org.gel.models.report.avro.VariantLevelQuestions Maven / Gradle / Ivy
/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.gel.models.report.avro;
@SuppressWarnings("all")
/** The variant level questions */
@org.apache.avro.specific.AvroGenerated
public class VariantLevelQuestions 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\":\"VariantLevelQuestions\",\"namespace\":\"org.gel.models.report.avro\",\"doc\":\"The variant level questions\",\"fields\":[{\"name\":\"variantCoordinates\",\"type\":{\"type\":\"record\",\"name\":\"VariantCoordinates\",\"doc\":\"The variant coordinates representing uniquely a small variant.\\n No multi-allelic variant supported, alternate only represents one alternate allele.\",\"fields\":[{\"name\":\"chromosome\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Chromosome without \\\"chr\\\" prefix (e.g. X rather than chrX)\"},{\"name\":\"position\",\"type\":\"int\",\"doc\":\"Genomic position\"},{\"name\":\"reference\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The reference bases.\"},{\"name\":\"alternate\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The alternate bases\"},{\"name\":\"assembly\",\"type\":{\"type\":\"enum\",\"name\":\"Assembly\",\"doc\":\"The reference genome assembly\",\"symbols\":[\"GRCh38\",\"GRCh37\"]},\"doc\":\"The assembly to which this variant corresponds\"}]},\"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$; }
/** Variant coordinates */
private org.gel.models.report.avro.VariantCoordinates variantCoordinates;
/** Did you carry out technical confirmation of this variant via an alternative test? */
private org.gel.models.report.avro.ConfirmationDecision confirmationDecision;
/** Did the test confirm that the variant is present? */
private org.gel.models.report.avro.ConfirmationOutcome confirmationOutcome;
/** Did you include the variant in your report to the clinician? */
private org.gel.models.report.avro.ReportingQuestion reportingQuestion;
/** What ACMG pathogenicity score (1-5) did you assign to this variant? */
private org.gel.models.report.avro.ACMGClassification acmgClassification;
/** Please provide PMIDs for papers which you have used to inform your assessment for this variant, separated by a `;` for multiple papers */
private java.lang.String publications;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public VariantLevelQuestions() {}
/**
* All-args constructor.
*/
public VariantLevelQuestions(org.gel.models.report.avro.VariantCoordinates variantCoordinates, org.gel.models.report.avro.ConfirmationDecision confirmationDecision, org.gel.models.report.avro.ConfirmationOutcome confirmationOutcome, org.gel.models.report.avro.ReportingQuestion reportingQuestion, org.gel.models.report.avro.ACMGClassification acmgClassification, java.lang.String publications) {
this.variantCoordinates = variantCoordinates;
this.confirmationDecision = confirmationDecision;
this.confirmationOutcome = confirmationOutcome;
this.reportingQuestion = reportingQuestion;
this.acmgClassification = acmgClassification;
this.publications = publications;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return variantCoordinates;
case 1: return confirmationDecision;
case 2: return confirmationOutcome;
case 3: return reportingQuestion;
case 4: return acmgClassification;
case 5: 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$) {
case 0: variantCoordinates = (org.gel.models.report.avro.VariantCoordinates)value$; break;
case 1: confirmationDecision = (org.gel.models.report.avro.ConfirmationDecision)value$; break;
case 2: confirmationOutcome = (org.gel.models.report.avro.ConfirmationOutcome)value$; break;
case 3: reportingQuestion = (org.gel.models.report.avro.ReportingQuestion)value$; break;
case 4: acmgClassification = (org.gel.models.report.avro.ACMGClassification)value$; break;
case 5: publications = (java.lang.String)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'variantCoordinates' field.
* Variant coordinates */
public org.gel.models.report.avro.VariantCoordinates getVariantCoordinates() {
return variantCoordinates;
}
/**
* Sets the value of the 'variantCoordinates' field.
* Variant coordinates * @param value the value to set.
*/
public void setVariantCoordinates(org.gel.models.report.avro.VariantCoordinates value) {
this.variantCoordinates = 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 VariantLevelQuestions RecordBuilder */
public static org.gel.models.report.avro.VariantLevelQuestions.Builder newBuilder() {
return new org.gel.models.report.avro.VariantLevelQuestions.Builder();
}
/** Creates a new VariantLevelQuestions RecordBuilder by copying an existing Builder */
public static org.gel.models.report.avro.VariantLevelQuestions.Builder newBuilder(org.gel.models.report.avro.VariantLevelQuestions.Builder other) {
return new org.gel.models.report.avro.VariantLevelQuestions.Builder(other);
}
/** Creates a new VariantLevelQuestions RecordBuilder by copying an existing VariantLevelQuestions instance */
public static org.gel.models.report.avro.VariantLevelQuestions.Builder newBuilder(org.gel.models.report.avro.VariantLevelQuestions other) {
return new org.gel.models.report.avro.VariantLevelQuestions.Builder(other);
}
/**
* RecordBuilder for VariantLevelQuestions instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private org.gel.models.report.avro.VariantCoordinates variantCoordinates;
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.VariantLevelQuestions.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.gel.models.report.avro.VariantLevelQuestions.Builder other) {
super(other);
if (isValidValue(fields()[0], other.variantCoordinates)) {
this.variantCoordinates = data().deepCopy(fields()[0].schema(), other.variantCoordinates);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.confirmationDecision)) {
this.confirmationDecision = data().deepCopy(fields()[1].schema(), other.confirmationDecision);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.confirmationOutcome)) {
this.confirmationOutcome = data().deepCopy(fields()[2].schema(), other.confirmationOutcome);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.reportingQuestion)) {
this.reportingQuestion = data().deepCopy(fields()[3].schema(), other.reportingQuestion);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.acmgClassification)) {
this.acmgClassification = data().deepCopy(fields()[4].schema(), other.acmgClassification);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.publications)) {
this.publications = data().deepCopy(fields()[5].schema(), other.publications);
fieldSetFlags()[5] = true;
}
}
/** Creates a Builder by copying an existing VariantLevelQuestions instance */
private Builder(org.gel.models.report.avro.VariantLevelQuestions other) {
super(org.gel.models.report.avro.VariantLevelQuestions.SCHEMA$);
if (isValidValue(fields()[0], other.variantCoordinates)) {
this.variantCoordinates = data().deepCopy(fields()[0].schema(), other.variantCoordinates);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.confirmationDecision)) {
this.confirmationDecision = data().deepCopy(fields()[1].schema(), other.confirmationDecision);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.confirmationOutcome)) {
this.confirmationOutcome = data().deepCopy(fields()[2].schema(), other.confirmationOutcome);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.reportingQuestion)) {
this.reportingQuestion = data().deepCopy(fields()[3].schema(), other.reportingQuestion);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.acmgClassification)) {
this.acmgClassification = data().deepCopy(fields()[4].schema(), other.acmgClassification);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.publications)) {
this.publications = data().deepCopy(fields()[5].schema(), other.publications);
fieldSetFlags()[5] = true;
}
}
/** Gets the value of the 'variantCoordinates' field */
public org.gel.models.report.avro.VariantCoordinates getVariantCoordinates() {
return variantCoordinates;
}
/** Sets the value of the 'variantCoordinates' field */
public org.gel.models.report.avro.VariantLevelQuestions.Builder setVariantCoordinates(org.gel.models.report.avro.VariantCoordinates value) {
validate(fields()[0], value);
this.variantCoordinates = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'variantCoordinates' field has been set */
public boolean hasVariantCoordinates() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'variantCoordinates' field */
public org.gel.models.report.avro.VariantLevelQuestions.Builder clearVariantCoordinates() {
variantCoordinates = null;
fieldSetFlags()[0] = 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.VariantLevelQuestions.Builder setConfirmationDecision(org.gel.models.report.avro.ConfirmationDecision value) {
validate(fields()[1], value);
this.confirmationDecision = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'confirmationDecision' field has been set */
public boolean hasConfirmationDecision() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'confirmationDecision' field */
public org.gel.models.report.avro.VariantLevelQuestions.Builder clearConfirmationDecision() {
confirmationDecision = null;
fieldSetFlags()[1] = 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.VariantLevelQuestions.Builder setConfirmationOutcome(org.gel.models.report.avro.ConfirmationOutcome value) {
validate(fields()[2], value);
this.confirmationOutcome = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'confirmationOutcome' field has been set */
public boolean hasConfirmationOutcome() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'confirmationOutcome' field */
public org.gel.models.report.avro.VariantLevelQuestions.Builder clearConfirmationOutcome() {
confirmationOutcome = null;
fieldSetFlags()[2] = 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.VariantLevelQuestions.Builder setReportingQuestion(org.gel.models.report.avro.ReportingQuestion value) {
validate(fields()[3], value);
this.reportingQuestion = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'reportingQuestion' field has been set */
public boolean hasReportingQuestion() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'reportingQuestion' field */
public org.gel.models.report.avro.VariantLevelQuestions.Builder clearReportingQuestion() {
reportingQuestion = null;
fieldSetFlags()[3] = 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.VariantLevelQuestions.Builder setAcmgClassification(org.gel.models.report.avro.ACMGClassification value) {
validate(fields()[4], value);
this.acmgClassification = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'acmgClassification' field has been set */
public boolean hasAcmgClassification() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'acmgClassification' field */
public org.gel.models.report.avro.VariantLevelQuestions.Builder clearAcmgClassification() {
acmgClassification = null;
fieldSetFlags()[4] = 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.VariantLevelQuestions.Builder setPublications(java.lang.String value) {
validate(fields()[5], value);
this.publications = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'publications' field has been set */
public boolean hasPublications() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'publications' field */
public org.gel.models.report.avro.VariantLevelQuestions.Builder clearPublications() {
publications = null;
fieldSetFlags()[5] = false;
return this;
}
@Override
public VariantLevelQuestions build() {
try {
VariantLevelQuestions record = new VariantLevelQuestions();
record.variantCoordinates = fieldSetFlags()[0] ? this.variantCoordinates : (org.gel.models.report.avro.VariantCoordinates) defaultValue(fields()[0]);
record.confirmationDecision = fieldSetFlags()[1] ? this.confirmationDecision : (org.gel.models.report.avro.ConfirmationDecision) defaultValue(fields()[1]);
record.confirmationOutcome = fieldSetFlags()[2] ? this.confirmationOutcome : (org.gel.models.report.avro.ConfirmationOutcome) defaultValue(fields()[2]);
record.reportingQuestion = fieldSetFlags()[3] ? this.reportingQuestion : (org.gel.models.report.avro.ReportingQuestion) defaultValue(fields()[3]);
record.acmgClassification = fieldSetFlags()[4] ? this.acmgClassification : (org.gel.models.report.avro.ACMGClassification) defaultValue(fields()[4]);
record.publications = fieldSetFlags()[5] ? this.publications : (java.lang.String) defaultValue(fields()[5]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
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