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Code generated by DATATOOL from 'seqfeat.asn' (module 'NCBI-Variation')

Choice variants.

No variant selected.

same location as variation-ref itself

Definition at line 105 of file Delta_item_.hpp.

Choice variants.

No variant selected.

free-form

actual sequence-edit at feat.location

variant is a complex and undescribed change at the location This type of variant is known to occur in dbVar submissions

Definition at line 363 of file Variation_ref_.hpp.

Choice variants.

No variant selected.

some effect on splicing

freeform

Describe resulting variation in the product, e.g. missense, nonsense, silent, neutral, etc in a protein, that arises from THIS variation.

Definition at line 827 of file Variation_ref_.hpp.

Maximum+1 value of the choice variant enumerator.

== e_This+1

Definition at line 112 of file Delta_item_.hpp.

Maximum+1 value of the choice variant enumerator.

== e_Complex+1

Definition at line 373 of file Variation_ref_.hpp.

Maximum+1 value of the choice variant enumerator.

== e_Loss_of_heterozygosity+1

Definition at line 837 of file Variation_ref_.hpp.

Definition at line 266 of file Delta_item_.hpp.

Definition at line 90 of file Ext_loc_.hpp.

Definition at line 112 of file Phenotype_.hpp.

Definition at line 110 of file Population_data_.hpp.

Definition at line 294 of file VariantProperties_.hpp.

Definition at line 1307 of file Variation_ref_.hpp.

replace len(seq) positions starting with location.start with seq

go downstream by distance specified by multiplier (upstream if < 0), in genomic context.

excise sequence at location if multiplier is specified, delete len(location)*multiplier positions downstream

insert seq before the location.start

Definition at line 249 of file Delta_item_.hpp.

origin of this allele, if known note that these are powers-of-two, and represent bits; thus, we can represent more than one state simultaneously through a bitwise OR

stopper - 2^31

Definition at line 242 of file VariantProperties_.hpp.

origin of this allele, if known note that these are powers-of-two, and represent bits; thus, we can represent more than one state simultaneously through a bitwise OR DEPRECATED: new field = VariantProperties.allele-origin

stopper - 2^31

Definition at line 138 of file Variation_ref_.hpp.

observed allele state, if known NOTE: THIS IS NOT A BITFIELD!

Definition at line 263 of file VariantProperties_.hpp.

observed allele state, if known DEPRECATED: new field = VariantProperties.allele-state

Definition at line 158 of file Variation_ref_.hpp.

does this variant have known clinical significance?

Definition at line 90 of file Phenotype_.hpp.

Definition at line 230 of file VariantProperties_.hpp.

complex change at the same location on the same molecule

different products arising from the same variation in a precursor, e.g. r.[13g>a, 13_88del]

changes on the same allele, e.g r.[13g>a;15u>c]

changes on different alleles in the same genotype, e.g. g.[476C>T]+[476C>T]

different genotypes in the same individual

same organism; allele relationship unknown, e.g. g.[476C>T(+)183G>C]

population

set represents a set of observed alleles

set represents a package of observations at a given location, generally containing asserted + reference

Definition at line 206 of file Variation_ref_.hpp.

known to cause no functional changes since 0 does not combine with any other bit value, 'no-change' specifically implies that there are no consequences

one allele in the set does not change the encoded amino acid (0x1)

one allele in the set changes to STOP codon (TER). (0x2)

one allele in the set changes protein peptide (0x4)

one allele in the set changes all downstream amino acids (0x8)

the variant causes increased transcription (0x10)

the variant causes decreased transcription (0x20)

reference codon is not stop codon, but the snp variant allele changes the codon to a terminating codon.

reverse of STOP-GAIN: reference codon is a stop codon, but a snp variant allele changes the codon to a non-terminating codon.

Definition at line 162 of file VariantProperties_.hpp.

This field is an explicit bit-field Valid values should be a bitwise combination (= simple sum) of any of the values below.

Definition at line 92 of file Population_data_.hpp.

low frequency variation that is cited in journal or other reputable sources (0x01)

>5% minor allele freq in each and all populations (0x02)

>5% minor allele freq in 1+ populations (0x04)

Bit is set if the variant has a minor allele observed in two or more separate chromosomes.

>1% minor allele freq in each and all populations (0x10)

>1% minor allele freq in 1+ populations (0x20)

Definition at line 199 of file VariantProperties_.hpp.

Sequence intervals covered by a gene ID but not having an aligned transcript (0x01)

Within 2kb of the 5' end of a gene feature.

Within 0.5kb of the 3' end of a gene feature.

In Intron (0x08)

In donor splice-site (0x10)

In acceptor splice-site (0x20)

In 5' UTR (0x40)

In 3' UTR (0x80)

the variant is observed in a start codon (0x100)

the variant is observed in a stop codon (0x200)

variant located between genes (0x400)

variant is located in a conserved non-coding region (0x800)

Definition at line 144 of file VariantProperties_.hpp.

Exists in a haplotype tagging set (0x01)

SNP has individual genotype (0x02)

Definition at line 211 of file VariantProperties_.hpp.

map-weight captures specificity of placement NOTE: This is *NOT* a bitfield

Definition at line 189 of file VariantProperties_.hpp.

Another SNP has the same mapped positions on reference assembly (0x01)

Weight 1 or 2 SNPs that map to different chromosomes on different assemblies (0x02)

Only maps to 1 assembly (0x04)

Definition at line 178 of file VariantProperties_.hpp.

Definition at line 100 of file Variation_ref_.hpp.

'observation' is used to label items in a Variation-ref package This field is explicitly a bit-field, so the bitwise OR (= sum) of any of the values may be observed.

inst represents the asserted base at a position

inst represents the reference base at the position

inst represent the observed variant at a given position

Definition at line 120 of file Variation_inst_.hpp.

Reference sequence allele at the mapped position is not present in the SNP allele list, adjusted for orientation (0x01)

One member SS is withdrawn by submitter (0x02)

RS set has 2+ alleles from different submissions and these sets share no alleles in common (0x04)

Straing specific fixed difference (0x08)

Has Genotype Conflict (0x10)

Definition at line 219 of file VariantProperties_.hpp.

NOTE: The format for most of these values is as an integer Unless otherwise noted, these integers represent a bitwise OR (= simple sum) of the possible values, and as such, these values represent the specific bit flags that may be set for each of the possible attributes here.

Clinical, Pubmed, Cited, (0x01)

Provisional Third Party Annotations (0x02)

Has 3D strcture SNP3D table (0x04)

SNP->SubSNP->Batch link_out (0x08)

Clinical if LSDB, OMIM, TPA, Diagnostic (0x10)

Marker exists on high density genotyping kit (0x20)

Definition at line 132 of file VariantProperties_.hpp.

delta=[]

delta=[]

delta=[del, ins.seq= RevComp(variation-location)]

delta=[morph of length 1] NOTE: this is snV not snP; the latter requires frequency-based validation to be established in VariantProperties the strict definition of SNP is an SNV with an established population frequency of at least 1% in at least 1 popuplation

delta=[morph of length >1]

delta=[del, ins]

delta=[del]

delta=[ins]

delta=[del, ins.seq= repeat-unit with fuzzy multiplier] variation-location is the microsat expansion on the sequence

delta=[del, ins.seq= known donor or 'this'] variation-location is equiv of transposon locs.

delta=[del, ins= 'this' with fuzzy multiplier]

delta=[ins.seq= upstream location on the same strand]

delta=[ins.seq= downstream location on the same strand]

delta=[ins.seq= upstream location on the opposite strand]

delta=[ins.seq= downstream location on the opposite strand]

delta=like delins

delta=[morph of length 1]

delta=[del]; variation-location is the tail of the protein being truncated

delta=[morph of length 1]

delta=[morph of length 1, same AA as at variation-location]

delta=any

delta=any

Definition at line 89 of file Variation_inst_.hpp.

Check if it is safe to call GetAction method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 608 of file Delta_item_.hpp.

Check if it is safe to call GetClinical_test method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 3228 of file Variation_ref_.hpp.

Check if it is safe to call GetCondition method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 2857 of file Variation_ref_.hpp.

Check if it is safe to call GetConsequence method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 3492 of file Variation_ref_.hpp.

Referenced by s_IsLOH().

Check if it is safe to call GetData method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 3462 of file Variation_ref_.hpp.

Check if it is safe to call GetId method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 205 of file Ext_loc_.hpp.

Check if it is safe to call GetLocation method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 235 of file Ext_loc_.hpp.

Check if it is safe to call GetObject_id method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 2811 of file Variation_ref_.hpp.

Check if it is safe to call GetOther_ids method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 2941 of file Variation_ref_.hpp.

Check if it is safe to call GetPhase method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 2485 of file Variation_ref_.hpp.

Check if it is safe to call GetPopulation_data method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 3135 of file Variation_ref_.hpp.

Check if it is safe to call GetProject_data method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 1346 of file VariantProperties_.hpp.

Check if it is safe to call GetReference method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 2579 of file Variation_ref_.hpp.

Check if it is safe to call GetSample_ids method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 518 of file Population_data_.hpp.

Check if it is safe to call GetSource method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 2836 of file Variation_ref_.hpp.

Check if it is safe to call GetSynonyms method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 3013 of file Variation_ref_.hpp.

Check if it is safe to call GetTest method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 2626 of file Variation_ref_.hpp.

Check if it is safe to call GetType method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 2269 of file Variation_ref_.hpp.

Check if it is safe to call GetVariations method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 2316 of file Variation_ref_.hpp.

Check if it is safe to call GetX_length method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 2532 of file Variation_ref_.hpp.

Check if it is safe to call GetXref method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 395 of file Phenotype_.hpp.

Definition at line 86 of file Ext_loc.hpp.

Verify selection, throw exception if it differs from the expected.

Parameters

index Expected selection.

Definition at line 466 of file Delta_item_.hpp.

Definition at line 86 of file Phenotype.hpp.

Access to EAction's attributes (values, names) as defined in spec.

Access to EAllele_origin's attributes (values, names) as defined in spec.

Access to EAllele_origin's attributes (values, names) as defined in spec.

Access to EAllele_state's attributes (values, names) as defined in spec.

Access to EAllele_state's attributes (values, names) as defined in spec.

Access to EClinical_significance's attributes (values, names) as defined in spec.

Access to EConfidence's attributes (values, names) as defined in spec.

Access to EData_set_type's attributes (values, names) as defined in spec.

Access to EEffect's attributes (values, names) as defined in spec.

Access to EFlags's attributes (values, names) as defined in spec.

Access to EFrequency_based_validation's attributes (values, names) as defined in spec.

Access to EGene_location's attributes (values, names) as defined in spec.

Access to EGenotype's attributes (values, names) as defined in spec.

Access to EMap_weight's attributes (values, names) as defined in spec.

Access to EMapping's attributes (values, names) as defined in spec.

Access to EMethod_E's attributes (values, names) as defined in spec.

Access to EObservation's attributes (values, names) as defined in spec.

Access to EQuality_check's attributes (values, names) as defined in spec.

Access to EResource_link's attributes (values, names) as defined in spec.

Access to EType's attributes (values, names) as defined in spec.

Get the Data member data.

Returns

Reference to the member data.

Definition at line 3468 of file Variation_ref_.hpp.

References CVariation_ref_Base::m_Data, and CVariation_ref_Base::ResetData().

Referenced by variation_ref::CVariationUtil::AdjustDelinsToInterval(), CGvfWriteRecord::AssignType(), variation_ref::CVariationUtil::ChangeToDelins(), variation_ref::CVariationUtil::CheckExonBoundary(), g_ValidateVariationSeqfeat(), CSeq_featHandler::GetLabel(), CGuiObjectInfoVariant::GetToolTip(), CVariationUtilities::GetVariationRefAlt(), CVariationUtilities::GetVariationType(), NSnpGui::GetVcfType(), CVariation_ref::IsCNV(), CVariation_ref::IsComplex(), CFeatGlyph::IsDbVar(), CVariation_ref::IsDeletion(), CVariation_ref::IsDeletionInsertion(), CVariation_ref::IsEversion(), CVariation_ref::IsGain(), CVariation_ref::IsInsertion(), CVariationUtilities::IsIntronicVariation(), CVariation_ref::IsInversion(), CVariation_ref::IsLoss(), CVariation_ref::IsMicrosatellite(), CVariation_ref::IsMNP(), CVariation_ref::IsOther(), CVariationUtilities::IsReferenceCorrect(), CVariation_ref::IsSNV(), CVariation_ref::IsTranslocation(), CVariation_ref::IsUniparentalDisomy(), CVariation_ref::IsUnknown(), variation_ref::CVariationUtil::PrecursorToProt(), variation_ref::RepackageAssertedSequence(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_FactorOutLocsInPlace(), s_GetLiteralLength(), variation_ref::CVariationUtil::s_PropagateLocsInPlace(), variation_ref::CVariationUtil::s_Remap(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), variation_ref::CVariationUtil::SetReferenceSequence(), variation_ref::CVariationUtil::SetVariantProperties(), variation::CVariationUtil::x_AsVariation(), NSNPVariationHelper::x_CommonConvertFeat(), CVariationUtilities::x_FixAlleles(), variation_ref::CVariationUtil::x_ProtToPrecursor(), CVariationUtilities::x_SetReference(), CVariationNormalization_base< T >::x_Shift(), variation_ref::CHgvsParser::x_unwrap_iff_singleton(), CModifySeqId::x_UpdateVariation(), CReportTrim::x_UpdateVariation(), and CVcfWriter::x_WriteFeature().

Get the Delta member data.

Returns

Reference to the member data.

Definition at line 337 of file Variation_inst_.hpp.

References CVariation_inst_Base::m_Delta.

Referenced by variation_ref::CVariationUtil::AdjustDelinsToInterval(), variation::CVariationUtil::AttachSeq(), variation::CVariationUtil::ChangeToDelins(), variation_ref::CVariationUtil::ChangeToDelins(), variation_ref::CVariationUtil::CheckExonBoundary(), CSeq_featHandler::GetLabel(), CGuiObjectInfoVariant::GetToolTip(), NSnpGui::GetVcfType(), CPostProcessUtils::HasIntronOffset(), CVariation_ref::IsGain(), CVariation_ref::IsLoss(), CVariationUtilities::IsReferenceCorrect(), variation_ref::CVariationUtil::PrecursorToProt(), s_ContainsOffset(), variation::CVariationUtil::s_ConvertInstOffsetsToPlacementOffsets(), variation::CVariationUtil::s_FindAssertedLiteral(), s_GetAltRefFromInst(), s_GetLiteralLength(), variation::CVariationUtil::s_IsInstStrandFlippable(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), variation_ref::CVariationUtil::SetReferenceSequence(), CValidateVariant::ValidateIdentityInst(), CValidateVariant::ValidateMicrosatelliteInst(), variation::CVariationUtil::x_AdjustDelinsToInterval(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), variation::CHgvsParser::x_AsHgvsInstExpression(), variation_ref::CHgvsParser::x_GetInstData(), variation_ref::CHgvsParser::x_GetInstLength(), variation::CHgvsParser::x_GetInstLength(), CVcfWriter::x_GetTypeRefAlt(), variation::CVariationUtil::x_InferNAfromAA(), variation_ref::CHgvsParser::x_InstToString(), variation_ref::CVariationUtil::x_ProtToPrecursor(), variation_ref::CVariationUtil::x_SetVariantProperties(), CVariationNormalization_base< T >::x_Shift(), and CReportTrim::x_UpdateVariation().

Get the Id member data.

Returns

Reference to the member data.

Definition at line 2884 of file Variation_ref_.hpp.

References CVariation_ref_Base::CanGetId(), CVariation_ref_Base::m_Id, and CSerialObject::ThrowUnassigned().

Referenced by CSeq_featHandler::GetLabel(), CGuiObjectInfoVariant::GetLinks(), CGuiObjectInfoVariant::GetToolTip(), CFeatGlyph::IsDbVar(), NSearchFeatPanel::s_GetFeatureLabel(), s_GetVariationLabel(), CGvfWriteRecord::x_AssignAttributeID(), variation::CVariationUtil::x_AsVariation(), CVcfWriter::x_WriteFeatureId(), and CVcfWriter::x_WriteFeatureInfo().

Get the variant data.

Returns

Reference to the data.

Definition at line 257 of file Variation_ref_.cpp.

References CVariation_ref_Base::C_Data::CheckSelected(), CVariation_ref_Base::C_Data::e_Instance, and CVariation_ref_Base::C_Data::m_object.

Referenced by CGvfWriteRecord::AssignType(), variation_ref::CVariationUtil::CheckExonBoundary(), g_ValidateVariationSeqfeat(), CSeq_featHandler::GetLabel(), CGuiObjectInfoVariant::GetToolTip(), CVariationUtilities::GetVariationRefAlt(), CVariationUtilities::GetVariationType(), CVariation_ref::IsCNV(), CVariation_ref::IsDeletion(), CVariation_ref::IsDeletionInsertion(), CVariation_ref::IsEversion(), CVariation_ref::IsGain(), CVariation_ref::IsInsertion(), CVariationUtilities::IsIntronicVariation(), CVariation_ref::IsInversion(), CVariation_ref::IsLoss(), CVariation_ref::IsMicrosatellite(), CVariation_ref::IsMNP(), CVariationUtilities::IsReferenceCorrect(), CVariation_ref::IsSNV(), CVariation_ref::IsTranslocation(), variation_ref::CVariationUtil::PrecursorToProt(), s_GetLiteralLength(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), variation_ref::CVariationUtil::SetReferenceSequence(), variation::CVariationUtil::x_AsVariation(), NSNPVariationHelper::x_CommonConvertFeat(), variation_ref::CVariationUtil::x_ProtToPrecursor(), CModifySeqId::x_UpdateVariation(), CReportTrim::x_UpdateVariation(), and CVcfWriter::x_WriteFeature().

Get the variant data.

Returns

Reference to the data.

Definition at line 104 of file Delta_item_.cpp.

Referenced by variation::CVariationUtil::ChangeToDelins(), variation_ref::CVariationUtil::ChangeToDelins(), variation::CVariationUtil::FlipStrand(), NSNPVariationHelper::GetDeltas(), CGuiObjectInfoVariant::GetToolTip(), NSnpGui::GetVcfType(), CVariationUtilities::IsReferenceCorrect(), s_ContainsSeqDataIupacna(), s_GetAltRefFromInst(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), variation::CVariationUtil::TranslateNAtoAA(), CFeatureItem::x_AddQualsVariation(), variation_ref::CHgvsParser::x_GetInstData(), variation_ref::CHgvsParser::x_GetInstLength(), variation::CHgvsParser::x_GetInstLength(), variation_ref::CVariationUtil::x_SetVariantProperties(), and CVariationNormalization_base< T >::x_Shift().

Get the Object_id member data.

Returns

Reference to the member data.

Definition at line 2817 of file Variation_ref_.hpp.

Get the Observation member data.

Returns

Copy of the member data.

Definition at line 369 of file Variation_inst_.hpp.

References CVariation_inst_Base::CanGetObservation(), CVariation_inst_Base::m_Observation, and CSerialObject::ThrowUnassigned().

Referenced by variation::CVariationUtil::AttachProteinConsequences(), variation::CVariationUtil::AttachSeq(), CGuiObjectInfoVariant::GetToolTip(), NSnpGui::GetVcfType(), variation::CVariationUtil::s_FindAssertedLiteral(), variation_ref::CVariationUtil::SetReferenceSequence(), variation_ref::CVariationUtil::SetVariantProperties(), variation::CVariationUtil::x_InferNAfromAA(), and variation_ref::CVariationUtil::x_ProtToPrecursor().

Get the Seq member data.

Returns

Reference to the member data.

Definition at line 525 of file Delta_item_.hpp.

References CDelta_item_Base::CanGetSeq(), CDelta_item_Base::m_Seq, and CSerialObject::ThrowUnassigned().

Referenced by variation::CVariationUtil::ChangeToDelins(), variation_ref::CVariationUtil::ChangeToDelins(), variation::CVariationUtil::FlipStrand(), CVariationUtilities::IsReferenceCorrect(), s_ContainsSeqDataIupacna(), s_GetAltRefFromInst(), variation_ref::CVariationUtil::s_Remap(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), variation::CVariationUtil::TranslateNAtoAA(), variation_ref::CHgvsParser::x_GetInstData(), variation_ref::CHgvsParser::x_GetInstLength(), variation::CHgvsParser::x_GetInstLength(), variation_ref::CVariationUtil::x_SetVariantProperties(), and CVariationNormalization_base< T >::x_Shift().

Get the variant data.

Returns

Reference to the data.

Definition at line 279 of file Variation_ref_.cpp.

References CVariation_ref_Base::C_Data::CheckSelected(), CVariation_ref_Base::C_Data::e_Set, and CVariation_ref_Base::C_Data::m_object.

Referenced by g_ValidateVariationSeqfeat(), CGuiObjectInfoVariant::GetToolTip(), CVariationUtilities::GetVariationRefAlt(), CVariationUtilities::GetVariationType(), NSnpGui::GetVcfType(), CVariationUtilities::IsIntronicVariation(), CVariation_ref::IsOther(), CVariationUtilities::IsReferenceCorrect(), variation_ref::CVariationUtil::SetReferenceSequence(), variation::CVariationUtil::x_AsVariation(), CVariationUtilities::x_SetReference(), CVariationNormalization_base< T >::x_Shift(), variation_ref::CHgvsParser::x_unwrap_iff_singleton(), CModifySeqId::x_UpdateVariation(), CReportTrim::x_UpdateVariation(), and CVcfWriter::x_WriteFeature().

Get the Type member data.

Returns

Copy of the member data.

Definition at line 297 of file Variation_inst_.hpp.

References CVariation_inst_Base::CanGetType(), CVariation_inst_Base::m_Type, and CSerialObject::ThrowUnassigned().

Referenced by CGvfWriteRecord::AssignType(), variation::CVariationUtil::ChangeToDelins(), CGuiObjectInfoVariant::GetToolTip(), CVariationUtilities::GetVariationType(), NSnpGui::GetVcfType(), CVariation_ref::IsCNV(), CVariation_ref::IsDeletion(), CVariation_ref::IsDeletionInsertion(), CVariation_ref::IsEversion(), CVariation_ref::IsGain(), CVariation_ref::IsInsertion(), CVariation_ref::IsInversion(), CVariation_ref::IsLoss(), CVariation_ref::IsMicrosatellite(), CVariation_ref::IsMNP(), CVariationUtilities::IsReferenceCorrect(), CVariation_ref::IsSNV(), CVariation_ref::IsTranslocation(), CNormalizeVariant::NormalizeIdentityInstance(), CVariationNormalization_base< CVariationNormalizationRight >::ResetFullyShifted(), s_GetAltRefFromInst(), CValidateVariant::ValidateIdentityInst(), CValidateVariant::ValidateMicrosatelliteInst(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), variation::CHgvsParser::x_AsHgvsInstExpression(), CVariationUtilities::x_FixAlleles(), CVcfWriter::x_GetTypeRefAlt(), variation_ref::CHgvsParser::x_InstToString(), CVariationUtilities::x_SetReference(), and CVariationNormalization_base< T >::x_Shift().

Get the Variant_prop member data.

Returns

Reference to the member data.

Definition at line 3166 of file Variation_ref_.hpp.

References CVariation_ref_Base::CanGetVariant_prop(), CVariation_ref_Base::m_Variant_prop, and CSerialObject::ThrowUnassigned().

Referenced by CVariation_ref::CanGetAllele_frequency(), CVariation_ref::CanGetAllele_origin(), CVariation_ref::CanGetAllele_state(), CVariation_ref::CanGetIs_ancestral_allele(), CVariation_ref::CanGetValidated(), CVariation_ref::GetAllele_frequency(), CVariation_ref::GetAllele_origin(), CVariation_ref::GetAllele_state(), CVariation_ref::GetIs_ancestral_allele(), CSeq_featHandler::GetLabel(), CGuiObjectInfoVariant::GetToolTip(), CVariation_ref::GetValidated(), CVariation_ref::IsSetAllele_frequency(), CVariation_ref::IsSetAllele_origin(), CVariation_ref::IsSetAllele_state(), CVariation_ref::IsSetIs_ancestral_allele(), CVariation_ref::IsSetValidated(), variation::CVariationUtil::x_AsVariation(), variation_ref::CVariationUtil::x_SetVariantProperties(), and CVcfWriter::x_WriteFeatureInfo().

Get the Variations member data.

Returns

Reference to the member data.

Definition at line 2322 of file Variation_ref_.hpp.

Referenced by g_ValidateVariationSeqfeat(), CGuiObjectInfoVariant::GetToolTip(), CVariationUtilities::GetVariationRefAlt(), CVariationUtilities::GetVariationType(), NSnpGui::GetVcfType(), CVariationUtilities::IsIntronicVariation(), CVariationUtilities::IsReferenceCorrect(), variation::CVariationUtil::x_AsVariation(), CVariationUtilities::x_SetReference(), CVariationNormalization_base< T >::x_Shift(), variation_ref::CHgvsParser::x_unwrap_iff_singleton(), and CVcfWriter::x_WriteFeature().

Check if variant Instance is selected.

Instance type is defined as 'typedef CVariation_inst TInstance'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 2455 of file Variation_ref_.hpp.

References CVariation_ref_Base::C_Data::e_Instance, and CVariation_ref_Base::C_Data::m_choice.

Referenced by variation_ref::CVariationUtil::AdjustDelinsToInterval(), CGvfWriteRecord::AssignType(), variation_ref::CVariationUtil::ChangeToDelins(), variation_ref::CVariationUtil::CheckExonBoundary(), g_ValidateVariationSeqfeat(), CSeq_featHandler::GetLabel(), CGuiObjectInfoVariant::GetToolTip(), CVariationUtilities::GetVariationRefAlt(), CVariationUtilities::GetVariationType(), CVariation_ref::IsCNV(), CVariation_ref::IsDeletion(), CVariation_ref::IsDeletionInsertion(), CVariation_ref::IsEversion(), CVariation_ref::IsGain(), CVariation_ref::IsInsertion(), CVariation_ref::IsInversion(), CVariation_ref::IsLoss(), CVariation_ref::IsMicrosatellite(), CVariation_ref::IsMNP(), CVariationUtilities::IsReferenceCorrect(), CVariation_ref::IsSNV(), CVariation_ref::IsTranslocation(), variation_ref::CVariationUtil::PrecursorToProt(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), s_GetLiteralLength(), variation_ref::CVariationUtil::s_Remap(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), variation_ref::CVariationUtil::SetReferenceSequence(), variation_ref::CVariationUtil::SetVariantProperties(), variation::CVariationUtil::x_AsVariation(), NSNPVariationHelper::x_CommonConvertFeat(), CVariationUtilities::x_FixAlleles(), variation_ref::CVariationUtil::x_ProtToPrecursor(), CVariationUtilities::x_SetReference(), CVariationNormalization_base< T >::x_Shift(), CModifySeqId::x_UpdateVariation(), and CReportTrim::x_UpdateVariation().

Check if variant Set is selected.

Set type is defined as 'typedef C_Set TSet'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 2461 of file Variation_ref_.hpp.

References CVariation_ref_Base::C_Data::e_Set, and CVariation_ref_Base::C_Data::m_choice.

Referenced by variation_ref::CVariationUtil::AdjustDelinsToInterval(), variation_ref::CVariationUtil::ChangeToDelins(), g_ValidateVariationSeqfeat(), CGuiObjectInfoVariant::GetToolTip(), NSnpGui::GetVcfType(), CVariation_ref::IsOther(), CVariationUtilities::IsReferenceCorrect(), variation_ref::RepackageAssertedSequence(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_FactorOutLocsInPlace(), variation_ref::CVariationUtil::s_PropagateLocsInPlace(), variation_ref::CVariationUtil::s_Remap(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), variation_ref::CVariationUtil::SetReferenceSequence(), variation::CVariationUtil::x_AsVariation(), variation_ref::CVariationUtil::x_ProtToPrecursor(), CVariationUtilities::x_SetReference(), CVariationNormalization_base< T >::x_Shift(), variation_ref::CHgvsParser::x_unwrap_iff_singleton(), CModifySeqId::x_UpdateVariation(), and CReportTrim::x_UpdateVariation().

Check if a value has been assigned to Action data member.

Data member Action is optional with default eAction_morph; its type is defined as 'typedef int TAction'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 602 of file Delta_item_.hpp.

References CDelta_item_Base::m_set_State.

Referenced by variation::CVariationUtil::ChangeToDelins(), variation_ref::CVariationUtil::ChangeToDelins(), variation_ref::CVariationUtil::CheckExonBoundary(), s_ContainsOffset(), variation::CVariationUtil::s_IsInstStrandFlippable(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), CDelta_item_Base::SetAction(), variation_ref::CVariationUtil::SetReferenceSequence(), and variation_ref::CVariationUtil::x_SetVariantProperties().

Check if a value has been assigned to Condition data member.

Data member Condition is optional; its type is defined as 'typedef C_Condition TCondition'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 2851 of file Variation_ref_.hpp.

Check if a value has been assigned to Data data member.

Data member Data is mandatory; its type is defined as 'typedef C_Data TData'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 3456 of file Variation_ref_.hpp.

References CVariation_ref_Base::m_Data, and CRef< C, Locker >::NotEmpty().

Referenced by g_ValidateVariationSeqfeat(), CGuiObjectInfoVariant::GetToolTip(), CVariationUtilities::GetVariationRefAlt(), CVariationUtilities::GetVariationType(), NSnpGui::GetVcfType(), CVariationUtilities::IsIntronicVariation(), CVariationUtilities::IsReferenceCorrect(), CAutogeneratedCleanup::x_BasicCleanupVariationRef(), CVariationUtilities::x_FixAlleles(), CVariationUtilities::x_SetReference(), CVariationNormalization_base< T >::x_Shift(), CModifySeqId::x_UpdateVariation(), and CReportTrim::x_UpdateVariation().

Sequence that replaces the location, in biological order.

Check if a value has been assigned to Delta data member.

Data member Delta is mandatory; its type is defined as 'typedef list< CRef< CDelta_item > > TDelta'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 325 of file Variation_inst_.hpp.

References CVariation_inst_Base::m_set_State.

Referenced by variation::CVariationUtil::FlipStrand(), CSeq_featHandler::GetLabel(), CGuiObjectInfoVariant::GetToolTip(), CPostProcessUtils::HasIntronOffset(), CVariation_ref::IsGain(), CVariation_ref::IsLoss(), CNormalizeVariant::NormalizeIdentityInstance(), s_ContainsOffset(), s_GetLiteralLength(), CValidateVariant::ValidateIdentityInst(), CValidateVariant::ValidateMicrosatelliteInst(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_ETC(), CVcfWriter::x_GetTypeRefAlt(), CVariationNormalization_base< T >::x_Shift(), CModifySeqId::x_UpdateVariation(), and CReportTrim::x_UpdateVariation().

Check if a value has been assigned to Description data member.

Data member Description is optional; its type is defined as 'typedef string TDescription'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 2758 of file Variation_ref_.hpp.

References CVariation_ref_Base::m_set_State.

Check if a value has been assigned to Id data member.

Data member Id is mandatory; its type is defined as 'typedef CObject_id TId'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 199 of file Ext_loc_.hpp.

References CExt_loc_Base::m_Id.

ids (i.e., SNP rsid / ssid, dbVar nsv/nssv) expected values include 'dbSNP|rs12334', 'dbSNP|ss12345', 'dbVar|nsv1'

we relate three kinds of IDs here:

• our current object's id
• the id of this object's parent, if it exists
• the sample ID that this item originates from Check if a value has been assigned to Id data member.

Data member Id is optional; its type is defined as 'typedef CDbtag TId'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 2872 of file Variation_ref_.hpp.

References CVariation_ref_Base::m_Id.

Referenced by CVariation_ref_Base::CanGetId(), CSeq_featHandler::GetLabel(), CGuiObjectInfoVariant::GetToolTip(), s_GetVariationLabel(), CGvfWriteRecord::x_AssignAttributeID(), variation::CVariationUtil::x_AsVariation(), CVcfWriter::x_WriteFeatureId(), and CVcfWriter::x_WriteFeatureInfo().

Check if a value has been assigned to Location data member.

Data member Location is mandatory; its type is defined as 'typedef CSeq_loc TLocation'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 229 of file Ext_loc_.hpp.

References CExt_loc_Base::m_Location.

Multiplier allows representing a tandem, e.g.

ATATAT as AT*3 This allows describing CNV/SSR where delta=self with a multiplier which specifies the count of the repeat unit. assumed 1 if not specified. Check if a value has been assigned to Multiplier data member.

Data member Multiplier is optional; its type is defined as 'typedef int TMultiplier'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 534 of file Delta_item_.hpp.

References CDelta_item_Base::m_set_State.

Referenced by CDelta_item_Base::CanGetMultiplier(), variation::CVariationUtil::ChangeToDelins(), variation_ref::CVariationUtil::ChangeToDelins(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), CDelta_item_Base::SetMultiplier(), variation_ref::CHgvsParser::x_GetInstData(), variation_ref::CHgvsParser::x_GetInstLength(), and variation::CHgvsParser::x_GetInstLength().

reference to BioTerm / other descriptive database Check if a value has been assigned to Object_id data member.

Data member Object_id is optional; its type is defined as 'typedef list< CRef< CDbtag > > TObject_id'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 2805 of file Variation_ref_.hpp.

References CVariation_ref_Base::m_set_State.

Check if a value has been assigned to Observation data member.

Data member Observation is optional; its type is defined as 'typedef int TObservation'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 350 of file Variation_inst_.hpp.

References CVariation_inst_Base::m_set_State.

Referenced by variation::CVariationUtil::AttachProteinConsequences(), variation::CVariationUtil::AttachSeq(), CVariation_inst_Base::CanGetObservation(), variation::CVariationUtil::s_FindAssertedLiteral(), CVariation_inst_Base::SetObservation(), variation_ref::CVariationUtil::SetReferenceSequence(), variation_ref::CVariationUtil::SetVariantProperties(), variation::CVariationUtil::x_InferNAfromAA(), and variation_ref::CVariationUtil::x_ProtToPrecursor().

Note about SNP representation and pretinent fields: allele-frequency, population, quality-codes: The case of multiple alleles for a SNP would be described by parent-feature of type Variation-set.diff-alleles, where the child features of type Variation-inst, all at the same location, would describe individual alleles.

population data DEPRECATED - do not use Check if a value has been assigned to Population_data data member.

Data member Population_data is optional; its type is defined as 'typedef list< CRef< CPopulation_data > > TPopulation_data'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 3129 of file Variation_ref_.hpp.

References CVariation_ref_Base::m_set_State.

Referenced by CVariation_ref::PostRead().

project IDs are IDs from BioProjects in order to report information about project relationships, we require projects to be registered This field in many ways duplicates dbxrefs; however, the intention of this field is to more adequately reflect ownership and data source

11/9/2010: DO NOT USE This field was changed in the spec in a breaking way; using it will break clients. We are officially suppressing / abandoning this field. Clients who need to use this should instead place the data in Seq-feat.dbxref, using the db name 'BioProject' Check if a value has been assigned to Project_data data member.

Data member Project_data is optional; its type is defined as 'typedef list< int > TProject_data'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 1340 of file VariantProperties_.hpp.

References CVariantProperties_Base::m_set_State.

publication support.

Note: made this pub instead of pub-equiv, since Pub can be pub-equiv and pub-equiv is a set of pubs, but it looks like Pub is more often used as top-level container DEPRECATED - do not use; use Seq-feat.dbxref instead Check if a value has been assigned to Pub data member.

Data member Pub is optional; its type is defined as 'typedef CPub TPub'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 3435 of file Variation_ref_.hpp.

References CVariation_ref_Base::m_Pub.

Referenced by CVariation_ref_Base::CanGetPub(), and CVariation_ref::PostRead().

In germline comparison, it will be reference genome assembly (default) or reference/normal population.

In somatic mutation, it will be a name of the normal tissue. Check if a value has been assigned to Reference data member.

Data member Reference is optional; its type is defined as 'typedef string TReference'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 2573 of file Variation_ref_.hpp.

References CVariation_ref_Base::m_set_State.

description of the somatic origin itself Check if a value has been assigned to Source data member.

Data member Source is optional; its type is defined as 'typedef CSubSource TSource'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 2830 of file Variation_ref_.hpp.

Name of the testing subject type or the testing tissue.

Check if a value has been assigned to Test data member.

Data member Test is optional; its type is defined as 'typedef string TTest'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 2620 of file Variation_ref_.hpp.

References CVariation_ref_Base::m_set_State.

Check if a value has been assigned to Type data member.

Data member Type is mandatory; its type is defined as 'typedef int TType'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 278 of file Variation_inst_.hpp.

References CVariation_inst_Base::m_set_State.

Referenced by CVariation_inst_Base::CanGetType(), CVariation_ref::IsCNV(), CVariation_ref::IsDeletion(), CVariation_ref::IsDeletionInsertion(), CVariation_ref::IsEversion(), CVariation_ref::IsGain(), CVariation_ref::IsInsertion(), CVariation_ref::IsInversion(), CVariation_ref::IsLoss(), CVariation_ref::IsMicrosatellite(), CVariation_ref::IsMNP(), CVariation_ref::IsSNV(), CVariation_ref::IsTranslocation(), CVariation_inst_Base::SetType(), CValidateVariant::ValidateIdentityInst(), and CValidateVariant::ValidateMicrosatelliteInst().

variant properties bit fields Check if a value has been assigned to Variant_prop data member.

Data member Variant_prop is optional; its type is defined as 'typedef CVariantProperties TVariant_prop'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 3154 of file Variation_ref_.hpp.

References CVariation_ref_Base::m_Variant_prop.

Referenced by CVariation_ref_Base::CanGetVariant_prop(), CVariation_ref::GetAllele_frequency(), CVariation_ref::GetAllele_origin(), CVariation_ref::GetAllele_state(), CVariation_ref::GetIs_ancestral_allele(), CSeq_featHandler::GetLabel(), CGuiObjectInfoVariant::GetToolTip(), CVariation_ref::GetValidated(), CVariation_ref::IsSetAllele_frequency(), CVariation_ref::IsSetAllele_origin(), CVariation_ref::IsSetAllele_state(), CVariation_ref::IsSetIs_ancestral_allele(), CVariation_ref::IsSetValidated(), CVariation_ref::ResetAllele_frequency(), CVariation_ref::ResetAllele_origin(), CVariation_ref::ResetAllele_state(), CVariation_ref::ResetIs_ancestral_allele(), CVariation_ref::ResetValidated(), variation::CVariationUtil::x_AsVariation(), and CVcfWriter::x_WriteFeatureInfo().

Check if a value has been assigned to X_length data member.

Data member X_length is optional; its type is defined as 'typedef int TX_length'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 2526 of file Variation_ref_.hpp.

References CVariation_ref_Base::m_set_State.

Reset the whole object.

Definition at line 203 of file VariantProperties_.cpp.

References CVariantProperties_Base::ResetAllele_frequency(), CVariantProperties_Base::ResetAllele_origin(), CVariantProperties_Base::ResetAllele_state(), CVariantProperties_Base::ResetConfidence(), CVariantProperties_Base::ResetEffect(), CVariantProperties_Base::ResetFrequency_based_validation(), CVariantProperties_Base::ResetGene_location(), CVariantProperties_Base::ResetGenotype(), CVariantProperties_Base::ResetIs_ancestral_allele(), CVariantProperties_Base::ResetMap_weight(), CVariantProperties_Base::ResetMapping(), CVariantProperties_Base::ResetOther_validation(), CVariantProperties_Base::ResetProject_data(), CVariantProperties_Base::ResetQuality_check(), CVariantProperties_Base::ResetResource_link(), and CVariantProperties_Base::ResetVersion().

Reset the whole object.

Definition at line 877 of file Variation_ref_.cpp.

References CVariation_ref_Base::ResetAllele_frequency(), CVariation_ref_Base::ResetAllele_origin(), CVariation_ref_Base::ResetAllele_state(), CVariation_ref_Base::ResetClinical_test(), CVariation_ref_Base::ResetConsequence(), CVariation_ref_Base::ResetData(), CVariation_ref_Base::ResetDescription(), CVariation_ref_Base::ResetExt(), CVariation_ref_Base::ResetExt_locs(), CVariation_ref_Base::ResetId(), CVariation_ref_Base::ResetIs_ancestral_allele(), CVariation_ref_Base::ResetLocation(), CVariation_ref_Base::ResetMethod(), CVariation_ref_Base::ResetName(), CVariation_ref_Base::ResetOther_ids(), CVariation_ref_Base::ResetParent_id(), CVariation_ref_Base::ResetPhenotype(), CVariation_ref_Base::ResetPopulation_data(), CVariation_ref_Base::ResetPub(), CVariation_ref_Base::ResetSample_id(), CVariation_ref_Base::ResetSomatic_origin(), CVariation_ref_Base::ResetSynonyms(), CVariation_ref_Base::ResetValidated(), and CVariation_ref_Base::ResetVariant_prop().

Referenced by CVariation_ref_Base::C_Data::~C_Data(), and CVariation_ref_Base::C_E_Consequence::~C_E_Consequence().

Reset the selection (set it to e_not_set).

Definition at line 411 of file Variation_ref_.cpp.

References CVariation_ref_Base::C_E_Consequence::e_Frameshift, CVariation_ref_Base::C_E_Consequence::e_Loss_of_heterozygosity, CVariation_ref_Base::C_E_Consequence::e_not_set, CVariation_ref_Base::C_E_Consequence::e_Note, CVariation_ref_Base::C_E_Consequence::e_Variation, CVariation_ref_Base::C_E_Consequence::m_choice, CVariation_ref_Base::C_E_Consequence::m_object, and CVariation_ref_Base::C_E_Consequence::m_string.

Referenced by CVariation_ref_Base::C_E_Consequence::Reset(), CVariation_ref_Base::C_E_Consequence::SetFrameshift(), CVariation_ref_Base::C_E_Consequence::SetLoss_of_heterozygosity(), and CVariation_ref_Base::C_E_Consequence::SetVariation().

Select the requested variant if needed, allocating CObject variants from memory pool.

Select the requested variant if needed, allocating CObject variants from memory pool.

Select the requested variant if needed, allocating CObject variants from memory pool.

Select the requested variant if needed.

Parameters

index New selection state. reset Flag that defines the resetting of the variant data. The data will be reset if either the current selection differs from the new one, or the flag is set to eDoResetVariant.

Retrieve selection name (for diagnostic purposes).

Parameters

index One of possible selection states.

Returns

Name string.

Definition at line 94 of file Delta_item_.cpp.

Assign a value to Data data member.

Parameters

value Reference to value.

Definition at line 820 of file Variation_ref_.cpp.

References CVariation_ref_Base::m_Data, CRef< C, Locker >::Reset(), and rapidjson::value.

Referenced by variation_ref::CVariationUtil::AdjustDelinsToInterval(), variation_ref::CVariationUtil::ChangeToDelins(), variation_ref::RepackageAssertedSequence(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_FactorOutLocsInPlace(), variation_ref::CVariationUtil::s_PropagateLocsInPlace(), variation_ref::CVariationUtil::s_Remap(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), s_SetReplaces(), variation_ref::CVariationUtil::SetReferenceSequence(), variation_ref::CVariationUtil::SetVariantProperties(), CAutogeneratedCleanup::x_BasicCleanupVariationRef(), NSNPVariationHelper::x_CommonConvertFeat(), CVariationUtilities::x_FixAlleles(), variation_ref::CVariationUtil::x_ProtToPrecursor(), CVariationUtilities::x_SetReference(), CVariationNormalization_base< T >::x_Shift(), variation_ref::CHgvsParser::x_unwrap_iff_singleton(), CModifySeqId::x_UpdateVariation(), and CReportTrim::x_UpdateVariation().

Assign a value to Data data member.

Returns

Reference to the data value.

Definition at line 3477 of file Variation_ref_.hpp.

References CVariation_ref_Base::m_Data, and CVariation_ref_Base::ResetData().

Referenced by CVariation_ref::SetCNV(), CVariation_ref::SetComplex(), CVariation_ref::SetDeletion(), CVariation_ref::SetDeletionInsertion(), CVariation_ref::SetDuplication(), CVariation_ref::SetEversion(), CVariation_ref::SetGain(), CVariation_ref::SetIdentity(), CVariation_ref::SetInsertion(), CVariation_ref::SetInversion(), CVariation_ref::SetLoss(), CVariation_ref::SetMicrosatellite(), CVariation_ref::SetMissense(), CVariation_ref::SetMNP(), CVariation_ref::SetOther(), CVariation_ref::SetSNV(), CVariation_ref::SetTranslocation(), CVariation_ref::SetUniparentalDisomy(), and CVariation_ref::SetUnknown().

Assign a value to Delta data member.

Returns

Reference to the data value.

Definition at line 343 of file Variation_inst_.hpp.

References CVariation_inst_Base::m_Delta, and CVariation_inst_Base::m_set_State.

Referenced by variation_ref::CVariationUtil::AdjustDelinsToInterval(), variation::CVariationUtil::ChangeToDelins(), variation_ref::CVariationUtil::ChangeToDelins(), variation::CVariationUtil::FlipStrand(), g_CreateDeletion(), CNormalizeVariant::NormalizeIdentityInstance(), CVariationNormalization_base< CVariationNormalizationRight >::ResetFullyShifted(), s_AddDeleteDeltaItem(), variation::CVariationUtil::s_AddInstOffsetsFromPlacementOffsets(), CVariation_ref::SetCNV(), CVariation_ref::SetDeletion(), CVariation_ref::SetDeletionInsertion(), CVariation_ref::SetEversion(), CVariation_ref::SetGain(), CVariation_ref::SetInsertion(), CVariation_ref::SetInversion(), CVariation_ref::SetLoss(), CVariation_ref::SetMicrosatellite(), CVariation_ref::SetMNP(), CVariation_ref::SetSNV(), CVariation_ref::SetTranslocation(), variation::CVariationUtil::x_AdjustDelinsToInterval(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_ETC(), variation_ref::CHgvsParser::x_conversion(), variation::CHgvsParser::x_conversion(), variation_ref::CHgvsParser::x_deletion(), variation::CHgvsParser::x_deletion(), variation_ref::CHgvsParser::x_delins(), variation_ref::CHgvsParser::x_duplication(), variation::CHgvsParser::x_duplication(), variation_ref::CHgvsParser::x_expr2(), variation::CHgvsParser::x_expr2(), variation::CHgvsParser::x_expr3(), CVariationUtilities::x_FixAlleles(), variation_ref::CHgvsParser::x_identity(), variation::CVariationUtil::x_InferNAfromAA(), variation_ref::CHgvsParser::x_insertion(), variation::CHgvsParser::x_insertion(), variation::CHgvsParser::x_no_change(), variation_ref::CHgvsParser::x_nuc_inv(), variation::CHgvsParser::x_nuc_inv(), variation_ref::CHgvsParser::x_nuc_subst(), variation::CHgvsParser::x_nuc_subst(), variation_ref::CHgvsParser::x_prot_ext(), variation::CHgvsParser::x_prot_ext(), variation_ref::CHgvsParser::x_prot_missense(), variation::CHgvsParser::x_prot_missense(), variation_ref::CVariationUtil::x_ProtToPrecursor(), CVariationUtilities::x_SetReference(), CVariationNormalization_base< T >::x_Shift(), variation_ref::CHgvsParser::x_translocation(), variation::CHgvsParser::x_translocation(), CVcfReader::xAssignVariantDelins(), and CVcfReader::xAssignVariantIns().