org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto Maven / Gradle / Ivy
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// Generated by the protocol buffer compiler. DO NOT EDIT!
// source: protobuf/opencb/evidence.proto
package org.opencb.biodata.models.variant.protobuf;
public final class EvidenceEntryProto {
private EvidenceEntryProto() {}
public static void registerAllExtensions(
com.google.protobuf.ExtensionRegistryLite registry) {
}
public static void registerAllExtensions(
com.google.protobuf.ExtensionRegistry registry) {
registerAllExtensions(
(com.google.protobuf.ExtensionRegistryLite) registry);
}
/**
*
**
*An enumeration for the different mode of inheritances:
* `monoallelic_not_imprinted`: MONOALLELIC, autosomal or pseudoautosomal, not imprinted
* `monoallelic_maternally_imprinted`: MONOALLELIC, autosomal or pseudoautosomal, maternally imprinted (paternal allele expressed)
* `monoallelic_paternally_imprinted`: MONOALLELIC, autosomal or pseudoautosomal, paternally imprinted (maternal allele expressed)
* `monoallelic`: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
* `biallelic`: BIALLELIC, autosomal or pseudoautosomal
* `monoallelic_and_biallelic`: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
* `monoallelic_and_more_severe_biallelic`: BOTH monoallelic and biallelic, autosomal or pseudoautosomal (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
* `xlinked_biallelic`: X-LINKED: hemizygous mutation in males, biallelic mutations in females
* `xlinked_monoallelic`: X linked: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
* `mitochondrial`: MITOCHONDRIAL
* `unknown`: Unknown
* `NA`: Not applicable
*
*
* Protobuf enum {@code protobuf.opencb.ModeOfInheritance}
*/
public enum ModeOfInheritance
implements com.google.protobuf.ProtocolMessageEnum {
/**
* monoallelic = 0;
*/
monoallelic(0),
/**
* monoallelic_not_imprinted = 1;
*/
monoallelic_not_imprinted(1),
/**
* monoallelic_maternally_imprinted = 2;
*/
monoallelic_maternally_imprinted(2),
/**
* monoallelic_paternally_imprinted = 3;
*/
monoallelic_paternally_imprinted(3),
/**
* biallelic = 4;
*/
biallelic(4),
/**
* monoallelic_and_biallelic = 5;
*/
monoallelic_and_biallelic(5),
/**
* monoallelic_and_more_severe_biallelic = 6;
*/
monoallelic_and_more_severe_biallelic(6),
/**
* xlinked_biallelic = 7;
*/
xlinked_biallelic(7),
/**
* xlinked_monoallelic = 8;
*/
xlinked_monoallelic(8),
/**
* mitochondrial = 9;
*/
mitochondrial(9),
/**
* unknown = 10;
*/
unknown(10),
/**
* NA = 11;
*/
NA(11),
UNRECOGNIZED(-1),
;
/**
* monoallelic = 0;
*/
public static final int monoallelic_VALUE = 0;
/**
* monoallelic_not_imprinted = 1;
*/
public static final int monoallelic_not_imprinted_VALUE = 1;
/**
* monoallelic_maternally_imprinted = 2;
*/
public static final int monoallelic_maternally_imprinted_VALUE = 2;
/**
* monoallelic_paternally_imprinted = 3;
*/
public static final int monoallelic_paternally_imprinted_VALUE = 3;
/**
* biallelic = 4;
*/
public static final int biallelic_VALUE = 4;
/**
* monoallelic_and_biallelic = 5;
*/
public static final int monoallelic_and_biallelic_VALUE = 5;
/**
* monoallelic_and_more_severe_biallelic = 6;
*/
public static final int monoallelic_and_more_severe_biallelic_VALUE = 6;
/**
* xlinked_biallelic = 7;
*/
public static final int xlinked_biallelic_VALUE = 7;
/**
* xlinked_monoallelic = 8;
*/
public static final int xlinked_monoallelic_VALUE = 8;
/**
* mitochondrial = 9;
*/
public static final int mitochondrial_VALUE = 9;
/**
* unknown = 10;
*/
public static final int unknown_VALUE = 10;
/**
* NA = 11;
*/
public static final int NA_VALUE = 11;
public final int getNumber() {
if (this == UNRECOGNIZED) {
throw new java.lang.IllegalArgumentException(
"Can't get the number of an unknown enum value.");
}
return value;
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
* @deprecated Use {@link #forNumber(int)} instead.
*/
@java.lang.Deprecated
public static ModeOfInheritance valueOf(int value) {
return forNumber(value);
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
*/
public static ModeOfInheritance forNumber(int value) {
switch (value) {
case 0: return monoallelic;
case 1: return monoallelic_not_imprinted;
case 2: return monoallelic_maternally_imprinted;
case 3: return monoallelic_paternally_imprinted;
case 4: return biallelic;
case 5: return monoallelic_and_biallelic;
case 6: return monoallelic_and_more_severe_biallelic;
case 7: return xlinked_biallelic;
case 8: return xlinked_monoallelic;
case 9: return mitochondrial;
case 10: return unknown;
case 11: return NA;
default: return null;
}
}
public static com.google.protobuf.Internal.EnumLiteMap
internalGetValueMap() {
return internalValueMap;
}
private static final com.google.protobuf.Internal.EnumLiteMap<
ModeOfInheritance> internalValueMap =
new com.google.protobuf.Internal.EnumLiteMap() {
public ModeOfInheritance findValueByNumber(int number) {
return ModeOfInheritance.forNumber(number);
}
};
public final com.google.protobuf.Descriptors.EnumValueDescriptor
getValueDescriptor() {
return getDescriptor().getValues().get(ordinal());
}
public final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptorForType() {
return getDescriptor();
}
public static final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.getDescriptor().getEnumTypes().get(0);
}
private static final ModeOfInheritance[] VALUES = values();
public static ModeOfInheritance valueOf(
com.google.protobuf.Descriptors.EnumValueDescriptor desc) {
if (desc.getType() != getDescriptor()) {
throw new java.lang.IllegalArgumentException(
"EnumValueDescriptor is not for this type.");
}
if (desc.getIndex() == -1) {
return UNRECOGNIZED;
}
return VALUES[desc.getIndex()];
}
private final int value;
private ModeOfInheritance(int value) {
this.value = value;
}
// @@protoc_insertion_point(enum_scope:protobuf.opencb.ModeOfInheritance)
}
/**
*
**
*The feature types
*
*
* Protobuf enum {@code protobuf.opencb.FeatureTypes}
*/
public enum FeatureTypes
implements com.google.protobuf.ProtocolMessageEnum {
/**
* regulatory_region = 0;
*/
regulatory_region(0),
/**
* gene = 1;
*/
gene(1),
/**
* transcript = 2;
*/
transcript(2),
/**
* protein = 3;
*/
protein(3),
UNRECOGNIZED(-1),
;
/**
* regulatory_region = 0;
*/
public static final int regulatory_region_VALUE = 0;
/**
* gene = 1;
*/
public static final int gene_VALUE = 1;
/**
* transcript = 2;
*/
public static final int transcript_VALUE = 2;
/**
* protein = 3;
*/
public static final int protein_VALUE = 3;
public final int getNumber() {
if (this == UNRECOGNIZED) {
throw new java.lang.IllegalArgumentException(
"Can't get the number of an unknown enum value.");
}
return value;
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
* @deprecated Use {@link #forNumber(int)} instead.
*/
@java.lang.Deprecated
public static FeatureTypes valueOf(int value) {
return forNumber(value);
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
*/
public static FeatureTypes forNumber(int value) {
switch (value) {
case 0: return regulatory_region;
case 1: return gene;
case 2: return transcript;
case 3: return protein;
default: return null;
}
}
public static com.google.protobuf.Internal.EnumLiteMap
internalGetValueMap() {
return internalValueMap;
}
private static final com.google.protobuf.Internal.EnumLiteMap<
FeatureTypes> internalValueMap =
new com.google.protobuf.Internal.EnumLiteMap() {
public FeatureTypes findValueByNumber(int number) {
return FeatureTypes.forNumber(number);
}
};
public final com.google.protobuf.Descriptors.EnumValueDescriptor
getValueDescriptor() {
return getDescriptor().getValues().get(ordinal());
}
public final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptorForType() {
return getDescriptor();
}
public static final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.getDescriptor().getEnumTypes().get(1);
}
private static final FeatureTypes[] VALUES = values();
public static FeatureTypes valueOf(
com.google.protobuf.Descriptors.EnumValueDescriptor desc) {
if (desc.getType() != getDescriptor()) {
throw new java.lang.IllegalArgumentException(
"EnumValueDescriptor is not for this type.");
}
if (desc.getIndex() == -1) {
return UNRECOGNIZED;
}
return VALUES[desc.getIndex()];
}
private final int value;
private FeatureTypes(int value) {
this.value = value;
}
// @@protoc_insertion_point(enum_scope:protobuf.opencb.FeatureTypes)
}
/**
*
**
*Mendelian variants classification with ACMG terminology as defined in Richards, S. et al. (2015). Standards and
*guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College
*of Medical Genetics and Genomics and the Association for Molecular Pathology. Genetics in Medicine, 17(5),
*405–423. https://doi.org/10.1038/gim.2015.30.
*Classification for pharmacogenomic variants, variants associated to
*disease and somatic variants based on the ACMG recommendations and ClinVar classification
*(https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/).
* `benign_variant` : Benign variants interpreted for Mendelian disorders
* `likely_benign_variant` : Likely benign variants interpreted for Mendelian disorders with a certainty of at least 90%
* `pathogenic_variant` : Pathogenic variants interpreted for Mendelian disorders
* `likely_pathogenic_variant` : Likely pathogenic variants interpreted for Mendelian disorders with a certainty of at
*least 90%
* `uncertain_significance` : Uncertain significance variants interpreted for Mendelian disorders. Variants with
*conflicting evidences should be classified as uncertain_significance
*
*
* Protobuf enum {@code protobuf.opencb.ClinicalSignificance}
*/
public enum ClinicalSignificance
implements com.google.protobuf.ProtocolMessageEnum {
/**
* benign = 0;
*/
benign(0),
/**
* likely_benign = 1;
*/
likely_benign(1),
/**
* VUS = 2;
*/
VUS(2),
/**
* likely_pathogenic = 3;
*/
likely_pathogenic(3),
/**
* pathogenic = 4;
*/
pathogenic(4),
/**
* uncertain_significance = 5;
*/
uncertain_significance(5),
UNRECOGNIZED(-1),
;
/**
* benign = 0;
*/
public static final int benign_VALUE = 0;
/**
* likely_benign = 1;
*/
public static final int likely_benign_VALUE = 1;
/**
* VUS = 2;
*/
public static final int VUS_VALUE = 2;
/**
* likely_pathogenic = 3;
*/
public static final int likely_pathogenic_VALUE = 3;
/**
* pathogenic = 4;
*/
public static final int pathogenic_VALUE = 4;
/**
* uncertain_significance = 5;
*/
public static final int uncertain_significance_VALUE = 5;
public final int getNumber() {
if (this == UNRECOGNIZED) {
throw new java.lang.IllegalArgumentException(
"Can't get the number of an unknown enum value.");
}
return value;
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
* @deprecated Use {@link #forNumber(int)} instead.
*/
@java.lang.Deprecated
public static ClinicalSignificance valueOf(int value) {
return forNumber(value);
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
*/
public static ClinicalSignificance forNumber(int value) {
switch (value) {
case 0: return benign;
case 1: return likely_benign;
case 2: return VUS;
case 3: return likely_pathogenic;
case 4: return pathogenic;
case 5: return uncertain_significance;
default: return null;
}
}
public static com.google.protobuf.Internal.EnumLiteMap
internalGetValueMap() {
return internalValueMap;
}
private static final com.google.protobuf.Internal.EnumLiteMap<
ClinicalSignificance> internalValueMap =
new com.google.protobuf.Internal.EnumLiteMap() {
public ClinicalSignificance findValueByNumber(int number) {
return ClinicalSignificance.forNumber(number);
}
};
public final com.google.protobuf.Descriptors.EnumValueDescriptor
getValueDescriptor() {
return getDescriptor().getValues().get(ordinal());
}
public final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptorForType() {
return getDescriptor();
}
public static final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.getDescriptor().getEnumTypes().get(2);
}
private static final ClinicalSignificance[] VALUES = values();
public static ClinicalSignificance valueOf(
com.google.protobuf.Descriptors.EnumValueDescriptor desc) {
if (desc.getType() != getDescriptor()) {
throw new java.lang.IllegalArgumentException(
"EnumValueDescriptor is not for this type.");
}
if (desc.getIndex() == -1) {
return UNRECOGNIZED;
}
return VALUES[desc.getIndex()];
}
private final int value;
private ClinicalSignificance(int value) {
this.value = value;
}
// @@protoc_insertion_point(enum_scope:protobuf.opencb.ClinicalSignificance)
}
/**
*
**
*Pharmacogenomics drug response variant classification
* `responsive` : A variant that confers response to a treatment
* `resistant` : A variant that confers resistance to a treatment
* `toxicity` : A variant that is associated with drug-induced toxicity
* `indication` : A variant that is required in order for a particular drug to be prescribed
* `contraindication` : A variant that if present, a particular drug should not be prescribed
* `dosing` : A variant that results in an alteration in dosing of a particular drug in order to achieve INR, reduce toxicity or increase efficacy
* `increased_monitoring` : increase vigilance or increased dosage monitoring may be required for a patient with this variant to look for signs of adverse drug reactions
* `efficacy` : a variant that affects the efficacy of the treatment
*
*
* Protobuf enum {@code protobuf.opencb.DrugResponseClassification}
*/
public enum DrugResponseClassification
implements com.google.protobuf.ProtocolMessageEnum {
/**
* responsive = 0;
*/
responsive(0),
/**
* resistant = 1;
*/
resistant(1),
/**
* toxicity = 2;
*/
toxicity(2),
/**
* indication = 3;
*/
indication(3),
/**
* contraindication = 4;
*/
contraindication(4),
/**
* dosing = 5;
*/
dosing(5),
/**
* increased_monitoring = 6;
*/
increased_monitoring(6),
/**
* efficacy = 7;
*/
efficacy(7),
UNRECOGNIZED(-1),
;
/**
* responsive = 0;
*/
public static final int responsive_VALUE = 0;
/**
* resistant = 1;
*/
public static final int resistant_VALUE = 1;
/**
* toxicity = 2;
*/
public static final int toxicity_VALUE = 2;
/**
* indication = 3;
*/
public static final int indication_VALUE = 3;
/**
* contraindication = 4;
*/
public static final int contraindication_VALUE = 4;
/**
* dosing = 5;
*/
public static final int dosing_VALUE = 5;
/**
* increased_monitoring = 6;
*/
public static final int increased_monitoring_VALUE = 6;
/**
* efficacy = 7;
*/
public static final int efficacy_VALUE = 7;
public final int getNumber() {
if (this == UNRECOGNIZED) {
throw new java.lang.IllegalArgumentException(
"Can't get the number of an unknown enum value.");
}
return value;
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
* @deprecated Use {@link #forNumber(int)} instead.
*/
@java.lang.Deprecated
public static DrugResponseClassification valueOf(int value) {
return forNumber(value);
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
*/
public static DrugResponseClassification forNumber(int value) {
switch (value) {
case 0: return responsive;
case 1: return resistant;
case 2: return toxicity;
case 3: return indication;
case 4: return contraindication;
case 5: return dosing;
case 6: return increased_monitoring;
case 7: return efficacy;
default: return null;
}
}
public static com.google.protobuf.Internal.EnumLiteMap
internalGetValueMap() {
return internalValueMap;
}
private static final com.google.protobuf.Internal.EnumLiteMap<
DrugResponseClassification> internalValueMap =
new com.google.protobuf.Internal.EnumLiteMap() {
public DrugResponseClassification findValueByNumber(int number) {
return DrugResponseClassification.forNumber(number);
}
};
public final com.google.protobuf.Descriptors.EnumValueDescriptor
getValueDescriptor() {
return getDescriptor().getValues().get(ordinal());
}
public final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptorForType() {
return getDescriptor();
}
public static final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.getDescriptor().getEnumTypes().get(3);
}
private static final DrugResponseClassification[] VALUES = values();
public static DrugResponseClassification valueOf(
com.google.protobuf.Descriptors.EnumValueDescriptor desc) {
if (desc.getType() != getDescriptor()) {
throw new java.lang.IllegalArgumentException(
"EnumValueDescriptor is not for this type.");
}
if (desc.getIndex() == -1) {
return UNRECOGNIZED;
}
return VALUES[desc.getIndex()];
}
private final int value;
private DrugResponseClassification(int value) {
this.value = value;
}
// @@protoc_insertion_point(enum_scope:protobuf.opencb.DrugResponseClassification)
}
/**
*
**
*Association of variants to a given trait.
* `established_risk_allele` : Established risk allele for variants associated to disease
* `likely_risk_allele` : Likely risk allele for variants associated to disease
* `uncertain_risk_allele` : Uncertain risk allele for variants associated to disease
* `protective` : Protective allele
*
*
* Protobuf enum {@code protobuf.opencb.TraitAssociation}
*/
public enum TraitAssociation
implements com.google.protobuf.ProtocolMessageEnum {
/**
* established_risk_allele = 0;
*/
established_risk_allele(0),
/**
* likely_risk_allele = 1;
*/
likely_risk_allele(1),
/**
* uncertain_risk_allele = 2;
*/
uncertain_risk_allele(2),
/**
* protective = 3;
*/
protective(3),
UNRECOGNIZED(-1),
;
/**
* established_risk_allele = 0;
*/
public static final int established_risk_allele_VALUE = 0;
/**
* likely_risk_allele = 1;
*/
public static final int likely_risk_allele_VALUE = 1;
/**
* uncertain_risk_allele = 2;
*/
public static final int uncertain_risk_allele_VALUE = 2;
/**
* protective = 3;
*/
public static final int protective_VALUE = 3;
public final int getNumber() {
if (this == UNRECOGNIZED) {
throw new java.lang.IllegalArgumentException(
"Can't get the number of an unknown enum value.");
}
return value;
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
* @deprecated Use {@link #forNumber(int)} instead.
*/
@java.lang.Deprecated
public static TraitAssociation valueOf(int value) {
return forNumber(value);
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
*/
public static TraitAssociation forNumber(int value) {
switch (value) {
case 0: return established_risk_allele;
case 1: return likely_risk_allele;
case 2: return uncertain_risk_allele;
case 3: return protective;
default: return null;
}
}
public static com.google.protobuf.Internal.EnumLiteMap
internalGetValueMap() {
return internalValueMap;
}
private static final com.google.protobuf.Internal.EnumLiteMap<
TraitAssociation> internalValueMap =
new com.google.protobuf.Internal.EnumLiteMap() {
public TraitAssociation findValueByNumber(int number) {
return TraitAssociation.forNumber(number);
}
};
public final com.google.protobuf.Descriptors.EnumValueDescriptor
getValueDescriptor() {
return getDescriptor().getValues().get(ordinal());
}
public final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptorForType() {
return getDescriptor();
}
public static final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.getDescriptor().getEnumTypes().get(4);
}
private static final TraitAssociation[] VALUES = values();
public static TraitAssociation valueOf(
com.google.protobuf.Descriptors.EnumValueDescriptor desc) {
if (desc.getType() != getDescriptor()) {
throw new java.lang.IllegalArgumentException(
"EnumValueDescriptor is not for this type.");
}
if (desc.getIndex() == -1) {
return UNRECOGNIZED;
}
return VALUES[desc.getIndex()];
}
private final int value;
private TraitAssociation(int value) {
this.value = value;
}
// @@protoc_insertion_point(enum_scope:protobuf.opencb.TraitAssociation)
}
/**
*
**
*Variant classification according to its relation to cancer aetiology.
* `driver` : Driver variants
* `passenger` : Passenger variants
* `modifier` : Modifier variants
*
*
* Protobuf enum {@code protobuf.opencb.TumorigenesisClassification}
*/
public enum TumorigenesisClassification
implements com.google.protobuf.ProtocolMessageEnum {
/**
* driver = 0;
*/
driver(0),
/**
* passenger = 1;
*/
passenger(1),
/**
* modifier = 2;
*/
modifier(2),
UNRECOGNIZED(-1),
;
/**
* driver = 0;
*/
public static final int driver_VALUE = 0;
/**
* passenger = 1;
*/
public static final int passenger_VALUE = 1;
/**
* modifier = 2;
*/
public static final int modifier_VALUE = 2;
public final int getNumber() {
if (this == UNRECOGNIZED) {
throw new java.lang.IllegalArgumentException(
"Can't get the number of an unknown enum value.");
}
return value;
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
* @deprecated Use {@link #forNumber(int)} instead.
*/
@java.lang.Deprecated
public static TumorigenesisClassification valueOf(int value) {
return forNumber(value);
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
*/
public static TumorigenesisClassification forNumber(int value) {
switch (value) {
case 0: return driver;
case 1: return passenger;
case 2: return modifier;
default: return null;
}
}
public static com.google.protobuf.Internal.EnumLiteMap
internalGetValueMap() {
return internalValueMap;
}
private static final com.google.protobuf.Internal.EnumLiteMap<
TumorigenesisClassification> internalValueMap =
new com.google.protobuf.Internal.EnumLiteMap() {
public TumorigenesisClassification findValueByNumber(int number) {
return TumorigenesisClassification.forNumber(number);
}
};
public final com.google.protobuf.Descriptors.EnumValueDescriptor
getValueDescriptor() {
return getDescriptor().getValues().get(ordinal());
}
public final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptorForType() {
return getDescriptor();
}
public static final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.getDescriptor().getEnumTypes().get(5);
}
private static final TumorigenesisClassification[] VALUES = values();
public static TumorigenesisClassification valueOf(
com.google.protobuf.Descriptors.EnumValueDescriptor desc) {
if (desc.getType() != getDescriptor()) {
throw new java.lang.IllegalArgumentException(
"EnumValueDescriptor is not for this type.");
}
if (desc.getIndex() == -1) {
return UNRECOGNIZED;
}
return VALUES[desc.getIndex()];
}
private final int value;
private TumorigenesisClassification(int value) {
this.value = value;
}
// @@protoc_insertion_point(enum_scope:protobuf.opencb.TumorigenesisClassification)
}
/**
*
**
*Evidence of pathogenicity and benign impact as defined in Richards, S. et al. (2015). Standards and guidelines for the interpretation
*of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and
*the Association for Molecular Pathology. Genetics in Medicine, 17(5), 405–423. https://doi.org/10.1038/gim.2015.30
*Evidence of pathogenicity:
* `very_strong`:
*- PVS1 null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multiexon
*deletion) in a gene where LOF is a known mechanism of disease
* `strong`:
*- PS1 Same amino acid change as a previously established pathogenic variant regardless of nucleotide change
*- PS2 De novo (both maternity and paternity confirmed) in a patient with the disease and no family history
*- PS3 Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene
*product
*- PS4 The prevalence of the variant in affected individuals is significantly increased compared with the prevalence
*in controls
* `moderate`:
*- PM1 Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of
*an enzyme) without benign variation
*- PM2 Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes
*Project, or Exome Aggregation Consortium
*- PM3 For recessive disorders, detected in trans with a pathogenic variant
*- PM4 Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss
*variants
*- PM5 Novel missense change at an amino acid residue where a different missense change determined to be pathogenic
*has been seen before
*- PM6 Assumed de novo, but without confirmation of paternity and maternity
* `supporting`:
*- PP1 Cosegregation with disease in multiple affected family members in a gene definitively known to cause the
*disease
*- PP2 Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are
*a common mechanism of disease
*- PP3 Multiple lines of computational evidence support a deleterious effect on the gene or gene product
*(conservation, evolutionary, splicing impact, etc.)
*- PP4 Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology
*- PP5 Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory
*to perform an independent evaluation
*Evidence of benign impact:
* `stand_alone`:
*- BA1 Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation
*Consortium
* `strong`:
*- BS1 Allele frequency is greater than expected for disorder
*- BS2 Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked
*(hemizygous) disorder, with full penetrance expected at an early age
*- BS3 Well-established in vitro or in vivo functional studies show no damaging effect on protein function or
*splicing
*- BS4 Lack of segregation in affected members of a family
* `supporting`:
*- BP1 Missense variant in a gene for which primarily truncating variants are known to cause disease
*- BP2 Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis
*with a pathogenic variant in any inheritance pattern
*- BP3 In-frame deletions/insertions in a repetitive region without a known function
*- BP4 Multiple lines of computational evidence suggest no impact on gene or gene product (conservation,
*evolutionary, splicing impact, etc.)
*- BP5 Variant found in a case with an alternate molecular basis for disease
*- BP6 Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to
*perform an independent evaluation
*- BP7 A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice
*consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
*
*
* Protobuf enum {@code protobuf.opencb.EvidenceImpact}
*/
public enum EvidenceImpact
implements com.google.protobuf.ProtocolMessageEnum {
/**
* very_strong = 0;
*/
very_strong(0),
/**
* strong = 1;
*/
strong(1),
/**
* moderate = 2;
*/
moderate(2),
/**
* supporting = 3;
*/
supporting(3),
/**
* stand_alone = 4;
*/
stand_alone(4),
UNRECOGNIZED(-1),
;
/**
* very_strong = 0;
*/
public static final int very_strong_VALUE = 0;
/**
* strong = 1;
*/
public static final int strong_VALUE = 1;
/**
* moderate = 2;
*/
public static final int moderate_VALUE = 2;
/**
* supporting = 3;
*/
public static final int supporting_VALUE = 3;
/**
* stand_alone = 4;
*/
public static final int stand_alone_VALUE = 4;
public final int getNumber() {
if (this == UNRECOGNIZED) {
throw new java.lang.IllegalArgumentException(
"Can't get the number of an unknown enum value.");
}
return value;
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
* @deprecated Use {@link #forNumber(int)} instead.
*/
@java.lang.Deprecated
public static EvidenceImpact valueOf(int value) {
return forNumber(value);
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
*/
public static EvidenceImpact forNumber(int value) {
switch (value) {
case 0: return very_strong;
case 1: return strong;
case 2: return moderate;
case 3: return supporting;
case 4: return stand_alone;
default: return null;
}
}
public static com.google.protobuf.Internal.EnumLiteMap
internalGetValueMap() {
return internalValueMap;
}
private static final com.google.protobuf.Internal.EnumLiteMap<
EvidenceImpact> internalValueMap =
new com.google.protobuf.Internal.EnumLiteMap() {
public EvidenceImpact findValueByNumber(int number) {
return EvidenceImpact.forNumber(number);
}
};
public final com.google.protobuf.Descriptors.EnumValueDescriptor
getValueDescriptor() {
return getDescriptor().getValues().get(ordinal());
}
public final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptorForType() {
return getDescriptor();
}
public static final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.getDescriptor().getEnumTypes().get(6);
}
private static final EvidenceImpact[] VALUES = values();
public static EvidenceImpact valueOf(
com.google.protobuf.Descriptors.EnumValueDescriptor desc) {
if (desc.getType() != getDescriptor()) {
throw new java.lang.IllegalArgumentException(
"EnumValueDescriptor is not for this type.");
}
if (desc.getIndex() == -1) {
return UNRECOGNIZED;
}
return VALUES[desc.getIndex()];
}
private final int value;
private EvidenceImpact(int value) {
this.value = value;
}
// @@protoc_insertion_point(enum_scope:protobuf.opencb.EvidenceImpact)
}
/**
*
**
*This is the list of ethnics in ONS16
* `D`: Mixed: White and Black Caribbean
* `E`: Mixed: White and Black African
* `F`: Mixed: White and Asian
* `G`: Mixed: Any other mixed background
* `A`: White: British
* `B`: White: Irish
* `C`: White: Any other White background
* `L`: Asian or Asian British: Any other Asian background
* `M`: Black or Black British: Caribbean
* `N`: Black or Black British: African
* `H`: Asian or Asian British: Indian
* `J`: Asian or Asian British: Pakistani
* `K`: Asian or Asian British: Bangladeshi
* `P`: Black or Black British: Any other Black background
* `S`: Other Ethnic Groups: Any other ethnic group
* `R`: Other Ethnic Groups: Chinese
* `Z`: Not stated
*
*
* Protobuf enum {@code protobuf.opencb.EthnicCategory}
*/
public enum EthnicCategory
implements com.google.protobuf.ProtocolMessageEnum {
/**
* D = 0;
*/
D(0),
/**
* E = 1;
*/
E(1),
/**
* F = 2;
*/
F(2),
/**
* G = 3;
*/
G(3),
/**
* A = 4;
*/
A(4),
/**
* B = 5;
*/
B(5),
/**
* C = 6;
*/
C(6),
/**
* L = 7;
*/
L(7),
/**
* M = 8;
*/
M(8),
/**
* N = 9;
*/
N(9),
/**
* H = 10;
*/
H(10),
/**
* J = 11;
*/
J(11),
/**
* K = 12;
*/
K(12),
/**
* P = 13;
*/
P(13),
/**
* S = 14;
*/
S(14),
/**
* R = 15;
*/
R(15),
/**
* Z = 16;
*/
Z(16),
UNRECOGNIZED(-1),
;
/**
* D = 0;
*/
public static final int D_VALUE = 0;
/**
* E = 1;
*/
public static final int E_VALUE = 1;
/**
* F = 2;
*/
public static final int F_VALUE = 2;
/**
* G = 3;
*/
public static final int G_VALUE = 3;
/**
* A = 4;
*/
public static final int A_VALUE = 4;
/**
* B = 5;
*/
public static final int B_VALUE = 5;
/**
* C = 6;
*/
public static final int C_VALUE = 6;
/**
* L = 7;
*/
public static final int L_VALUE = 7;
/**
* M = 8;
*/
public static final int M_VALUE = 8;
/**
* N = 9;
*/
public static final int N_VALUE = 9;
/**
* H = 10;
*/
public static final int H_VALUE = 10;
/**
* J = 11;
*/
public static final int J_VALUE = 11;
/**
* K = 12;
*/
public static final int K_VALUE = 12;
/**
* P = 13;
*/
public static final int P_VALUE = 13;
/**
* S = 14;
*/
public static final int S_VALUE = 14;
/**
* R = 15;
*/
public static final int R_VALUE = 15;
/**
* Z = 16;
*/
public static final int Z_VALUE = 16;
public final int getNumber() {
if (this == UNRECOGNIZED) {
throw new java.lang.IllegalArgumentException(
"Can't get the number of an unknown enum value.");
}
return value;
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
* @deprecated Use {@link #forNumber(int)} instead.
*/
@java.lang.Deprecated
public static EthnicCategory valueOf(int value) {
return forNumber(value);
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
*/
public static EthnicCategory forNumber(int value) {
switch (value) {
case 0: return D;
case 1: return E;
case 2: return F;
case 3: return G;
case 4: return A;
case 5: return B;
case 6: return C;
case 7: return L;
case 8: return M;
case 9: return N;
case 10: return H;
case 11: return J;
case 12: return K;
case 13: return P;
case 14: return S;
case 15: return R;
case 16: return Z;
default: return null;
}
}
public static com.google.protobuf.Internal.EnumLiteMap
internalGetValueMap() {
return internalValueMap;
}
private static final com.google.protobuf.Internal.EnumLiteMap<
EthnicCategory> internalValueMap =
new com.google.protobuf.Internal.EnumLiteMap() {
public EthnicCategory findValueByNumber(int number) {
return EthnicCategory.forNumber(number);
}
};
public final com.google.protobuf.Descriptors.EnumValueDescriptor
getValueDescriptor() {
return getDescriptor().getValues().get(ordinal());
}
public final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptorForType() {
return getDescriptor();
}
public static final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.getDescriptor().getEnumTypes().get(7);
}
private static final EthnicCategory[] VALUES = values();
public static EthnicCategory valueOf(
com.google.protobuf.Descriptors.EnumValueDescriptor desc) {
if (desc.getType() != getDescriptor()) {
throw new java.lang.IllegalArgumentException(
"EnumValueDescriptor is not for this type.");
}
if (desc.getIndex() == -1) {
return UNRECOGNIZED;
}
return VALUES[desc.getIndex()];
}
private final int value;
private EthnicCategory(int value) {
this.value = value;
}
// @@protoc_insertion_point(enum_scope:protobuf.opencb.EthnicCategory)
}
/**
*
**
*Penetrance assumed in the analysis
*
*
* Protobuf enum {@code protobuf.opencb.Penetrance}
*/
public enum Penetrance
implements com.google.protobuf.ProtocolMessageEnum {
/**
* complete = 0;
*/
complete(0),
/**
* incomplete = 1;
*/
incomplete(1),
UNRECOGNIZED(-1),
;
/**
* complete = 0;
*/
public static final int complete_VALUE = 0;
/**
* incomplete = 1;
*/
public static final int incomplete_VALUE = 1;
public final int getNumber() {
if (this == UNRECOGNIZED) {
throw new java.lang.IllegalArgumentException(
"Can't get the number of an unknown enum value.");
}
return value;
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
* @deprecated Use {@link #forNumber(int)} instead.
*/
@java.lang.Deprecated
public static Penetrance valueOf(int value) {
return forNumber(value);
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
*/
public static Penetrance forNumber(int value) {
switch (value) {
case 0: return complete;
case 1: return incomplete;
default: return null;
}
}
public static com.google.protobuf.Internal.EnumLiteMap
internalGetValueMap() {
return internalValueMap;
}
private static final com.google.protobuf.Internal.EnumLiteMap<
Penetrance> internalValueMap =
new com.google.protobuf.Internal.EnumLiteMap() {
public Penetrance findValueByNumber(int number) {
return Penetrance.forNumber(number);
}
};
public final com.google.protobuf.Descriptors.EnumValueDescriptor
getValueDescriptor() {
return getDescriptor().getValues().get(ordinal());
}
public final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptorForType() {
return getDescriptor();
}
public static final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.getDescriptor().getEnumTypes().get(8);
}
private static final Penetrance[] VALUES = values();
public static Penetrance valueOf(
com.google.protobuf.Descriptors.EnumValueDescriptor desc) {
if (desc.getType() != getDescriptor()) {
throw new java.lang.IllegalArgumentException(
"EnumValueDescriptor is not for this type.");
}
if (desc.getIndex() == -1) {
return UNRECOGNIZED;
}
return VALUES[desc.getIndex()];
}
private final int value;
private Penetrance(int value) {
this.value = value;
}
// @@protoc_insertion_point(enum_scope:protobuf.opencb.Penetrance)
}
/**
*
**
*Variant effect with Sequence Ontology terms.
* `SO_0002052`: dominant_negative_variant (http://purl.obolibrary.org/obo/SO_0002052)
* `SO_0002053`: gain_of_function_variant (http://purl.obolibrary.org/obo/SO_0002053)
* `SO_0001773`: lethal_variant (http://purl.obolibrary.org/obo/SO_0001773)
* `SO_0002054`: loss_of_function_variant (http://purl.obolibrary.org/obo/SO_0002054)
* `SO_0001786`: loss_of_heterozygosity (http://purl.obolibrary.org/obo/SO_0001786)
* `SO_0002055`: null_variant (http://purl.obolibrary.org/obo/SO_0002055)
*
*
* Protobuf enum {@code protobuf.opencb.VariantFunctionalEffect}
*/
public enum VariantFunctionalEffect
implements com.google.protobuf.ProtocolMessageEnum {
/**
* dominant_negative_variant = 0;
*/
dominant_negative_variant(0),
/**
* gain_of_function_variant = 1;
*/
gain_of_function_variant(1),
/**
* lethal_variant = 2;
*/
lethal_variant(2),
/**
* loss_of_function_variant = 3;
*/
loss_of_function_variant(3),
/**
* loss_of_heterozygosity = 4;
*/
loss_of_heterozygosity(4),
/**
* null_variant = 5;
*/
null_variant(5),
UNRECOGNIZED(-1),
;
/**
* dominant_negative_variant = 0;
*/
public static final int dominant_negative_variant_VALUE = 0;
/**
* gain_of_function_variant = 1;
*/
public static final int gain_of_function_variant_VALUE = 1;
/**
* lethal_variant = 2;
*/
public static final int lethal_variant_VALUE = 2;
/**
* loss_of_function_variant = 3;
*/
public static final int loss_of_function_variant_VALUE = 3;
/**
* loss_of_heterozygosity = 4;
*/
public static final int loss_of_heterozygosity_VALUE = 4;
/**
* null_variant = 5;
*/
public static final int null_variant_VALUE = 5;
public final int getNumber() {
if (this == UNRECOGNIZED) {
throw new java.lang.IllegalArgumentException(
"Can't get the number of an unknown enum value.");
}
return value;
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
* @deprecated Use {@link #forNumber(int)} instead.
*/
@java.lang.Deprecated
public static VariantFunctionalEffect valueOf(int value) {
return forNumber(value);
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
*/
public static VariantFunctionalEffect forNumber(int value) {
switch (value) {
case 0: return dominant_negative_variant;
case 1: return gain_of_function_variant;
case 2: return lethal_variant;
case 3: return loss_of_function_variant;
case 4: return loss_of_heterozygosity;
case 5: return null_variant;
default: return null;
}
}
public static com.google.protobuf.Internal.EnumLiteMap
internalGetValueMap() {
return internalValueMap;
}
private static final com.google.protobuf.Internal.EnumLiteMap<
VariantFunctionalEffect> internalValueMap =
new com.google.protobuf.Internal.EnumLiteMap() {
public VariantFunctionalEffect findValueByNumber(int number) {
return VariantFunctionalEffect.forNumber(number);
}
};
public final com.google.protobuf.Descriptors.EnumValueDescriptor
getValueDescriptor() {
return getDescriptor().getValues().get(ordinal());
}
public final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptorForType() {
return getDescriptor();
}
public static final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.getDescriptor().getEnumTypes().get(9);
}
private static final VariantFunctionalEffect[] VALUES = values();
public static VariantFunctionalEffect valueOf(
com.google.protobuf.Descriptors.EnumValueDescriptor desc) {
if (desc.getType() != getDescriptor()) {
throw new java.lang.IllegalArgumentException(
"EnumValueDescriptor is not for this type.");
}
if (desc.getIndex() == -1) {
return UNRECOGNIZED;
}
return VALUES[desc.getIndex()];
}
private final int value;
private VariantFunctionalEffect(int value) {
this.value = value;
}
// @@protoc_insertion_point(enum_scope:protobuf.opencb.VariantFunctionalEffect)
}
/**
*
**
*Variant origin.
* `SO_0001781`: de novo variant. http://purl.obolibrary.org/obo/SO_0001781
* `SO_0001778`: germline variant. http://purl.obolibrary.org/obo/SO_0001778
* `SO_0001775`: maternal variant. http://purl.obolibrary.org/obo/SO_0001775
* `SO_0001776`: paternal variant. http://purl.obolibrary.org/obo/SO_0001776
* `SO_0001779`: pedigree specific variant. http://purl.obolibrary.org/obo/SO_0001779
* `SO_0001780`: population specific variant. http://purl.obolibrary.org/obo/SO_0001780
* `SO_0001777`: somatic variant. http://purl.obolibrary.org/obo/SO_0001777
*
*
* Protobuf enum {@code protobuf.opencb.AlleleOrigin}
*/
public enum AlleleOrigin
implements com.google.protobuf.ProtocolMessageEnum {
/**
* de_novo_variant = 0;
*/
de_novo_variant(0),
/**
* germline_variant = 1;
*/
germline_variant(1),
/**
* maternal_variant = 2;
*/
maternal_variant(2),
/**
* paternal_variant = 3;
*/
paternal_variant(3),
/**
* pedigree_specific_variant = 4;
*/
pedigree_specific_variant(4),
/**
* population_specific_variant = 5;
*/
population_specific_variant(5),
/**
* somatic_variant = 6;
*/
somatic_variant(6),
UNRECOGNIZED(-1),
;
/**
* de_novo_variant = 0;
*/
public static final int de_novo_variant_VALUE = 0;
/**
* germline_variant = 1;
*/
public static final int germline_variant_VALUE = 1;
/**
* maternal_variant = 2;
*/
public static final int maternal_variant_VALUE = 2;
/**
* paternal_variant = 3;
*/
public static final int paternal_variant_VALUE = 3;
/**
* pedigree_specific_variant = 4;
*/
public static final int pedigree_specific_variant_VALUE = 4;
/**
* population_specific_variant = 5;
*/
public static final int population_specific_variant_VALUE = 5;
/**
* somatic_variant = 6;
*/
public static final int somatic_variant_VALUE = 6;
public final int getNumber() {
if (this == UNRECOGNIZED) {
throw new java.lang.IllegalArgumentException(
"Can't get the number of an unknown enum value.");
}
return value;
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
* @deprecated Use {@link #forNumber(int)} instead.
*/
@java.lang.Deprecated
public static AlleleOrigin valueOf(int value) {
return forNumber(value);
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
*/
public static AlleleOrigin forNumber(int value) {
switch (value) {
case 0: return de_novo_variant;
case 1: return germline_variant;
case 2: return maternal_variant;
case 3: return paternal_variant;
case 4: return pedigree_specific_variant;
case 5: return population_specific_variant;
case 6: return somatic_variant;
default: return null;
}
}
public static com.google.protobuf.Internal.EnumLiteMap
internalGetValueMap() {
return internalValueMap;
}
private static final com.google.protobuf.Internal.EnumLiteMap<
AlleleOrigin> internalValueMap =
new com.google.protobuf.Internal.EnumLiteMap() {
public AlleleOrigin findValueByNumber(int number) {
return AlleleOrigin.forNumber(number);
}
};
public final com.google.protobuf.Descriptors.EnumValueDescriptor
getValueDescriptor() {
return getDescriptor().getValues().get(ordinal());
}
public final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptorForType() {
return getDescriptor();
}
public static final com.google.protobuf.Descriptors.EnumDescriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.getDescriptor().getEnumTypes().get(10);
}
private static final AlleleOrigin[] VALUES = values();
public static AlleleOrigin valueOf(
com.google.protobuf.Descriptors.EnumValueDescriptor desc) {
if (desc.getType() != getDescriptor()) {
throw new java.lang.IllegalArgumentException(
"EnumValueDescriptor is not for this type.");
}
if (desc.getIndex() == -1) {
return UNRECOGNIZED;
}
return VALUES[desc.getIndex()];
}
private final int value;
private AlleleOrigin(int value) {
this.value = value;
}
// @@protoc_insertion_point(enum_scope:protobuf.opencb.AlleleOrigin)
}
/**
*
**
*Confidence based on the Confidence Information Ontology
* `CIO_0000029`: high confidence level http://purl.obolibrary.org/obo/CIO_0000029
* `CIO_0000031`: low confidence level http://purl.obolibrary.org/obo/CIO_0000031
* `CIO_0000030`: medium confidence level http://purl.obolibrary.org/obo/CIO_0000030
* `CIO_0000039`: rejected http://purl.obolibrary.org/obo/CIO_0000039
*
*
* Protobuf enum {@code protobuf.opencb.Confidence}
*/
public enum Confidence
implements com.google.protobuf.ProtocolMessageEnum {
/**
*
* CIO_0000031
*
*
* low_confidence_level = 0;
*/
low_confidence_level(0),
/**
*
* CIO_0000030
*
*
* medium_confidence_level = 1;
*/
medium_confidence_level(1),
/**
*
* CIO_0000029
*
*
* high_confidence_level = 2;
*/
high_confidence_level(2),
/**
*
* CIO_0000039
*
*
* rejected = 3;
*/
rejected(3),
UNRECOGNIZED(-1),
;
/**
*
* CIO_0000031
*
*
* low_confidence_level = 0;
*/
public static final int low_confidence_level_VALUE = 0;
/**
*
* CIO_0000030
*
*
* medium_confidence_level = 1;
*/
public static final int medium_confidence_level_VALUE = 1;
/**
*
* CIO_0000029
*
*
* high_confidence_level = 2;
*/
public static final int high_confidence_level_VALUE = 2;
/**
*
* CIO_0000039
*
*
* rejected = 3;
*/
public static final int rejected_VALUE = 3;
public final int getNumber() {
if (this == UNRECOGNIZED) {
throw new java.lang.IllegalArgumentException(
"Can't get the number of an unknown enum value.");
}
return value;
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
* @deprecated Use {@link #forNumber(int)} instead.
*/
@java.lang.Deprecated
public static Confidence valueOf(int value) {
return forNumber(value);
}
/**
* @param value The numeric wire value of the corresponding enum entry.
* @return The enum associated with the given numeric wire value.
*/
public static Confidence forNumber(int value) {
switch (value) {
case 0: return low_confidence_level;
case 1: return medium_confidence_level;
case 2: return high_confidence_level;
case 3: return rejected;
default: return null;
}
}
public static com.google.protobuf.Internal.EnumLiteMap
internalGetValueMap() {
return internalValueMap;
}
private static final com.google.protobuf.Internal.EnumLiteMap<
Confidence> internalValueMap =
new com.google.protobuf.Internal.EnumLiteMap() {
public Confidence findValueByNumber(int number) {
return Confidence.forNumber(number);
}
};
public final com.google.protobuf.Descriptors.EnumValueDescriptor
getValueDescriptor() {
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// @@protoc_insertion_point(enum_scope:protobuf.opencb.Confidence)
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/**
*
**
*The consistency of evidences for a given phenotype. This aggregates all evidences for a given phenotype and all
*evidences with no phenotype associated (e.g.: in silico impact prediction, population frequency).
*This is based on the Confidence Information Ontology terms.
* `CIO_0000033`: congruent, all evidences are consistent. http://purl.obolibrary.org/obo/CIO_0000033
* `CIO_0000034`: conflict, there are conflicting evidences. This should correspond to a `VariantClassification` of
*`uncertain_significance` for mendelian disorders. http://purl.obolibrary.org/obo/CIO_0000034
* `CIO_0000035`: strongly conflicting. http://purl.obolibrary.org/obo/CIO_0000035
* `CIO_0000036`: weakly conflicting. http://purl.obolibrary.org/obo/CIO_0000036
*
*
* Protobuf enum {@code protobuf.opencb.ConsistencyStatus}
*/
public enum ConsistencyStatus
implements com.google.protobuf.ProtocolMessageEnum {
/**
*
* CIO_0000033
*
*
* congruent = 0;
*/
congruent(0),
/**
*
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*
*
* conflict = 1;
*/
conflict(1),
/**
*
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*
*
* weakly_conflicting = 2;
*/
weakly_conflicting(2),
/**
*
* CIO_0000036
*
*
* strongly_conflicting = 3;
*/
strongly_conflicting(3),
UNRECOGNIZED(-1),
;
/**
*
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*
*
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*/
public static final int congruent_VALUE = 0;
/**
*
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*
*
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*/
public static final int conflict_VALUE = 1;
/**
*
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*
*
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*/
public static final int weakly_conflicting_VALUE = 2;
/**
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*
*
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*/
public static final int strongly_conflicting_VALUE = 3;
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*/
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case 2: return weakly_conflicting;
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public com.google.protobuf.ByteString
getSubmitterBytes() {
java.lang.Object ref = submitter_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
submitter_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
**
*The submitter
*
*
* string submitter = 1;
* @param value The submitter to set.
* @return This builder for chaining.
*/
public Builder setSubmitter(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
submitter_ = value;
onChanged();
return this;
}
/**
*
**
*The submitter
*
*
* string submitter = 1;
* @return This builder for chaining.
*/
public Builder clearSubmitter() {
submitter_ = getDefaultInstance().getSubmitter();
onChanged();
return this;
}
/**
*
**
*The submitter
*
*
* string submitter = 1;
* @param value The bytes for submitter to set.
* @return This builder for chaining.
*/
public Builder setSubmitterBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
submitter_ = value;
onChanged();
return this;
}
private java.lang.Object date_ = "";
/**
*
**
*The submission date
*
*
* string date = 2;
* @return The date.
*/
public java.lang.String getDate() {
java.lang.Object ref = date_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
date_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
**
*The submission date
*
*
* string date = 2;
* @return The bytes for date.
*/
public com.google.protobuf.ByteString
getDateBytes() {
java.lang.Object ref = date_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
date_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
**
*The submission date
*
*
* string date = 2;
* @param value The date to set.
* @return This builder for chaining.
*/
public Builder setDate(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
date_ = value;
onChanged();
return this;
}
/**
*
**
*The submission date
*
*
* string date = 2;
* @return This builder for chaining.
*/
public Builder clearDate() {
date_ = getDefaultInstance().getDate();
onChanged();
return this;
}
/**
*
**
*The submission date
*
*
* string date = 2;
* @param value The bytes for date to set.
* @return This builder for chaining.
*/
public Builder setDateBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
date_ = value;
onChanged();
return this;
}
private java.lang.Object id_ = "";
/**
*
**
*The submission id
*
*
* string id = 3;
* @return The id.
*/
public java.lang.String getId() {
java.lang.Object ref = id_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
id_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
**
*The submission id
*
*
* string id = 3;
* @return The bytes for id.
*/
public com.google.protobuf.ByteString
getIdBytes() {
java.lang.Object ref = id_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
id_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
**
*The submission id
*
*
* string id = 3;
* @param value The id to set.
* @return This builder for chaining.
*/
public Builder setId(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
id_ = value;
onChanged();
return this;
}
/**
*
**
*The submission id
*
*
* string id = 3;
* @return This builder for chaining.
*/
public Builder clearId() {
id_ = getDefaultInstance().getId();
onChanged();
return this;
}
/**
*
**
*The submission id
*
*
* string id = 3;
* @param value The bytes for id to set.
* @return This builder for chaining.
*/
public Builder setIdBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
id_ = value;
onChanged();
return this;
}
@java.lang.Override
public final Builder setUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
return super.setUnknownFields(unknownFields);
}
@java.lang.Override
public final Builder mergeUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
return super.mergeUnknownFields(unknownFields);
}
// @@protoc_insertion_point(builder_scope:protobuf.opencb.EvidenceSubmission)
}
// @@protoc_insertion_point(class_scope:protobuf.opencb.EvidenceSubmission)
private static final org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission();
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public EvidenceSubmission parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new EvidenceSubmission(input, extensionRegistry);
}
};
public static com.google.protobuf.Parser parser() {
return PARSER;
}
@java.lang.Override
public com.google.protobuf.Parser getParserForType() {
return PARSER;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}
public interface SomaticInformationOrBuilder extends
// @@protoc_insertion_point(interface_extends:protobuf.opencb.SomaticInformation)
com.google.protobuf.MessageOrBuilder {
/**
*
**
*The primary site
*
*
* string primarySite = 1;
* @return The primarySite.
*/
java.lang.String getPrimarySite();
/**
*
**
*The primary site
*
*
* string primarySite = 1;
* @return The bytes for primarySite.
*/
com.google.protobuf.ByteString
getPrimarySiteBytes();
/**
*
**
*The primary site subtype
*
*
* string siteSubtype = 2;
* @return The siteSubtype.
*/
java.lang.String getSiteSubtype();
/**
*
**
*The primary site subtype
*
*
* string siteSubtype = 2;
* @return The bytes for siteSubtype.
*/
com.google.protobuf.ByteString
getSiteSubtypeBytes();
/**
*
**
*The primary histology
*
*
* string primaryHistology = 3;
* @return The primaryHistology.
*/
java.lang.String getPrimaryHistology();
/**
*
**
*The primary histology
*
*
* string primaryHistology = 3;
* @return The bytes for primaryHistology.
*/
com.google.protobuf.ByteString
getPrimaryHistologyBytes();
/**
*
**
*The histology subtype
*
*
* string histologySubtype = 4;
* @return The histologySubtype.
*/
java.lang.String getHistologySubtype();
/**
*
**
*The histology subtype
*
*
* string histologySubtype = 4;
* @return The bytes for histologySubtype.
*/
com.google.protobuf.ByteString
getHistologySubtypeBytes();
/**
*
**
*The tumour origin
*
*
* string tumourOrigin = 5;
* @return The tumourOrigin.
*/
java.lang.String getTumourOrigin();
/**
*
**
*The tumour origin
*
*
* string tumourOrigin = 5;
* @return The bytes for tumourOrigin.
*/
com.google.protobuf.ByteString
getTumourOriginBytes();
/**
*
**
*The sample source, e.g. blood-bone marrow, cell-line, pancreatic
*
*
* string sampleSource = 6;
* @return The sampleSource.
*/
java.lang.String getSampleSource();
/**
*
**
*The sample source, e.g. blood-bone marrow, cell-line, pancreatic
*
*
* string sampleSource = 6;
* @return The bytes for sampleSource.
*/
com.google.protobuf.ByteString
getSampleSourceBytes();
}
/**
*
**
*The somatic information.
*
*
* Protobuf type {@code protobuf.opencb.SomaticInformation}
*/
public static final class SomaticInformation extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:protobuf.opencb.SomaticInformation)
SomaticInformationOrBuilder {
private static final long serialVersionUID = 0L;
// Use SomaticInformation.newBuilder() to construct.
private SomaticInformation(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private SomaticInformation() {
primarySite_ = "";
siteSubtype_ = "";
primaryHistology_ = "";
histologySubtype_ = "";
tumourOrigin_ = "";
sampleSource_ = "";
}
@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new SomaticInformation();
}
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private SomaticInformation(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
this();
if (extensionRegistry == null) {
throw new java.lang.NullPointerException();
}
com.google.protobuf.UnknownFieldSet.Builder unknownFields =
com.google.protobuf.UnknownFieldSet.newBuilder();
try {
boolean done = false;
while (!done) {
int tag = input.readTag();
switch (tag) {
case 0:
done = true;
break;
case 10: {
java.lang.String s = input.readStringRequireUtf8();
primarySite_ = s;
break;
}
case 18: {
java.lang.String s = input.readStringRequireUtf8();
siteSubtype_ = s;
break;
}
case 26: {
java.lang.String s = input.readStringRequireUtf8();
primaryHistology_ = s;
break;
}
case 34: {
java.lang.String s = input.readStringRequireUtf8();
histologySubtype_ = s;
break;
}
case 42: {
java.lang.String s = input.readStringRequireUtf8();
tumourOrigin_ = s;
break;
}
case 50: {
java.lang.String s = input.readStringRequireUtf8();
sampleSource_ = s;
break;
}
default: {
if (!parseUnknownField(
input, unknownFields, extensionRegistry, tag)) {
done = true;
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break;
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}
}
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
e).setUnfinishedMessage(this);
} finally {
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.internal_static_protobuf_opencb_SomaticInformation_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.internal_static_protobuf_opencb_SomaticInformation_fieldAccessorTable
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org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.class, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.Builder.class);
}
public static final int PRIMARYSITE_FIELD_NUMBER = 1;
private volatile java.lang.Object primarySite_;
/**
*
**
*The primary site
*
*
* string primarySite = 1;
* @return The primarySite.
*/
public java.lang.String getPrimarySite() {
java.lang.Object ref = primarySite_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
} else {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
primarySite_ = s;
return s;
}
}
/**
*
**
*The primary site
*
*
* string primarySite = 1;
* @return The bytes for primarySite.
*/
public com.google.protobuf.ByteString
getPrimarySiteBytes() {
java.lang.Object ref = primarySite_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
primarySite_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int SITESUBTYPE_FIELD_NUMBER = 2;
private volatile java.lang.Object siteSubtype_;
/**
*
**
*The primary site subtype
*
*
* string siteSubtype = 2;
* @return The siteSubtype.
*/
public java.lang.String getSiteSubtype() {
java.lang.Object ref = siteSubtype_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
} else {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
siteSubtype_ = s;
return s;
}
}
/**
*
**
*The primary site subtype
*
*
* string siteSubtype = 2;
* @return The bytes for siteSubtype.
*/
public com.google.protobuf.ByteString
getSiteSubtypeBytes() {
java.lang.Object ref = siteSubtype_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
siteSubtype_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int PRIMARYHISTOLOGY_FIELD_NUMBER = 3;
private volatile java.lang.Object primaryHistology_;
/**
*
**
*The primary histology
*
*
* string primaryHistology = 3;
* @return The primaryHistology.
*/
public java.lang.String getPrimaryHistology() {
java.lang.Object ref = primaryHistology_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
} else {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
primaryHistology_ = s;
return s;
}
}
/**
*
**
*The primary histology
*
*
* string primaryHistology = 3;
* @return The bytes for primaryHistology.
*/
public com.google.protobuf.ByteString
getPrimaryHistologyBytes() {
java.lang.Object ref = primaryHistology_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
primaryHistology_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int HISTOLOGYSUBTYPE_FIELD_NUMBER = 4;
private volatile java.lang.Object histologySubtype_;
/**
*
**
*The histology subtype
*
*
* string histologySubtype = 4;
* @return The histologySubtype.
*/
public java.lang.String getHistologySubtype() {
java.lang.Object ref = histologySubtype_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
} else {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
histologySubtype_ = s;
return s;
}
}
/**
*
**
*The histology subtype
*
*
* string histologySubtype = 4;
* @return The bytes for histologySubtype.
*/
public com.google.protobuf.ByteString
getHistologySubtypeBytes() {
java.lang.Object ref = histologySubtype_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
histologySubtype_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int TUMOURORIGIN_FIELD_NUMBER = 5;
private volatile java.lang.Object tumourOrigin_;
/**
*
**
*The tumour origin
*
*
* string tumourOrigin = 5;
* @return The tumourOrigin.
*/
public java.lang.String getTumourOrigin() {
java.lang.Object ref = tumourOrigin_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
} else {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
tumourOrigin_ = s;
return s;
}
}
/**
*
**
*The tumour origin
*
*
* string tumourOrigin = 5;
* @return The bytes for tumourOrigin.
*/
public com.google.protobuf.ByteString
getTumourOriginBytes() {
java.lang.Object ref = tumourOrigin_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
tumourOrigin_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int SAMPLESOURCE_FIELD_NUMBER = 6;
private volatile java.lang.Object sampleSource_;
/**
*
**
*The sample source, e.g. blood-bone marrow, cell-line, pancreatic
*
*
* string sampleSource = 6;
* @return The sampleSource.
*/
public java.lang.String getSampleSource() {
java.lang.Object ref = sampleSource_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
} else {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
sampleSource_ = s;
return s;
}
}
/**
*
**
*The sample source, e.g. blood-bone marrow, cell-line, pancreatic
*
*
* string sampleSource = 6;
* @return The bytes for sampleSource.
*/
public com.google.protobuf.ByteString
getSampleSourceBytes() {
java.lang.Object ref = sampleSource_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
sampleSource_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
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private byte memoizedIsInitialized = -1;
@java.lang.Override
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byte isInitialized = memoizedIsInitialized;
if (isInitialized == 1) return true;
if (isInitialized == 0) return false;
memoizedIsInitialized = 1;
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@java.lang.Override
public void writeTo(com.google.protobuf.CodedOutputStream output)
throws java.io.IOException {
if (!getPrimarySiteBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 1, primarySite_);
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if (!getSiteSubtypeBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 2, siteSubtype_);
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if (!getPrimaryHistologyBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 3, primaryHistology_);
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if (!getHistologySubtypeBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 4, histologySubtype_);
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if (!getTumourOriginBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 5, tumourOrigin_);
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if (!getSampleSourceBytes().isEmpty()) {
com.google.protobuf.GeneratedMessageV3.writeString(output, 6, sampleSource_);
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unknownFields.writeTo(output);
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int size = memoizedSize;
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size = 0;
if (!getPrimarySiteBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(1, primarySite_);
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if (!getSiteSubtypeBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(2, siteSubtype_);
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if (!getPrimaryHistologyBytes().isEmpty()) {
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if (!getTumourOriginBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(5, tumourOrigin_);
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if (!getSampleSourceBytes().isEmpty()) {
size += com.google.protobuf.GeneratedMessageV3.computeStringSize(6, sampleSource_);
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size += unknownFields.getSerializedSize();
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@java.lang.Override
public boolean equals(final java.lang.Object obj) {
if (obj == this) {
return true;
}
if (!(obj instanceof org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation)) {
return super.equals(obj);
}
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation other = (org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation) obj;
if (!getPrimarySite()
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if (!getSiteSubtype()
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if (!getPrimaryHistology()
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if (!getHistologySubtype()
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if (!getTumourOrigin()
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if (!getSampleSource()
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if (memoizedHashCode != 0) {
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int hash = 41;
hash = (19 * hash) + getDescriptor().hashCode();
hash = (37 * hash) + PRIMARYSITE_FIELD_NUMBER;
hash = (53 * hash) + getPrimarySite().hashCode();
hash = (37 * hash) + SITESUBTYPE_FIELD_NUMBER;
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public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation parseFrom(
java.nio.ByteBuffer data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation parseFrom(
java.nio.ByteBuffer data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation parseFrom(
com.google.protobuf.ByteString data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation parseFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation parseFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation parseDelimitedFrom(java.io.InputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation parseDelimitedFrom(
java.io.InputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseDelimitedWithIOException(PARSER, input, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input);
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
.parseWithIOException(PARSER, input, extensionRegistry);
}
@java.lang.Override
public Builder newBuilderForType() { return newBuilder(); }
public static Builder newBuilder() {
return DEFAULT_INSTANCE.toBuilder();
}
public static Builder newBuilder(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation prototype) {
return DEFAULT_INSTANCE.toBuilder().mergeFrom(prototype);
}
@java.lang.Override
public Builder toBuilder() {
return this == DEFAULT_INSTANCE
? new Builder() : new Builder().mergeFrom(this);
}
@java.lang.Override
protected Builder newBuilderForType(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
Builder builder = new Builder(parent);
return builder;
}
/**
*
**
*The somatic information.
*
*
* Protobuf type {@code protobuf.opencb.SomaticInformation}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:protobuf.opencb.SomaticInformation)
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformationOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.internal_static_protobuf_opencb_SomaticInformation_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.internal_static_protobuf_opencb_SomaticInformation_fieldAccessorTable
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org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.class, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.Builder.class);
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// Construct using org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.newBuilder()
private Builder() {
maybeForceBuilderInitialization();
}
private Builder(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessageV3
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}
}
@java.lang.Override
public Builder clear() {
super.clear();
primarySite_ = "";
siteSubtype_ = "";
primaryHistology_ = "";
histologySubtype_ = "";
tumourOrigin_ = "";
sampleSource_ = "";
return this;
}
@java.lang.Override
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.internal_static_protobuf_opencb_SomaticInformation_descriptor;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation getDefaultInstanceForType() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.getDefaultInstance();
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation build() {
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation buildPartial() {
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation result = new org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation(this);
result.primarySite_ = primarySite_;
result.siteSubtype_ = siteSubtype_;
result.primaryHistology_ = primaryHistology_;
result.histologySubtype_ = histologySubtype_;
result.tumourOrigin_ = tumourOrigin_;
result.sampleSource_ = sampleSource_;
onBuilt();
return result;
}
@java.lang.Override
public Builder clone() {
return super.clone();
}
@java.lang.Override
public Builder setField(
com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
return super.setField(field, value);
}
@java.lang.Override
public Builder clearField(
com.google.protobuf.Descriptors.FieldDescriptor field) {
return super.clearField(field);
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@java.lang.Override
public Builder clearOneof(
com.google.protobuf.Descriptors.OneofDescriptor oneof) {
return super.clearOneof(oneof);
}
@java.lang.Override
public Builder setRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
int index, java.lang.Object value) {
return super.setRepeatedField(field, index, value);
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@java.lang.Override
public Builder addRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
return super.addRepeatedField(field, value);
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@java.lang.Override
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation) {
return mergeFrom((org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation)other);
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return this;
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public Builder mergeFrom(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation other) {
if (other == org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.getDefaultInstance()) return this;
if (!other.getPrimarySite().isEmpty()) {
primarySite_ = other.primarySite_;
onChanged();
}
if (!other.getSiteSubtype().isEmpty()) {
siteSubtype_ = other.siteSubtype_;
onChanged();
}
if (!other.getPrimaryHistology().isEmpty()) {
primaryHistology_ = other.primaryHistology_;
onChanged();
}
if (!other.getHistologySubtype().isEmpty()) {
histologySubtype_ = other.histologySubtype_;
onChanged();
}
if (!other.getTumourOrigin().isEmpty()) {
tumourOrigin_ = other.tumourOrigin_;
onChanged();
}
if (!other.getSampleSource().isEmpty()) {
sampleSource_ = other.sampleSource_;
onChanged();
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this.mergeUnknownFields(other.unknownFields);
onChanged();
return this;
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@java.lang.Override
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return true;
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@java.lang.Override
public Builder mergeFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private java.lang.Object primarySite_ = "";
/**
*
**
*The primary site
*
*
* string primarySite = 1;
* @return The primarySite.
*/
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java.lang.Object ref = primarySite_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
primarySite_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
**
*The primary site
*
*
* string primarySite = 1;
* @return The bytes for primarySite.
*/
public com.google.protobuf.ByteString
getPrimarySiteBytes() {
java.lang.Object ref = primarySite_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
primarySite_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
**
*The primary site
*
*
* string primarySite = 1;
* @param value The primarySite to set.
* @return This builder for chaining.
*/
public Builder setPrimarySite(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
primarySite_ = value;
onChanged();
return this;
}
/**
*
**
*The primary site
*
*
* string primarySite = 1;
* @return This builder for chaining.
*/
public Builder clearPrimarySite() {
primarySite_ = getDefaultInstance().getPrimarySite();
onChanged();
return this;
}
/**
*
**
*The primary site
*
*
* string primarySite = 1;
* @param value The bytes for primarySite to set.
* @return This builder for chaining.
*/
public Builder setPrimarySiteBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
primarySite_ = value;
onChanged();
return this;
}
private java.lang.Object siteSubtype_ = "";
/**
*
**
*The primary site subtype
*
*
* string siteSubtype = 2;
* @return The siteSubtype.
*/
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java.lang.Object ref = siteSubtype_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
siteSubtype_ = s;
return s;
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return (java.lang.String) ref;
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/**
*
**
*The primary site subtype
*
*
* string siteSubtype = 2;
* @return The bytes for siteSubtype.
*/
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getSiteSubtypeBytes() {
java.lang.Object ref = siteSubtype_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
siteSubtype_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
**
*The primary site subtype
*
*
* string siteSubtype = 2;
* @param value The siteSubtype to set.
* @return This builder for chaining.
*/
public Builder setSiteSubtype(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
siteSubtype_ = value;
onChanged();
return this;
}
/**
*
**
*The primary site subtype
*
*
* string siteSubtype = 2;
* @return This builder for chaining.
*/
public Builder clearSiteSubtype() {
siteSubtype_ = getDefaultInstance().getSiteSubtype();
onChanged();
return this;
}
/**
*
**
*The primary site subtype
*
*
* string siteSubtype = 2;
* @param value The bytes for siteSubtype to set.
* @return This builder for chaining.
*/
public Builder setSiteSubtypeBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
siteSubtype_ = value;
onChanged();
return this;
}
private java.lang.Object primaryHistology_ = "";
/**
*
**
*The primary histology
*
*
* string primaryHistology = 3;
* @return The primaryHistology.
*/
public java.lang.String getPrimaryHistology() {
java.lang.Object ref = primaryHistology_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
primaryHistology_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
**
*The primary histology
*
*
* string primaryHistology = 3;
* @return The bytes for primaryHistology.
*/
public com.google.protobuf.ByteString
getPrimaryHistologyBytes() {
java.lang.Object ref = primaryHistology_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
primaryHistology_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
**
*The primary histology
*
*
* string primaryHistology = 3;
* @param value The primaryHistology to set.
* @return This builder for chaining.
*/
public Builder setPrimaryHistology(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
primaryHistology_ = value;
onChanged();
return this;
}
/**
*
**
*The primary histology
*
*
* string primaryHistology = 3;
* @return This builder for chaining.
*/
public Builder clearPrimaryHistology() {
primaryHistology_ = getDefaultInstance().getPrimaryHistology();
onChanged();
return this;
}
/**
*
**
*The primary histology
*
*
* string primaryHistology = 3;
* @param value The bytes for primaryHistology to set.
* @return This builder for chaining.
*/
public Builder setPrimaryHistologyBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
primaryHistology_ = value;
onChanged();
return this;
}
private java.lang.Object histologySubtype_ = "";
/**
*
**
*The histology subtype
*
*
* string histologySubtype = 4;
* @return The histologySubtype.
*/
public java.lang.String getHistologySubtype() {
java.lang.Object ref = histologySubtype_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
histologySubtype_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
**
*The histology subtype
*
*
* string histologySubtype = 4;
* @return The bytes for histologySubtype.
*/
public com.google.protobuf.ByteString
getHistologySubtypeBytes() {
java.lang.Object ref = histologySubtype_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
histologySubtype_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
**
*The histology subtype
*
*
* string histologySubtype = 4;
* @param value The histologySubtype to set.
* @return This builder for chaining.
*/
public Builder setHistologySubtype(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
histologySubtype_ = value;
onChanged();
return this;
}
/**
*
**
*The histology subtype
*
*
* string histologySubtype = 4;
* @return This builder for chaining.
*/
public Builder clearHistologySubtype() {
histologySubtype_ = getDefaultInstance().getHistologySubtype();
onChanged();
return this;
}
/**
*
**
*The histology subtype
*
*
* string histologySubtype = 4;
* @param value The bytes for histologySubtype to set.
* @return This builder for chaining.
*/
public Builder setHistologySubtypeBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
histologySubtype_ = value;
onChanged();
return this;
}
private java.lang.Object tumourOrigin_ = "";
/**
*
**
*The tumour origin
*
*
* string tumourOrigin = 5;
* @return The tumourOrigin.
*/
public java.lang.String getTumourOrigin() {
java.lang.Object ref = tumourOrigin_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
tumourOrigin_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
**
*The tumour origin
*
*
* string tumourOrigin = 5;
* @return The bytes for tumourOrigin.
*/
public com.google.protobuf.ByteString
getTumourOriginBytes() {
java.lang.Object ref = tumourOrigin_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
tumourOrigin_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
**
*The tumour origin
*
*
* string tumourOrigin = 5;
* @param value The tumourOrigin to set.
* @return This builder for chaining.
*/
public Builder setTumourOrigin(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
tumourOrigin_ = value;
onChanged();
return this;
}
/**
*
**
*The tumour origin
*
*
* string tumourOrigin = 5;
* @return This builder for chaining.
*/
public Builder clearTumourOrigin() {
tumourOrigin_ = getDefaultInstance().getTumourOrigin();
onChanged();
return this;
}
/**
*
**
*The tumour origin
*
*
* string tumourOrigin = 5;
* @param value The bytes for tumourOrigin to set.
* @return This builder for chaining.
*/
public Builder setTumourOriginBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
tumourOrigin_ = value;
onChanged();
return this;
}
private java.lang.Object sampleSource_ = "";
/**
*
**
*The sample source, e.g. blood-bone marrow, cell-line, pancreatic
*
*
* string sampleSource = 6;
* @return The sampleSource.
*/
public java.lang.String getSampleSource() {
java.lang.Object ref = sampleSource_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
sampleSource_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
**
*The sample source, e.g. blood-bone marrow, cell-line, pancreatic
*
*
* string sampleSource = 6;
* @return The bytes for sampleSource.
*/
public com.google.protobuf.ByteString
getSampleSourceBytes() {
java.lang.Object ref = sampleSource_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
sampleSource_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
**
*The sample source, e.g. blood-bone marrow, cell-line, pancreatic
*
*
* string sampleSource = 6;
* @param value The sampleSource to set.
* @return This builder for chaining.
*/
public Builder setSampleSource(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
sampleSource_ = value;
onChanged();
return this;
}
/**
*
**
*The sample source, e.g. blood-bone marrow, cell-line, pancreatic
*
*
* string sampleSource = 6;
* @return This builder for chaining.
*/
public Builder clearSampleSource() {
sampleSource_ = getDefaultInstance().getSampleSource();
onChanged();
return this;
}
/**
*
**
*The sample source, e.g. blood-bone marrow, cell-line, pancreatic
*
*
* string sampleSource = 6;
* @param value The bytes for sampleSource to set.
* @return This builder for chaining.
*/
public Builder setSampleSourceBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
sampleSource_ = value;
onChanged();
return this;
}
@java.lang.Override
public final Builder setUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
return super.setUnknownFields(unknownFields);
}
@java.lang.Override
public final Builder mergeUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
return super.mergeUnknownFields(unknownFields);
}
// @@protoc_insertion_point(builder_scope:protobuf.opencb.SomaticInformation)
}
// @@protoc_insertion_point(class_scope:protobuf.opencb.SomaticInformation)
private static final org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation();
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public SomaticInformation parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new SomaticInformation(input, extensionRegistry);
}
};
public static com.google.protobuf.Parser parser() {
return PARSER;
}
@java.lang.Override
public com.google.protobuf.Parser getParserForType() {
return PARSER;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}
public interface HeritableTraitOrBuilder extends
// @@protoc_insertion_point(interface_extends:protobuf.opencb.HeritableTrait)
com.google.protobuf.MessageOrBuilder {
/**
*
**
*The trait (e.g.: HPO term, MIM term, DO term etc.)
*
*
* string trait = 1;
* @return The trait.
*/
java.lang.String getTrait();
/**
*
**
*The trait (e.g.: HPO term, MIM term, DO term etc.)
*
*
* string trait = 1;
* @return The bytes for trait.
*/
com.google.protobuf.ByteString
getTraitBytes();
/**
*
**
*The mode of inheritance
*
*
* .protobuf.opencb.ModeOfInheritance inheritanceMode = 2;
* @return The enum numeric value on the wire for inheritanceMode.
*/
int getInheritanceModeValue();
/**
*
**
*The mode of inheritance
*
*
* .protobuf.opencb.ModeOfInheritance inheritanceMode = 2;
* @return The inheritanceMode.
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ModeOfInheritance getInheritanceMode();
}
/**
*
**
*The entity representing a phenotype and its inheritance pattern.
*
*
* Protobuf type {@code protobuf.opencb.HeritableTrait}
*/
public static final class HeritableTrait extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:protobuf.opencb.HeritableTrait)
HeritableTraitOrBuilder {
private static final long serialVersionUID = 0L;
// Use HeritableTrait.newBuilder() to construct.
private HeritableTrait(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private HeritableTrait() {
trait_ = "";
inheritanceMode_ = 0;
}
@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new HeritableTrait();
}
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
}
private HeritableTrait(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
this();
if (extensionRegistry == null) {
throw new java.lang.NullPointerException();
}
com.google.protobuf.UnknownFieldSet.Builder unknownFields =
com.google.protobuf.UnknownFieldSet.newBuilder();
try {
boolean done = false;
while (!done) {
int tag = input.readTag();
switch (tag) {
case 0:
done = true;
break;
case 10: {
java.lang.String s = input.readStringRequireUtf8();
trait_ = s;
break;
}
case 16: {
int rawValue = input.readEnum();
inheritanceMode_ = rawValue;
break;
}
default: {
if (!parseUnknownField(
input, unknownFields, extensionRegistry, tag)) {
done = true;
}
break;
}
}
}
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
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public com.google.protobuf.ByteString
getNameBytes() {
java.lang.Object ref = name_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
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name_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
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}
/**
*
**
*The ontology term name
*
*
* string name = 2;
* @param value The name to set.
* @return This builder for chaining.
*/
public Builder setName(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
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name_ = value;
onChanged();
return this;
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/**
*
**
*The ontology term name
*
*
* string name = 2;
* @return This builder for chaining.
*/
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name_ = getDefaultInstance().getName();
onChanged();
return this;
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/**
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**
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com.google.protobuf.ByteString value) {
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}
checkByteStringIsUtf8(value);
name_ = value;
onChanged();
return this;
}
private java.lang.Object value_ = "";
/**
*
**
*Optional value for the ontology term, the type of the value is not checked
*(i.e.: we could set the pvalue term to "significant" or to "0.0001")
*
*
* string value = 3;
* @return The value.
*/
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java.lang.Object ref = value_;
if (!(ref instanceof java.lang.String)) {
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java.lang.String s = bs.toStringUtf8();
value_ = s;
return s;
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return (java.lang.String) ref;
}
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/**
*
**
*Optional value for the ontology term, the type of the value is not checked
*(i.e.: we could set the pvalue term to "significant" or to "0.0001")
*
*
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* @return The bytes for value.
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java.lang.Object ref = value_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
value_ = b;
return b;
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return (com.google.protobuf.ByteString) ref;
}
}
/**
*
**
*Optional value for the ontology term, the type of the value is not checked
*(i.e.: we could set the pvalue term to "significant" or to "0.0001")
*
*
* string value = 3;
* @param value The value to set.
* @return This builder for chaining.
*/
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java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
value_ = value;
onChanged();
return this;
}
/**
*
**
*Optional value for the ontology term, the type of the value is not checked
*(i.e.: we could set the pvalue term to "significant" or to "0.0001")
*
*
* string value = 3;
* @return This builder for chaining.
*/
public Builder clearValue() {
value_ = getDefaultInstance().getValue();
onChanged();
return this;
}
/**
*
**
*Optional value for the ontology term, the type of the value is not checked
*(i.e.: we could set the pvalue term to "significant" or to "0.0001")
*
*
* string value = 3;
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* @return This builder for chaining.
*/
public Builder setValueBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
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checkByteStringIsUtf8(value);
value_ = value;
onChanged();
return this;
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@java.lang.Override
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}
// @@protoc_insertion_point(builder_scope:protobuf.opencb.Property)
}
// @@protoc_insertion_point(class_scope:protobuf.opencb.Property)
private static final org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property();
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public Property parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new Property(input, extensionRegistry);
}
};
public static com.google.protobuf.Parser parser() {
return PARSER;
}
@java.lang.Override
public com.google.protobuf.Parser getParserForType() {
return PARSER;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}
public interface VariantClassificationOrBuilder extends
// @@protoc_insertion_point(interface_extends:protobuf.opencb.VariantClassification)
com.google.protobuf.MessageOrBuilder {
/**
*
**
*The variant's clinical significance.
*
*
* .protobuf.opencb.ClinicalSignificance clinicalSignificance = 1;
* @return The enum numeric value on the wire for clinicalSignificance.
*/
int getClinicalSignificanceValue();
/**
*
**
*The variant's clinical significance.
*
*
* .protobuf.opencb.ClinicalSignificance clinicalSignificance = 1;
* @return The clinicalSignificance.
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ClinicalSignificance getClinicalSignificance();
/**
*
**
*The variant's pharmacogenomics classification.
*
*
* .protobuf.opencb.DrugResponseClassification drugResponseClassification = 2;
* @return The enum numeric value on the wire for drugResponseClassification.
*/
int getDrugResponseClassificationValue();
/**
*
**
*The variant's pharmacogenomics classification.
*
*
* .protobuf.opencb.DrugResponseClassification drugResponseClassification = 2;
* @return The drugResponseClassification.
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.DrugResponseClassification getDrugResponseClassification();
/**
*
**
*The variant's trait association.
*
*
* .protobuf.opencb.TraitAssociation traitAssociation = 3;
* @return The enum numeric value on the wire for traitAssociation.
*/
int getTraitAssociationValue();
/**
*
**
*The variant's trait association.
*
*
* .protobuf.opencb.TraitAssociation traitAssociation = 3;
* @return The traitAssociation.
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TraitAssociation getTraitAssociation();
/**
*
**
*The variant's tumorigenesis classification.
*
*
* .protobuf.opencb.TumorigenesisClassification tumorigenesisClassification = 4;
* @return The enum numeric value on the wire for tumorigenesisClassification.
*/
int getTumorigenesisClassificationValue();
/**
*
**
*The variant's tumorigenesis classification.
*
*
* .protobuf.opencb.TumorigenesisClassification tumorigenesisClassification = 4;
* @return The tumorigenesisClassification.
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TumorigenesisClassification getTumorigenesisClassification();
/**
*
**
*The variant functional effect
*
*
* .protobuf.opencb.VariantFunctionalEffect functionalEffect = 5;
* @return The enum numeric value on the wire for functionalEffect.
*/
int getFunctionalEffectValue();
/**
*
**
*The variant functional effect
*
*
* .protobuf.opencb.VariantFunctionalEffect functionalEffect = 5;
* @return The functionalEffect.
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantFunctionalEffect getFunctionalEffect();
}
/**
*
**
*The variant classification according to different properties.
*
*
* Protobuf type {@code protobuf.opencb.VariantClassification}
*/
public static final class VariantClassification extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:protobuf.opencb.VariantClassification)
VariantClassificationOrBuilder {
private static final long serialVersionUID = 0L;
// Use VariantClassification.newBuilder() to construct.
private VariantClassification(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
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drugResponseClassification_ = 0;
traitAssociation_ = 0;
tumorigenesisClassification_ = 0;
functionalEffect_ = 0;
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protected java.lang.Object newInstance(
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return new VariantClassification();
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private VariantClassification(
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this();
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clinicalSignificance_ = rawValue;
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drugResponseClassification_ = rawValue;
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case 24: {
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traitAssociation_ = rawValue;
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tumorigenesisClassification_ = rawValue;
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this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
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public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.internal_static_protobuf_opencb_VariantClassification_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
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public static final int CLINICALSIGNIFICANCE_FIELD_NUMBER = 1;
private int clinicalSignificance_;
/**
*
**
*The variant's clinical significance.
*
*
* .protobuf.opencb.ClinicalSignificance clinicalSignificance = 1;
* @return The enum numeric value on the wire for clinicalSignificance.
*/
public int getClinicalSignificanceValue() {
return clinicalSignificance_;
}
/**
*
**
*The variant's clinical significance.
*
*
* .protobuf.opencb.ClinicalSignificance clinicalSignificance = 1;
* @return The clinicalSignificance.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ClinicalSignificance getClinicalSignificance() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ClinicalSignificance result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ClinicalSignificance.valueOf(clinicalSignificance_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ClinicalSignificance.UNRECOGNIZED : result;
}
public static final int DRUGRESPONSECLASSIFICATION_FIELD_NUMBER = 2;
private int drugResponseClassification_;
/**
*
**
*The variant's pharmacogenomics classification.
*
*
* .protobuf.opencb.DrugResponseClassification drugResponseClassification = 2;
* @return The enum numeric value on the wire for drugResponseClassification.
*/
public int getDrugResponseClassificationValue() {
return drugResponseClassification_;
}
/**
*
**
*The variant's pharmacogenomics classification.
*
*
* .protobuf.opencb.DrugResponseClassification drugResponseClassification = 2;
* @return The drugResponseClassification.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.DrugResponseClassification getDrugResponseClassification() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.DrugResponseClassification result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.DrugResponseClassification.valueOf(drugResponseClassification_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.DrugResponseClassification.UNRECOGNIZED : result;
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public static final int TRAITASSOCIATION_FIELD_NUMBER = 3;
private int traitAssociation_;
/**
*
**
*The variant's trait association.
*
*
* .protobuf.opencb.TraitAssociation traitAssociation = 3;
* @return The enum numeric value on the wire for traitAssociation.
*/
public int getTraitAssociationValue() {
return traitAssociation_;
}
/**
*
**
*The variant's trait association.
*
*
* .protobuf.opencb.TraitAssociation traitAssociation = 3;
* @return The traitAssociation.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TraitAssociation getTraitAssociation() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TraitAssociation result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TraitAssociation.valueOf(traitAssociation_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TraitAssociation.UNRECOGNIZED : result;
}
public static final int TUMORIGENESISCLASSIFICATION_FIELD_NUMBER = 4;
private int tumorigenesisClassification_;
/**
*
**
*The variant's tumorigenesis classification.
*
*
* .protobuf.opencb.TumorigenesisClassification tumorigenesisClassification = 4;
* @return The enum numeric value on the wire for tumorigenesisClassification.
*/
public int getTumorigenesisClassificationValue() {
return tumorigenesisClassification_;
}
/**
*
**
*The variant's tumorigenesis classification.
*
*
* .protobuf.opencb.TumorigenesisClassification tumorigenesisClassification = 4;
* @return The tumorigenesisClassification.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TumorigenesisClassification getTumorigenesisClassification() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TumorigenesisClassification result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TumorigenesisClassification.valueOf(tumorigenesisClassification_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TumorigenesisClassification.UNRECOGNIZED : result;
}
public static final int FUNCTIONALEFFECT_FIELD_NUMBER = 5;
private int functionalEffect_;
/**
*
**
*The variant functional effect
*
*
* .protobuf.opencb.VariantFunctionalEffect functionalEffect = 5;
* @return The enum numeric value on the wire for functionalEffect.
*/
public int getFunctionalEffectValue() {
return functionalEffect_;
}
/**
*
**
*The variant functional effect
*
*
* .protobuf.opencb.VariantFunctionalEffect functionalEffect = 5;
* @return The functionalEffect.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantFunctionalEffect getFunctionalEffect() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantFunctionalEffect result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantFunctionalEffect.valueOf(functionalEffect_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantFunctionalEffect.UNRECOGNIZED : result;
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if (functionalEffect_ != org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantFunctionalEffect.dominant_negative_variant.getNumber()) {
output.writeEnum(5, functionalEffect_);
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unknownFields.writeTo(output);
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if (obj == this) {
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if (!(obj instanceof org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification)) {
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}
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification other = (org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification) obj;
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if (drugResponseClassification_ != other.drugResponseClassification_) return false;
if (traitAssociation_ != other.traitAssociation_) return false;
if (tumorigenesisClassification_ != other.tumorigenesisClassification_) return false;
if (functionalEffect_ != other.functionalEffect_) return false;
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return true;
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if (memoizedHashCode != 0) {
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int hash = 41;
hash = (19 * hash) + getDescriptor().hashCode();
hash = (37 * hash) + CLINICALSIGNIFICANCE_FIELD_NUMBER;
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public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification parseFrom(
java.nio.ByteBuffer data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
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public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification parseFrom(
com.google.protobuf.ByteString data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification parseFrom(
com.google.protobuf.ByteString data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification parseFrom(byte[] data)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data);
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public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification parseFrom(
byte[] data,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return PARSER.parseFrom(data, extensionRegistry);
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public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification parseFrom(java.io.InputStream input)
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public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification parseFrom(
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com.google.protobuf.ExtensionRegistryLite extensionRegistry)
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return com.google.protobuf.GeneratedMessageV3
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public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification parseDelimitedFrom(
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com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification parseFrom(
com.google.protobuf.CodedInputStream input)
throws java.io.IOException {
return com.google.protobuf.GeneratedMessageV3
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public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification parseFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
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/**
*
**
*The variant classification according to different properties.
*
*
* Protobuf type {@code protobuf.opencb.VariantClassification}
*/
public static final class Builder extends
com.google.protobuf.GeneratedMessageV3.Builder implements
// @@protoc_insertion_point(builder_implements:protobuf.opencb.VariantClassification)
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassificationOrBuilder {
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.internal_static_protobuf_opencb_VariantClassification_descriptor;
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private Builder(
com.google.protobuf.GeneratedMessageV3.BuilderParent parent) {
super(parent);
maybeForceBuilderInitialization();
}
private void maybeForceBuilderInitialization() {
if (com.google.protobuf.GeneratedMessageV3
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}
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@java.lang.Override
public Builder clear() {
super.clear();
clinicalSignificance_ = 0;
drugResponseClassification_ = 0;
traitAssociation_ = 0;
tumorigenesisClassification_ = 0;
functionalEffect_ = 0;
return this;
}
@java.lang.Override
public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.internal_static_protobuf_opencb_VariantClassification_descriptor;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification getDefaultInstanceForType() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification.getDefaultInstance();
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification build() {
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification buildPartial() {
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification result = new org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification(this);
result.clinicalSignificance_ = clinicalSignificance_;
result.drugResponseClassification_ = drugResponseClassification_;
result.traitAssociation_ = traitAssociation_;
result.tumorigenesisClassification_ = tumorigenesisClassification_;
result.functionalEffect_ = functionalEffect_;
onBuilt();
return result;
}
@java.lang.Override
public Builder clone() {
return super.clone();
}
@java.lang.Override
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com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
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com.google.protobuf.Descriptors.FieldDescriptor field) {
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com.google.protobuf.Descriptors.OneofDescriptor oneof) {
return super.clearOneof(oneof);
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com.google.protobuf.Descriptors.FieldDescriptor field,
int index, java.lang.Object value) {
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public Builder addRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
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@java.lang.Override
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification) {
return mergeFrom((org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification other) {
if (other == org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification.getDefaultInstance()) return this;
if (other.clinicalSignificance_ != 0) {
setClinicalSignificanceValue(other.getClinicalSignificanceValue());
}
if (other.drugResponseClassification_ != 0) {
setDrugResponseClassificationValue(other.getDrugResponseClassificationValue());
}
if (other.traitAssociation_ != 0) {
setTraitAssociationValue(other.getTraitAssociationValue());
}
if (other.tumorigenesisClassification_ != 0) {
setTumorigenesisClassificationValue(other.getTumorigenesisClassificationValue());
}
if (other.functionalEffect_ != 0) {
setFunctionalEffectValue(other.getFunctionalEffectValue());
}
this.mergeUnknownFields(other.unknownFields);
onChanged();
return this;
}
@java.lang.Override
public final boolean isInitialized() {
return true;
}
@java.lang.Override
public Builder mergeFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int clinicalSignificance_ = 0;
/**
*
**
*The variant's clinical significance.
*
*
* .protobuf.opencb.ClinicalSignificance clinicalSignificance = 1;
* @return The enum numeric value on the wire for clinicalSignificance.
*/
public int getClinicalSignificanceValue() {
return clinicalSignificance_;
}
/**
*
**
*The variant's clinical significance.
*
*
* .protobuf.opencb.ClinicalSignificance clinicalSignificance = 1;
* @param value The enum numeric value on the wire for clinicalSignificance to set.
* @return This builder for chaining.
*/
public Builder setClinicalSignificanceValue(int value) {
clinicalSignificance_ = value;
onChanged();
return this;
}
/**
*
**
*The variant's clinical significance.
*
*
* .protobuf.opencb.ClinicalSignificance clinicalSignificance = 1;
* @return The clinicalSignificance.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ClinicalSignificance getClinicalSignificance() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ClinicalSignificance result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ClinicalSignificance.valueOf(clinicalSignificance_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ClinicalSignificance.UNRECOGNIZED : result;
}
/**
*
**
*The variant's clinical significance.
*
*
* .protobuf.opencb.ClinicalSignificance clinicalSignificance = 1;
* @param value The clinicalSignificance to set.
* @return This builder for chaining.
*/
public Builder setClinicalSignificance(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ClinicalSignificance value) {
if (value == null) {
throw new NullPointerException();
}
clinicalSignificance_ = value.getNumber();
onChanged();
return this;
}
/**
*
**
*The variant's clinical significance.
*
*
* .protobuf.opencb.ClinicalSignificance clinicalSignificance = 1;
* @return This builder for chaining.
*/
public Builder clearClinicalSignificance() {
clinicalSignificance_ = 0;
onChanged();
return this;
}
private int drugResponseClassification_ = 0;
/**
*
**
*The variant's pharmacogenomics classification.
*
*
* .protobuf.opencb.DrugResponseClassification drugResponseClassification = 2;
* @return The enum numeric value on the wire for drugResponseClassification.
*/
public int getDrugResponseClassificationValue() {
return drugResponseClassification_;
}
/**
*
**
*The variant's pharmacogenomics classification.
*
*
* .protobuf.opencb.DrugResponseClassification drugResponseClassification = 2;
* @param value The enum numeric value on the wire for drugResponseClassification to set.
* @return This builder for chaining.
*/
public Builder setDrugResponseClassificationValue(int value) {
drugResponseClassification_ = value;
onChanged();
return this;
}
/**
*
**
*The variant's pharmacogenomics classification.
*
*
* .protobuf.opencb.DrugResponseClassification drugResponseClassification = 2;
* @return The drugResponseClassification.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.DrugResponseClassification getDrugResponseClassification() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.DrugResponseClassification result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.DrugResponseClassification.valueOf(drugResponseClassification_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.DrugResponseClassification.UNRECOGNIZED : result;
}
/**
*
**
*The variant's pharmacogenomics classification.
*
*
* .protobuf.opencb.DrugResponseClassification drugResponseClassification = 2;
* @param value The drugResponseClassification to set.
* @return This builder for chaining.
*/
public Builder setDrugResponseClassification(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.DrugResponseClassification value) {
if (value == null) {
throw new NullPointerException();
}
drugResponseClassification_ = value.getNumber();
onChanged();
return this;
}
/**
*
**
*The variant's pharmacogenomics classification.
*
*
* .protobuf.opencb.DrugResponseClassification drugResponseClassification = 2;
* @return This builder for chaining.
*/
public Builder clearDrugResponseClassification() {
drugResponseClassification_ = 0;
onChanged();
return this;
}
private int traitAssociation_ = 0;
/**
*
**
*The variant's trait association.
*
*
* .protobuf.opencb.TraitAssociation traitAssociation = 3;
* @return The enum numeric value on the wire for traitAssociation.
*/
public int getTraitAssociationValue() {
return traitAssociation_;
}
/**
*
**
*The variant's trait association.
*
*
* .protobuf.opencb.TraitAssociation traitAssociation = 3;
* @param value The enum numeric value on the wire for traitAssociation to set.
* @return This builder for chaining.
*/
public Builder setTraitAssociationValue(int value) {
traitAssociation_ = value;
onChanged();
return this;
}
/**
*
**
*The variant's trait association.
*
*
* .protobuf.opencb.TraitAssociation traitAssociation = 3;
* @return The traitAssociation.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TraitAssociation getTraitAssociation() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TraitAssociation result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TraitAssociation.valueOf(traitAssociation_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TraitAssociation.UNRECOGNIZED : result;
}
/**
*
**
*The variant's trait association.
*
*
* .protobuf.opencb.TraitAssociation traitAssociation = 3;
* @param value The traitAssociation to set.
* @return This builder for chaining.
*/
public Builder setTraitAssociation(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TraitAssociation value) {
if (value == null) {
throw new NullPointerException();
}
traitAssociation_ = value.getNumber();
onChanged();
return this;
}
/**
*
**
*The variant's trait association.
*
*
* .protobuf.opencb.TraitAssociation traitAssociation = 3;
* @return This builder for chaining.
*/
public Builder clearTraitAssociation() {
traitAssociation_ = 0;
onChanged();
return this;
}
private int tumorigenesisClassification_ = 0;
/**
*
**
*The variant's tumorigenesis classification.
*
*
* .protobuf.opencb.TumorigenesisClassification tumorigenesisClassification = 4;
* @return The enum numeric value on the wire for tumorigenesisClassification.
*/
public int getTumorigenesisClassificationValue() {
return tumorigenesisClassification_;
}
/**
*
**
*The variant's tumorigenesis classification.
*
*
* .protobuf.opencb.TumorigenesisClassification tumorigenesisClassification = 4;
* @param value The enum numeric value on the wire for tumorigenesisClassification to set.
* @return This builder for chaining.
*/
public Builder setTumorigenesisClassificationValue(int value) {
tumorigenesisClassification_ = value;
onChanged();
return this;
}
/**
*
**
*The variant's tumorigenesis classification.
*
*
* .protobuf.opencb.TumorigenesisClassification tumorigenesisClassification = 4;
* @return The tumorigenesisClassification.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TumorigenesisClassification getTumorigenesisClassification() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TumorigenesisClassification result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TumorigenesisClassification.valueOf(tumorigenesisClassification_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TumorigenesisClassification.UNRECOGNIZED : result;
}
/**
*
**
*The variant's tumorigenesis classification.
*
*
* .protobuf.opencb.TumorigenesisClassification tumorigenesisClassification = 4;
* @param value The tumorigenesisClassification to set.
* @return This builder for chaining.
*/
public Builder setTumorigenesisClassification(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.TumorigenesisClassification value) {
if (value == null) {
throw new NullPointerException();
}
tumorigenesisClassification_ = value.getNumber();
onChanged();
return this;
}
/**
*
**
*The variant's tumorigenesis classification.
*
*
* .protobuf.opencb.TumorigenesisClassification tumorigenesisClassification = 4;
* @return This builder for chaining.
*/
public Builder clearTumorigenesisClassification() {
tumorigenesisClassification_ = 0;
onChanged();
return this;
}
private int functionalEffect_ = 0;
/**
*
**
*The variant functional effect
*
*
* .protobuf.opencb.VariantFunctionalEffect functionalEffect = 5;
* @return The enum numeric value on the wire for functionalEffect.
*/
public int getFunctionalEffectValue() {
return functionalEffect_;
}
/**
*
**
*The variant functional effect
*
*
* .protobuf.opencb.VariantFunctionalEffect functionalEffect = 5;
* @param value The enum numeric value on the wire for functionalEffect to set.
* @return This builder for chaining.
*/
public Builder setFunctionalEffectValue(int value) {
functionalEffect_ = value;
onChanged();
return this;
}
/**
*
**
*The variant functional effect
*
*
* .protobuf.opencb.VariantFunctionalEffect functionalEffect = 5;
* @return The functionalEffect.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantFunctionalEffect getFunctionalEffect() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantFunctionalEffect result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantFunctionalEffect.valueOf(functionalEffect_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantFunctionalEffect.UNRECOGNIZED : result;
}
/**
*
**
*The variant functional effect
*
*
* .protobuf.opencb.VariantFunctionalEffect functionalEffect = 5;
* @param value The functionalEffect to set.
* @return This builder for chaining.
*/
public Builder setFunctionalEffect(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantFunctionalEffect value) {
if (value == null) {
throw new NullPointerException();
}
functionalEffect_ = value.getNumber();
onChanged();
return this;
}
/**
*
**
*The variant functional effect
*
*
* .protobuf.opencb.VariantFunctionalEffect functionalEffect = 5;
* @return This builder for chaining.
*/
public Builder clearFunctionalEffect() {
functionalEffect_ = 0;
onChanged();
return this;
}
@java.lang.Override
public final Builder setUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
return super.setUnknownFields(unknownFields);
}
@java.lang.Override
public final Builder mergeUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
return super.mergeUnknownFields(unknownFields);
}
// @@protoc_insertion_point(builder_scope:protobuf.opencb.VariantClassification)
}
// @@protoc_insertion_point(class_scope:protobuf.opencb.VariantClassification)
private static final org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification();
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public VariantClassification parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new VariantClassification(input, extensionRegistry);
}
};
public static com.google.protobuf.Parser parser() {
return PARSER;
}
@java.lang.Override
public com.google.protobuf.Parser getParserForType() {
return PARSER;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}
public interface EvidenceEntryOrBuilder extends
// @@protoc_insertion_point(interface_extends:protobuf.opencb.EvidenceEntry)
com.google.protobuf.MessageOrBuilder {
/**
*
**
*Source of the evidence
*
*
* .protobuf.opencb.EvidenceSource source = 1;
* @return Whether the source field is set.
*/
boolean hasSource();
/**
*
**
*Source of the evidence
*
*
* .protobuf.opencb.EvidenceSource source = 1;
* @return The source.
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource getSource();
/**
*
**
*Source of the evidence
*
*
* .protobuf.opencb.EvidenceSource source = 1;
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSourceOrBuilder getSourceOrBuilder();
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
java.util.List
getSubmissionsList();
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission getSubmissions(int index);
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
int getSubmissionsCount();
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
java.util.List
getSubmissionsOrBuilderList();
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmissionOrBuilder getSubmissionsOrBuilder(
int index);
/**
*
**
*The somatic information
*
*
* .protobuf.opencb.SomaticInformation somaticInformation = 3;
* @return Whether the somaticInformation field is set.
*/
boolean hasSomaticInformation();
/**
*
**
*The somatic information
*
*
* .protobuf.opencb.SomaticInformation somaticInformation = 3;
* @return The somaticInformation.
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation getSomaticInformation();
/**
*
**
*The somatic information
*
*
* .protobuf.opencb.SomaticInformation somaticInformation = 3;
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformationOrBuilder getSomaticInformationOrBuilder();
/**
*
**
*URL of source if any
*
*
* string url = 4;
* @return The url.
*/
java.lang.String getUrl();
/**
*
**
*URL of source if any
*
*
* string url = 4;
* @return The bytes for url.
*/
com.google.protobuf.ByteString
getUrlBytes();
/**
*
**
*ID of record in the source
*
*
* string id = 5;
* @return The id.
*/
java.lang.String getId();
/**
*
**
*ID of record in the source
*
*
* string id = 5;
* @return The bytes for id.
*/
com.google.protobuf.ByteString
getIdBytes();
/**
*
**
*The reference genome assembly
*
*
* string assembly = 6;
* @return The assembly.
*/
java.lang.String getAssembly();
/**
*
**
*The reference genome assembly
*
*
* string assembly = 6;
* @return The bytes for assembly.
*/
com.google.protobuf.ByteString
getAssemblyBytes();
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @return A list containing the alleleOrigin.
*/
java.util.List getAlleleOriginList();
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @return The count of alleleOrigin.
*/
int getAlleleOriginCount();
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @param index The index of the element to return.
* @return The alleleOrigin at the given index.
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.AlleleOrigin getAlleleOrigin(int index);
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @return A list containing the enum numeric values on the wire for alleleOrigin.
*/
java.util.List
getAlleleOriginValueList();
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @param index The index of the value to return.
* @return The enum numeric value on the wire of alleleOrigin at the given index.
*/
int getAlleleOriginValue(int index);
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
java.util.List
getHeritableTraitsList();
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait getHeritableTraits(int index);
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
int getHeritableTraitsCount();
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
java.util.List
getHeritableTraitsOrBuilderList();
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTraitOrBuilder getHeritableTraitsOrBuilder(
int index);
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
java.util.List
getGenomicFeaturesList();
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature getGenomicFeatures(int index);
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
int getGenomicFeaturesCount();
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
java.util.List
getGenomicFeaturesOrBuilderList();
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeatureOrBuilder getGenomicFeaturesOrBuilder(
int index);
/**
*
**
*The variant classification
*
*
* .protobuf.opencb.VariantClassification variantClassification = 10;
* @return Whether the variantClassification field is set.
*/
boolean hasVariantClassification();
/**
*
**
*The variant classification
*
*
* .protobuf.opencb.VariantClassification variantClassification = 10;
* @return The variantClassification.
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification getVariantClassification();
/**
*
**
*The variant classification
*
*
* .protobuf.opencb.VariantClassification variantClassification = 10;
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassificationOrBuilder getVariantClassificationOrBuilder();
/**
*
**
*Impact of evidence. Should be coherent with the classification of impact if provided.
*
*
* .protobuf.opencb.EvidenceImpact impact = 11;
* @return The enum numeric value on the wire for impact.
*/
int getImpactValue();
/**
*
**
*Impact of evidence. Should be coherent with the classification of impact if provided.
*
*
* .protobuf.opencb.EvidenceImpact impact = 11;
* @return The impact.
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceImpact getImpact();
/**
*
**
*The curation confidence.
*
*
* .protobuf.opencb.Confidence confidence = 12;
* @return The enum numeric value on the wire for confidence.
*/
int getConfidenceValue();
/**
*
**
*The curation confidence.
*
*
* .protobuf.opencb.Confidence confidence = 12;
* @return The confidence.
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Confidence getConfidence();
/**
*
**
*The consistency status. This is applicable to complex evidences (e.g.: ClinVar)
*
*
* .protobuf.opencb.ConsistencyStatus consistencyStatus = 13;
* @return The enum numeric value on the wire for consistencyStatus.
*/
int getConsistencyStatusValue();
/**
*
**
*The consistency status. This is applicable to complex evidences (e.g.: ClinVar)
*
*
* .protobuf.opencb.ConsistencyStatus consistencyStatus = 13;
* @return The consistencyStatus.
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ConsistencyStatus getConsistencyStatus();
/**
*
**
*Ethnicity
*
*
* .protobuf.opencb.EthnicCategory ethnicity = 14;
* @return The enum numeric value on the wire for ethnicity.
*/
int getEthnicityValue();
/**
*
**
*Ethnicity
*
*
* .protobuf.opencb.EthnicCategory ethnicity = 14;
* @return The ethnicity.
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EthnicCategory getEthnicity();
/**
*
**
*The penetrance of the phenotype for this genotype. Value in the range [0, 1]
*
*
* .protobuf.opencb.Penetrance penetrance = 15;
* @return The enum numeric value on the wire for penetrance.
*/
int getPenetranceValue();
/**
*
**
*The penetrance of the phenotype for this genotype. Value in the range [0, 1]
*
*
* .protobuf.opencb.Penetrance penetrance = 15;
* @return The penetrance.
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Penetrance getPenetrance();
/**
*
**
*Variable expressivity of a given phenotype for the same genotype
*
*
* bool variableExpressivity = 16;
* @return The variableExpressivity.
*/
boolean getVariableExpressivity();
/**
*
**
*Evidence description
*
*
* string description = 17;
* @return The description.
*/
java.lang.String getDescription();
/**
*
**
*Evidence description
*
*
* string description = 17;
* @return The bytes for description.
*/
com.google.protobuf.ByteString
getDescriptionBytes();
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
java.util.List
getAdditionalPropertiesList();
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property getAdditionalProperties(int index);
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
int getAdditionalPropertiesCount();
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
java.util.List
getAdditionalPropertiesOrBuilderList();
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.PropertyOrBuilder getAdditionalPropertiesOrBuilder(
int index);
/**
*
**
*Bibliography
*
*
* repeated string bibliography = 19;
* @return A list containing the bibliography.
*/
java.util.List
getBibliographyList();
/**
*
**
*Bibliography
*
*
* repeated string bibliography = 19;
* @return The count of bibliography.
*/
int getBibliographyCount();
/**
*
**
*Bibliography
*
*
* repeated string bibliography = 19;
* @param index The index of the element to return.
* @return The bibliography at the given index.
*/
java.lang.String getBibliography(int index);
/**
*
**
*Bibliography
*
*
* repeated string bibliography = 19;
* @param index The index of the value to return.
* @return The bytes of the bibliography at the given index.
*/
com.google.protobuf.ByteString
getBibliographyBytes(int index);
}
/**
*
**
*An entry for an evidence
*
*
* Protobuf type {@code protobuf.opencb.EvidenceEntry}
*/
public static final class EvidenceEntry extends
com.google.protobuf.GeneratedMessageV3 implements
// @@protoc_insertion_point(message_implements:protobuf.opencb.EvidenceEntry)
EvidenceEntryOrBuilder {
private static final long serialVersionUID = 0L;
// Use EvidenceEntry.newBuilder() to construct.
private EvidenceEntry(com.google.protobuf.GeneratedMessageV3.Builder builder) {
super(builder);
}
private EvidenceEntry() {
submissions_ = java.util.Collections.emptyList();
url_ = "";
id_ = "";
assembly_ = "";
alleleOrigin_ = java.util.Collections.emptyList();
heritableTraits_ = java.util.Collections.emptyList();
genomicFeatures_ = java.util.Collections.emptyList();
impact_ = 0;
confidence_ = 0;
consistencyStatus_ = 0;
ethnicity_ = 0;
penetrance_ = 0;
description_ = "";
additionalProperties_ = java.util.Collections.emptyList();
bibliography_ = com.google.protobuf.LazyStringArrayList.EMPTY;
}
@java.lang.Override
@SuppressWarnings({"unused"})
protected java.lang.Object newInstance(
UnusedPrivateParameter unused) {
return new EvidenceEntry();
}
@java.lang.Override
public final com.google.protobuf.UnknownFieldSet
getUnknownFields() {
return this.unknownFields;
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private EvidenceEntry(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
this();
if (extensionRegistry == null) {
throw new java.lang.NullPointerException();
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int mutable_bitField0_ = 0;
com.google.protobuf.UnknownFieldSet.Builder unknownFields =
com.google.protobuf.UnknownFieldSet.newBuilder();
try {
boolean done = false;
while (!done) {
int tag = input.readTag();
switch (tag) {
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org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource.Builder subBuilder = null;
if (source_ != null) {
subBuilder = source_.toBuilder();
}
source_ = input.readMessage(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(source_);
source_ = subBuilder.buildPartial();
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break;
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case 18: {
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submissions_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000001;
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submissions_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission.parser(), extensionRegistry));
break;
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case 26: {
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.Builder subBuilder = null;
if (somaticInformation_ != null) {
subBuilder = somaticInformation_.toBuilder();
}
somaticInformation_ = input.readMessage(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(somaticInformation_);
somaticInformation_ = subBuilder.buildPartial();
}
break;
}
case 34: {
java.lang.String s = input.readStringRequireUtf8();
url_ = s;
break;
}
case 42: {
java.lang.String s = input.readStringRequireUtf8();
id_ = s;
break;
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case 50: {
java.lang.String s = input.readStringRequireUtf8();
assembly_ = s;
break;
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case 56: {
int rawValue = input.readEnum();
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alleleOrigin_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000002;
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alleleOrigin_.add(rawValue);
break;
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int length = input.readRawVarint32();
int oldLimit = input.pushLimit(length);
while(input.getBytesUntilLimit() > 0) {
int rawValue = input.readEnum();
if (!((mutable_bitField0_ & 0x00000002) != 0)) {
alleleOrigin_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000002;
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alleleOrigin_.add(rawValue);
}
input.popLimit(oldLimit);
break;
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case 66: {
if (!((mutable_bitField0_ & 0x00000004) != 0)) {
heritableTraits_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000004;
}
heritableTraits_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait.parser(), extensionRegistry));
break;
}
case 74: {
if (!((mutable_bitField0_ & 0x00000008) != 0)) {
genomicFeatures_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000008;
}
genomicFeatures_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature.parser(), extensionRegistry));
break;
}
case 82: {
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification.Builder subBuilder = null;
if (variantClassification_ != null) {
subBuilder = variantClassification_.toBuilder();
}
variantClassification_ = input.readMessage(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification.parser(), extensionRegistry);
if (subBuilder != null) {
subBuilder.mergeFrom(variantClassification_);
variantClassification_ = subBuilder.buildPartial();
}
break;
}
case 88: {
int rawValue = input.readEnum();
impact_ = rawValue;
break;
}
case 96: {
int rawValue = input.readEnum();
confidence_ = rawValue;
break;
}
case 104: {
int rawValue = input.readEnum();
consistencyStatus_ = rawValue;
break;
}
case 112: {
int rawValue = input.readEnum();
ethnicity_ = rawValue;
break;
}
case 120: {
int rawValue = input.readEnum();
penetrance_ = rawValue;
break;
}
case 128: {
variableExpressivity_ = input.readBool();
break;
}
case 138: {
java.lang.String s = input.readStringRequireUtf8();
description_ = s;
break;
}
case 146: {
if (!((mutable_bitField0_ & 0x00000010) != 0)) {
additionalProperties_ = new java.util.ArrayList();
mutable_bitField0_ |= 0x00000010;
}
additionalProperties_.add(
input.readMessage(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property.parser(), extensionRegistry));
break;
}
case 154: {
java.lang.String s = input.readStringRequireUtf8();
if (!((mutable_bitField0_ & 0x00000020) != 0)) {
bibliography_ = new com.google.protobuf.LazyStringArrayList();
mutable_bitField0_ |= 0x00000020;
}
bibliography_.add(s);
break;
}
default: {
if (!parseUnknownField(
input, unknownFields, extensionRegistry, tag)) {
done = true;
}
break;
}
}
}
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
throw e.setUnfinishedMessage(this);
} catch (java.io.IOException e) {
throw new com.google.protobuf.InvalidProtocolBufferException(
e).setUnfinishedMessage(this);
} finally {
if (((mutable_bitField0_ & 0x00000001) != 0)) {
submissions_ = java.util.Collections.unmodifiableList(submissions_);
}
if (((mutable_bitField0_ & 0x00000002) != 0)) {
alleleOrigin_ = java.util.Collections.unmodifiableList(alleleOrigin_);
}
if (((mutable_bitField0_ & 0x00000004) != 0)) {
heritableTraits_ = java.util.Collections.unmodifiableList(heritableTraits_);
}
if (((mutable_bitField0_ & 0x00000008) != 0)) {
genomicFeatures_ = java.util.Collections.unmodifiableList(genomicFeatures_);
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if (((mutable_bitField0_ & 0x00000010) != 0)) {
additionalProperties_ = java.util.Collections.unmodifiableList(additionalProperties_);
}
if (((mutable_bitField0_ & 0x00000020) != 0)) {
bibliography_ = bibliography_.getUnmodifiableView();
}
this.unknownFields = unknownFields.build();
makeExtensionsImmutable();
}
}
public static final com.google.protobuf.Descriptors.Descriptor
getDescriptor() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.internal_static_protobuf_opencb_EvidenceEntry_descriptor;
}
@java.lang.Override
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internalGetFieldAccessorTable() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.internal_static_protobuf_opencb_EvidenceEntry_fieldAccessorTable
.ensureFieldAccessorsInitialized(
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry.class, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry.Builder.class);
}
public static final int SOURCE_FIELD_NUMBER = 1;
private org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource source_;
/**
*
**
*Source of the evidence
*
*
* .protobuf.opencb.EvidenceSource source = 1;
* @return Whether the source field is set.
*/
public boolean hasSource() {
return source_ != null;
}
/**
*
**
*Source of the evidence
*
*
* .protobuf.opencb.EvidenceSource source = 1;
* @return The source.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource getSource() {
return source_ == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource.getDefaultInstance() : source_;
}
/**
*
**
*Source of the evidence
*
*
* .protobuf.opencb.EvidenceSource source = 1;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSourceOrBuilder getSourceOrBuilder() {
return getSource();
}
public static final int SUBMISSIONS_FIELD_NUMBER = 2;
private java.util.List submissions_;
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public java.util.List getSubmissionsList() {
return submissions_;
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public java.util.List
getSubmissionsOrBuilderList() {
return submissions_;
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public int getSubmissionsCount() {
return submissions_.size();
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission getSubmissions(int index) {
return submissions_.get(index);
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmissionOrBuilder getSubmissionsOrBuilder(
int index) {
return submissions_.get(index);
}
public static final int SOMATICINFORMATION_FIELD_NUMBER = 3;
private org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation somaticInformation_;
/**
*
**
*The somatic information
*
*
* .protobuf.opencb.SomaticInformation somaticInformation = 3;
* @return Whether the somaticInformation field is set.
*/
public boolean hasSomaticInformation() {
return somaticInformation_ != null;
}
/**
*
**
*The somatic information
*
*
* .protobuf.opencb.SomaticInformation somaticInformation = 3;
* @return The somaticInformation.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation getSomaticInformation() {
return somaticInformation_ == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.getDefaultInstance() : somaticInformation_;
}
/**
*
**
*The somatic information
*
*
* .protobuf.opencb.SomaticInformation somaticInformation = 3;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformationOrBuilder getSomaticInformationOrBuilder() {
return getSomaticInformation();
}
public static final int URL_FIELD_NUMBER = 4;
private volatile java.lang.Object url_;
/**
*
**
*URL of source if any
*
*
* string url = 4;
* @return The url.
*/
public java.lang.String getUrl() {
java.lang.Object ref = url_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
} else {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
url_ = s;
return s;
}
}
/**
*
**
*URL of source if any
*
*
* string url = 4;
* @return The bytes for url.
*/
public com.google.protobuf.ByteString
getUrlBytes() {
java.lang.Object ref = url_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
url_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int ID_FIELD_NUMBER = 5;
private volatile java.lang.Object id_;
/**
*
**
*ID of record in the source
*
*
* string id = 5;
* @return The id.
*/
public java.lang.String getId() {
java.lang.Object ref = id_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
} else {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
id_ = s;
return s;
}
}
/**
*
**
*ID of record in the source
*
*
* string id = 5;
* @return The bytes for id.
*/
public com.google.protobuf.ByteString
getIdBytes() {
java.lang.Object ref = id_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
id_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int ASSEMBLY_FIELD_NUMBER = 6;
private volatile java.lang.Object assembly_;
/**
*
**
*The reference genome assembly
*
*
* string assembly = 6;
* @return The assembly.
*/
public java.lang.String getAssembly() {
java.lang.Object ref = assembly_;
if (ref instanceof java.lang.String) {
return (java.lang.String) ref;
} else {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
assembly_ = s;
return s;
}
}
/**
*
**
*The reference genome assembly
*
*
* string assembly = 6;
* @return The bytes for assembly.
*/
public com.google.protobuf.ByteString
getAssemblyBytes() {
java.lang.Object ref = assembly_;
if (ref instanceof java.lang.String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
assembly_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
public static final int ALLELEORIGIN_FIELD_NUMBER = 7;
private java.util.List alleleOrigin_;
private static final com.google.protobuf.Internal.ListAdapter.Converter<
java.lang.Integer, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.AlleleOrigin> alleleOrigin_converter_ =
new com.google.protobuf.Internal.ListAdapter.Converter<
java.lang.Integer, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.AlleleOrigin>() {
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.AlleleOrigin convert(java.lang.Integer from) {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.AlleleOrigin result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.AlleleOrigin.valueOf(from);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.AlleleOrigin.UNRECOGNIZED : result;
}
};
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @return A list containing the alleleOrigin.
*/
public java.util.List getAlleleOriginList() {
return new com.google.protobuf.Internal.ListAdapter<
java.lang.Integer, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.AlleleOrigin>(alleleOrigin_, alleleOrigin_converter_);
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @return The count of alleleOrigin.
*/
public int getAlleleOriginCount() {
return alleleOrigin_.size();
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @param index The index of the element to return.
* @return The alleleOrigin at the given index.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.AlleleOrigin getAlleleOrigin(int index) {
return alleleOrigin_converter_.convert(alleleOrigin_.get(index));
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @return A list containing the enum numeric values on the wire for alleleOrigin.
*/
public java.util.List
getAlleleOriginValueList() {
return alleleOrigin_;
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @param index The index of the value to return.
* @return The enum numeric value on the wire of alleleOrigin at the given index.
*/
public int getAlleleOriginValue(int index) {
return alleleOrigin_.get(index);
}
private int alleleOriginMemoizedSerializedSize;
public static final int HERITABLETRAITS_FIELD_NUMBER = 8;
private java.util.List heritableTraits_;
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public java.util.List getHeritableTraitsList() {
return heritableTraits_;
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public java.util.List
getHeritableTraitsOrBuilderList() {
return heritableTraits_;
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public int getHeritableTraitsCount() {
return heritableTraits_.size();
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait getHeritableTraits(int index) {
return heritableTraits_.get(index);
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTraitOrBuilder getHeritableTraitsOrBuilder(
int index) {
return heritableTraits_.get(index);
}
public static final int GENOMICFEATURES_FIELD_NUMBER = 9;
private java.util.List genomicFeatures_;
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public java.util.List getGenomicFeaturesList() {
return genomicFeatures_;
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public java.util.List
getGenomicFeaturesOrBuilderList() {
return genomicFeatures_;
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public int getGenomicFeaturesCount() {
return genomicFeatures_.size();
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature getGenomicFeatures(int index) {
return genomicFeatures_.get(index);
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeatureOrBuilder getGenomicFeaturesOrBuilder(
int index) {
return genomicFeatures_.get(index);
}
public static final int VARIANTCLASSIFICATION_FIELD_NUMBER = 10;
private org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification variantClassification_;
/**
*
**
*The variant classification
*
*
* .protobuf.opencb.VariantClassification variantClassification = 10;
* @return Whether the variantClassification field is set.
*/
public boolean hasVariantClassification() {
return variantClassification_ != null;
}
/**
*
**
*The variant classification
*
*
* .protobuf.opencb.VariantClassification variantClassification = 10;
* @return The variantClassification.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification getVariantClassification() {
return variantClassification_ == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification.getDefaultInstance() : variantClassification_;
}
/**
*
**
*The variant classification
*
*
* .protobuf.opencb.VariantClassification variantClassification = 10;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassificationOrBuilder getVariantClassificationOrBuilder() {
return getVariantClassification();
}
public static final int IMPACT_FIELD_NUMBER = 11;
private int impact_;
/**
*
**
*Impact of evidence. Should be coherent with the classification of impact if provided.
*
*
* .protobuf.opencb.EvidenceImpact impact = 11;
* @return The enum numeric value on the wire for impact.
*/
public int getImpactValue() {
return impact_;
}
/**
*
**
*Impact of evidence. Should be coherent with the classification of impact if provided.
*
*
* .protobuf.opencb.EvidenceImpact impact = 11;
* @return The impact.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceImpact getImpact() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceImpact result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceImpact.valueOf(impact_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceImpact.UNRECOGNIZED : result;
}
public static final int CONFIDENCE_FIELD_NUMBER = 12;
private int confidence_;
/**
*
**
*The curation confidence.
*
*
* .protobuf.opencb.Confidence confidence = 12;
* @return The enum numeric value on the wire for confidence.
*/
public int getConfidenceValue() {
return confidence_;
}
/**
*
**
*The curation confidence.
*
*
* .protobuf.opencb.Confidence confidence = 12;
* @return The confidence.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Confidence getConfidence() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Confidence result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Confidence.valueOf(confidence_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Confidence.UNRECOGNIZED : result;
}
public static final int CONSISTENCYSTATUS_FIELD_NUMBER = 13;
private int consistencyStatus_;
/**
*
**
*The consistency status. This is applicable to complex evidences (e.g.: ClinVar)
*
*
* .protobuf.opencb.ConsistencyStatus consistencyStatus = 13;
* @return The enum numeric value on the wire for consistencyStatus.
*/
public int getConsistencyStatusValue() {
return consistencyStatus_;
}
/**
*
**
*The consistency status. This is applicable to complex evidences (e.g.: ClinVar)
*
*
* .protobuf.opencb.ConsistencyStatus consistencyStatus = 13;
* @return The consistencyStatus.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ConsistencyStatus getConsistencyStatus() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ConsistencyStatus result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ConsistencyStatus.valueOf(consistencyStatus_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ConsistencyStatus.UNRECOGNIZED : result;
}
public static final int ETHNICITY_FIELD_NUMBER = 14;
private int ethnicity_;
/**
*
**
*Ethnicity
*
*
* .protobuf.opencb.EthnicCategory ethnicity = 14;
* @return The enum numeric value on the wire for ethnicity.
*/
public int getEthnicityValue() {
return ethnicity_;
}
/**
*
**
*Ethnicity
*
*
* .protobuf.opencb.EthnicCategory ethnicity = 14;
* @return The ethnicity.
*/
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@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EthnicCategory result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EthnicCategory.valueOf(ethnicity_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EthnicCategory.UNRECOGNIZED : result;
}
public static final int PENETRANCE_FIELD_NUMBER = 15;
private int penetrance_;
/**
*
**
*The penetrance of the phenotype for this genotype. Value in the range [0, 1]
*
*
* .protobuf.opencb.Penetrance penetrance = 15;
* @return The enum numeric value on the wire for penetrance.
*/
public int getPenetranceValue() {
return penetrance_;
}
/**
*
**
*The penetrance of the phenotype for this genotype. Value in the range [0, 1]
*
*
* .protobuf.opencb.Penetrance penetrance = 15;
* @return The penetrance.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Penetrance getPenetrance() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Penetrance result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Penetrance.valueOf(penetrance_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Penetrance.UNRECOGNIZED : result;
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public static final int VARIABLEEXPRESSIVITY_FIELD_NUMBER = 16;
private boolean variableExpressivity_;
/**
*
**
*Variable expressivity of a given phenotype for the same genotype
*
*
* bool variableExpressivity = 16;
* @return The variableExpressivity.
*/
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return variableExpressivity_;
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/**
*
**
*Evidence description
*
*
* string description = 17;
* @return The description.
*/
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java.lang.String s = bs.toStringUtf8();
description_ = s;
return s;
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/**
*
**
*Evidence description
*
*
* string description = 17;
* @return The bytes for description.
*/
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description_ = b;
return b;
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/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
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return additionalProperties_;
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*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
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*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
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}
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*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
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*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
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private com.google.protobuf.LazyStringList bibliography_;
/**
*
**
*Bibliography
*
*
* repeated string bibliography = 19;
* @return A list containing the bibliography.
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return bibliography_;
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*
**
*Bibliography
*
*
* repeated string bibliography = 19;
* @return The count of bibliography.
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return bibliography_.size();
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*
**
*Bibliography
*
*
* repeated string bibliography = 19;
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*
**
*Bibliography
*
*
* repeated string bibliography = 19;
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getAdditionalPropertiesFieldBuilder();
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public Builder clear() {
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source_ = null;
} else {
source_ = null;
sourceBuilder_ = null;
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somaticInformationBuilder_ = null;
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alleleOrigin_ = java.util.Collections.emptyList();
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variantClassificationBuilder_ = null;
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ethnicity_ = 0;
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bibliography_ = com.google.protobuf.LazyStringArrayList.EMPTY;
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public com.google.protobuf.Descriptors.Descriptor
getDescriptorForType() {
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}
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public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry getDefaultInstanceForType() {
return org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry.getDefaultInstance();
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry build() {
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry result = buildPartial();
if (!result.isInitialized()) {
throw newUninitializedMessageException(result);
}
return result;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry buildPartial() {
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry result = new org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry(this);
int from_bitField0_ = bitField0_;
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} else {
result.submissions_ = submissionsBuilder_.build();
}
if (somaticInformationBuilder_ == null) {
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}
result.url_ = url_;
result.id_ = id_;
result.assembly_ = assembly_;
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alleleOrigin_ = java.util.Collections.unmodifiableList(alleleOrigin_);
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result.alleleOrigin_ = alleleOrigin_;
if (heritableTraitsBuilder_ == null) {
if (((bitField0_ & 0x00000004) != 0)) {
heritableTraits_ = java.util.Collections.unmodifiableList(heritableTraits_);
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result.heritableTraits_ = heritableTraits_;
} else {
result.heritableTraits_ = heritableTraitsBuilder_.build();
}
if (genomicFeaturesBuilder_ == null) {
if (((bitField0_ & 0x00000008) != 0)) {
genomicFeatures_ = java.util.Collections.unmodifiableList(genomicFeatures_);
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result.genomicFeatures_ = genomicFeatures_;
} else {
result.genomicFeatures_ = genomicFeaturesBuilder_.build();
}
if (variantClassificationBuilder_ == null) {
result.variantClassification_ = variantClassification_;
} else {
result.variantClassification_ = variantClassificationBuilder_.build();
}
result.impact_ = impact_;
result.confidence_ = confidence_;
result.consistencyStatus_ = consistencyStatus_;
result.ethnicity_ = ethnicity_;
result.penetrance_ = penetrance_;
result.variableExpressivity_ = variableExpressivity_;
result.description_ = description_;
if (additionalPropertiesBuilder_ == null) {
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bitField0_ = (bitField0_ & ~0x00000010);
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result.additionalProperties_ = additionalProperties_;
} else {
result.additionalProperties_ = additionalPropertiesBuilder_.build();
}
if (((bitField0_ & 0x00000020) != 0)) {
bibliography_ = bibliography_.getUnmodifiableView();
bitField0_ = (bitField0_ & ~0x00000020);
}
result.bibliography_ = bibliography_;
onBuilt();
return result;
}
@java.lang.Override
public Builder clone() {
return super.clone();
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@java.lang.Override
public Builder setField(
com.google.protobuf.Descriptors.FieldDescriptor field,
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@java.lang.Override
public Builder clearField(
com.google.protobuf.Descriptors.FieldDescriptor field) {
return super.clearField(field);
}
@java.lang.Override
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com.google.protobuf.Descriptors.OneofDescriptor oneof) {
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@java.lang.Override
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com.google.protobuf.Descriptors.FieldDescriptor field,
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@java.lang.Override
public Builder addRepeatedField(
com.google.protobuf.Descriptors.FieldDescriptor field,
java.lang.Object value) {
return super.addRepeatedField(field, value);
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@java.lang.Override
public Builder mergeFrom(com.google.protobuf.Message other) {
if (other instanceof org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry) {
return mergeFrom((org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry)other);
} else {
super.mergeFrom(other);
return this;
}
}
public Builder mergeFrom(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry other) {
if (other == org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry.getDefaultInstance()) return this;
if (other.hasSource()) {
mergeSource(other.getSource());
}
if (submissionsBuilder_ == null) {
if (!other.submissions_.isEmpty()) {
if (submissions_.isEmpty()) {
submissions_ = other.submissions_;
bitField0_ = (bitField0_ & ~0x00000001);
} else {
ensureSubmissionsIsMutable();
submissions_.addAll(other.submissions_);
}
onChanged();
}
} else {
if (!other.submissions_.isEmpty()) {
if (submissionsBuilder_.isEmpty()) {
submissionsBuilder_.dispose();
submissionsBuilder_ = null;
submissions_ = other.submissions_;
bitField0_ = (bitField0_ & ~0x00000001);
submissionsBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getSubmissionsFieldBuilder() : null;
} else {
submissionsBuilder_.addAllMessages(other.submissions_);
}
}
}
if (other.hasSomaticInformation()) {
mergeSomaticInformation(other.getSomaticInformation());
}
if (!other.getUrl().isEmpty()) {
url_ = other.url_;
onChanged();
}
if (!other.getId().isEmpty()) {
id_ = other.id_;
onChanged();
}
if (!other.getAssembly().isEmpty()) {
assembly_ = other.assembly_;
onChanged();
}
if (!other.alleleOrigin_.isEmpty()) {
if (alleleOrigin_.isEmpty()) {
alleleOrigin_ = other.alleleOrigin_;
bitField0_ = (bitField0_ & ~0x00000002);
} else {
ensureAlleleOriginIsMutable();
alleleOrigin_.addAll(other.alleleOrigin_);
}
onChanged();
}
if (heritableTraitsBuilder_ == null) {
if (!other.heritableTraits_.isEmpty()) {
if (heritableTraits_.isEmpty()) {
heritableTraits_ = other.heritableTraits_;
bitField0_ = (bitField0_ & ~0x00000004);
} else {
ensureHeritableTraitsIsMutable();
heritableTraits_.addAll(other.heritableTraits_);
}
onChanged();
}
} else {
if (!other.heritableTraits_.isEmpty()) {
if (heritableTraitsBuilder_.isEmpty()) {
heritableTraitsBuilder_.dispose();
heritableTraitsBuilder_ = null;
heritableTraits_ = other.heritableTraits_;
bitField0_ = (bitField0_ & ~0x00000004);
heritableTraitsBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getHeritableTraitsFieldBuilder() : null;
} else {
heritableTraitsBuilder_.addAllMessages(other.heritableTraits_);
}
}
}
if (genomicFeaturesBuilder_ == null) {
if (!other.genomicFeatures_.isEmpty()) {
if (genomicFeatures_.isEmpty()) {
genomicFeatures_ = other.genomicFeatures_;
bitField0_ = (bitField0_ & ~0x00000008);
} else {
ensureGenomicFeaturesIsMutable();
genomicFeatures_.addAll(other.genomicFeatures_);
}
onChanged();
}
} else {
if (!other.genomicFeatures_.isEmpty()) {
if (genomicFeaturesBuilder_.isEmpty()) {
genomicFeaturesBuilder_.dispose();
genomicFeaturesBuilder_ = null;
genomicFeatures_ = other.genomicFeatures_;
bitField0_ = (bitField0_ & ~0x00000008);
genomicFeaturesBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getGenomicFeaturesFieldBuilder() : null;
} else {
genomicFeaturesBuilder_.addAllMessages(other.genomicFeatures_);
}
}
}
if (other.hasVariantClassification()) {
mergeVariantClassification(other.getVariantClassification());
}
if (other.impact_ != 0) {
setImpactValue(other.getImpactValue());
}
if (other.confidence_ != 0) {
setConfidenceValue(other.getConfidenceValue());
}
if (other.consistencyStatus_ != 0) {
setConsistencyStatusValue(other.getConsistencyStatusValue());
}
if (other.ethnicity_ != 0) {
setEthnicityValue(other.getEthnicityValue());
}
if (other.penetrance_ != 0) {
setPenetranceValue(other.getPenetranceValue());
}
if (other.getVariableExpressivity() != false) {
setVariableExpressivity(other.getVariableExpressivity());
}
if (!other.getDescription().isEmpty()) {
description_ = other.description_;
onChanged();
}
if (additionalPropertiesBuilder_ == null) {
if (!other.additionalProperties_.isEmpty()) {
if (additionalProperties_.isEmpty()) {
additionalProperties_ = other.additionalProperties_;
bitField0_ = (bitField0_ & ~0x00000010);
} else {
ensureAdditionalPropertiesIsMutable();
additionalProperties_.addAll(other.additionalProperties_);
}
onChanged();
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} else {
if (!other.additionalProperties_.isEmpty()) {
if (additionalPropertiesBuilder_.isEmpty()) {
additionalPropertiesBuilder_.dispose();
additionalPropertiesBuilder_ = null;
additionalProperties_ = other.additionalProperties_;
bitField0_ = (bitField0_ & ~0x00000010);
additionalPropertiesBuilder_ =
com.google.protobuf.GeneratedMessageV3.alwaysUseFieldBuilders ?
getAdditionalPropertiesFieldBuilder() : null;
} else {
additionalPropertiesBuilder_.addAllMessages(other.additionalProperties_);
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if (!other.bibliography_.isEmpty()) {
if (bibliography_.isEmpty()) {
bibliography_ = other.bibliography_;
bitField0_ = (bitField0_ & ~0x00000020);
} else {
ensureBibliographyIsMutable();
bibliography_.addAll(other.bibliography_);
}
onChanged();
}
this.mergeUnknownFields(other.unknownFields);
onChanged();
return this;
}
@java.lang.Override
public final boolean isInitialized() {
return true;
}
@java.lang.Override
public Builder mergeFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws java.io.IOException {
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry parsedMessage = null;
try {
parsedMessage = PARSER.parsePartialFrom(input, extensionRegistry);
} catch (com.google.protobuf.InvalidProtocolBufferException e) {
parsedMessage = (org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry) e.getUnfinishedMessage();
throw e.unwrapIOException();
} finally {
if (parsedMessage != null) {
mergeFrom(parsedMessage);
}
}
return this;
}
private int bitField0_;
private org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource source_;
private com.google.protobuf.SingleFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSourceOrBuilder> sourceBuilder_;
/**
*
**
*Source of the evidence
*
*
* .protobuf.opencb.EvidenceSource source = 1;
* @return Whether the source field is set.
*/
public boolean hasSource() {
return sourceBuilder_ != null || source_ != null;
}
/**
*
**
*Source of the evidence
*
*
* .protobuf.opencb.EvidenceSource source = 1;
* @return The source.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource getSource() {
if (sourceBuilder_ == null) {
return source_ == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource.getDefaultInstance() : source_;
} else {
return sourceBuilder_.getMessage();
}
}
/**
*
**
*Source of the evidence
*
*
* .protobuf.opencb.EvidenceSource source = 1;
*/
public Builder setSource(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource value) {
if (sourceBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
source_ = value;
onChanged();
} else {
sourceBuilder_.setMessage(value);
}
return this;
}
/**
*
**
*Source of the evidence
*
*
* .protobuf.opencb.EvidenceSource source = 1;
*/
public Builder setSource(
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource.Builder builderForValue) {
if (sourceBuilder_ == null) {
source_ = builderForValue.build();
onChanged();
} else {
sourceBuilder_.setMessage(builderForValue.build());
}
return this;
}
/**
*
**
*Source of the evidence
*
*
* .protobuf.opencb.EvidenceSource source = 1;
*/
public Builder mergeSource(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource value) {
if (sourceBuilder_ == null) {
if (source_ != null) {
source_ =
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource.newBuilder(source_).mergeFrom(value).buildPartial();
} else {
source_ = value;
}
onChanged();
} else {
sourceBuilder_.mergeFrom(value);
}
return this;
}
/**
*
**
*Source of the evidence
*
*
* .protobuf.opencb.EvidenceSource source = 1;
*/
public Builder clearSource() {
if (sourceBuilder_ == null) {
source_ = null;
onChanged();
} else {
source_ = null;
sourceBuilder_ = null;
}
return this;
}
/**
*
**
*Source of the evidence
*
*
* .protobuf.opencb.EvidenceSource source = 1;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource.Builder getSourceBuilder() {
onChanged();
return getSourceFieldBuilder().getBuilder();
}
/**
*
**
*Source of the evidence
*
*
* .protobuf.opencb.EvidenceSource source = 1;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSourceOrBuilder getSourceOrBuilder() {
if (sourceBuilder_ != null) {
return sourceBuilder_.getMessageOrBuilder();
} else {
return source_ == null ?
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource.getDefaultInstance() : source_;
}
}
/**
*
**
*Source of the evidence
*
*
* .protobuf.opencb.EvidenceSource source = 1;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSourceOrBuilder>
getSourceFieldBuilder() {
if (sourceBuilder_ == null) {
sourceBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSource.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSourceOrBuilder>(
getSource(),
getParentForChildren(),
isClean());
source_ = null;
}
return sourceBuilder_;
}
private java.util.List submissions_ =
java.util.Collections.emptyList();
private void ensureSubmissionsIsMutable() {
if (!((bitField0_ & 0x00000001) != 0)) {
submissions_ = new java.util.ArrayList(submissions_);
bitField0_ |= 0x00000001;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmissionOrBuilder> submissionsBuilder_;
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public java.util.List getSubmissionsList() {
if (submissionsBuilder_ == null) {
return java.util.Collections.unmodifiableList(submissions_);
} else {
return submissionsBuilder_.getMessageList();
}
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public int getSubmissionsCount() {
if (submissionsBuilder_ == null) {
return submissions_.size();
} else {
return submissionsBuilder_.getCount();
}
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission getSubmissions(int index) {
if (submissionsBuilder_ == null) {
return submissions_.get(index);
} else {
return submissionsBuilder_.getMessage(index);
}
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public Builder setSubmissions(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission value) {
if (submissionsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureSubmissionsIsMutable();
submissions_.set(index, value);
onChanged();
} else {
submissionsBuilder_.setMessage(index, value);
}
return this;
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public Builder setSubmissions(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission.Builder builderForValue) {
if (submissionsBuilder_ == null) {
ensureSubmissionsIsMutable();
submissions_.set(index, builderForValue.build());
onChanged();
} else {
submissionsBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public Builder addSubmissions(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission value) {
if (submissionsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureSubmissionsIsMutable();
submissions_.add(value);
onChanged();
} else {
submissionsBuilder_.addMessage(value);
}
return this;
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public Builder addSubmissions(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission value) {
if (submissionsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureSubmissionsIsMutable();
submissions_.add(index, value);
onChanged();
} else {
submissionsBuilder_.addMessage(index, value);
}
return this;
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public Builder addSubmissions(
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission.Builder builderForValue) {
if (submissionsBuilder_ == null) {
ensureSubmissionsIsMutable();
submissions_.add(builderForValue.build());
onChanged();
} else {
submissionsBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public Builder addSubmissions(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission.Builder builderForValue) {
if (submissionsBuilder_ == null) {
ensureSubmissionsIsMutable();
submissions_.add(index, builderForValue.build());
onChanged();
} else {
submissionsBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public Builder addAllSubmissions(
java.lang.Iterable values) {
if (submissionsBuilder_ == null) {
ensureSubmissionsIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, submissions_);
onChanged();
} else {
submissionsBuilder_.addAllMessages(values);
}
return this;
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public Builder clearSubmissions() {
if (submissionsBuilder_ == null) {
submissions_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000001);
onChanged();
} else {
submissionsBuilder_.clear();
}
return this;
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public Builder removeSubmissions(int index) {
if (submissionsBuilder_ == null) {
ensureSubmissionsIsMutable();
submissions_.remove(index);
onChanged();
} else {
submissionsBuilder_.remove(index);
}
return this;
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission.Builder getSubmissionsBuilder(
int index) {
return getSubmissionsFieldBuilder().getBuilder(index);
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmissionOrBuilder getSubmissionsOrBuilder(
int index) {
if (submissionsBuilder_ == null) {
return submissions_.get(index); } else {
return submissionsBuilder_.getMessageOrBuilder(index);
}
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public java.util.List
getSubmissionsOrBuilderList() {
if (submissionsBuilder_ != null) {
return submissionsBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(submissions_);
}
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission.Builder addSubmissionsBuilder() {
return getSubmissionsFieldBuilder().addBuilder(
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission.getDefaultInstance());
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission.Builder addSubmissionsBuilder(
int index) {
return getSubmissionsFieldBuilder().addBuilder(
index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission.getDefaultInstance());
}
/**
*
**
*The list of submissions
*
*
* repeated .protobuf.opencb.EvidenceSubmission submissions = 2;
*/
public java.util.List
getSubmissionsBuilderList() {
return getSubmissionsFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmissionOrBuilder>
getSubmissionsFieldBuilder() {
if (submissionsBuilder_ == null) {
submissionsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmission.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceSubmissionOrBuilder>(
submissions_,
((bitField0_ & 0x00000001) != 0),
getParentForChildren(),
isClean());
submissions_ = null;
}
return submissionsBuilder_;
}
private org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation somaticInformation_;
private com.google.protobuf.SingleFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformationOrBuilder> somaticInformationBuilder_;
/**
*
**
*The somatic information
*
*
* .protobuf.opencb.SomaticInformation somaticInformation = 3;
* @return Whether the somaticInformation field is set.
*/
public boolean hasSomaticInformation() {
return somaticInformationBuilder_ != null || somaticInformation_ != null;
}
/**
*
**
*The somatic information
*
*
* .protobuf.opencb.SomaticInformation somaticInformation = 3;
* @return The somaticInformation.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation getSomaticInformation() {
if (somaticInformationBuilder_ == null) {
return somaticInformation_ == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.getDefaultInstance() : somaticInformation_;
} else {
return somaticInformationBuilder_.getMessage();
}
}
/**
*
**
*The somatic information
*
*
* .protobuf.opencb.SomaticInformation somaticInformation = 3;
*/
public Builder setSomaticInformation(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation value) {
if (somaticInformationBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
somaticInformation_ = value;
onChanged();
} else {
somaticInformationBuilder_.setMessage(value);
}
return this;
}
/**
*
**
*The somatic information
*
*
* .protobuf.opencb.SomaticInformation somaticInformation = 3;
*/
public Builder setSomaticInformation(
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.Builder builderForValue) {
if (somaticInformationBuilder_ == null) {
somaticInformation_ = builderForValue.build();
onChanged();
} else {
somaticInformationBuilder_.setMessage(builderForValue.build());
}
return this;
}
/**
*
**
*The somatic information
*
*
* .protobuf.opencb.SomaticInformation somaticInformation = 3;
*/
public Builder mergeSomaticInformation(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation value) {
if (somaticInformationBuilder_ == null) {
if (somaticInformation_ != null) {
somaticInformation_ =
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.newBuilder(somaticInformation_).mergeFrom(value).buildPartial();
} else {
somaticInformation_ = value;
}
onChanged();
} else {
somaticInformationBuilder_.mergeFrom(value);
}
return this;
}
/**
*
**
*The somatic information
*
*
* .protobuf.opencb.SomaticInformation somaticInformation = 3;
*/
public Builder clearSomaticInformation() {
if (somaticInformationBuilder_ == null) {
somaticInformation_ = null;
onChanged();
} else {
somaticInformation_ = null;
somaticInformationBuilder_ = null;
}
return this;
}
/**
*
**
*The somatic information
*
*
* .protobuf.opencb.SomaticInformation somaticInformation = 3;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.Builder getSomaticInformationBuilder() {
onChanged();
return getSomaticInformationFieldBuilder().getBuilder();
}
/**
*
**
*The somatic information
*
*
* .protobuf.opencb.SomaticInformation somaticInformation = 3;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformationOrBuilder getSomaticInformationOrBuilder() {
if (somaticInformationBuilder_ != null) {
return somaticInformationBuilder_.getMessageOrBuilder();
} else {
return somaticInformation_ == null ?
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.getDefaultInstance() : somaticInformation_;
}
}
/**
*
**
*The somatic information
*
*
* .protobuf.opencb.SomaticInformation somaticInformation = 3;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformationOrBuilder>
getSomaticInformationFieldBuilder() {
if (somaticInformationBuilder_ == null) {
somaticInformationBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformation.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.SomaticInformationOrBuilder>(
getSomaticInformation(),
getParentForChildren(),
isClean());
somaticInformation_ = null;
}
return somaticInformationBuilder_;
}
private java.lang.Object url_ = "";
/**
*
**
*URL of source if any
*
*
* string url = 4;
* @return The url.
*/
public java.lang.String getUrl() {
java.lang.Object ref = url_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
url_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
**
*URL of source if any
*
*
* string url = 4;
* @return The bytes for url.
*/
public com.google.protobuf.ByteString
getUrlBytes() {
java.lang.Object ref = url_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
url_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
**
*URL of source if any
*
*
* string url = 4;
* @param value The url to set.
* @return This builder for chaining.
*/
public Builder setUrl(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
url_ = value;
onChanged();
return this;
}
/**
*
**
*URL of source if any
*
*
* string url = 4;
* @return This builder for chaining.
*/
public Builder clearUrl() {
url_ = getDefaultInstance().getUrl();
onChanged();
return this;
}
/**
*
**
*URL of source if any
*
*
* string url = 4;
* @param value The bytes for url to set.
* @return This builder for chaining.
*/
public Builder setUrlBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
url_ = value;
onChanged();
return this;
}
private java.lang.Object id_ = "";
/**
*
**
*ID of record in the source
*
*
* string id = 5;
* @return The id.
*/
public java.lang.String getId() {
java.lang.Object ref = id_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
id_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
**
*ID of record in the source
*
*
* string id = 5;
* @return The bytes for id.
*/
public com.google.protobuf.ByteString
getIdBytes() {
java.lang.Object ref = id_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
id_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
**
*ID of record in the source
*
*
* string id = 5;
* @param value The id to set.
* @return This builder for chaining.
*/
public Builder setId(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
id_ = value;
onChanged();
return this;
}
/**
*
**
*ID of record in the source
*
*
* string id = 5;
* @return This builder for chaining.
*/
public Builder clearId() {
id_ = getDefaultInstance().getId();
onChanged();
return this;
}
/**
*
**
*ID of record in the source
*
*
* string id = 5;
* @param value The bytes for id to set.
* @return This builder for chaining.
*/
public Builder setIdBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
id_ = value;
onChanged();
return this;
}
private java.lang.Object assembly_ = "";
/**
*
**
*The reference genome assembly
*
*
* string assembly = 6;
* @return The assembly.
*/
public java.lang.String getAssembly() {
java.lang.Object ref = assembly_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
assembly_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
**
*The reference genome assembly
*
*
* string assembly = 6;
* @return The bytes for assembly.
*/
public com.google.protobuf.ByteString
getAssemblyBytes() {
java.lang.Object ref = assembly_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
assembly_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
**
*The reference genome assembly
*
*
* string assembly = 6;
* @param value The assembly to set.
* @return This builder for chaining.
*/
public Builder setAssembly(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
assembly_ = value;
onChanged();
return this;
}
/**
*
**
*The reference genome assembly
*
*
* string assembly = 6;
* @return This builder for chaining.
*/
public Builder clearAssembly() {
assembly_ = getDefaultInstance().getAssembly();
onChanged();
return this;
}
/**
*
**
*The reference genome assembly
*
*
* string assembly = 6;
* @param value The bytes for assembly to set.
* @return This builder for chaining.
*/
public Builder setAssemblyBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
assembly_ = value;
onChanged();
return this;
}
private java.util.List alleleOrigin_ =
java.util.Collections.emptyList();
private void ensureAlleleOriginIsMutable() {
if (!((bitField0_ & 0x00000002) != 0)) {
alleleOrigin_ = new java.util.ArrayList(alleleOrigin_);
bitField0_ |= 0x00000002;
}
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @return A list containing the alleleOrigin.
*/
public java.util.List getAlleleOriginList() {
return new com.google.protobuf.Internal.ListAdapter<
java.lang.Integer, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.AlleleOrigin>(alleleOrigin_, alleleOrigin_converter_);
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @return The count of alleleOrigin.
*/
public int getAlleleOriginCount() {
return alleleOrigin_.size();
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @param index The index of the element to return.
* @return The alleleOrigin at the given index.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.AlleleOrigin getAlleleOrigin(int index) {
return alleleOrigin_converter_.convert(alleleOrigin_.get(index));
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @param index The index to set the value at.
* @param value The alleleOrigin to set.
* @return This builder for chaining.
*/
public Builder setAlleleOrigin(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.AlleleOrigin value) {
if (value == null) {
throw new NullPointerException();
}
ensureAlleleOriginIsMutable();
alleleOrigin_.set(index, value.getNumber());
onChanged();
return this;
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @param value The alleleOrigin to add.
* @return This builder for chaining.
*/
public Builder addAlleleOrigin(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.AlleleOrigin value) {
if (value == null) {
throw new NullPointerException();
}
ensureAlleleOriginIsMutable();
alleleOrigin_.add(value.getNumber());
onChanged();
return this;
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @param values The alleleOrigin to add.
* @return This builder for chaining.
*/
public Builder addAllAlleleOrigin(
java.lang.Iterable values) {
ensureAlleleOriginIsMutable();
for (org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.AlleleOrigin value : values) {
alleleOrigin_.add(value.getNumber());
}
onChanged();
return this;
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @return This builder for chaining.
*/
public Builder clearAlleleOrigin() {
alleleOrigin_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000002);
onChanged();
return this;
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @return A list containing the enum numeric values on the wire for alleleOrigin.
*/
public java.util.List
getAlleleOriginValueList() {
return java.util.Collections.unmodifiableList(alleleOrigin_);
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @param index The index of the value to return.
* @return The enum numeric value on the wire of alleleOrigin at the given index.
*/
public int getAlleleOriginValue(int index) {
return alleleOrigin_.get(index);
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @param index The index of the value to return.
* @return The enum numeric value on the wire of alleleOrigin at the given index.
* @return This builder for chaining.
*/
public Builder setAlleleOriginValue(
int index, int value) {
ensureAlleleOriginIsMutable();
alleleOrigin_.set(index, value);
onChanged();
return this;
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @param value The enum numeric value on the wire for alleleOrigin to add.
* @return This builder for chaining.
*/
public Builder addAlleleOriginValue(int value) {
ensureAlleleOriginIsMutable();
alleleOrigin_.add(value);
onChanged();
return this;
}
/**
*
**
*List of allele origins
*
*
* repeated .protobuf.opencb.AlleleOrigin alleleOrigin = 7;
* @param values The enum numeric values on the wire for alleleOrigin to add.
* @return This builder for chaining.
*/
public Builder addAllAlleleOriginValue(
java.lang.Iterable values) {
ensureAlleleOriginIsMutable();
for (int value : values) {
alleleOrigin_.add(value);
}
onChanged();
return this;
}
private java.util.List heritableTraits_ =
java.util.Collections.emptyList();
private void ensureHeritableTraitsIsMutable() {
if (!((bitField0_ & 0x00000004) != 0)) {
heritableTraits_ = new java.util.ArrayList(heritableTraits_);
bitField0_ |= 0x00000004;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTraitOrBuilder> heritableTraitsBuilder_;
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public java.util.List getHeritableTraitsList() {
if (heritableTraitsBuilder_ == null) {
return java.util.Collections.unmodifiableList(heritableTraits_);
} else {
return heritableTraitsBuilder_.getMessageList();
}
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public int getHeritableTraitsCount() {
if (heritableTraitsBuilder_ == null) {
return heritableTraits_.size();
} else {
return heritableTraitsBuilder_.getCount();
}
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait getHeritableTraits(int index) {
if (heritableTraitsBuilder_ == null) {
return heritableTraits_.get(index);
} else {
return heritableTraitsBuilder_.getMessage(index);
}
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public Builder setHeritableTraits(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait value) {
if (heritableTraitsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureHeritableTraitsIsMutable();
heritableTraits_.set(index, value);
onChanged();
} else {
heritableTraitsBuilder_.setMessage(index, value);
}
return this;
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public Builder setHeritableTraits(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait.Builder builderForValue) {
if (heritableTraitsBuilder_ == null) {
ensureHeritableTraitsIsMutable();
heritableTraits_.set(index, builderForValue.build());
onChanged();
} else {
heritableTraitsBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public Builder addHeritableTraits(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait value) {
if (heritableTraitsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureHeritableTraitsIsMutable();
heritableTraits_.add(value);
onChanged();
} else {
heritableTraitsBuilder_.addMessage(value);
}
return this;
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public Builder addHeritableTraits(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait value) {
if (heritableTraitsBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureHeritableTraitsIsMutable();
heritableTraits_.add(index, value);
onChanged();
} else {
heritableTraitsBuilder_.addMessage(index, value);
}
return this;
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public Builder addHeritableTraits(
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait.Builder builderForValue) {
if (heritableTraitsBuilder_ == null) {
ensureHeritableTraitsIsMutable();
heritableTraits_.add(builderForValue.build());
onChanged();
} else {
heritableTraitsBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public Builder addHeritableTraits(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait.Builder builderForValue) {
if (heritableTraitsBuilder_ == null) {
ensureHeritableTraitsIsMutable();
heritableTraits_.add(index, builderForValue.build());
onChanged();
} else {
heritableTraitsBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public Builder addAllHeritableTraits(
java.lang.Iterable values) {
if (heritableTraitsBuilder_ == null) {
ensureHeritableTraitsIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, heritableTraits_);
onChanged();
} else {
heritableTraitsBuilder_.addAllMessages(values);
}
return this;
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public Builder clearHeritableTraits() {
if (heritableTraitsBuilder_ == null) {
heritableTraits_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000004);
onChanged();
} else {
heritableTraitsBuilder_.clear();
}
return this;
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public Builder removeHeritableTraits(int index) {
if (heritableTraitsBuilder_ == null) {
ensureHeritableTraitsIsMutable();
heritableTraits_.remove(index);
onChanged();
} else {
heritableTraitsBuilder_.remove(index);
}
return this;
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait.Builder getHeritableTraitsBuilder(
int index) {
return getHeritableTraitsFieldBuilder().getBuilder(index);
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTraitOrBuilder getHeritableTraitsOrBuilder(
int index) {
if (heritableTraitsBuilder_ == null) {
return heritableTraits_.get(index); } else {
return heritableTraitsBuilder_.getMessageOrBuilder(index);
}
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public java.util.List
getHeritableTraitsOrBuilderList() {
if (heritableTraitsBuilder_ != null) {
return heritableTraitsBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(heritableTraits_);
}
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait.Builder addHeritableTraitsBuilder() {
return getHeritableTraitsFieldBuilder().addBuilder(
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait.getDefaultInstance());
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait.Builder addHeritableTraitsBuilder(
int index) {
return getHeritableTraitsFieldBuilder().addBuilder(
index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait.getDefaultInstance());
}
/**
*
**
*Heritable traits associated to this evidence
*
*
* repeated .protobuf.opencb.HeritableTrait heritableTraits = 8;
*/
public java.util.List
getHeritableTraitsBuilderList() {
return getHeritableTraitsFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTraitOrBuilder>
getHeritableTraitsFieldBuilder() {
if (heritableTraitsBuilder_ == null) {
heritableTraitsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTrait.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.HeritableTraitOrBuilder>(
heritableTraits_,
((bitField0_ & 0x00000004) != 0),
getParentForChildren(),
isClean());
heritableTraits_ = null;
}
return heritableTraitsBuilder_;
}
private java.util.List genomicFeatures_ =
java.util.Collections.emptyList();
private void ensureGenomicFeaturesIsMutable() {
if (!((bitField0_ & 0x00000008) != 0)) {
genomicFeatures_ = new java.util.ArrayList(genomicFeatures_);
bitField0_ |= 0x00000008;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeatureOrBuilder> genomicFeaturesBuilder_;
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public java.util.List getGenomicFeaturesList() {
if (genomicFeaturesBuilder_ == null) {
return java.util.Collections.unmodifiableList(genomicFeatures_);
} else {
return genomicFeaturesBuilder_.getMessageList();
}
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public int getGenomicFeaturesCount() {
if (genomicFeaturesBuilder_ == null) {
return genomicFeatures_.size();
} else {
return genomicFeaturesBuilder_.getCount();
}
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature getGenomicFeatures(int index) {
if (genomicFeaturesBuilder_ == null) {
return genomicFeatures_.get(index);
} else {
return genomicFeaturesBuilder_.getMessage(index);
}
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public Builder setGenomicFeatures(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature value) {
if (genomicFeaturesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureGenomicFeaturesIsMutable();
genomicFeatures_.set(index, value);
onChanged();
} else {
genomicFeaturesBuilder_.setMessage(index, value);
}
return this;
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public Builder setGenomicFeatures(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature.Builder builderForValue) {
if (genomicFeaturesBuilder_ == null) {
ensureGenomicFeaturesIsMutable();
genomicFeatures_.set(index, builderForValue.build());
onChanged();
} else {
genomicFeaturesBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public Builder addGenomicFeatures(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature value) {
if (genomicFeaturesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureGenomicFeaturesIsMutable();
genomicFeatures_.add(value);
onChanged();
} else {
genomicFeaturesBuilder_.addMessage(value);
}
return this;
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public Builder addGenomicFeatures(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature value) {
if (genomicFeaturesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureGenomicFeaturesIsMutable();
genomicFeatures_.add(index, value);
onChanged();
} else {
genomicFeaturesBuilder_.addMessage(index, value);
}
return this;
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public Builder addGenomicFeatures(
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature.Builder builderForValue) {
if (genomicFeaturesBuilder_ == null) {
ensureGenomicFeaturesIsMutable();
genomicFeatures_.add(builderForValue.build());
onChanged();
} else {
genomicFeaturesBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public Builder addGenomicFeatures(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature.Builder builderForValue) {
if (genomicFeaturesBuilder_ == null) {
ensureGenomicFeaturesIsMutable();
genomicFeatures_.add(index, builderForValue.build());
onChanged();
} else {
genomicFeaturesBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public Builder addAllGenomicFeatures(
java.lang.Iterable values) {
if (genomicFeaturesBuilder_ == null) {
ensureGenomicFeaturesIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, genomicFeatures_);
onChanged();
} else {
genomicFeaturesBuilder_.addAllMessages(values);
}
return this;
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public Builder clearGenomicFeatures() {
if (genomicFeaturesBuilder_ == null) {
genomicFeatures_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000008);
onChanged();
} else {
genomicFeaturesBuilder_.clear();
}
return this;
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public Builder removeGenomicFeatures(int index) {
if (genomicFeaturesBuilder_ == null) {
ensureGenomicFeaturesIsMutable();
genomicFeatures_.remove(index);
onChanged();
} else {
genomicFeaturesBuilder_.remove(index);
}
return this;
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature.Builder getGenomicFeaturesBuilder(
int index) {
return getGenomicFeaturesFieldBuilder().getBuilder(index);
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeatureOrBuilder getGenomicFeaturesOrBuilder(
int index) {
if (genomicFeaturesBuilder_ == null) {
return genomicFeatures_.get(index); } else {
return genomicFeaturesBuilder_.getMessageOrBuilder(index);
}
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public java.util.List
getGenomicFeaturesOrBuilderList() {
if (genomicFeaturesBuilder_ != null) {
return genomicFeaturesBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(genomicFeatures_);
}
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature.Builder addGenomicFeaturesBuilder() {
return getGenomicFeaturesFieldBuilder().addBuilder(
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature.getDefaultInstance());
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature.Builder addGenomicFeaturesBuilder(
int index) {
return getGenomicFeaturesFieldBuilder().addBuilder(
index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature.getDefaultInstance());
}
/**
*
**
*The transcript to which the evidence refers
*
*
* repeated .protobuf.opencb.GenomicFeature genomicFeatures = 9;
*/
public java.util.List
getGenomicFeaturesBuilderList() {
return getGenomicFeaturesFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeatureOrBuilder>
getGenomicFeaturesFieldBuilder() {
if (genomicFeaturesBuilder_ == null) {
genomicFeaturesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeature.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.GenomicFeatureOrBuilder>(
genomicFeatures_,
((bitField0_ & 0x00000008) != 0),
getParentForChildren(),
isClean());
genomicFeatures_ = null;
}
return genomicFeaturesBuilder_;
}
private org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification variantClassification_;
private com.google.protobuf.SingleFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassificationOrBuilder> variantClassificationBuilder_;
/**
*
**
*The variant classification
*
*
* .protobuf.opencb.VariantClassification variantClassification = 10;
* @return Whether the variantClassification field is set.
*/
public boolean hasVariantClassification() {
return variantClassificationBuilder_ != null || variantClassification_ != null;
}
/**
*
**
*The variant classification
*
*
* .protobuf.opencb.VariantClassification variantClassification = 10;
* @return The variantClassification.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification getVariantClassification() {
if (variantClassificationBuilder_ == null) {
return variantClassification_ == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification.getDefaultInstance() : variantClassification_;
} else {
return variantClassificationBuilder_.getMessage();
}
}
/**
*
**
*The variant classification
*
*
* .protobuf.opencb.VariantClassification variantClassification = 10;
*/
public Builder setVariantClassification(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification value) {
if (variantClassificationBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
variantClassification_ = value;
onChanged();
} else {
variantClassificationBuilder_.setMessage(value);
}
return this;
}
/**
*
**
*The variant classification
*
*
* .protobuf.opencb.VariantClassification variantClassification = 10;
*/
public Builder setVariantClassification(
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification.Builder builderForValue) {
if (variantClassificationBuilder_ == null) {
variantClassification_ = builderForValue.build();
onChanged();
} else {
variantClassificationBuilder_.setMessage(builderForValue.build());
}
return this;
}
/**
*
**
*The variant classification
*
*
* .protobuf.opencb.VariantClassification variantClassification = 10;
*/
public Builder mergeVariantClassification(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification value) {
if (variantClassificationBuilder_ == null) {
if (variantClassification_ != null) {
variantClassification_ =
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification.newBuilder(variantClassification_).mergeFrom(value).buildPartial();
} else {
variantClassification_ = value;
}
onChanged();
} else {
variantClassificationBuilder_.mergeFrom(value);
}
return this;
}
/**
*
**
*The variant classification
*
*
* .protobuf.opencb.VariantClassification variantClassification = 10;
*/
public Builder clearVariantClassification() {
if (variantClassificationBuilder_ == null) {
variantClassification_ = null;
onChanged();
} else {
variantClassification_ = null;
variantClassificationBuilder_ = null;
}
return this;
}
/**
*
**
*The variant classification
*
*
* .protobuf.opencb.VariantClassification variantClassification = 10;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification.Builder getVariantClassificationBuilder() {
onChanged();
return getVariantClassificationFieldBuilder().getBuilder();
}
/**
*
**
*The variant classification
*
*
* .protobuf.opencb.VariantClassification variantClassification = 10;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassificationOrBuilder getVariantClassificationOrBuilder() {
if (variantClassificationBuilder_ != null) {
return variantClassificationBuilder_.getMessageOrBuilder();
} else {
return variantClassification_ == null ?
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification.getDefaultInstance() : variantClassification_;
}
}
/**
*
**
*The variant classification
*
*
* .protobuf.opencb.VariantClassification variantClassification = 10;
*/
private com.google.protobuf.SingleFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassificationOrBuilder>
getVariantClassificationFieldBuilder() {
if (variantClassificationBuilder_ == null) {
variantClassificationBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassification.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.VariantClassificationOrBuilder>(
getVariantClassification(),
getParentForChildren(),
isClean());
variantClassification_ = null;
}
return variantClassificationBuilder_;
}
private int impact_ = 0;
/**
*
**
*Impact of evidence. Should be coherent with the classification of impact if provided.
*
*
* .protobuf.opencb.EvidenceImpact impact = 11;
* @return The enum numeric value on the wire for impact.
*/
public int getImpactValue() {
return impact_;
}
/**
*
**
*Impact of evidence. Should be coherent with the classification of impact if provided.
*
*
* .protobuf.opencb.EvidenceImpact impact = 11;
* @param value The enum numeric value on the wire for impact to set.
* @return This builder for chaining.
*/
public Builder setImpactValue(int value) {
impact_ = value;
onChanged();
return this;
}
/**
*
**
*Impact of evidence. Should be coherent with the classification of impact if provided.
*
*
* .protobuf.opencb.EvidenceImpact impact = 11;
* @return The impact.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceImpact getImpact() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceImpact result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceImpact.valueOf(impact_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceImpact.UNRECOGNIZED : result;
}
/**
*
**
*Impact of evidence. Should be coherent with the classification of impact if provided.
*
*
* .protobuf.opencb.EvidenceImpact impact = 11;
* @param value The impact to set.
* @return This builder for chaining.
*/
public Builder setImpact(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceImpact value) {
if (value == null) {
throw new NullPointerException();
}
impact_ = value.getNumber();
onChanged();
return this;
}
/**
*
**
*Impact of evidence. Should be coherent with the classification of impact if provided.
*
*
* .protobuf.opencb.EvidenceImpact impact = 11;
* @return This builder for chaining.
*/
public Builder clearImpact() {
impact_ = 0;
onChanged();
return this;
}
private int confidence_ = 0;
/**
*
**
*The curation confidence.
*
*
* .protobuf.opencb.Confidence confidence = 12;
* @return The enum numeric value on the wire for confidence.
*/
public int getConfidenceValue() {
return confidence_;
}
/**
*
**
*The curation confidence.
*
*
* .protobuf.opencb.Confidence confidence = 12;
* @param value The enum numeric value on the wire for confidence to set.
* @return This builder for chaining.
*/
public Builder setConfidenceValue(int value) {
confidence_ = value;
onChanged();
return this;
}
/**
*
**
*The curation confidence.
*
*
* .protobuf.opencb.Confidence confidence = 12;
* @return The confidence.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Confidence getConfidence() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Confidence result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Confidence.valueOf(confidence_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Confidence.UNRECOGNIZED : result;
}
/**
*
**
*The curation confidence.
*
*
* .protobuf.opencb.Confidence confidence = 12;
* @param value The confidence to set.
* @return This builder for chaining.
*/
public Builder setConfidence(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Confidence value) {
if (value == null) {
throw new NullPointerException();
}
confidence_ = value.getNumber();
onChanged();
return this;
}
/**
*
**
*The curation confidence.
*
*
* .protobuf.opencb.Confidence confidence = 12;
* @return This builder for chaining.
*/
public Builder clearConfidence() {
confidence_ = 0;
onChanged();
return this;
}
private int consistencyStatus_ = 0;
/**
*
**
*The consistency status. This is applicable to complex evidences (e.g.: ClinVar)
*
*
* .protobuf.opencb.ConsistencyStatus consistencyStatus = 13;
* @return The enum numeric value on the wire for consistencyStatus.
*/
public int getConsistencyStatusValue() {
return consistencyStatus_;
}
/**
*
**
*The consistency status. This is applicable to complex evidences (e.g.: ClinVar)
*
*
* .protobuf.opencb.ConsistencyStatus consistencyStatus = 13;
* @param value The enum numeric value on the wire for consistencyStatus to set.
* @return This builder for chaining.
*/
public Builder setConsistencyStatusValue(int value) {
consistencyStatus_ = value;
onChanged();
return this;
}
/**
*
**
*The consistency status. This is applicable to complex evidences (e.g.: ClinVar)
*
*
* .protobuf.opencb.ConsistencyStatus consistencyStatus = 13;
* @return The consistencyStatus.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ConsistencyStatus getConsistencyStatus() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ConsistencyStatus result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ConsistencyStatus.valueOf(consistencyStatus_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ConsistencyStatus.UNRECOGNIZED : result;
}
/**
*
**
*The consistency status. This is applicable to complex evidences (e.g.: ClinVar)
*
*
* .protobuf.opencb.ConsistencyStatus consistencyStatus = 13;
* @param value The consistencyStatus to set.
* @return This builder for chaining.
*/
public Builder setConsistencyStatus(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.ConsistencyStatus value) {
if (value == null) {
throw new NullPointerException();
}
consistencyStatus_ = value.getNumber();
onChanged();
return this;
}
/**
*
**
*The consistency status. This is applicable to complex evidences (e.g.: ClinVar)
*
*
* .protobuf.opencb.ConsistencyStatus consistencyStatus = 13;
* @return This builder for chaining.
*/
public Builder clearConsistencyStatus() {
consistencyStatus_ = 0;
onChanged();
return this;
}
private int ethnicity_ = 0;
/**
*
**
*Ethnicity
*
*
* .protobuf.opencb.EthnicCategory ethnicity = 14;
* @return The enum numeric value on the wire for ethnicity.
*/
public int getEthnicityValue() {
return ethnicity_;
}
/**
*
**
*Ethnicity
*
*
* .protobuf.opencb.EthnicCategory ethnicity = 14;
* @param value The enum numeric value on the wire for ethnicity to set.
* @return This builder for chaining.
*/
public Builder setEthnicityValue(int value) {
ethnicity_ = value;
onChanged();
return this;
}
/**
*
**
*Ethnicity
*
*
* .protobuf.opencb.EthnicCategory ethnicity = 14;
* @return The ethnicity.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EthnicCategory getEthnicity() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EthnicCategory result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EthnicCategory.valueOf(ethnicity_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EthnicCategory.UNRECOGNIZED : result;
}
/**
*
**
*Ethnicity
*
*
* .protobuf.opencb.EthnicCategory ethnicity = 14;
* @param value The ethnicity to set.
* @return This builder for chaining.
*/
public Builder setEthnicity(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EthnicCategory value) {
if (value == null) {
throw new NullPointerException();
}
ethnicity_ = value.getNumber();
onChanged();
return this;
}
/**
*
**
*Ethnicity
*
*
* .protobuf.opencb.EthnicCategory ethnicity = 14;
* @return This builder for chaining.
*/
public Builder clearEthnicity() {
ethnicity_ = 0;
onChanged();
return this;
}
private int penetrance_ = 0;
/**
*
**
*The penetrance of the phenotype for this genotype. Value in the range [0, 1]
*
*
* .protobuf.opencb.Penetrance penetrance = 15;
* @return The enum numeric value on the wire for penetrance.
*/
public int getPenetranceValue() {
return penetrance_;
}
/**
*
**
*The penetrance of the phenotype for this genotype. Value in the range [0, 1]
*
*
* .protobuf.opencb.Penetrance penetrance = 15;
* @param value The enum numeric value on the wire for penetrance to set.
* @return This builder for chaining.
*/
public Builder setPenetranceValue(int value) {
penetrance_ = value;
onChanged();
return this;
}
/**
*
**
*The penetrance of the phenotype for this genotype. Value in the range [0, 1]
*
*
* .protobuf.opencb.Penetrance penetrance = 15;
* @return The penetrance.
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Penetrance getPenetrance() {
@SuppressWarnings("deprecation")
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Penetrance result = org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Penetrance.valueOf(penetrance_);
return result == null ? org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Penetrance.UNRECOGNIZED : result;
}
/**
*
**
*The penetrance of the phenotype for this genotype. Value in the range [0, 1]
*
*
* .protobuf.opencb.Penetrance penetrance = 15;
* @param value The penetrance to set.
* @return This builder for chaining.
*/
public Builder setPenetrance(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Penetrance value) {
if (value == null) {
throw new NullPointerException();
}
penetrance_ = value.getNumber();
onChanged();
return this;
}
/**
*
**
*The penetrance of the phenotype for this genotype. Value in the range [0, 1]
*
*
* .protobuf.opencb.Penetrance penetrance = 15;
* @return This builder for chaining.
*/
public Builder clearPenetrance() {
penetrance_ = 0;
onChanged();
return this;
}
private boolean variableExpressivity_ ;
/**
*
**
*Variable expressivity of a given phenotype for the same genotype
*
*
* bool variableExpressivity = 16;
* @return The variableExpressivity.
*/
public boolean getVariableExpressivity() {
return variableExpressivity_;
}
/**
*
**
*Variable expressivity of a given phenotype for the same genotype
*
*
* bool variableExpressivity = 16;
* @param value The variableExpressivity to set.
* @return This builder for chaining.
*/
public Builder setVariableExpressivity(boolean value) {
variableExpressivity_ = value;
onChanged();
return this;
}
/**
*
**
*Variable expressivity of a given phenotype for the same genotype
*
*
* bool variableExpressivity = 16;
* @return This builder for chaining.
*/
public Builder clearVariableExpressivity() {
variableExpressivity_ = false;
onChanged();
return this;
}
private java.lang.Object description_ = "";
/**
*
**
*Evidence description
*
*
* string description = 17;
* @return The description.
*/
public java.lang.String getDescription() {
java.lang.Object ref = description_;
if (!(ref instanceof java.lang.String)) {
com.google.protobuf.ByteString bs =
(com.google.protobuf.ByteString) ref;
java.lang.String s = bs.toStringUtf8();
description_ = s;
return s;
} else {
return (java.lang.String) ref;
}
}
/**
*
**
*Evidence description
*
*
* string description = 17;
* @return The bytes for description.
*/
public com.google.protobuf.ByteString
getDescriptionBytes() {
java.lang.Object ref = description_;
if (ref instanceof String) {
com.google.protobuf.ByteString b =
com.google.protobuf.ByteString.copyFromUtf8(
(java.lang.String) ref);
description_ = b;
return b;
} else {
return (com.google.protobuf.ByteString) ref;
}
}
/**
*
**
*Evidence description
*
*
* string description = 17;
* @param value The description to set.
* @return This builder for chaining.
*/
public Builder setDescription(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
description_ = value;
onChanged();
return this;
}
/**
*
**
*Evidence description
*
*
* string description = 17;
* @return This builder for chaining.
*/
public Builder clearDescription() {
description_ = getDefaultInstance().getDescription();
onChanged();
return this;
}
/**
*
**
*Evidence description
*
*
* string description = 17;
* @param value The bytes for description to set.
* @return This builder for chaining.
*/
public Builder setDescriptionBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
description_ = value;
onChanged();
return this;
}
private java.util.List additionalProperties_ =
java.util.Collections.emptyList();
private void ensureAdditionalPropertiesIsMutable() {
if (!((bitField0_ & 0x00000010) != 0)) {
additionalProperties_ = new java.util.ArrayList(additionalProperties_);
bitField0_ |= 0x00000010;
}
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.PropertyOrBuilder> additionalPropertiesBuilder_;
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public java.util.List getAdditionalPropertiesList() {
if (additionalPropertiesBuilder_ == null) {
return java.util.Collections.unmodifiableList(additionalProperties_);
} else {
return additionalPropertiesBuilder_.getMessageList();
}
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public int getAdditionalPropertiesCount() {
if (additionalPropertiesBuilder_ == null) {
return additionalProperties_.size();
} else {
return additionalPropertiesBuilder_.getCount();
}
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property getAdditionalProperties(int index) {
if (additionalPropertiesBuilder_ == null) {
return additionalProperties_.get(index);
} else {
return additionalPropertiesBuilder_.getMessage(index);
}
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public Builder setAdditionalProperties(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property value) {
if (additionalPropertiesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureAdditionalPropertiesIsMutable();
additionalProperties_.set(index, value);
onChanged();
} else {
additionalPropertiesBuilder_.setMessage(index, value);
}
return this;
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public Builder setAdditionalProperties(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property.Builder builderForValue) {
if (additionalPropertiesBuilder_ == null) {
ensureAdditionalPropertiesIsMutable();
additionalProperties_.set(index, builderForValue.build());
onChanged();
} else {
additionalPropertiesBuilder_.setMessage(index, builderForValue.build());
}
return this;
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public Builder addAdditionalProperties(org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property value) {
if (additionalPropertiesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureAdditionalPropertiesIsMutable();
additionalProperties_.add(value);
onChanged();
} else {
additionalPropertiesBuilder_.addMessage(value);
}
return this;
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public Builder addAdditionalProperties(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property value) {
if (additionalPropertiesBuilder_ == null) {
if (value == null) {
throw new NullPointerException();
}
ensureAdditionalPropertiesIsMutable();
additionalProperties_.add(index, value);
onChanged();
} else {
additionalPropertiesBuilder_.addMessage(index, value);
}
return this;
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public Builder addAdditionalProperties(
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property.Builder builderForValue) {
if (additionalPropertiesBuilder_ == null) {
ensureAdditionalPropertiesIsMutable();
additionalProperties_.add(builderForValue.build());
onChanged();
} else {
additionalPropertiesBuilder_.addMessage(builderForValue.build());
}
return this;
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public Builder addAdditionalProperties(
int index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property.Builder builderForValue) {
if (additionalPropertiesBuilder_ == null) {
ensureAdditionalPropertiesIsMutable();
additionalProperties_.add(index, builderForValue.build());
onChanged();
} else {
additionalPropertiesBuilder_.addMessage(index, builderForValue.build());
}
return this;
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public Builder addAllAdditionalProperties(
java.lang.Iterable values) {
if (additionalPropertiesBuilder_ == null) {
ensureAdditionalPropertiesIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, additionalProperties_);
onChanged();
} else {
additionalPropertiesBuilder_.addAllMessages(values);
}
return this;
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public Builder clearAdditionalProperties() {
if (additionalPropertiesBuilder_ == null) {
additionalProperties_ = java.util.Collections.emptyList();
bitField0_ = (bitField0_ & ~0x00000010);
onChanged();
} else {
additionalPropertiesBuilder_.clear();
}
return this;
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public Builder removeAdditionalProperties(int index) {
if (additionalPropertiesBuilder_ == null) {
ensureAdditionalPropertiesIsMutable();
additionalProperties_.remove(index);
onChanged();
} else {
additionalPropertiesBuilder_.remove(index);
}
return this;
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property.Builder getAdditionalPropertiesBuilder(
int index) {
return getAdditionalPropertiesFieldBuilder().getBuilder(index);
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.PropertyOrBuilder getAdditionalPropertiesOrBuilder(
int index) {
if (additionalPropertiesBuilder_ == null) {
return additionalProperties_.get(index); } else {
return additionalPropertiesBuilder_.getMessageOrBuilder(index);
}
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public java.util.List
getAdditionalPropertiesOrBuilderList() {
if (additionalPropertiesBuilder_ != null) {
return additionalPropertiesBuilder_.getMessageOrBuilderList();
} else {
return java.util.Collections.unmodifiableList(additionalProperties_);
}
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property.Builder addAdditionalPropertiesBuilder() {
return getAdditionalPropertiesFieldBuilder().addBuilder(
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property.getDefaultInstance());
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property.Builder addAdditionalPropertiesBuilder(
int index) {
return getAdditionalPropertiesFieldBuilder().addBuilder(
index, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property.getDefaultInstance());
}
/**
*
**
*A list of additional properties in the form name-value.
*
*
* repeated .protobuf.opencb.Property additionalProperties = 18;
*/
public java.util.List
getAdditionalPropertiesBuilderList() {
return getAdditionalPropertiesFieldBuilder().getBuilderList();
}
private com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.PropertyOrBuilder>
getAdditionalPropertiesFieldBuilder() {
if (additionalPropertiesBuilder_ == null) {
additionalPropertiesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<
org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.Property.Builder, org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.PropertyOrBuilder>(
additionalProperties_,
((bitField0_ & 0x00000010) != 0),
getParentForChildren(),
isClean());
additionalProperties_ = null;
}
return additionalPropertiesBuilder_;
}
private com.google.protobuf.LazyStringList bibliography_ = com.google.protobuf.LazyStringArrayList.EMPTY;
private void ensureBibliographyIsMutable() {
if (!((bitField0_ & 0x00000020) != 0)) {
bibliography_ = new com.google.protobuf.LazyStringArrayList(bibliography_);
bitField0_ |= 0x00000020;
}
}
/**
*
**
*Bibliography
*
*
* repeated string bibliography = 19;
* @return A list containing the bibliography.
*/
public com.google.protobuf.ProtocolStringList
getBibliographyList() {
return bibliography_.getUnmodifiableView();
}
/**
*
**
*Bibliography
*
*
* repeated string bibliography = 19;
* @return The count of bibliography.
*/
public int getBibliographyCount() {
return bibliography_.size();
}
/**
*
**
*Bibliography
*
*
* repeated string bibliography = 19;
* @param index The index of the element to return.
* @return The bibliography at the given index.
*/
public java.lang.String getBibliography(int index) {
return bibliography_.get(index);
}
/**
*
**
*Bibliography
*
*
* repeated string bibliography = 19;
* @param index The index of the value to return.
* @return The bytes of the bibliography at the given index.
*/
public com.google.protobuf.ByteString
getBibliographyBytes(int index) {
return bibliography_.getByteString(index);
}
/**
*
**
*Bibliography
*
*
* repeated string bibliography = 19;
* @param index The index to set the value at.
* @param value The bibliography to set.
* @return This builder for chaining.
*/
public Builder setBibliography(
int index, java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
ensureBibliographyIsMutable();
bibliography_.set(index, value);
onChanged();
return this;
}
/**
*
**
*Bibliography
*
*
* repeated string bibliography = 19;
* @param value The bibliography to add.
* @return This builder for chaining.
*/
public Builder addBibliography(
java.lang.String value) {
if (value == null) {
throw new NullPointerException();
}
ensureBibliographyIsMutable();
bibliography_.add(value);
onChanged();
return this;
}
/**
*
**
*Bibliography
*
*
* repeated string bibliography = 19;
* @param values The bibliography to add.
* @return This builder for chaining.
*/
public Builder addAllBibliography(
java.lang.Iterable values) {
ensureBibliographyIsMutable();
com.google.protobuf.AbstractMessageLite.Builder.addAll(
values, bibliography_);
onChanged();
return this;
}
/**
*
**
*Bibliography
*
*
* repeated string bibliography = 19;
* @return This builder for chaining.
*/
public Builder clearBibliography() {
bibliography_ = com.google.protobuf.LazyStringArrayList.EMPTY;
bitField0_ = (bitField0_ & ~0x00000020);
onChanged();
return this;
}
/**
*
**
*Bibliography
*
*
* repeated string bibliography = 19;
* @param value The bytes of the bibliography to add.
* @return This builder for chaining.
*/
public Builder addBibliographyBytes(
com.google.protobuf.ByteString value) {
if (value == null) {
throw new NullPointerException();
}
checkByteStringIsUtf8(value);
ensureBibliographyIsMutable();
bibliography_.add(value);
onChanged();
return this;
}
@java.lang.Override
public final Builder setUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
return super.setUnknownFields(unknownFields);
}
@java.lang.Override
public final Builder mergeUnknownFields(
final com.google.protobuf.UnknownFieldSet unknownFields) {
return super.mergeUnknownFields(unknownFields);
}
// @@protoc_insertion_point(builder_scope:protobuf.opencb.EvidenceEntry)
}
// @@protoc_insertion_point(class_scope:protobuf.opencb.EvidenceEntry)
private static final org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry DEFAULT_INSTANCE;
static {
DEFAULT_INSTANCE = new org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry();
}
public static org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry getDefaultInstance() {
return DEFAULT_INSTANCE;
}
private static final com.google.protobuf.Parser
PARSER = new com.google.protobuf.AbstractParser() {
@java.lang.Override
public EvidenceEntry parsePartialFrom(
com.google.protobuf.CodedInputStream input,
com.google.protobuf.ExtensionRegistryLite extensionRegistry)
throws com.google.protobuf.InvalidProtocolBufferException {
return new EvidenceEntry(input, extensionRegistry);
}
};
public static com.google.protobuf.Parser parser() {
return PARSER;
}
@java.lang.Override
public com.google.protobuf.Parser getParserForType() {
return PARSER;
}
@java.lang.Override
public org.opencb.biodata.models.variant.protobuf.EvidenceEntryProto.EvidenceEntry getDefaultInstanceForType() {
return DEFAULT_INSTANCE;
}
}
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internal_static_protobuf_opencb_EvidenceSource_descriptor;
private static final
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internal_static_protobuf_opencb_EvidenceSource_fieldAccessorTable;
private static final com.google.protobuf.Descriptors.Descriptor
internal_static_protobuf_opencb_EvidenceSubmission_descriptor;
private static final
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private static final com.google.protobuf.Descriptors.Descriptor
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private static com.google.protobuf.Descriptors.FileDescriptor
descriptor;
static {
java.lang.String[] descriptorData = {
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"uf.opencb\"=\n\016EvidenceSource\022\014\n\004name\030\001 \001(" +
"\t\022\017\n\007version\030\002 \001(\t\022\014\n\004date\030\003 \001(\t\"A\n\022Evid" +
"enceSubmission\022\021\n\tsubmitter\030\001 \001(\t\022\014\n\004dat" +
"e\030\002 \001(\t\022\n\n\002id\030\003 \001(\t\"\236\001\n\022SomaticInformati" +
"on\022\023\n\013primarySite\030\001 \001(\t\022\023\n\013siteSubtype\030\002" +
" \001(\t\022\030\n\020primaryHistology\030\003 \001(\t\022\030\n\020histol" +
"ogySubtype\030\004 \001(\t\022\024\n\014tumourOrigin\030\005 \001(\t\022\024" +
"\n\014sampleSource\030\006 \001(\t\"\\\n\016HeritableTrait\022\r" +
"\n\005trait\030\001 \001(\t\022;\n\017inheritanceMode\030\002 \001(\0162\"" +
".protobuf.opencb.ModeOfInheritance\"\300\001\n\016G" +
"enomicFeature\0222\n\013featureType\030\001 \001(\0162\035.pro" +
"tobuf.opencb.FeatureTypes\022\021\n\tensemblId\030\002" +
" \001(\t\0229\n\005xrefs\030\003 \003(\0132*.protobuf.opencb.Ge" +
"nomicFeature.XrefsEntry\032,\n\nXrefsEntry\022\013\n" +
"\003key\030\001 \001(\t\022\r\n\005value\030\002 \001(\t:\0028\001\"3\n\010Propert" +
"y\022\n\n\002id\030\001 \001(\t\022\014\n\004name\030\002 \001(\t\022\r\n\005value\030\003 \001" +
"(\t\"\201\003\n\025VariantClassification\022C\n\024clinical" +
"Significance\030\001 \001(\0162%.protobuf.opencb.Cli" +
"nicalSignificance\022O\n\032drugResponseClassif" +
"ication\030\002 \001(\0162+.protobuf.opencb.DrugResp" +
"onseClassification\022;\n\020traitAssociation\030\003" +
" \001(\0162!.protobuf.opencb.TraitAssociation\022" +
"Q\n\033tumorigenesisClassification\030\004 \001(\0162,.p" +
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"opencb.VariantFunctionalEffect\"\336\006\n\rEvide" +
"nceEntry\022/\n\006source\030\001 \001(\0132\037.protobuf.open" +
"cb.EvidenceSource\0228\n\013submissions\030\002 \003(\0132#" +
".protobuf.opencb.EvidenceSubmission\022?\n\022s" +
"omaticInformation\030\003 \001(\0132#.protobuf.openc" +
"b.SomaticInformation\022\013\n\003url\030\004 \001(\t\022\n\n\002id\030" +
"\005 \001(\t\022\020\n\010assembly\030\006 \001(\t\0223\n\014alleleOrigin\030" +
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"b.VariantClassification\022/\n\006impact\030\013 \001(\0162" +
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"idence\030\014 \001(\0162\033.protobuf.opencb.Confidenc" +
"e\022=\n\021consistencyStatus\030\r \001(\0162\".protobuf." +
"opencb.ConsistencyStatus\0222\n\tethnicity\030\016 " +
"\001(\0162\037.protobuf.opencb.EthnicCategory\022/\n\n" +
"penetrance\030\017 \001(\0162\033.protobuf.opencb.Penet" +
"rance\022\034\n\024variableExpressivity\030\020 \001(\010\022\023\n\013d" +
"escription\030\021 \001(\t\0227\n\024additionalProperties" +
"\030\022 \003(\0132\031.protobuf.opencb.Property\022\024\n\014bib" +
"liography\030\023 \003(\t*\300\002\n\021ModeOfInheritance\022\017\n" +
"\013monoallelic\020\000\022\035\n\031monoallelic_not_imprin" +
"ted\020\001\022$\n monoallelic_maternally_imprinte" +
"d\020\002\022$\n monoallelic_paternally_imprinted\020" +
"\003\022\r\n\tbiallelic\020\004\022\035\n\031monoallelic_and_bial" +
"lelic\020\005\022)\n%monoallelic_and_more_severe_b" +
"iallelic\020\006\022\025\n\021xlinked_biallelic\020\007\022\027\n\023xli" +
"nked_monoallelic\020\010\022\021\n\rmitochondrial\020\t\022\013\n" +
"\007unknown\020\n\022\006\n\002NA\020\013*L\n\014FeatureTypes\022\025\n\021re" +
"gulatory_region\020\000\022\010\n\004gene\020\001\022\016\n\ntranscrip" +
"t\020\002\022\013\n\007protein\020\003*\201\001\n\024ClinicalSignificanc" +
"e\022\n\n\006benign\020\000\022\021\n\rlikely_benign\020\001\022\007\n\003VUS\020" +
"\002\022\025\n\021likely_pathogenic\020\003\022\016\n\npathogenic\020\004" +
"\022\032\n\026uncertain_significance\020\005*\243\001\n\032DrugRes" +
"ponseClassification\022\016\n\nresponsive\020\000\022\r\n\tr" +
"esistant\020\001\022\014\n\010toxicity\020\002\022\016\n\nindication\020\003" +
"\022\024\n\020contraindication\020\004\022\n\n\006dosing\020\005\022\030\n\024in" +
"creased_monitoring\020\006\022\014\n\010efficacy\020\007*r\n\020Tr" +
"aitAssociation\022\033\n\027established_risk_allel" +
"e\020\000\022\026\n\022likely_risk_allele\020\001\022\031\n\025uncertain" +
"_risk_allele\020\002\022\016\n\nprotective\020\003*F\n\033Tumori" +
"genesisClassification\022\n\n\006driver\020\000\022\r\n\tpas" +
"senger\020\001\022\014\n\010modifier\020\002*\\\n\016EvidenceImpact" +
"\022\017\n\013very_strong\020\000\022\n\n\006strong\020\001\022\014\n\010moderat" +
"e\020\002\022\016\n\nsupporting\020\003\022\017\n\013stand_alone\020\004*\207\001\n" +
"\016EthnicCategory\022\005\n\001D\020\000\022\005\n\001E\020\001\022\005\n\001F\020\002\022\005\n\001" +
"G\020\003\022\005\n\001A\020\004\022\005\n\001B\020\005\022\005\n\001C\020\006\022\005\n\001L\020\007\022\005\n\001M\020\010\022\005" +
"\n\001N\020\t\022\005\n\001H\020\n\022\005\n\001J\020\013\022\005\n\001K\020\014\022\005\n\001P\020\r\022\005\n\001S\020\016" +
"\022\005\n\001R\020\017\022\005\n\001Z\020\020**\n\nPenetrance\022\014\n\010complete" +
"\020\000\022\016\n\nincomplete\020\001*\266\001\n\027VariantFunctional" +
"Effect\022\035\n\031dominant_negative_variant\020\000\022\034\n" +
"\030gain_of_function_variant\020\001\022\022\n\016lethal_va" +
"riant\020\002\022\034\n\030loss_of_function_variant\020\003\022\032\n" +
"\026loss_of_heterozygosity\020\004\022\020\n\014null_varian" +
"t\020\005*\272\001\n\014AlleleOrigin\022\023\n\017de_novo_variant\020" +
"\000\022\024\n\020germline_variant\020\001\022\024\n\020maternal_vari" +
"ant\020\002\022\024\n\020paternal_variant\020\003\022\035\n\031pedigree_" +
"specific_variant\020\004\022\037\n\033population_specifi" +
"c_variant\020\005\022\023\n\017somatic_variant\020\006*l\n\nConf" +
"idence\022\030\n\024low_confidence_level\020\000\022\033\n\027medi" +
"um_confidence_level\020\001\022\031\n\025high_confidence" +
"_level\020\002\022\014\n\010rejected\020\003*b\n\021ConsistencySta" +
"tus\022\r\n\tcongruent\020\000\022\014\n\010conflict\020\001\022\026\n\022weak" +
"ly_conflicting\020\002\022\030\n\024strongly_conflicting" +
"\020\003BC\n*org.opencb.biodata.models.variant." +
"protobufB\022EvidenceEntryProto\240\001\001b\006proto3"
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}
// @@protoc_insertion_point(outer_class_scope)
}