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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.gel.models.report.avro;
@SuppressWarnings("all")
/** The questions for the cancer program exit questionnaire for somatic variants */
@org.apache.avro.specific.AvroGenerated
public class CancerSomaticVariantLevelQuestions 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\":\"CancerSomaticVariantLevelQuestions\",\"namespace\":\"org.gel.models.report.avro\",\"doc\":\"The questions for the cancer program exit questionnaire for somatic variants\",\"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 following format `chromosome:position:reference:alternate`\"},{\"name\":\"variantActionability\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"enum\",\"name\":\"CancerActionabilitySomatic\",\"doc\":\"The variant actionabilities:\\n* `predicts_therapeutic_response`: Predicts therapeutic response\\n* `prognostic`: Prognostic\\n* `defines_diagnosis_group`: Defines diagnosis group\\n* `eligibility_for_trial`: Eligibility for trial\\n* `other`: Other (please specify)\",\"symbols\":[\"predicts_therapeutic_response\",\"prognostic\",\"defines_diagnosis_group\",\"eligibility_for_trial\",\"other\"]}},\"doc\":\"Type of potential actionability:\"},{\"name\":\"otherVariantActionability\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Other information about variant actionability\"},{\"name\":\"variantUsability\",\"type\":{\"type\":\"enum\",\"name\":\"CancerUsabilitySomatic\",\"doc\":\"Variant usability for somatic variants:\\n* `already_actioned`: Already actioned (i.e. prior to receiving this WGA)\\n* `actioned_result_of_this_wga`: actioned as a result of receiving this WGA\\n* `not_yet_actioned`: not yet actioned, but potentially actionable in the future\",\"symbols\":[\"already_actioned\",\"actioned_result_of_this_wga\",\"not_yet_actioned\"]},\"doc\":\"How has/will this potentially actionable variant been/be used?\"},{\"name\":\"variantTested\",\"type\":{\"type\":\"enum\",\"name\":\"CancerTested\",\"doc\":\"Was the variant validated with an orthogonal technology?\\n* `not_indicated_for_patient_care`: No: not indicated for patient care at this time\\n* `no_orthologous_test_available`: No: no orthologous test available\\n* `test_performed_prior_to_wga`: Yes: test performed prior to receiving WGA (eg using standard-of-care assay such as panel testing, or sanger sequencing)\\n* `technical_validation_following_WGA`: Yes: technical validation performed/planned following receiving this WGA\",\"symbols\":[\"not_indicated_for_patient_care\",\"no_orthologous_test_available\",\"test_performed_prior_to_wga\",\"technical_validation_following_wga\"]},\"doc\":\"Has this variant been tested by another method (either prior to or following receipt of this WGA)?\"},{\"name\":\"validationAssayType\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Please enter validation assay type e.g Pyrosequencing, NGS panel, COBAS, Sanger sequencing. If not applicable enter NA;\"}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** Variant coordinates following format `chromosome:position:reference:alternate` */
private org.gel.models.report.avro.VariantCoordinates variantCoordinates;
/** Type of potential actionability: */
private java.util.List variantActionability;
/** Other information about variant actionability */
private java.lang.String otherVariantActionability;
/** How has/will this potentially actionable variant been/be used? */
private org.gel.models.report.avro.CancerUsabilitySomatic variantUsability;
/** Has this variant been tested by another method (either prior to or following receipt of this WGA)? */
private org.gel.models.report.avro.CancerTested variantTested;
/** Please enter validation assay type e.g Pyrosequencing, NGS panel, COBAS, Sanger sequencing. If not applicable enter NA; */
private java.lang.String validationAssayType;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public CancerSomaticVariantLevelQuestions() {}
/**
* All-args constructor.
*/
public CancerSomaticVariantLevelQuestions(org.gel.models.report.avro.VariantCoordinates variantCoordinates, java.util.List variantActionability, java.lang.String otherVariantActionability, org.gel.models.report.avro.CancerUsabilitySomatic variantUsability, org.gel.models.report.avro.CancerTested variantTested, java.lang.String validationAssayType) {
this.variantCoordinates = variantCoordinates;
this.variantActionability = variantActionability;
this.otherVariantActionability = otherVariantActionability;
this.variantUsability = variantUsability;
this.variantTested = variantTested;
this.validationAssayType = validationAssayType;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return variantCoordinates;
case 1: return variantActionability;
case 2: return otherVariantActionability;
case 3: return variantUsability;
case 4: return variantTested;
case 5: return validationAssayType;
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: variantActionability = (java.util.List)value$; break;
case 2: otherVariantActionability = (java.lang.String)value$; break;
case 3: variantUsability = (org.gel.models.report.avro.CancerUsabilitySomatic)value$; break;
case 4: variantTested = (org.gel.models.report.avro.CancerTested)value$; break;
case 5: validationAssayType = (java.lang.String)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'variantCoordinates' field.
* Variant coordinates following format `chromosome:position:reference:alternate` */
public org.gel.models.report.avro.VariantCoordinates getVariantCoordinates() {
return variantCoordinates;
}
/**
* Sets the value of the 'variantCoordinates' field.
* Variant coordinates following format `chromosome:position:reference:alternate` * @param value the value to set.
*/
public void setVariantCoordinates(org.gel.models.report.avro.VariantCoordinates value) {
this.variantCoordinates = value;
}
/**
* Gets the value of the 'variantActionability' field.
* Type of potential actionability: */
public java.util.List getVariantActionability() {
return variantActionability;
}
/**
* Sets the value of the 'variantActionability' field.
* Type of potential actionability: * @param value the value to set.
*/
public void setVariantActionability(java.util.List value) {
this.variantActionability = value;
}
/**
* Gets the value of the 'otherVariantActionability' field.
* Other information about variant actionability */
public java.lang.String getOtherVariantActionability() {
return otherVariantActionability;
}
/**
* Sets the value of the 'otherVariantActionability' field.
* Other information about variant actionability * @param value the value to set.
*/
public void setOtherVariantActionability(java.lang.String value) {
this.otherVariantActionability = value;
}
/**
* Gets the value of the 'variantUsability' field.
* How has/will this potentially actionable variant been/be used? */
public org.gel.models.report.avro.CancerUsabilitySomatic getVariantUsability() {
return variantUsability;
}
/**
* Sets the value of the 'variantUsability' field.
* How has/will this potentially actionable variant been/be used? * @param value the value to set.
*/
public void setVariantUsability(org.gel.models.report.avro.CancerUsabilitySomatic value) {
this.variantUsability = value;
}
/**
* Gets the value of the 'variantTested' field.
* Has this variant been tested by another method (either prior to or following receipt of this WGA)? */
public org.gel.models.report.avro.CancerTested getVariantTested() {
return variantTested;
}
/**
* Sets the value of the 'variantTested' field.
* Has this variant been tested by another method (either prior to or following receipt of this WGA)? * @param value the value to set.
*/
public void setVariantTested(org.gel.models.report.avro.CancerTested value) {
this.variantTested = value;
}
/**
* Gets the value of the 'validationAssayType' field.
* Please enter validation assay type e.g Pyrosequencing, NGS panel, COBAS, Sanger sequencing. If not applicable enter NA; */
public java.lang.String getValidationAssayType() {
return validationAssayType;
}
/**
* Sets the value of the 'validationAssayType' field.
* Please enter validation assay type e.g Pyrosequencing, NGS panel, COBAS, Sanger sequencing. If not applicable enter NA; * @param value the value to set.
*/
public void setValidationAssayType(java.lang.String value) {
this.validationAssayType = value;
}
/** Creates a new CancerSomaticVariantLevelQuestions RecordBuilder */
public static org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder newBuilder() {
return new org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder();
}
/** Creates a new CancerSomaticVariantLevelQuestions RecordBuilder by copying an existing Builder */
public static org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder newBuilder(org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder other) {
return new org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder(other);
}
/** Creates a new CancerSomaticVariantLevelQuestions RecordBuilder by copying an existing CancerSomaticVariantLevelQuestions instance */
public static org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder newBuilder(org.gel.models.report.avro.CancerSomaticVariantLevelQuestions other) {
return new org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder(other);
}
/**
* RecordBuilder for CancerSomaticVariantLevelQuestions 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 java.util.List variantActionability;
private java.lang.String otherVariantActionability;
private org.gel.models.report.avro.CancerUsabilitySomatic variantUsability;
private org.gel.models.report.avro.CancerTested variantTested;
private java.lang.String validationAssayType;
/** Creates a new Builder */
private Builder() {
super(org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.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.variantActionability)) {
this.variantActionability = data().deepCopy(fields()[1].schema(), other.variantActionability);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.otherVariantActionability)) {
this.otherVariantActionability = data().deepCopy(fields()[2].schema(), other.otherVariantActionability);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.variantUsability)) {
this.variantUsability = data().deepCopy(fields()[3].schema(), other.variantUsability);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.variantTested)) {
this.variantTested = data().deepCopy(fields()[4].schema(), other.variantTested);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.validationAssayType)) {
this.validationAssayType = data().deepCopy(fields()[5].schema(), other.validationAssayType);
fieldSetFlags()[5] = true;
}
}
/** Creates a Builder by copying an existing CancerSomaticVariantLevelQuestions instance */
private Builder(org.gel.models.report.avro.CancerSomaticVariantLevelQuestions other) {
super(org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.SCHEMA$);
if (isValidValue(fields()[0], other.variantCoordinates)) {
this.variantCoordinates = data().deepCopy(fields()[0].schema(), other.variantCoordinates);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.variantActionability)) {
this.variantActionability = data().deepCopy(fields()[1].schema(), other.variantActionability);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.otherVariantActionability)) {
this.otherVariantActionability = data().deepCopy(fields()[2].schema(), other.otherVariantActionability);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.variantUsability)) {
this.variantUsability = data().deepCopy(fields()[3].schema(), other.variantUsability);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.variantTested)) {
this.variantTested = data().deepCopy(fields()[4].schema(), other.variantTested);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.validationAssayType)) {
this.validationAssayType = data().deepCopy(fields()[5].schema(), other.validationAssayType);
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.CancerSomaticVariantLevelQuestions.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.CancerSomaticVariantLevelQuestions.Builder clearVariantCoordinates() {
variantCoordinates = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'variantActionability' field */
public java.util.List getVariantActionability() {
return variantActionability;
}
/** Sets the value of the 'variantActionability' field */
public org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder setVariantActionability(java.util.List value) {
validate(fields()[1], value);
this.variantActionability = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'variantActionability' field has been set */
public boolean hasVariantActionability() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'variantActionability' field */
public org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder clearVariantActionability() {
variantActionability = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'otherVariantActionability' field */
public java.lang.String getOtherVariantActionability() {
return otherVariantActionability;
}
/** Sets the value of the 'otherVariantActionability' field */
public org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder setOtherVariantActionability(java.lang.String value) {
validate(fields()[2], value);
this.otherVariantActionability = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'otherVariantActionability' field has been set */
public boolean hasOtherVariantActionability() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'otherVariantActionability' field */
public org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder clearOtherVariantActionability() {
otherVariantActionability = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'variantUsability' field */
public org.gel.models.report.avro.CancerUsabilitySomatic getVariantUsability() {
return variantUsability;
}
/** Sets the value of the 'variantUsability' field */
public org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder setVariantUsability(org.gel.models.report.avro.CancerUsabilitySomatic value) {
validate(fields()[3], value);
this.variantUsability = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'variantUsability' field has been set */
public boolean hasVariantUsability() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'variantUsability' field */
public org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder clearVariantUsability() {
variantUsability = null;
fieldSetFlags()[3] = false;
return this;
}
/** Gets the value of the 'variantTested' field */
public org.gel.models.report.avro.CancerTested getVariantTested() {
return variantTested;
}
/** Sets the value of the 'variantTested' field */
public org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder setVariantTested(org.gel.models.report.avro.CancerTested value) {
validate(fields()[4], value);
this.variantTested = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'variantTested' field has been set */
public boolean hasVariantTested() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'variantTested' field */
public org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder clearVariantTested() {
variantTested = null;
fieldSetFlags()[4] = false;
return this;
}
/** Gets the value of the 'validationAssayType' field */
public java.lang.String getValidationAssayType() {
return validationAssayType;
}
/** Sets the value of the 'validationAssayType' field */
public org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder setValidationAssayType(java.lang.String value) {
validate(fields()[5], value);
this.validationAssayType = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'validationAssayType' field has been set */
public boolean hasValidationAssayType() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'validationAssayType' field */
public org.gel.models.report.avro.CancerSomaticVariantLevelQuestions.Builder clearValidationAssayType() {
validationAssayType = null;
fieldSetFlags()[5] = false;
return this;
}
@Override
public CancerSomaticVariantLevelQuestions build() {
try {
CancerSomaticVariantLevelQuestions record = new CancerSomaticVariantLevelQuestions();
record.variantCoordinates = fieldSetFlags()[0] ? this.variantCoordinates : (org.gel.models.report.avro.VariantCoordinates) defaultValue(fields()[0]);
record.variantActionability = fieldSetFlags()[1] ? this.variantActionability : (java.util.List) defaultValue(fields()[1]);
record.otherVariantActionability = fieldSetFlags()[2] ? this.otherVariantActionability : (java.lang.String) defaultValue(fields()[2]);
record.variantUsability = fieldSetFlags()[3] ? this.variantUsability : (org.gel.models.report.avro.CancerUsabilitySomatic) defaultValue(fields()[3]);
record.variantTested = fieldSetFlags()[4] ? this.variantTested : (org.gel.models.report.avro.CancerTested) defaultValue(fields()[4]);
record.validationAssayType = fieldSetFlags()[5] ? this.validationAssayType : (java.lang.String) defaultValue(fields()[5]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
