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◆ CpGeneticCodePtr() ◆ CpTheQualValueNext() static string CpTheQualValueNext ( TQualVector::const_iterator & cur_qual, const TQualVector::const_iterator & end_qual, const char * qual ) static ◆ DbxrefToSeqID() ◆ EndAdded()

Definition at line 1382 of file nucprot.cpp.

Referenced by InternalStopCodon().

◆ ErrByteStorePtr()

Definition at line 1144 of file nucprot.cpp.

References CpTheQualValue(), ERR_CDREGION_TranslationDiff, ErrLogPrintStr(), FtaErrPost, CSeq_feat_Base::GetExcept(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetQual(), CSeq_feat_Base::IsSetExcept(), location_to_string(), prot, and SEV_WARNING.

Referenced by CkProteinTransl(), and InternalStopCodon().

◆ ExtractDescrs() ◆ FindCd()

Definition at line 2297 of file nucprot.cpp.

References Begin(), ProtBlk::biosep, CpSeqId(), CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), ProtBlk::ibp, ProtBlk::IsBioseqSet, CSeq_annot::IsFtable(), CSeq_entry_Base::IsSet(), Parser::pbp, Parser::source, SrchCdRegion(), and Parser::USPTO.

Referenced by ProcNucProt().

◆ FixCreateDates() ◆ FixDupDates()

Definition at line 2505 of file nucprot.cpp.

References Begin(), CDate::Compare(), CSeqdesc_Base::e_Create_date, CSeqdesc_Base::e_Update_date, CDate::eCompare_same, CSeq_descr_Base::Get(), GetDateFromDescrs(), CBioseq_set_Base::GetDescr(), CBioseq_set_Base::IsSetDescr(), CBioseq_set_Base::IsSetSeq_set(), CBioseq_set_Base::SetDescr(), and CBioseq_set_Base::SetSeq_set().

Referenced by FixCreateDates(), and FixUpdateDates().

◆ FixEmblUpdateDates()

Definition at line 2561 of file nucprot.cpp.

References CSerialObject::Assign(), Begin(), CDate::Compare(), CSeqdesc_Base::e_Update_date, CDate::eCompare_same, CSeq_descr_Base::Get(), GetDateFromDescrs(), CBioseq_set_Base::GetDescr(), CEMBL_block_Base::GetUpdate_date(), CBioseq_set_Base::IsSetDescr(), CBioseq_set_Base::IsSetSeq_set(), CEMBL_block_Base::IsSetUpdate_date(), CBioseq_set_Base::SetDescr(), CBioseq_set_Base::SetSeq_set(), and CSeqdesc_Base::SetUpdate_date().

Referenced by CheckDupDates().

◆ FixUpdateDates() ◆ fta_check_codon_quals() ◆ fta_check_exception()

Definition at line 1882 of file nucprot.cpp.

References b, NStr::EqualNocase(), ERR_QUALIFIER_InvalidException, fta_concat_except_text(), FtaErrPost, GBExceptionQualVals, CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetQual(), CSeq_feat_Base::IsSetQual(), location_to_string(), Parser::Refseq, CSeq_feat_Base::ResetQual(), RSExceptionQualVals, CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetQual(), SEV_ERROR, SEV_REJECT, and rapidjson::source.

Referenced by CkCdRegion().

◆ fta_concat_except_text() ◆ fta_get_genetic_code() ◆ GetBioseqSetDescr() ◆ GetCdRegionCB()

Definition at line 1012 of file nucprot.cpp.

References Compare(), CpTheQualValueNext(), eContains, eExtreme_Positional, ERR_FEATURE_LocationParsing, fCompareOverlapping, FtaErrPost, CCode_break_Base::GetLoc(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetQual(), GetQualValueAa(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), i, InfoBioseq::ids, CCode_break_Base::IsSetLoc(), CSeq_feat_Base::IsSetLocation(), CSeq_feat_Base::IsSetQual(), CSeq_loc::IsSetStrand(), location, CRef< C, Locker >::NotEmpty(), CCode_break_Base::SetAa(), CCode_break_Base::SetLoc(), SEV_WARNING, SimpleValuePos(), and xgbparseint_ver().

Referenced by CkCdRegion().

◆ GetDateFromDescrs() ◆ GetGcode() ◆ GetProtRefAnnot()

Definition at line 501 of file nucprot.cpp.

Referenced by BldProtRefSeqEntry().

◆ GetProtRefDescr()

Definition at line 591 of file nucprot.cpp.

References Compare(), CpTheQualValue(), CMolInfo_Base::eBiomol_peptide, CMolInfo_Base::eCompleteness_no_ends, CMolInfo_Base::eCompleteness_no_left, CMolInfo_Base::eCompleteness_no_right, CMolInfo_Base::eCompleteness_partial, eContained, eExtreme_Biological, eGIBB_method_concept_trans, eGIBB_method_concept_trans_a, eNoOverlap, eOverlap, eSame, CMolInfo_Base::eTech_concept_trans, CMolInfo_Base::eTech_concept_trans_a, fCompareOverlapping, fta_if_special_org(), CSeq_descr_Base::Get(), CBioseq_Base::GetAnnot(), CBioseq_Base::GetDescr(), GetLength(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetPartial(), CSeq_feat_Base::GetQual(), CSeq_loc::GetStrand(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_feat_Base::IsSetPartial(), CRef< C, Locker >::Reset(), CSeqdesc_Base::SetMolinfo(), CSeqdesc_Base::SetTitle(), and rapidjson::source.

Referenced by BldProtRefSeqEntry().

◆ GetProtRefSeqId()

Definition at line 285 of file nucprot.cpp.

References Parser::accver, CpTheQualValue(), Parser::curindx, Parser::DDBJ, CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, Parser::EMBL, Parser::entrylist, ERR_CDREGION_IncorrectProteinAccession, ERR_CDREGION_IncorrectProteinVersion, ERR_CDREGION_MissingProteinId, ERR_CDREGION_MissingProteinVersion, fta_atoi(), FtaErrPost, CTextseq_id_Base::GetAccession(), CScope::GetBioseqHandle(), CSeq_feat_Base::GetLocation(), GetNewProtId(), GetNucAccOwner(), GetProtAccOwner(), Parser::HTGSCON, InfoBioseq::ids, Parser::ign_prot_src, location_to_string(), InfoBioseq::mAccNum, MakeUsptoPatSeqId(), Parser::mode, Parser::NCBI, CSeq_id::ParseIDs(), r(), Parser::Relaxed, CRef< C, Locker >::Reset(), CDbtag_Base::SetDb(), CSeq_id_Base::SetGeneral(), CSeq_id_Base::SetLocal(), CSeq_id_Base::SetPatent(), CSeq_feat_Base::SetProduct(), CSeq_feat_Base::SetQual(), CObject_id_Base::SetStr(), CDbtag_Base::SetTag(), SetTextId(), SEV_FATAL, SEV_WARNING, Parser::source, StringChr, and Parser::USPTO.

Referenced by CkCdRegion().

◆ GuessGeneticCode() ◆ IfOnlyStopCodon()

Definition at line 1832 of file nucprot.cpp.

References eExtreme_Positional, ERR_CDREGION_StopCodonBadInterval, ERR_CDREGION_StopCodonOnly, FtaErrPost, CBioseq::GetLength(), CSeq_feat_Base::GetLocation(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), i, CSeq_feat_Base::IsSetLocation(), CSeq_loc::IsSetStrand(), kInvalidSeqPos, len, location_to_string(), SEV_INFO, and SEV_REJECT.

Referenced by CkCdRegion().

◆ InternalStopCodon()

Definition at line 1591 of file nucprot.cpp.

References check_end_internal(), check_short_CDS(), check_translation(), CkEndStop(), CkProteinTransl(), CpTheQualValue(), Parser::curindx, Parser::debug, eGIBB_method_concept_trans, EndAdded(), Parser::entrylist, ERR_CDREGION_GeneticCodeAssumed, ERR_CDREGION_IllegalStart, ERR_CDREGION_InternalStopCodonFound, ERR_CDREGION_NoProteinSeq, ERR_CDREGION_TerminalStopCodonMissing, ERR_CDREGION_TranslationAdded, ErrByteStorePtr(), FtaErrPost, CSeq_feat_Base::GetExcept(), CCdregion_Base::GetFrame(), CGenetic_code_Base::C_E::GetId(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetPartial(), CSeq_feat_Base::GetQual(), CCdregion_Base::IsSetCode(), CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetPartial(), location_to_string(), Parser::no_code, prot, r(), SeqLocHaveFuzz(), CGenetic_code_Base::Set(), CCdregion_Base::SetCode(), CSeq_feat_Base::SetData(), CGenetic_code_Base::C_E::SetId(), CCdregion_Base::SetStops(), SEV_ERROR, SEV_INFO, SEV_WARNING, Parser::taxserver, and Translate().

Referenced by CkCdRegion().

◆ ProcessForDbxref() ◆ ProcNucProt()

Definition at line 2445 of file nucprot.cpp.

References BuildProtBioseqSet(), Parser::curindx, ProtBlk::entries, Parser::entrylist, ERR_CDREGION_GeneticCodeAssumed, FindCd(), FtaErrPost, ProtBlk::gcode, ProtBlk::genome, GetGcode(), Parser::no_code, ProtBlk::orig_gcode, Parser::pbp, ProtBlkFree(), ProtBlkInit(), CRef< C, Locker >::Reset(), SEV_INFO, SEV_WARNING, and Parser::taxserver.

Referenced by DealWithGenes(), and CXml2Asn::xGetEntry().

◆ ProtBlkFree() ◆ ProtBlkInit() ◆ QualsToSeqID()

Definition at line 757 of file nucprot.cpp.

References Parser::DDBJ, Parser::EMBL, CRef< C, Locker >::Empty(), ERR_CDREGION_InvalidDb_xref, FtaErrPost, CSeq_feat_Base::GetQual(), CSeq_feat_Base::IsSetQual(), CRef< C, Locker >::Reset(), CSeq_feat_Base::ResetQual(), CSeq_feat_Base::SetQual(), SEV_ERROR, rapidjson::source, StringIStr(), and StrToSeqId().

Referenced by ProcessForDbxref().

◆ s_ProcessCdsQuals() ◆ SimpleValuePos() static string_view SimpleValuePos ( const string_view & qval ) static ◆ SrchCdRegion()

Definition at line 2237 of file nucprot.cpp.

References CkCdRegion(), Parser::curindx, Parser::entrylist, ERR_CDREGION_BadLocForTranslation, ProtBlk::feats, FtaErrPost, CSeq_annot_Base::GetData(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetImp(), CImp_feat_Base::GetKey(), CSeq_feat_Base::GetLocation(), i, CSeq_loc_Base::IsBond(), CSeq_loc_Base::IsEmpty(), CSeq_loc_Base::IsEquiv(), CSeq_annot_Base::C_Data::IsFtable(), CSeqFeatData_Base::IsImp(), CSeq_annot_Base::IsSetData(), CSeq_feat_Base::IsSetData(), CImp_feat_Base::IsSetKey(), location_to_string(), Parser::pbp, CSeq_annot_Base::SetData(), SEV_REJECT, and StripCDSComment().

Referenced by FindCd().

◆ StripCDSComment() ◆ stripStr() static char* stripStr ( char * base, const char * str ) static ◆ Translate()

Definition at line 1333 of file nucprot.cpp.

References FtaErrPost, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CSeq_loc::GetId(), CSeq_feat_Base::GetLocation(), CException::GetMsg(), CCdregion_Base::IsSetCode_break(), CSeq_feat_Base::IsSetLocation(), prot, CSeq_feat_Base::SetData(), SEV_REJECT, and CSeqTranslator::Translate().

Referenced by EndAdded(), CGeneModel::GetProtein(), and InternalStopCodon().

◆ USING_SCOPE() ◆ ValidateQualSeqId() ◆ ValNodeExtractUserObject() ◆ GBExceptionQualVals const char* GBExceptionQualVals[] Initial value:

= {

"RNA editing",

"reasons given in citation",

"rearrangement required for product",

"annotated by transcript or proteomic data",

nullptr

}

Definition at line 109 of file nucprot.cpp.

Referenced by fta_check_exception().

◆ RSExceptionQualVals const char* RSExceptionQualVals[] Initial value:

= {

"RNA editing",

"reasons given in citation",

"ribosomal slippage",

"trans-splicing",

"alternative processing",

"artificial frameshift",

"nonconsensus splice site",

"rearrangement required for product",

"modified codon recognition",

"alternative start codon",

"unclassified transcription discrepancy",

"unclassified translation discrepancy",

"mismatches in transcription",

"mismatches in translation",

nullptr

}

Definition at line 117 of file nucprot.cpp.

Referenced by fta_check_exception().

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