_control_region",

"insulator",

"locus_control_region",

"matrix_attachment_region",

"minus_35_signal",

"minus_10_signal",

"response_element",

"polyA_signal_sequence",

"promoter",

"recoding_stimulatory_region",

"replication_regulatory_region",

"ribosome_binding_site",

"riboswitch",

"silencer",

"TATA_box",

"terminator",

"transcriptional_cis_regulatory_region",

"other",

nullptr

}

Definition at line 506 of file loadfeat.cpp.

Referenced by fta_check_replace_regulatory().

= {

{ "alanine", 'A' },

{ "arginine", 'R' },

{ "asparagine", 'N' },

{ "aspartic acid", 'D' },

{ "aspartate", 'D' },

{ "cysteine", 'C' },

{ "glutamine", 'Q' },

{ "glutamic acid", 'E' },

{ "glutamate", 'E' },

{ "glycine", 'G' },

{ "histidine", 'H' },

{ "isoleucine", 'I' },

{ "leucine", 'L' },

{ "lysine", 'K' },

{ "methionine", 'M' },

{ "phenylalanine", 'F' },

{ "proline", 'P' },

{ "selenocysteine", 'U' },

{ "serine", 'S' },

{ "threonine", 'T' },

{ "tryptophan", 'W' },

{ "tyrosine", 'Y' },

{ "valine", 'V' },

{ nullptr, '\0' }

}

Definition at line 126 of file loadfeat.cpp.

Referenced by fta_get_aa_from_string(), s_CodonToAA(), CFeatureTableReader_Imp::x_AddQualifierToRna(), CNewCleanup_imp::x_IsCodonCorrect(), and CRNAValidator::x_ValidateTrnaCodons().

= {

"3'UTR",

"5'UTR",

"CDS",

"gene",

"mRNA",

"misc_RNA",

"precursor_RNA",

"tRNA",

nullptr

}

Definition at line 453 of file loadfeat.cpp.

Referenced by ProcFeatBlk().

= {

"TRANSFERN RNA",

"TRANSFER RRNA",

"TRANSFER TRNA",

"TRANSFER RNA",

"TRASNFER RNA",

"TRANSDER RNA",

"TRANSFERRNA",

"TRANFER RNA",

"T RNA",

"TRNA",

nullptr

}

Definition at line 240 of file loadfeat.cpp.

Referenced by fta_get_trna_from_product().

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