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NCBI C++ ToolKit: include/objtools/validator/utilities.hpp File Reference

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enum   EAccessionFormatError {
  eAccessionFormat_valid = 0 , eAccessionFormat_no_start_letters , eAccessionFormat_wrong_number_of_digits , eAccessionFormat_null ,
  eAccessionFormat_too_long , eAccessionFormat_missing_version , eAccessionFormat_bad_version
}   enum   EDateValid {
  eDateValid_valid = 0x0 , eDateValid_bad_str = 0x01 , eDateValid_bad_year = 0x02 , eDateValid_bad_month = 0x04 ,
  eDateValid_bad_day = 0x08 , eDateValid_bad_season = 0x10 , eDateValid_bad_other = 0x20 , eDateValid_empty_date = 0x40
}   enum   EBioseqEndIsType { eBioseqEndIsType_None = 0 , eBioseqEndIsType_Last , eBioseqEndIsType_All }   enum   EDuplicateFeatureType {
  eDuplicate_Not = 0 , eDuplicate_Duplicate , eDuplicate_SameIntervalDifferentLabel , eDuplicate_DuplicateDifferentTable ,
  eDuplicate_SameIntervalDifferentLabelDifferentTable
}   bool  IsClassInEntry (const CSeq_entry &se, CBioseq_set::EClass clss)   bool  IsDeltaOrFarSeg (const CSeq_loc &loc, CScope *scope)   bool  IsBlankStringList (const list< string > &str_list)   TGi  GetGIForSeqId (const CSeq_id &id)   CScope::TIds  GetSeqIdsForGI (TGi gi)   bool  IsFarLocation (const CSeq_loc &loc, const CSeq_entry_Handle &seh)   CSeqVector  GetSequenceFromLoc (const CSeq_loc &loc, CScope &scope, CBioseq_Handle::EVectorCoding coding=CBioseq_Handle::eCoding_Iupac)   CSeqVector  GetSequenceFromFeature (const CSeq_feat &feat, CScope &scope, CBioseq_Handle::EVectorCoding coding=CBioseq_Handle::eCoding_Iupac, bool product=false)   string  GetSequenceStringFromLoc (const CSeq_loc &loc, CScope &scope)   bool  IsResidue (unsigned char residue)   CConstRef< CSeq_id >  GetReportableSeqIdForAlignment (const CSeq_align &align, CScope &scope)   string  GetAccessionFromObjects (const CSerialObject *obj, const CSeq_entry *ctx, CScope &scope, int *version)   string  GetAccessionFromBioseq (const CBioseq &bioseq, int *version)   string  GetAccessionFromBioseqSet (const CBioseq_set &bsst, int *version)   CBioseq_set_Handle  GetSetParent (const CBioseq_set_Handle &set, CBioseq_set::TClass set_class)   CBioseq_set_Handle  GetSetParent (const CBioseq_Handle &bioseq, CBioseq_set::TClass set_class)   CBioseq_set_Handle  GetGenProdSetParent (const CBioseq_set_Handle &set)   CBioseq_set_Handle  GetGenProdSetParent (const CBioseq_Handle &set)   CBioseq_set_Handle  GetNucProtSetParent (const CBioseq_Handle &bioseq)   CBioseq_Handle  GetNucBioseq (const CBioseq_set_Handle &bioseq_set)   CBioseq_Handle  GetNucBioseq (const CBioseq_Handle &bioseq)   EAccessionFormatError  ValidateAccessionString (const string &accession, bool require_version)   bool  s_IdXrefsAreReciprocal (const CSeq_feat &cds, const CSeq_feat &mrna)   bool  s_FeatureIdsMatch (const CFeat_id &f1, const CFeat_id &f2)   bool  s_StringHasPMID (const string &str)   bool  HasBadCharacter (const string &str)   bool  EndsWithBadCharacter (const string &str)   int  CheckDate (const CDate &date, bool require_full_date=false)   bool  IsDateInPast (const CDate &date)   string  GetDateErrorDescription (int flags)   bool  IsBioseqTSA (const CBioseq &seq, CScope *scope)   string  GetValidatorLocationLabel (const CSeq_loc &loc, CScope &scope)   void  AppendBioseqLabel (string &str, const CBioseq &sq, bool supress_context)   string  GetBioseqIdLabel (const CBioseq &sq)   bool  HasECnumberPattern (const string &str)   bool  SeqIsPatent (const CBioseq &seq)   bool  SeqIsPatent (const CBioseq_Handle &seq)   bool  s_PartialAtGapOrNs (CScope *scope, const CSeq_loc &loc, unsigned int tag, bool only_gap=false)   CBioseq_Handle  BioseqHandleFromLocation (CScope *m_Scope, const CSeq_loc &loc)   void  CheckBioseqEndsForNAndGap (const CBioseq_Handle &bsh, EBioseqEndIsType &begin_n, EBioseqEndIsType &begin_gap, EBioseqEndIsType &end_n, EBioseqEndIsType &end_gap, bool &begin_ambig, bool &end_ambig)   bool  ShouldCheckForNsAndGap (const CBioseq_Handle &bsh)   void  CheckBioseqEndsForNAndGap (const CSeqVector &vec, EBioseqEndIsType &begin_n, EBioseqEndIsType &begin_gap, EBioseqEndIsType &end_n, EBioseqEndIsType &end_gap, bool &begin_ambig, bool &end_ambig)   bool  IsDicistronicGene (const CSeq_feat_Handle &f)   Indicates whether feature is a dicistronic gene. More...
  bool  IsDicistronic (const CSeq_feat_Handle &f)   EDuplicateFeatureType  IsDuplicate (const CSeq_feat_Handle &f1, const CSeq_feat_Handle &f2, bool check_partials=false, bool case_sensitive=false)   Reports how two features duplicate each other. More...
  bool  IsLocFullLength (const CSeq_loc &loc, const CBioseq_Handle &bsh)   bool  PartialsSame (const CSeq_loc &loc1, const CSeq_loc &loc2)   bool  IsSpecificHostValid (const string &host, string &error_msg)   returns true and error_msg will be empty, if specific host is valid returns true and error_msg will be "Host is empty", if specific host is empty returns false if specific host is invalid More...
  string  FixSpecificHost (const string &host)   returns the corrected specific host, if the specific host is invalid and can be corrected returns an empty string, if the specific host is invalid and cannot be corrected returns the original value except the preceding/trailing spaces, if the specific host is valid More...
  bool  IsCommonName (const CT3Data &data)   bool  HasMisSpellFlag (const CT3Data &data)   bool  FindMatchInOrgRef (const string &str, const COrg_ref &org)   string  SpecificHostValueToCheck (const string &val)   bool  IsLikelyTaxname (const string &val)   string  InterpretSpecificHostResult (const string &host, const CT3Reply &reply, const string &orig_host=kEmptyStr)   void  AdjustSpecificHostForTaxServer (string &spec_host)   void  ConvertToEntrezTerm (string &title)   string  TranslateCodingRegionForValidation (const CSeq_feat &feat, CScope &scope, bool &alt_start)   bool  ReportTranslationErrors (const string &except_text)   bool  HasBadStartCodon (const CSeq_feat &feat, CScope &scope, bool ignore_exceptions)   bool  HasBadStartCodon (const CSeq_loc &loc, const string &transl_prot)   size_t  CountInternalStopCodons (const string &transl_prot)   bool  HasInternalStop (const CSeq_feat &feat, CScope &scope, bool ignore_exceptions)   CRef< CSeqVector >  MakeSeqVectorForResidueCounting (const CBioseq_Handle &bsh)   bool  HasBadProteinStart (const CSeqVector &sv)   bool  HasBadProteinStart (const CSeq_feat &cds, CScope &scope)   size_t  CountProteinStops (const CSeqVector &sv)   bool  HasStopInProtein (const CSeq_feat &feat, CScope &scope)   void  FeatureHasEnds (const CSeq_feat &feat, CScope *scope, bool &no_beg, bool &no_end)   CBioseq_Handle  GetCDSProductSequence (const CSeq_feat &feat, CScope *scope, const CTSE_Handle &tse, bool far_fetch, bool &is_far)   vector< TSeqPos >  GetMismatches (const CSeq_feat &feat, const CBioseq_Handle &prot_handle, const string &transl_prot)   vector< TSeqPos >  GetMismatches (const CSeq_feat &feat, const CSeqVector &prot_vec, const string &transl_prot)   void  CalculateEffectiveTranslationLengths (const string &transl_prot, const CSeqVector &prot_vec, size_t &len, size_t &prot_len)   bool  HasNoStop (const CSeq_feat &feat, CScope *scope)   bool  IsSequenceFetchable (const CSeq_id &id, CScope *scope=nullptr)   bool  IsSequenceFetchable (const string &seq_id, CScope *scope=nullptr)   bool  DoesFeatureHaveUnnecessaryException (const CSeq_feat &feat, CScope &scope)   bool  IsNTNCNWACAccession (const string &acc)   bool  IsNTNCNWACAccession (const CSeq_id &id)   bool  IsNTNCNWACAccession (const CBioseq &seq)   bool  IsNG (const CSeq_id &id)   bool  IsNG (const CBioseq &seq)   bool  IsTemporary (const CSeq_id &id)   bool  IsOrganelle (int genome)   bool  IsOrganelle (const CBioseq_Handle &seq)   bool  IsInOrganelleSmallGenomeSet (const CSeq_id &id, CScope &scope)   bool  BadMultipleSequenceLocation (const CSeq_loc &loc, CScope &scope)   bool  ConsistentWithA (Char ch)   bool  ConsistentWithC (Char ch)   bool  ConsistentWithG (Char ch)   bool  ConsistentWithT (Char ch)   bool  IsBadSubmissionFirstName (const string &first)   bool  IsBadSubmissionLastName (const string &last)   bool  g_IsMasterAccession (const CSeq_id &id)   ◆ TDbtags ◆ EAccessionFormatError Enumerator eAccessionFormat_valid  eAccessionFormat_no_start_letters  eAccessionFormat_wrong_number_of_digits  eAccessionFormat_null  eAccessionFormat_too_long  eAccessionFormat_missing_version  eAccessionFormat_bad_version 

Definition at line 105 of file utilities.hpp.

◆ EBioseqEndIsType Enumerator eBioseqEndIsType_None  eBioseqEndIsType_Last  eBioseqEndIsType_All 

Definition at line 156 of file utilities.hpp.

◆ EDateValid Enumerator eDateValid_valid  eDateValid_bad_str  eDateValid_bad_year  eDateValid_bad_month  eDateValid_bad_day  eDateValid_bad_season  eDateValid_bad_other  eDateValid_empty_date 

Definition at line 122 of file utilities.hpp.

◆ EDuplicateFeatureType Enumerator eDuplicate_Not  eDuplicate_Duplicate  eDuplicate_SameIntervalDifferentLabel  eDuplicate_DuplicateDifferentTable  eDuplicate_SameIntervalDifferentLabelDifferentTable 

Definition at line 191 of file utilities.hpp.

◆ AdjustSpecificHostForTaxServer() ◆ AppendBioseqLabel()

Definition at line 1066 of file utilities.cpp.

References ENUM_METHOD_NAME, CEnumeratedTypeValues::FindName(), GetBioseqIdLabel(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_inst_Base::GetMol(), CSeq_inst_Base::GetRepr(), NStr::IntToString(), CSeq_inst_Base::IsSetLength(), str(), and string.

Referenced by CValidErrorFormat::GetDescriptorLabel(), CValidError_imp::PostErr(), and CValidError_bioseq::x_ReportOverlappingPeptidePair().

◆ BadMultipleSequenceLocation() ◆ BioseqHandleFromLocation() ◆ CalculateEffectiveTranslationLengths() void CalculateEffectiveTranslationLengths ( const string &  transl_prot, const CSeqVector &  prot_vec, size_t &  len, size_t &  prot_len  ) ◆ CheckBioseqEndsForNAndGap() [1/2] ◆ CheckBioseqEndsForNAndGap() [2/2] ◆ CheckDate()

Definition at line 782 of file utilities.cpp.

References eDateValid_bad_day, eDateValid_bad_month, eDateValid_bad_other, eDateValid_bad_season, eDateValid_bad_str, eDateValid_bad_year, eDateValid_valid, NStr::Equal(), CDate_Base::GetStd(), CDate_Base::GetStr(), isalpha(), NStr::IsBlank(), CDate_Base::IsStd(), and CDate_Base::IsStr().

Referenced by CValidError_imp::ValidateCitSub(), CValidError_imp::ValidatePubArticleNoPMID(), CValidError_imp::ValidatePubGen(), and CValidError_desc::ValidateSeqDesc().

◆ ConsistentWithA() ◆ ConsistentWithC() ◆ ConsistentWithG() ◆ ConsistentWithT() ◆ ConvertToEntrezTerm() void ConvertToEntrezTerm ( string &  title ) ◆ CountInternalStopCodons() size_t CountInternalStopCodons ( const string &  transl_prot ) ◆ CountProteinStops() ◆ DoesFeatureHaveUnnecessaryException()

Definition at line 2942 of file utilities.cpp.

References CSpliceProblems::CalculateSpliceProblems(), DoesCodingRegionHaveUnnecessaryException(), DoesmRNAHaveUnnecessaryException(), CSeqFeatData::eSubtype_mRNA, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), CSeqFeatData::GetSubtype(), CSeqFeatData_Base::IsCdregion(), CSpliceProblems::IsExceptionUnnecessary(), IsPseudo(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetExcept_text(), and CSeq_feat_Base::IsSetLocation().

Referenced by CRemoveUnnecessaryExceptions::apply(), and BOOST_AUTO_TEST_CASE().

◆ EndsWithBadCharacter() ◆ FeatureHasEnds() ◆ FindMatchInOrgRef()

Definition at line 1987 of file utilities.cpp.

References NStr::EqualCase(), NStr::EqualNocase(), COrgMod_Base::eSubtype_gb_synonym, COrgMod_Base::eSubtype_old_name, FOR_EACH_SYN_ON_ORGREF, COrg_ref_Base::GetCommon(), COrgName_Base::GetMod(), COrg_ref_Base::GetOrgname(), COrg_ref_Base::GetTaxname(), NStr::IsBlank(), COrg_ref_Base::IsSetCommon(), COrgName_Base::IsSetMod(), COrg_ref_Base::IsSetOrgname(), COrg_ref_Base::IsSetTaxname(), match(), and str().

Referenced by CSpecificHostRequest::AddReply(), and InterpretSpecificHostResult().

◆ FixSpecificHost()

returns the corrected specific host, if the specific host is invalid and can be corrected returns an empty string, if the specific host is invalid and cannot be corrected returns the original value except the preceding/trailing spaces, if the specific host is valid

Definition at line 2192 of file utilities.cpp.

References val.

Referenced by BOOST_AUTO_TEST_CASE().

◆ g_IsMasterAccession() ◆ GetAccessionFromBioseq() ◆ GetAccessionFromBioseqSet() ◆ GetAccessionFromObjects()

Definition at line 445 of file utilities.cpp.

References ctx, CScope::GetBioseqHandle(), CBioseq_set_Handle::GetCompleteBioseq_set(), CSeq_loc::GetId(), CSeq_graph_Base::GetLoc(), CSeq_annot_Handle::GetParentEntry(), GetReportableSeqIdForAlignment(), CSeq_entry_Base::GetSeq(), CSeq_entry_Handle::GetSeq(), CScope::GetSeq_annotHandle(), CScope::GetSeq_entryHandle(), CSeq_entry_Base::GetSet(), CSeq_entry_Handle::GetSet(), CSerialObject::GetThisTypeInfo(), NStr::IsBlank(), CSeq_entry_Base::IsSeq(), CSeq_entry_Handle::IsSeq(), CSeq_entry_Base::IsSet(), CSeq_entry_Handle::IsSet(), s_GetAccessionForSeqdesc(), s_GetBioseqAcc(), s_GetSeq_featAcc(), s_GetSeqFromSet(), and dtl::version.

Referenced by CValidError_imp::PostErr(), CTable2AsnValidator::Validate(), and CValidError_align::x_ValidateDim().

◆ GetBioseqIdLabel() ◆ GetCDSProductSequence() ◆ GetDateErrorDescription() ◆ GetGenProdSetParent() [1/2] ◆ GetGenProdSetParent() [2/2] ◆ GetGIForSeqId() ◆ GetMismatches() [1/2] ◆ GetMismatches() [2/2] ◆ GetNucBioseq() [1/2] ◆ GetNucBioseq() [2/2] ◆ GetNucProtSetParent() ◆ GetReportableSeqIdForAlignment()

Definition at line 401 of file utilities.cpp.

References CScope::GetBioseqHandle(), CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::GetDim(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), i, IsBioseqInSameSeqEntryAsAlign(), CSeq_align_Base::C_Segs::IsDendiag(), CSeq_align_Base::IsSetDim(), CSeq_align_Base::IsSetSegs(), and CSeq_align_Base::C_Segs::IsStd().

Referenced by GetAccessionFromObjects(), CValidError_imp::PostErr(), and CValidError_align::x_ValidateDim().

◆ GetSeqIdsForGI() ◆ GetSequenceFromFeature() ◆ GetSequenceFromLoc() ◆ GetSequenceStringFromLoc() ◆ GetSetParent() [1/2] ◆ GetSetParent() [2/2] ◆ GetValidatorLocationLabel()

Definition at line 960 of file utilities.cpp.

References CSeq_loc::Assign(), CScope::GetBioseqHandle(), GetBioseqIdLabel(), CBioseq_Handle::GetCompleteBioseq(), CSeq_loc::GetLabel(), CSeq_loc_Base::GetWhole(), NStr::IsBlank(), CSeq_loc_Base::IsWhole(), NStr::ReplaceInPlace(), and UpdateToBestId().

Referenced by CValidErrorFormat::GetFeatureLocationLabel(), CValidErrorFormat::GetFeatureProductLocLabel(), CCdregionValidator::MapToNTCoords(), CValidError_imp::ValidateSeqLoc(), CValidError_imp::x_CheckLoc(), CCdregionValidator::x_ValidateCodebreak(), and CValidError_graph::x_ValidateGraphLocation().

◆ HasBadCharacter() ◆ HasBadProteinStart() [1/2] ◆ HasBadProteinStart() [2/2] ◆ HasBadStartCodon() [1/2]

Definition at line 2365 of file utilities.cpp.

References CSeq_feat_Base::CanGetExcept(), CSeq_feat_Base::CanGetExcept_text(), NStr::EqualNocase(), FOR_EACH_GBQUAL_ON_FEATURE, CSeq_feat_Base::GetData(), CSeq_feat_Base::GetExcept(), CSeq_feat_Base::GetExcept_text(), CSeq_feat_Base::GetLocation(), HasBadStartCodon(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Base::IsSetData(), ReportTranslationErrors(), and TranslateCodingRegionForValidation().

Referenced by CConvertBadCdsAndRnaToMiscFeat::apply(), BOOST_AUTO_TEST_CASE(), CCDSTranslationProblems::CalculateTranslationProblems(), and GetInternalStopErrorMessage().

◆ HasBadStartCodon() [2/2] ◆ HasECnumberPattern() ◆ HasInternalStop()

Definition at line 2419 of file utilities.cpp.

References CSeq_feat_Base::CanGetExcept(), CSeq_feat_Base::CanGetExcept_text(), CountInternalStopCodons(), NStr::EqualNocase(), NStr::Find(), FOR_EACH_GBQUAL_ON_FEATURE, CSeq_feat_Base::GetData(), CSeq_feat_Base::GetExcept(), CSeq_feat_Base::GetExcept_text(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Base::IsSetData(), kUnclassifiedTranslationDiscrepancy, ReportTranslationErrors(), and TranslateCodingRegionForValidation().

Referenced by CConvertBadCdsAndRnaToMiscFeat::apply(), and BOOST_AUTO_TEST_CASE().

◆ HasMisSpellFlag() ◆ HasNoStop()

Definition at line 2676 of file utilities.cpp.

References NStr::EndsWith(), FeatureHasEnds(), CScope::GetBioseqHandle(), GetCDSProductSequence(), CSeq_feat_Base::GetLocation(), GetMismatches(), CSeq_feat_Base::GetPartial(), CBioseq_Handle::GetTSE_Handle(), CSeq_feat_Base::IsSetPartial(), and TranslateCodingRegionForValidation().

Referenced by CConvertBadCdsAndRnaToMiscFeat::apply(), and BOOST_AUTO_TEST_CASE().

◆ HasStopInProtein() ◆ InterpretSpecificHostResult()

Definition at line 2088 of file utilities.cpp.

References FindMatchInOrgRef(), NStr::FindNoCase(), CT3Reply_Base::GetData(), CT3Reply_Base::GetError(), CT3Error_Base::GetMessage(), CT3Data_Base::GetOrg(), COrg_ref_Base::GetTaxname(), HasMisSpellFlag(), NStr::IsBlank(), IsCommonName(), CT3Reply_Base::IsData(), CT3Reply_Base::IsError(), CT3Error_Base::IsSetMessage(), and NStr::StartsWith().

Referenced by CSpecificHostRequest::AddReply().

◆ IsBadSubmissionFirstName() ◆ IsBadSubmissionLastName() ◆ IsBioseqTSA() ◆ IsBlankStringList() ◆ IsClassInEntry() ◆ IsCommonName() ◆ IsDateInPast() ◆ IsDeltaOrFarSeg() ◆ IsDicistronic() ◆ IsDicistronicGene() ◆ IsDuplicate()

Reports how two features duplicate each other.

Parameters
f1 Seq-feat-Handle [in] f2 Seq-feat-Handle [in]
Returns
EDuplicateFeatureType return value indicates how features are duplicates

Definition at line 1840 of file utilities.cpp.

References Compare(), eDuplicate_Duplicate, eDuplicate_DuplicateDifferentTable, eDuplicate_Not, eDuplicate_SameIntervalDifferentLabel, eDuplicate_SameIntervalDifferentLabelDifferentTable, eSame, CSeqFeatData::eSubtype_pub, CSeqFeatData::eSubtype_region, CSeqFeatData::eSubtype_variation, fCompareOverlapping, CSeq_feat_Handle::GetData(), CSeq_feat_Handle::GetDbxref(), CSeq_feat_Handle::GetLocation(), CSeq_feat_Handle::GetScope(), CSeqFeatData::GetSubtype(), CSeq_feat_Handle::IsSetDbxref(), PartialsSame(), s_AreCodingRegionsLinkedToDifferentmRNAs(), s_AreDifferentVariations(), s_AreFeatureLabelsSame(), s_AreFullLengthCodingRegionsWithDifferentFrames(), s_AremRNAsLinkedToDifferentCodingRegions(), s_IsDifferentDbxrefs(), s_IsSameSeqAnnot(), and s_IsSameStrand().

Referenced by CRmDupFeaturesDlg::GetCommand(), GetDuplicateFeaturesForRemoval(), CRemoveFeaturesDlg::RemoveDuplicateFeatures(), and CValidError_bioseq::x_ReportDupOverlapFeaturePair().

◆ IsFarLocation() ◆ IsInOrganelleSmallGenomeSet() ◆ IsLikelyTaxname()

Definition at line 2153 of file utilities.cpp.

References NStr::Find(), CTaxon1::GetOrgRef(), CTaxon1::GetTaxIdByName(), CTaxon1::Init(), INVALID_TAX_ID, isalpha(), IsCommon(), NPOS, val, and ZERO_TAX_ID.

Referenced by CSpecificHostRequest::AddReply(), and BOOST_AUTO_TEST_CASE().

◆ IsLocFullLength() ◆ IsNG() [1/2] ◆ IsNG() [2/2] ◆ IsNTNCNWACAccession() [1/3] ◆ IsNTNCNWACAccession() [2/3] ◆ IsNTNCNWACAccession() [3/3] ◆ IsOrganelle() [1/2] ◆ IsOrganelle() [2/2]

Definition at line 2834 of file utilities.cpp.

References CBioSource_Base::eGenome_apicoplast, CBioSource_Base::eGenome_chloroplast, CBioSource_Base::eGenome_chromatophore, CBioSource_Base::eGenome_chromoplast, CBioSource_Base::eGenome_cyanelle, CBioSource_Base::eGenome_hydrogenosome, CBioSource_Base::eGenome_kinetoplast, CBioSource_Base::eGenome_leucoplast, CBioSource_Base::eGenome_mitochondrion, CBioSource_Base::eGenome_nucleomorph, CBioSource_Base::eGenome_plastid, and CBioSource_Base::eGenome_proplastid.

Referenced by CSpliceProblems::CalculateSpliceProblems(), IsInOrganelleSmallGenomeSet(), CValidError_feat::IsIntronShort(), IsOrganelle(), CAdjustForConsensusSpliceSite::s_IsBioseqGood_AdjustEnds(), CIntronValidator::Validate(), CValidError_bioseq::ValidateFeatPartialInContext(), CMRnaForCDS::x_ChkAndMakeMRna(), CIntronValidator::x_IsIntronShort(), CValidError_bioseq::x_ReportStartStopPartialProblem(), CValidError_bioseq::x_SetupCommonFlags(), and CValidError_bioseq::x_ValidateAbuttingRNA().

◆ IsResidue() bool IsResidue ( unsigned char  residue ) inline ◆ IsSequenceFetchable() [1/2] ◆ IsSequenceFetchable() [2/2] ◆ IsSpecificHostValid() ◆ IsTemporary() ◆ MakeSeqVectorForResidueCounting()

Definition at line 2458 of file utilities.cpp.

References CSeq_data_Base::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, CSeq_data_Base::e_not_set, CBioseq_Handle::eCoding_Iupac, CBioseq_Handle::GetInst(), CSeq_inst_Base::GetSeq_data(), CSeq_inst_Base::IsSetSeq_data(), CSeqVector::SetCoding(), and CSeq_data_Base::Which().

Referenced by HasBadProteinStart(), HasStopInProtein(), and CValidError_bioseq::ValidateRawConst().

◆ PartialsSame() ◆ ReportTranslationErrors() ◆ s_FeatureIdsMatch() ◆ s_IdXrefsAreReciprocal() ◆ s_PartialAtGapOrNs()

Definition at line 1178 of file utilities.cpp.

References CBioseq_Handle::eCoding_Iupac, eNa_strand_minus, eSeqlocPartial_Nostart, eSeqlocPartial_Nostop, first(), CScope::GetBioseqHandle(), CRange_Base::GetFrom(), CSeq_loc::GetId(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetRangeAsSeq_loc(), CBioseq_Handle::GetSeqVector(), CSeq_loc_CI::GetStrand(), CRange_Base::GetTo(), isalpha(), CSeqVector::IsInGap(), IsResidue(), last(), len, result, CSeqVector::size(), swap(), and tag.

Referenced by CValidError_bioseq::ValidateFeatPartialInContext(), and CCDSTranslationProblems::x_CheckCDSFrame().

◆ s_StringHasPMID() ◆ SeqIsPatent() [1/2] ◆ SeqIsPatent() [2/2] ◆ ShouldCheckForNsAndGap() ◆ SpecificHostValueToCheck() ◆ TranslateCodingRegionForValidation()

Definition at line 2269 of file utilities.cpp.

References CSerialObject::Assign(), FixGeneticCode(), CScope::GetBioseqHandle(), CSeqFeatData_Base::GetCdregion(), CCdregion_Base::GetCode(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CBioseq_Handle::GetInst_Length(), CSeq_feat_Base::GetLocation(), CSeq_loc_Base::GetWhole(), CCdregion_Base::IsSetCode(), CCdregion_Base::IsSetFrame(), CSeq_loc_Base::IsWhole(), kEmptyStr, CSeq_feat_Base::SetData(), tmp, and CSeqTranslator::Translate().

Referenced by CCDSTranslationProblems::CalculateTranslationProblems(), HasBadStartCodon(), HasInternalStop(), HasNoStop(), and CCDSTranslationProblems::x_IsThreeBaseNonsense().

◆ ValidateAccessionString()

Definition at line 626 of file utilities.cpp.

References eAccessionFormat_bad_version, eAccessionFormat_missing_version, eAccessionFormat_no_start_letters, eAccessionFormat_null, eAccessionFormat_too_long, eAccessionFormat_valid, eAccessionFormat_wrong_number_of_digits, isalpha(), NStr::IsBlank(), isdigit(), isupper(), NStr::StartsWith(), and str().

Referenced by CValidError_bioseq::ValidateSeqId(), CSingleFeatValidator::x_ValidateCompareVal(), and CSingleFeatValidator::x_ValidateSeqFeatProduct().

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