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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.gel.models.report.avro;
@SuppressWarnings("all")
/** Full Variant classification acording to AMP guideline, including all supporting evidences and the final
assessment */
@org.apache.avro.specific.AvroGenerated
public class AmpVariantClassification 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\":\"AmpVariantClassification\",\"namespace\":\"org.gel.models.report.avro\",\"doc\":\"Full Variant classification acording to AMP guideline, including all supporting evidences and the final\\n assessment\",\"fields\":[{\"name\":\"ampEvidences\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"AmpEvidence\",\"doc\":\"Evidences as defined in AMP guidelines, they are composed by a evidence type (first column in the evidence table of\\n the guidlines) and a assessment of the evicence, this last one will define the streght of the evidence, supporting\\n the variant to be classified as TierI-IV\",\"fields\":[{\"name\":\"type\",\"type\":{\"type\":\"enum\",\"name\":\"AmpEvidenceType\",\"doc\":\"Type of evidence in the AMP guideline\",\"symbols\":[\"mutation_type\",\"therapies\",\"variant_frequencies\",\"potential_germline\",\"population_database_presence\",\"germline_database_presence\",\"somatic_database_presence\",\"impact_predictive_software\",\"pathway_involvement\",\"publications\"]},\"doc\":\"AMP evidence type according to Guidlines, i.e germline_database_presence\"},{\"name\":\"evidenceAssessment\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Assessment for AMP evidence, i.e Present in ClinVar\"}]}},\"doc\":\"List of AMP evidences\"},{\"name\":\"ampTier\",\"type\":{\"type\":\"enum\",\"name\":\"AmpTier\",\"doc\":\"AMP tier:\\n* `TierI`: Variants of Strong Clinical Significance\\n* `TierII`: Variants of Potential Clinical Significance\\n* `TierIII`: Variants of Unknown Clinical Significance\\n* `TierIV`: Benign or Likely Benign Variants\",\"symbols\":[\"tierI\",\"tierII\",\"tierIII\",\"tierIV\"]},\"doc\":\"Final Clasification taken in account the evidences\"},{\"name\":\"ampClincialOrExperimentalEvidence\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"AmpClincialOrExperimentalEvidence\",\"doc\":\"Amp Clinical or Experimental Evidence, the level will define the overal clasification of the variant together with\\n the tiering.\",\"fields\":[{\"name\":\"category\",\"type\":{\"type\":\"enum\",\"name\":\"AmpClinicalOrExperimentalEvidenceCategory\",\"doc\":\"Categories of Clinical and/or Experimental Evidence as defined in AMP guidelines\",\"symbols\":[\"therapeutic\",\"diagnosis\",\"prognosis\"]},\"doc\":\"As denined in AMP guidelines: therapeutic, diagnosis or prognosis\"},{\"name\":\"level\",\"type\":{\"type\":\"enum\",\"name\":\"AmpClinicalOrExperimentalEvidenceLevel\",\"doc\":\"Levels for categories of Clinical and/or Experimental Evidence as defined in AMP guidelines\",\"symbols\":[\"levelA\",\"levelB\",\"levelC\",\"levelD\"]},\"doc\":\"As denined in AMP guidelines: levelA, levelB, levelC, levelD\"},{\"name\":\"description\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Description of the evidence\"}]}}],\"doc\":\"Clinical or Experimental evicence\"},{\"name\":\"assessment\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Final Assessment\"}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** List of AMP evidences */
private java.util.List ampEvidences;
/** Final Clasification taken in account the evidences */
private org.gel.models.report.avro.AmpTier ampTier;
/** Clinical or Experimental evicence */
private java.util.List ampClincialOrExperimentalEvidence;
/** Final Assessment */
private java.lang.String assessment;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public AmpVariantClassification() {}
/**
* All-args constructor.
*/
public AmpVariantClassification(java.util.List ampEvidences, org.gel.models.report.avro.AmpTier ampTier, java.util.List ampClincialOrExperimentalEvidence, java.lang.String assessment) {
this.ampEvidences = ampEvidences;
this.ampTier = ampTier;
this.ampClincialOrExperimentalEvidence = ampClincialOrExperimentalEvidence;
this.assessment = assessment;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return ampEvidences;
case 1: return ampTier;
case 2: return ampClincialOrExperimentalEvidence;
case 3: return assessment;
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$) {
case 0: ampEvidences = (java.util.List)value$; break;
case 1: ampTier = (org.gel.models.report.avro.AmpTier)value$; break;
case 2: ampClincialOrExperimentalEvidence = (java.util.List)value$; break;
case 3: assessment = (java.lang.String)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'ampEvidences' field.
* List of AMP evidences */
public java.util.List getAmpEvidences() {
return ampEvidences;
}
/**
* Sets the value of the 'ampEvidences' field.
* List of AMP evidences * @param value the value to set.
*/
public void setAmpEvidences(java.util.List value) {
this.ampEvidences = value;
}
/**
* Gets the value of the 'ampTier' field.
* Final Clasification taken in account the evidences */
public org.gel.models.report.avro.AmpTier getAmpTier() {
return ampTier;
}
/**
* Sets the value of the 'ampTier' field.
* Final Clasification taken in account the evidences * @param value the value to set.
*/
public void setAmpTier(org.gel.models.report.avro.AmpTier value) {
this.ampTier = value;
}
/**
* Gets the value of the 'ampClincialOrExperimentalEvidence' field.
* Clinical or Experimental evicence */
public java.util.List getAmpClincialOrExperimentalEvidence() {
return ampClincialOrExperimentalEvidence;
}
/**
* Sets the value of the 'ampClincialOrExperimentalEvidence' field.
* Clinical or Experimental evicence * @param value the value to set.
*/
public void setAmpClincialOrExperimentalEvidence(java.util.List value) {
this.ampClincialOrExperimentalEvidence = value;
}
/**
* Gets the value of the 'assessment' field.
* Final Assessment */
public java.lang.String getAssessment() {
return assessment;
}
/**
* Sets the value of the 'assessment' field.
* Final Assessment * @param value the value to set.
*/
public void setAssessment(java.lang.String value) {
this.assessment = value;
}
/** Creates a new AmpVariantClassification RecordBuilder */
public static org.gel.models.report.avro.AmpVariantClassification.Builder newBuilder() {
return new org.gel.models.report.avro.AmpVariantClassification.Builder();
}
/** Creates a new AmpVariantClassification RecordBuilder by copying an existing Builder */
public static org.gel.models.report.avro.AmpVariantClassification.Builder newBuilder(org.gel.models.report.avro.AmpVariantClassification.Builder other) {
return new org.gel.models.report.avro.AmpVariantClassification.Builder(other);
}
/** Creates a new AmpVariantClassification RecordBuilder by copying an existing AmpVariantClassification instance */
public static org.gel.models.report.avro.AmpVariantClassification.Builder newBuilder(org.gel.models.report.avro.AmpVariantClassification other) {
return new org.gel.models.report.avro.AmpVariantClassification.Builder(other);
}
/**
* RecordBuilder for AmpVariantClassification instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private java.util.List ampEvidences;
private org.gel.models.report.avro.AmpTier ampTier;
private java.util.List ampClincialOrExperimentalEvidence;
private java.lang.String assessment;
/** Creates a new Builder */
private Builder() {
super(org.gel.models.report.avro.AmpVariantClassification.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.gel.models.report.avro.AmpVariantClassification.Builder other) {
super(other);
if (isValidValue(fields()[0], other.ampEvidences)) {
this.ampEvidences = data().deepCopy(fields()[0].schema(), other.ampEvidences);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.ampTier)) {
this.ampTier = data().deepCopy(fields()[1].schema(), other.ampTier);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.ampClincialOrExperimentalEvidence)) {
this.ampClincialOrExperimentalEvidence = data().deepCopy(fields()[2].schema(), other.ampClincialOrExperimentalEvidence);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.assessment)) {
this.assessment = data().deepCopy(fields()[3].schema(), other.assessment);
fieldSetFlags()[3] = true;
}
}
/** Creates a Builder by copying an existing AmpVariantClassification instance */
private Builder(org.gel.models.report.avro.AmpVariantClassification other) {
super(org.gel.models.report.avro.AmpVariantClassification.SCHEMA$);
if (isValidValue(fields()[0], other.ampEvidences)) {
this.ampEvidences = data().deepCopy(fields()[0].schema(), other.ampEvidences);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.ampTier)) {
this.ampTier = data().deepCopy(fields()[1].schema(), other.ampTier);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.ampClincialOrExperimentalEvidence)) {
this.ampClincialOrExperimentalEvidence = data().deepCopy(fields()[2].schema(), other.ampClincialOrExperimentalEvidence);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.assessment)) {
this.assessment = data().deepCopy(fields()[3].schema(), other.assessment);
fieldSetFlags()[3] = true;
}
}
/** Gets the value of the 'ampEvidences' field */
public java.util.List getAmpEvidences() {
return ampEvidences;
}
/** Sets the value of the 'ampEvidences' field */
public org.gel.models.report.avro.AmpVariantClassification.Builder setAmpEvidences(java.util.List value) {
validate(fields()[0], value);
this.ampEvidences = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'ampEvidences' field has been set */
public boolean hasAmpEvidences() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'ampEvidences' field */
public org.gel.models.report.avro.AmpVariantClassification.Builder clearAmpEvidences() {
ampEvidences = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'ampTier' field */
public org.gel.models.report.avro.AmpTier getAmpTier() {
return ampTier;
}
/** Sets the value of the 'ampTier' field */
public org.gel.models.report.avro.AmpVariantClassification.Builder setAmpTier(org.gel.models.report.avro.AmpTier value) {
validate(fields()[1], value);
this.ampTier = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'ampTier' field has been set */
public boolean hasAmpTier() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'ampTier' field */
public org.gel.models.report.avro.AmpVariantClassification.Builder clearAmpTier() {
ampTier = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'ampClincialOrExperimentalEvidence' field */
public java.util.List getAmpClincialOrExperimentalEvidence() {
return ampClincialOrExperimentalEvidence;
}
/** Sets the value of the 'ampClincialOrExperimentalEvidence' field */
public org.gel.models.report.avro.AmpVariantClassification.Builder setAmpClincialOrExperimentalEvidence(java.util.List value) {
validate(fields()[2], value);
this.ampClincialOrExperimentalEvidence = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'ampClincialOrExperimentalEvidence' field has been set */
public boolean hasAmpClincialOrExperimentalEvidence() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'ampClincialOrExperimentalEvidence' field */
public org.gel.models.report.avro.AmpVariantClassification.Builder clearAmpClincialOrExperimentalEvidence() {
ampClincialOrExperimentalEvidence = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'assessment' field */
public java.lang.String getAssessment() {
return assessment;
}
/** Sets the value of the 'assessment' field */
public org.gel.models.report.avro.AmpVariantClassification.Builder setAssessment(java.lang.String value) {
validate(fields()[3], value);
this.assessment = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'assessment' field has been set */
public boolean hasAssessment() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'assessment' field */
public org.gel.models.report.avro.AmpVariantClassification.Builder clearAssessment() {
assessment = null;
fieldSetFlags()[3] = false;
return this;
}
@Override
public AmpVariantClassification build() {
try {
AmpVariantClassification record = new AmpVariantClassification();
record.ampEvidences = fieldSetFlags()[0] ? this.ampEvidences : (java.util.List) defaultValue(fields()[0]);
record.ampTier = fieldSetFlags()[1] ? this.ampTier : (org.gel.models.report.avro.AmpTier) defaultValue(fields()[1]);
record.ampClincialOrExperimentalEvidence = fieldSetFlags()[2] ? this.ampClincialOrExperimentalEvidence : (java.util.List) defaultValue(fields()[2]);
record.assessment = fieldSetFlags()[3] ? this.assessment : (java.lang.String) defaultValue(fields()[3]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
