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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.gel.models.report.avro;
@SuppressWarnings("all")
/** Structural variant level questions */
@org.apache.avro.specific.AvroGenerated
public class StructuralVariantLevelQuestions extends org.apache.avro.specific.SpecificRecordBase implements org.apache.avro.specific.SpecificRecord {
public static final org.apache.avro.Schema SCHEMA$ = new org.apache.avro.Schema.Parser().parse("{\"type\":\"record\",\"name\":\"StructuralVariantLevelQuestions\",\"namespace\":\"org.gel.models.report.avro\",\"doc\":\"Structural variant level questions\",\"fields\":[{\"name\":\"variantType\",\"type\":{\"type\":\"enum\",\"name\":\"StructuralVariantType\",\"symbols\":[\"ins\",\"dup\",\"inv\",\"amplification\",\"deletion\",\"dup_tandem\",\"del_me\",\"ins_me\"]},\"doc\":\"Structural variant type\"},{\"name\":\"coordinates\",\"type\":{\"type\":\"record\",\"name\":\"Coordinates\",\"fields\":[{\"name\":\"assembly\",\"type\":{\"type\":\"enum\",\"name\":\"Assembly\",\"doc\":\"The reference genome assembly\",\"symbols\":[\"GRCh38\",\"GRCh37\"]},\"doc\":\"The assembly to which this variant corresponds\"},{\"name\":\"chromosome\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Chromosome without \\\"chr\\\" prefix (e.g. X rather than chrX)\"},{\"name\":\"start\",\"type\":\"int\",\"doc\":\"Start genomic position for variant (1-based)\"},{\"name\":\"end\",\"type\":\"int\",\"doc\":\"End genomic position for variant\"},{\"name\":\"ciStart\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"ConfidenceInterval\",\"fields\":[{\"name\":\"left\",\"type\":\"int\"},{\"name\":\"right\",\"type\":\"int\"}]}]},{\"name\":\"ciEnd\",\"type\":[\"null\",\"ConfidenceInterval\"]}]},\"doc\":\"Variant coordinates\"},{\"name\":\"confirmationDecision\",\"type\":{\"type\":\"enum\",\"name\":\"ConfirmationDecision\",\"symbols\":[\"yes\",\"no\",\"na\"]},\"doc\":\"Did you carry out technical confirmation of this variant via an alternative test?\"},{\"name\":\"confirmationOutcome\",\"type\":{\"type\":\"enum\",\"name\":\"ConfirmationOutcome\",\"symbols\":[\"yes\",\"no\",\"na\"]},\"doc\":\"Did the test confirm that the variant is present?\"},{\"name\":\"reportingQuestion\",\"type\":{\"type\":\"enum\",\"name\":\"ReportingQuestion\",\"symbols\":[\"yes\",\"no\",\"na\"]},\"doc\":\"Did you include the variant in your report to the clinician?\"},{\"name\":\"acmgClassification\",\"type\":{\"type\":\"enum\",\"name\":\"ACMGClassification\",\"symbols\":[\"pathogenic_variant\",\"likely_pathogenic_variant\",\"variant_of_unknown_clinical_significance\",\"likely_benign_variant\",\"benign_variant\",\"not_assessed\",\"na\"]},\"doc\":\"What ACMG pathogenicity score (1-5) did you assign to this variant?\"},{\"name\":\"publications\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Please provide PMIDs for papers which you have used to inform your assessment for this variant, separated by a `;` for multiple papers\"}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** Structural variant type */
private org.gel.models.report.avro.StructuralVariantType variantType;
/** Variant coordinates */
private org.gel.models.report.avro.Coordinates coordinates;
/** Did you carry out technical confirmation of this variant via an alternative test? */
private org.gel.models.report.avro.ConfirmationDecision confirmationDecision;
/** Did the test confirm that the variant is present? */
private org.gel.models.report.avro.ConfirmationOutcome confirmationOutcome;
/** Did you include the variant in your report to the clinician? */
private org.gel.models.report.avro.ReportingQuestion reportingQuestion;
/** What ACMG pathogenicity score (1-5) did you assign to this variant? */
private org.gel.models.report.avro.ACMGClassification acmgClassification;
/** Please provide PMIDs for papers which you have used to inform your assessment for this variant, separated by a `;` for multiple papers */
private java.lang.String publications;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public StructuralVariantLevelQuestions() {}
/**
* All-args constructor.
*/
public StructuralVariantLevelQuestions(org.gel.models.report.avro.StructuralVariantType variantType, org.gel.models.report.avro.Coordinates coordinates, org.gel.models.report.avro.ConfirmationDecision confirmationDecision, org.gel.models.report.avro.ConfirmationOutcome confirmationOutcome, org.gel.models.report.avro.ReportingQuestion reportingQuestion, org.gel.models.report.avro.ACMGClassification acmgClassification, java.lang.String publications) {
this.variantType = variantType;
this.coordinates = coordinates;
this.confirmationDecision = confirmationDecision;
this.confirmationOutcome = confirmationOutcome;
this.reportingQuestion = reportingQuestion;
this.acmgClassification = acmgClassification;
this.publications = publications;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return variantType;
case 1: return coordinates;
case 2: return confirmationDecision;
case 3: return confirmationOutcome;
case 4: return reportingQuestion;
case 5: return acmgClassification;
case 6: return publications;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
// Used by DatumReader. Applications should not call.
@SuppressWarnings(value="unchecked")
public void put(int field$, java.lang.Object value$) {
switch (field$) {
case 0: variantType = (org.gel.models.report.avro.StructuralVariantType)value$; break;
case 1: coordinates = (org.gel.models.report.avro.Coordinates)value$; break;
case 2: confirmationDecision = (org.gel.models.report.avro.ConfirmationDecision)value$; break;
case 3: confirmationOutcome = (org.gel.models.report.avro.ConfirmationOutcome)value$; break;
case 4: reportingQuestion = (org.gel.models.report.avro.ReportingQuestion)value$; break;
case 5: acmgClassification = (org.gel.models.report.avro.ACMGClassification)value$; break;
case 6: publications = (java.lang.String)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'variantType' field.
* Structural variant type */
public org.gel.models.report.avro.StructuralVariantType getVariantType() {
return variantType;
}
/**
* Sets the value of the 'variantType' field.
* Structural variant type * @param value the value to set.
*/
public void setVariantType(org.gel.models.report.avro.StructuralVariantType value) {
this.variantType = value;
}
/**
* Gets the value of the 'coordinates' field.
* Variant coordinates */
public org.gel.models.report.avro.Coordinates getCoordinates() {
return coordinates;
}
/**
* Sets the value of the 'coordinates' field.
* Variant coordinates * @param value the value to set.
*/
public void setCoordinates(org.gel.models.report.avro.Coordinates value) {
this.coordinates = value;
}
/**
* Gets the value of the 'confirmationDecision' field.
* Did you carry out technical confirmation of this variant via an alternative test? */
public org.gel.models.report.avro.ConfirmationDecision getConfirmationDecision() {
return confirmationDecision;
}
/**
* Sets the value of the 'confirmationDecision' field.
* Did you carry out technical confirmation of this variant via an alternative test? * @param value the value to set.
*/
public void setConfirmationDecision(org.gel.models.report.avro.ConfirmationDecision value) {
this.confirmationDecision = value;
}
/**
* Gets the value of the 'confirmationOutcome' field.
* Did the test confirm that the variant is present? */
public org.gel.models.report.avro.ConfirmationOutcome getConfirmationOutcome() {
return confirmationOutcome;
}
/**
* Sets the value of the 'confirmationOutcome' field.
* Did the test confirm that the variant is present? * @param value the value to set.
*/
public void setConfirmationOutcome(org.gel.models.report.avro.ConfirmationOutcome value) {
this.confirmationOutcome = value;
}
/**
* Gets the value of the 'reportingQuestion' field.
* Did you include the variant in your report to the clinician? */
public org.gel.models.report.avro.ReportingQuestion getReportingQuestion() {
return reportingQuestion;
}
/**
* Sets the value of the 'reportingQuestion' field.
* Did you include the variant in your report to the clinician? * @param value the value to set.
*/
public void setReportingQuestion(org.gel.models.report.avro.ReportingQuestion value) {
this.reportingQuestion = value;
}
/**
* Gets the value of the 'acmgClassification' field.
* What ACMG pathogenicity score (1-5) did you assign to this variant? */
public org.gel.models.report.avro.ACMGClassification getAcmgClassification() {
return acmgClassification;
}
/**
* Sets the value of the 'acmgClassification' field.
* What ACMG pathogenicity score (1-5) did you assign to this variant? * @param value the value to set.
*/
public void setAcmgClassification(org.gel.models.report.avro.ACMGClassification value) {
this.acmgClassification = value;
}
/**
* Gets the value of the 'publications' field.
* Please provide PMIDs for papers which you have used to inform your assessment for this variant, separated by a `;` for multiple papers */
public java.lang.String getPublications() {
return publications;
}
/**
* Sets the value of the 'publications' field.
* Please provide PMIDs for papers which you have used to inform your assessment for this variant, separated by a `;` for multiple papers * @param value the value to set.
*/
public void setPublications(java.lang.String value) {
this.publications = value;
}
/** Creates a new StructuralVariantLevelQuestions RecordBuilder */
public static org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder newBuilder() {
return new org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder();
}
/** Creates a new StructuralVariantLevelQuestions RecordBuilder by copying an existing Builder */
public static org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder newBuilder(org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder other) {
return new org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder(other);
}
/** Creates a new StructuralVariantLevelQuestions RecordBuilder by copying an existing StructuralVariantLevelQuestions instance */
public static org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder newBuilder(org.gel.models.report.avro.StructuralVariantLevelQuestions other) {
return new org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder(other);
}
/**
* RecordBuilder for StructuralVariantLevelQuestions instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private org.gel.models.report.avro.StructuralVariantType variantType;
private org.gel.models.report.avro.Coordinates coordinates;
private org.gel.models.report.avro.ConfirmationDecision confirmationDecision;
private org.gel.models.report.avro.ConfirmationOutcome confirmationOutcome;
private org.gel.models.report.avro.ReportingQuestion reportingQuestion;
private org.gel.models.report.avro.ACMGClassification acmgClassification;
private java.lang.String publications;
/** Creates a new Builder */
private Builder() {
super(org.gel.models.report.avro.StructuralVariantLevelQuestions.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder other) {
super(other);
if (isValidValue(fields()[0], other.variantType)) {
this.variantType = data().deepCopy(fields()[0].schema(), other.variantType);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.coordinates)) {
this.coordinates = data().deepCopy(fields()[1].schema(), other.coordinates);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.confirmationDecision)) {
this.confirmationDecision = data().deepCopy(fields()[2].schema(), other.confirmationDecision);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.confirmationOutcome)) {
this.confirmationOutcome = data().deepCopy(fields()[3].schema(), other.confirmationOutcome);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.reportingQuestion)) {
this.reportingQuestion = data().deepCopy(fields()[4].schema(), other.reportingQuestion);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.acmgClassification)) {
this.acmgClassification = data().deepCopy(fields()[5].schema(), other.acmgClassification);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.publications)) {
this.publications = data().deepCopy(fields()[6].schema(), other.publications);
fieldSetFlags()[6] = true;
}
}
/** Creates a Builder by copying an existing StructuralVariantLevelQuestions instance */
private Builder(org.gel.models.report.avro.StructuralVariantLevelQuestions other) {
super(org.gel.models.report.avro.StructuralVariantLevelQuestions.SCHEMA$);
if (isValidValue(fields()[0], other.variantType)) {
this.variantType = data().deepCopy(fields()[0].schema(), other.variantType);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.coordinates)) {
this.coordinates = data().deepCopy(fields()[1].schema(), other.coordinates);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.confirmationDecision)) {
this.confirmationDecision = data().deepCopy(fields()[2].schema(), other.confirmationDecision);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.confirmationOutcome)) {
this.confirmationOutcome = data().deepCopy(fields()[3].schema(), other.confirmationOutcome);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.reportingQuestion)) {
this.reportingQuestion = data().deepCopy(fields()[4].schema(), other.reportingQuestion);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.acmgClassification)) {
this.acmgClassification = data().deepCopy(fields()[5].schema(), other.acmgClassification);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.publications)) {
this.publications = data().deepCopy(fields()[6].schema(), other.publications);
fieldSetFlags()[6] = true;
}
}
/** Gets the value of the 'variantType' field */
public org.gel.models.report.avro.StructuralVariantType getVariantType() {
return variantType;
}
/** Sets the value of the 'variantType' field */
public org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder setVariantType(org.gel.models.report.avro.StructuralVariantType value) {
validate(fields()[0], value);
this.variantType = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'variantType' field has been set */
public boolean hasVariantType() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'variantType' field */
public org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder clearVariantType() {
variantType = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'coordinates' field */
public org.gel.models.report.avro.Coordinates getCoordinates() {
return coordinates;
}
/** Sets the value of the 'coordinates' field */
public org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder setCoordinates(org.gel.models.report.avro.Coordinates value) {
validate(fields()[1], value);
this.coordinates = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'coordinates' field has been set */
public boolean hasCoordinates() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'coordinates' field */
public org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder clearCoordinates() {
coordinates = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'confirmationDecision' field */
public org.gel.models.report.avro.ConfirmationDecision getConfirmationDecision() {
return confirmationDecision;
}
/** Sets the value of the 'confirmationDecision' field */
public org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder setConfirmationDecision(org.gel.models.report.avro.ConfirmationDecision value) {
validate(fields()[2], value);
this.confirmationDecision = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'confirmationDecision' field has been set */
public boolean hasConfirmationDecision() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'confirmationDecision' field */
public org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder clearConfirmationDecision() {
confirmationDecision = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'confirmationOutcome' field */
public org.gel.models.report.avro.ConfirmationOutcome getConfirmationOutcome() {
return confirmationOutcome;
}
/** Sets the value of the 'confirmationOutcome' field */
public org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder setConfirmationOutcome(org.gel.models.report.avro.ConfirmationOutcome value) {
validate(fields()[3], value);
this.confirmationOutcome = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'confirmationOutcome' field has been set */
public boolean hasConfirmationOutcome() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'confirmationOutcome' field */
public org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder clearConfirmationOutcome() {
confirmationOutcome = null;
fieldSetFlags()[3] = false;
return this;
}
/** Gets the value of the 'reportingQuestion' field */
public org.gel.models.report.avro.ReportingQuestion getReportingQuestion() {
return reportingQuestion;
}
/** Sets the value of the 'reportingQuestion' field */
public org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder setReportingQuestion(org.gel.models.report.avro.ReportingQuestion value) {
validate(fields()[4], value);
this.reportingQuestion = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'reportingQuestion' field has been set */
public boolean hasReportingQuestion() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'reportingQuestion' field */
public org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder clearReportingQuestion() {
reportingQuestion = null;
fieldSetFlags()[4] = false;
return this;
}
/** Gets the value of the 'acmgClassification' field */
public org.gel.models.report.avro.ACMGClassification getAcmgClassification() {
return acmgClassification;
}
/** Sets the value of the 'acmgClassification' field */
public org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder setAcmgClassification(org.gel.models.report.avro.ACMGClassification value) {
validate(fields()[5], value);
this.acmgClassification = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'acmgClassification' field has been set */
public boolean hasAcmgClassification() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'acmgClassification' field */
public org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder clearAcmgClassification() {
acmgClassification = null;
fieldSetFlags()[5] = false;
return this;
}
/** Gets the value of the 'publications' field */
public java.lang.String getPublications() {
return publications;
}
/** Sets the value of the 'publications' field */
public org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder setPublications(java.lang.String value) {
validate(fields()[6], value);
this.publications = value;
fieldSetFlags()[6] = true;
return this;
}
/** Checks whether the 'publications' field has been set */
public boolean hasPublications() {
return fieldSetFlags()[6];
}
/** Clears the value of the 'publications' field */
public org.gel.models.report.avro.StructuralVariantLevelQuestions.Builder clearPublications() {
publications = null;
fieldSetFlags()[6] = false;
return this;
}
@Override
public StructuralVariantLevelQuestions build() {
try {
StructuralVariantLevelQuestions record = new StructuralVariantLevelQuestions();
record.variantType = fieldSetFlags()[0] ? this.variantType : (org.gel.models.report.avro.StructuralVariantType) defaultValue(fields()[0]);
record.coordinates = fieldSetFlags()[1] ? this.coordinates : (org.gel.models.report.avro.Coordinates) defaultValue(fields()[1]);
record.confirmationDecision = fieldSetFlags()[2] ? this.confirmationDecision : (org.gel.models.report.avro.ConfirmationDecision) defaultValue(fields()[2]);
record.confirmationOutcome = fieldSetFlags()[3] ? this.confirmationOutcome : (org.gel.models.report.avro.ConfirmationOutcome) defaultValue(fields()[3]);
record.reportingQuestion = fieldSetFlags()[4] ? this.reportingQuestion : (org.gel.models.report.avro.ReportingQuestion) defaultValue(fields()[4]);
record.acmgClassification = fieldSetFlags()[5] ? this.acmgClassification : (org.gel.models.report.avro.ACMGClassification) defaultValue(fields()[5]);
record.publications = fieldSetFlags()[6] ? this.publications : (java.lang.String) defaultValue(fields()[6]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
