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NCBI C++ ToolKit: variation Namespace Reference

  USING_SCOPE (objects)   CVariantPlacement &  SetFirstPlacement (CVariation &v)   void  SetComputational (CVariation &variation)   bool  SeqsMatch (const string &query, const char *text)   CRef< CSeq_loc >  FindSSRLoc (const CSeq_loc &loc, const string &seq, CScope &scope)   void  RepackageAssertedSequence (CVariation &vr)   void  AdjustMoltype (CVariation &vr, CScope &scope)   template<typename T > T  AdjustHgvsCoord (T val, TSeqPos offset, bool adjust)   bool  IsPureFuzzPoint (const CSeq_point &p)   CSeq_id_Handle  GetUniquePrimaryTranscriptId (CBioseq_Handle &bsh)   bool  IsLRG (CBioseq_Handle &bsh)   int  GetDeltaLength (const CDelta_item &delta, int loc_len)   CVariation_inst::EType  GetDelInsSubtype (int del_len, int ins_len)   string  Ncbieaa2HgvsAA (const string &prot_str)   bool  IsMitochondrion (CBioseq_Handle bsh)   bool  ContainsAnyFuzz (CConstRef< CVariantPlacement > p)   static CRef< CVariationException >  CreateException (const string &message, CVariationException::ECode code=static_cast< CVariationException::ECode >(0))   template<typename T > static void  ChangeIdsInPlace (T &container, sequence::EGetIdType id_type, CScope &scope)   static bool  ValidExonTerminal (const set< TSeqPos > &exon_biostarts, const set< TSeqPos > &exon_biostops, TSeqPos exon_anchor_pos, int offset_pos)   static int  GetFuzzSign (const CInt_fuzz &fuzz, int loc_sign)   static bool  ValidExonTerminals (const set< TSeqPos > &exon_biostarts, const set< TSeqPos > &exon_biostops, const CVariantPlacement &p)   static void  SwapLtGtFuzz (CInt_fuzz &fuzz)   static void  ApplyOffsetFuzz (CSeq_loc &loc, const CInt_fuzz &offset_fuzz, bool is_start)   static CRef< CSeq_align >  CreateSplicedSeqAlignFromFeat (const CSeq_feat &rna_feat)   template<typename T > static bool  ContainsIupacNaAmbiguities (const T &obj)   static bool  IsRightPartial (CBioseq_Handle bsh)   static string  Translate (const string &nuc_str, bool is_mito)   CVariation_inst::EType  CalcInstTypeForAA (const string &prot_ref_str, const string &prot_delta_str)   static CVariantProperties::TEffect  CalcEffectForProt (const string &prot_ref_str, const string &prot_delta_str)   static CVariationUtil::TSOTerms  CalcSOTermsForProt (TSignedSeqPos nuc_delta_len, const string &prot_ref_str, const string &prot_variant_str)   static bool  Contains (const CSeq_loc &a, const CSeq_loc &b, CScope *scope)   static CRef< CVariation >  CreateUnknownProtConsequenceVariation (const CVariantPlacement &nuc_p, const CSeq_feat &cds_feat, bool is_frameshifting, CScope &scope)   static size_t  GetCommonPrefixLen (const string &a, const string &b)   static size_t  GetCommonSuffixLen (const string &a, const string &b)   static bool  HasProblematicExceptions (const CSeq_feat &cds_feat)   static bool  Equals (const CVariation::TPlacements &p1, const CVariation::TPlacements &p2)   static bool  IsRefSeqGene (const CBioseq_Handle &bsh)   static set< int >  GetFocusLocusIDs (const CBioseq_Handle &bsh)   CRef< CVariation >  InheritParentAttributes (const CVariation &child, const CVariation &parent)   static CRef< CDelta_item >  CreateDeltaForOffset (int offset, const CInt_fuzz *fuzz)   static int  GetSignedOffset (const CDelta_item &delta)   static const CInt_fuzz *  GetFuzz (const CDelta_item &delta)   ◆ AdjustHgvsCoord()

template<typename T >

T variation::AdjustHgvsCoord ( T  val, TSeqPos  offset, bool  adjust  ) ◆ AdjustMoltype() ◆ ApplyOffsetFuzz() ◆ CalcEffectForProt() ◆ CalcInstTypeForAA() ◆ CalcSOTermsForProt() ◆ ChangeIdsInPlace()

Definition at line 112 of file variation_util2.cpp.

References Begin(), eGetId_ForceAcc, eGetId_ForceGi, GetId(), CSeq_id_Handle::GetSeqId(), and NCBI_USER_THROW.

Referenced by CreateUnknownProtConsequenceVariation(), variation::CVariationUtil::CCdregionIndex::Get(), variation::CVariationUtil::CCdregionIndex::GetCachedLiteralAtLoc(), variation::CVariationUtil::CVariantPropertiesIndex::GetLocationProperties(), variation::CVariationUtil::RemapToAnnotatedTarget(), variation::CVariationUtil::TranslateNAtoAA(), variation::CVariationUtil::x_CreateUnknownVariation(), variation::CVariationUtil::x_InferNAfromAA(), and variation::CVariationUtil::x_Remap().

◆ Contains()

Definition at line 2259 of file variation_util2.cpp.

References a, CSeq_loc::Assign(), b, Compare(), eContains, fCompareOverlapping, and CSeq_loc::ResetStrand().

Referenced by CSimpleDesktopItem::FindItem(), CCompositeDesktopItem::FindItem(), CNoFocusBitmapButton::OnMotion(), CNoFocusBitmapButton::OnMouseUp(), variation::CVariationUtil::TranslateNAtoAA(), and CwxTableListCtrl::x_ShowTooltip().

◆ ContainsAnyFuzz() ◆ ContainsIupacNaAmbiguities() ◆ CreateDeltaForOffset() ◆ CreateException() ◆ CreateSplicedSeqAlignFromFeat()

Definition at line 603 of file variation_util2.cpp.

References CSeq_loc_CI::eEmpty_Skip, eNa_strand_plus, CSeq_loc_CI::eOrder_Biological, CSpliced_seg_Base::eProduct_type_transcript, CSeq_align_Base::eType_other, GetId(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), GetStrand(), NULL, CSpliced_seg_Base::SetExons(), CSpliced_seg_Base::SetGenomic_id(), CSpliced_seg_Base::SetGenomic_strand(), CSpliced_seg_Base::SetProduct_id(), CSpliced_seg_Base::SetProduct_strand(), CSpliced_seg_Base::SetProduct_type(), CSeq_align_Base::SetSegs(), and CSeq_align_Base::SetType().

Referenced by variation::CVariationUtil::RemapToAnnotatedTarget().

◆ CreateUnknownProtConsequenceVariation()

Definition at line 2286 of file variation_util2.cpp.

References ChangeIdsInPlace(), CreateException(), CVariationException_Base::eCode_inconsistent_consequence, eGetId_ForceAcc, CSeq_loc_Mapper_Base::eLocationToProduct, CVariationMethod_Base::eMethod_E_computational, CVariantPlacement_Base::eMol_protein, CSeq_loc_Mapper_Base::eProductToLocation, variation::CVariationUtil::eSO_frameshift_variant, eUnknown, GetId(), CVariantPlacement_Base::GetLoc(), CVariantPlacement_Base::GetMol(), CSeq_feat_Base::GetProduct(), CSeq_loc_Base::IsNull(), CSeq_loc_Mapper_Base::Map(), NCBI_THROW, NULL, CRef< C, Locker >::Reset(), SerialClone(), CVariantPlacement_Base::SetExceptions(), CVariantPlacement_Base::SetLoc(), CVariationMethod_Base::SetMethod(), CVariantPlacement_Base::SetMol(), and CSeq_loc::SetWhole().

Referenced by variation::CVariationUtil::TranslateNAtoAA().

◆ Equals()

Definition at line 2925 of file variation_util2.cpp.

References CSerialObject::Equals().

Referenced by BOOST_AUTO_TEST_CASE(), CachedTaxonomyLookupCommand(), CCharVectorTypeInfo< Char >::CCharVectorTypeInfo(), ConvertToPairwise(), CPrimitiveTypeInfo::CPrimitiveTypeInfo(), CPrimitiveTypeInfoAnyContent::CPrimitiveTypeInfoAnyContent(), CPrimitiveTypeInfoBitString::CPrimitiveTypeInfoBitString(), CPrimitiveTypeInfoCharPtr< T >::CPrimitiveTypeInfoCharPtr(), CStdTypeInfo< bool >::CreateTypeInfoNullBool(), CTimeTypeInfo::CTimeTypeInfo(), CTaxValidationAndCleanup::DoTaxonomyUpdate(), CGffRecord::GetSubtypeOf(), CBam2Seq_graph::MakeSeq_entry(), variation::CVariationUtil::s_FactorOutPlacements(), SpecificHostCleanupCommand(), TaxonomyLookupCommand(), and CwxChooseSeqDlg::x_GetIdIndex().

◆ FindSSRLoc()

Definition at line 182 of file hgvs_parser2.cpp.

References CSeq_loc::Assign(), CSeqVector::begin(), CSeq_loc::ChangeToMix(), Compare(), CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Null, CBioseq_Handle::eCoding_Iupac, eExtreme_Positional, eNa_strand_minus, CSeqVector::end(), eNoOverlap, fCompareOverlapping, CSeq_loc::fMerge_SingleRange, CSeq_loc::fSortAndMerge_All, CScope::GetBioseqHandle(), CSeq_interval_Base::GetFrom(), GetId(), CBioseq_Handle::GetInst_Length(), CSeq_loc_Base::GetInt(), CSeqVector::GetSeqData(), GetStrand(), CSeq_interval_Base::GetTo(), HGVS_THROW, i, min(), NULL, result, Seq_loc_Merge(), SeqsMatch(), CSeq_loc::SetInt(), and CSeq_loc::SetMix().

Referenced by variation::CHgvsParser::x_ssr().

◆ GetCommonPrefixLen() ◆ GetCommonSuffixLen() ◆ GetDelInsSubtype() ◆ GetDeltaLength() ◆ GetFocusLocusIDs()

Definition at line 3516 of file variation_util2.cpp.

References CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Rna, set< Key, Compare >::end(), set< Key, Compare >::find(), CDbtag_Base::GetDb(), CSeq_feat_Handle::GetDbxref(), CSeq_id_Handle::GetHandle(), GetId(), CObject_id_Base::GetId(), CMappedFeat::GetProduct(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CDbtag_Base::GetTag(), SAnnotSelector::IncludeFeatType(), set< Key, Compare >::insert(), IsRefSeqGene(), CSeq_feat_Handle::IsSetDbxref(), CSeq_feat_Handle::IsSetProduct(), CSeq_align_Base::C_Segs::IsSpliced(), ITERATE, and NULL.

Referenced by variation::CVariationUtil::CVariantPropertiesIndex::x_Index().

◆ GetFuzz() ◆ GetFuzzSign() ◆ GetSignedOffset() ◆ GetUniquePrimaryTranscriptId()

Definition at line 793 of file hgvs_parser2.cpp.

References set< Key, Compare >::begin(), CSeqFeatData_Base::e_Rna, eGetId_ForceAcc, set< Key, Compare >::end(), CSeq_id_Handle::GetHandle(), GetId(), CMappedFeat::GetProduct(), CBioseq_Handle::GetScope(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), SAnnotSelector::IncludeFeatType(), set< Key, Compare >::insert(), CSeq_feat_Handle::IsSetProduct(), CSeq_align_Base::C_Segs::IsSpliced(), and SAnnotSelector::SetResolveTSE().

Referenced by variation::CHgvsParser::x_header().

◆ HasProblematicExceptions() ◆ InheritParentAttributes() ◆ IsLRG() ◆ IsMitochondrion() ◆ IsPureFuzzPoint() ◆ IsRefSeqGene() ◆ IsRightPartial() ◆ Ncbieaa2HgvsAA() ◆ RepackageAssertedSequence() void variation::RepackageAssertedSequence ( CVariation &  vr )

Definition at line 299 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), delta(), CVariation_Base::C_Data::C_Set::eData_set_type_package, CVariation_inst_Base::eObservation_asserted, CVariation_inst_Base::eType_identity, CVariation_Base::GetData(), CVariation_Base::C_Data::IsSet(), CVariation_Base::IsSetPlacements(), NON_CONST_ITERATE, orig, CVariantPlacement_Base::ResetSeq(), CVariation_Base::SetData(), SetFirstPlacement(), and CVariation_Base::SetPlacements().

Referenced by variation::CHgvsParser::x_root().

◆ SeqsMatch() ◆ SetComputational() void variation::SetComputational ( CVariation &  variation ) ◆ SetFirstPlacement()

Definition at line 145 of file hgvs_parser2.cpp.

References CVariation_Base::SetPlacements().

Referenced by RepackageAssertedSequence(), variation::CHgvsParser::x_conversion(), variation::CHgvsParser::x_deletion(), variation::CHgvsParser::x_delins(), variation::CHgvsParser::x_duplication(), variation::CHgvsParser::x_expr2(), variation::CHgvsParser::x_insertion(), variation::CHgvsParser::x_mut_inst(), variation::CHgvsParser::x_no_change(), variation::CHgvsParser::x_nuc_inv(), variation::CHgvsParser::x_nuc_subst(), variation::CHgvsParser::x_prot_ext(), variation::CHgvsParser::x_prot_fs(), variation::CHgvsParser::x_prot_missense(), variation::CHgvsParser::x_ssr(), variation::CHgvsParser::x_string_content(), and variation::CHgvsParser::x_translocation().

◆ SwapLtGtFuzz() ◆ Translate() ◆ USING_SCOPE() variation::USING_SCOPE ( objects  ) ◆ ValidExonTerminal() ◆ ValidExonTerminals()

Definition at line 185 of file variation_util2.cpp.

References eExtreme_Biological, eNa_strand_minus, GetFuzzSign(), CVariantPlacement_Base::GetLoc(), GetStart(), CVariantPlacement_Base::GetStart_offset(), CVariantPlacement_Base::GetStart_offset_fuzz(), GetStop(), CVariantPlacement_Base::GetStop_offset(), CVariantPlacement_Base::GetStop_offset_fuzz(), GetStrand(), CVariantPlacement_Base::IsSetStart_offset(), CVariantPlacement_Base::IsSetStart_offset_fuzz(), CVariantPlacement_Base::IsSetStop_offset(), CVariantPlacement_Base::IsSetStop_offset_fuzz(), NULL, and ValidExonTerminal().

Referenced by variation::CVariationUtil::CheckExonBoundary().

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