org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation Maven / Gradle / Ivy
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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.opencb.biodata.models.variant.avro;
@SuppressWarnings("all")
@org.apache.avro.specific.AvroGenerated
public class PharmacogenomicsClinicalAnnotation 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\":\"PharmacogenomicsClinicalAnnotation\",\"namespace\":\"org.opencb.biodata.models.variant.avro\",\"fields\":[{\"name\":\"variantId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"geneNames\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"phenotypes\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"phenotypeTypes\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"confidence\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"score\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"url\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"summary\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"pubmed\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"alleles\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"PharmacogenomicsAlleles\",\"fields\":[{\"name\":\"allele\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"annotation\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"description\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]}]}}]}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
private java.lang.String variantId;
private java.util.List geneNames;
private java.util.List phenotypes;
private java.util.List phenotypeTypes;
private java.lang.String confidence;
private java.lang.String score;
private java.lang.String url;
private java.lang.String summary;
private java.util.List pubmed;
private java.util.List alleles;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public PharmacogenomicsClinicalAnnotation() {}
/**
* All-args constructor.
*/
public PharmacogenomicsClinicalAnnotation(java.lang.String variantId, java.util.List geneNames, java.util.List phenotypes, java.util.List phenotypeTypes, java.lang.String confidence, java.lang.String score, java.lang.String url, java.lang.String summary, java.util.List pubmed, java.util.List alleles) {
this.variantId = variantId;
this.geneNames = geneNames;
this.phenotypes = phenotypes;
this.phenotypeTypes = phenotypeTypes;
this.confidence = confidence;
this.score = score;
this.url = url;
this.summary = summary;
this.pubmed = pubmed;
this.alleles = alleles;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return variantId;
case 1: return geneNames;
case 2: return phenotypes;
case 3: return phenotypeTypes;
case 4: return confidence;
case 5: return score;
case 6: return url;
case 7: return summary;
case 8: return pubmed;
case 9: return alleles;
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$) {
case 0: variantId = (java.lang.String)value$; break;
case 1: geneNames = (java.util.List)value$; break;
case 2: phenotypes = (java.util.List)value$; break;
case 3: phenotypeTypes = (java.util.List)value$; break;
case 4: confidence = (java.lang.String)value$; break;
case 5: score = (java.lang.String)value$; break;
case 6: url = (java.lang.String)value$; break;
case 7: summary = (java.lang.String)value$; break;
case 8: pubmed = (java.util.List)value$; break;
case 9: alleles = (java.util.List)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'variantId' field.
*/
public java.lang.String getVariantId() {
return variantId;
}
/**
* Sets the value of the 'variantId' field.
* @param value the value to set.
*/
public void setVariantId(java.lang.String value) {
this.variantId = value;
}
/**
* Gets the value of the 'geneNames' field.
*/
public java.util.List getGeneNames() {
return geneNames;
}
/**
* Sets the value of the 'geneNames' field.
* @param value the value to set.
*/
public void setGeneNames(java.util.List value) {
this.geneNames = value;
}
/**
* Gets the value of the 'phenotypes' field.
*/
public java.util.List getPhenotypes() {
return phenotypes;
}
/**
* Sets the value of the 'phenotypes' field.
* @param value the value to set.
*/
public void setPhenotypes(java.util.List value) {
this.phenotypes = value;
}
/**
* Gets the value of the 'phenotypeTypes' field.
*/
public java.util.List getPhenotypeTypes() {
return phenotypeTypes;
}
/**
* Sets the value of the 'phenotypeTypes' field.
* @param value the value to set.
*/
public void setPhenotypeTypes(java.util.List value) {
this.phenotypeTypes = value;
}
/**
* Gets the value of the 'confidence' field.
*/
public java.lang.String getConfidence() {
return confidence;
}
/**
* Sets the value of the 'confidence' field.
* @param value the value to set.
*/
public void setConfidence(java.lang.String value) {
this.confidence = value;
}
/**
* Gets the value of the 'score' field.
*/
public java.lang.String getScore() {
return score;
}
/**
* Sets the value of the 'score' field.
* @param value the value to set.
*/
public void setScore(java.lang.String value) {
this.score = value;
}
/**
* Gets the value of the 'url' field.
*/
public java.lang.String getUrl() {
return url;
}
/**
* Sets the value of the 'url' field.
* @param value the value to set.
*/
public void setUrl(java.lang.String value) {
this.url = value;
}
/**
* Gets the value of the 'summary' field.
*/
public java.lang.String getSummary() {
return summary;
}
/**
* Sets the value of the 'summary' field.
* @param value the value to set.
*/
public void setSummary(java.lang.String value) {
this.summary = value;
}
/**
* Gets the value of the 'pubmed' field.
*/
public java.util.List getPubmed() {
return pubmed;
}
/**
* Sets the value of the 'pubmed' field.
* @param value the value to set.
*/
public void setPubmed(java.util.List value) {
this.pubmed = value;
}
/**
* Gets the value of the 'alleles' field.
*/
public java.util.List getAlleles() {
return alleles;
}
/**
* Sets the value of the 'alleles' field.
* @param value the value to set.
*/
public void setAlleles(java.util.List value) {
this.alleles = value;
}
/** Creates a new PharmacogenomicsClinicalAnnotation RecordBuilder */
public static org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder newBuilder() {
return new org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder();
}
/** Creates a new PharmacogenomicsClinicalAnnotation RecordBuilder by copying an existing Builder */
public static org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder newBuilder(org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder other) {
return new org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder(other);
}
/** Creates a new PharmacogenomicsClinicalAnnotation RecordBuilder by copying an existing PharmacogenomicsClinicalAnnotation instance */
public static org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder newBuilder(org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation other) {
return new org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder(other);
}
/**
* RecordBuilder for PharmacogenomicsClinicalAnnotation instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private java.lang.String variantId;
private java.util.List geneNames;
private java.util.List phenotypes;
private java.util.List phenotypeTypes;
private java.lang.String confidence;
private java.lang.String score;
private java.lang.String url;
private java.lang.String summary;
private java.util.List pubmed;
private java.util.List alleles;
/** Creates a new Builder */
private Builder() {
super(org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder other) {
super(other);
if (isValidValue(fields()[0], other.variantId)) {
this.variantId = data().deepCopy(fields()[0].schema(), other.variantId);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.geneNames)) {
this.geneNames = data().deepCopy(fields()[1].schema(), other.geneNames);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.phenotypes)) {
this.phenotypes = data().deepCopy(fields()[2].schema(), other.phenotypes);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.phenotypeTypes)) {
this.phenotypeTypes = data().deepCopy(fields()[3].schema(), other.phenotypeTypes);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.confidence)) {
this.confidence = data().deepCopy(fields()[4].schema(), other.confidence);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.score)) {
this.score = data().deepCopy(fields()[5].schema(), other.score);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.url)) {
this.url = data().deepCopy(fields()[6].schema(), other.url);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.summary)) {
this.summary = data().deepCopy(fields()[7].schema(), other.summary);
fieldSetFlags()[7] = true;
}
if (isValidValue(fields()[8], other.pubmed)) {
this.pubmed = data().deepCopy(fields()[8].schema(), other.pubmed);
fieldSetFlags()[8] = true;
}
if (isValidValue(fields()[9], other.alleles)) {
this.alleles = data().deepCopy(fields()[9].schema(), other.alleles);
fieldSetFlags()[9] = true;
}
}
/** Creates a Builder by copying an existing PharmacogenomicsClinicalAnnotation instance */
private Builder(org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation other) {
super(org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.SCHEMA$);
if (isValidValue(fields()[0], other.variantId)) {
this.variantId = data().deepCopy(fields()[0].schema(), other.variantId);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.geneNames)) {
this.geneNames = data().deepCopy(fields()[1].schema(), other.geneNames);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.phenotypes)) {
this.phenotypes = data().deepCopy(fields()[2].schema(), other.phenotypes);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.phenotypeTypes)) {
this.phenotypeTypes = data().deepCopy(fields()[3].schema(), other.phenotypeTypes);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.confidence)) {
this.confidence = data().deepCopy(fields()[4].schema(), other.confidence);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.score)) {
this.score = data().deepCopy(fields()[5].schema(), other.score);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.url)) {
this.url = data().deepCopy(fields()[6].schema(), other.url);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.summary)) {
this.summary = data().deepCopy(fields()[7].schema(), other.summary);
fieldSetFlags()[7] = true;
}
if (isValidValue(fields()[8], other.pubmed)) {
this.pubmed = data().deepCopy(fields()[8].schema(), other.pubmed);
fieldSetFlags()[8] = true;
}
if (isValidValue(fields()[9], other.alleles)) {
this.alleles = data().deepCopy(fields()[9].schema(), other.alleles);
fieldSetFlags()[9] = true;
}
}
/** Gets the value of the 'variantId' field */
public java.lang.String getVariantId() {
return variantId;
}
/** Sets the value of the 'variantId' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder setVariantId(java.lang.String value) {
validate(fields()[0], value);
this.variantId = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'variantId' field has been set */
public boolean hasVariantId() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'variantId' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder clearVariantId() {
variantId = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'geneNames' field */
public java.util.List getGeneNames() {
return geneNames;
}
/** Sets the value of the 'geneNames' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder setGeneNames(java.util.List value) {
validate(fields()[1], value);
this.geneNames = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'geneNames' field has been set */
public boolean hasGeneNames() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'geneNames' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder clearGeneNames() {
geneNames = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'phenotypes' field */
public java.util.List getPhenotypes() {
return phenotypes;
}
/** Sets the value of the 'phenotypes' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder setPhenotypes(java.util.List value) {
validate(fields()[2], value);
this.phenotypes = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'phenotypes' field has been set */
public boolean hasPhenotypes() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'phenotypes' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder clearPhenotypes() {
phenotypes = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'phenotypeTypes' field */
public java.util.List getPhenotypeTypes() {
return phenotypeTypes;
}
/** Sets the value of the 'phenotypeTypes' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder setPhenotypeTypes(java.util.List value) {
validate(fields()[3], value);
this.phenotypeTypes = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'phenotypeTypes' field has been set */
public boolean hasPhenotypeTypes() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'phenotypeTypes' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder clearPhenotypeTypes() {
phenotypeTypes = null;
fieldSetFlags()[3] = false;
return this;
}
/** Gets the value of the 'confidence' field */
public java.lang.String getConfidence() {
return confidence;
}
/** Sets the value of the 'confidence' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder setConfidence(java.lang.String value) {
validate(fields()[4], value);
this.confidence = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'confidence' field has been set */
public boolean hasConfidence() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'confidence' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder clearConfidence() {
confidence = null;
fieldSetFlags()[4] = false;
return this;
}
/** Gets the value of the 'score' field */
public java.lang.String getScore() {
return score;
}
/** Sets the value of the 'score' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder setScore(java.lang.String value) {
validate(fields()[5], value);
this.score = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'score' field has been set */
public boolean hasScore() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'score' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder clearScore() {
score = null;
fieldSetFlags()[5] = false;
return this;
}
/** Gets the value of the 'url' field */
public java.lang.String getUrl() {
return url;
}
/** Sets the value of the 'url' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder setUrl(java.lang.String value) {
validate(fields()[6], value);
this.url = value;
fieldSetFlags()[6] = true;
return this;
}
/** Checks whether the 'url' field has been set */
public boolean hasUrl() {
return fieldSetFlags()[6];
}
/** Clears the value of the 'url' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder clearUrl() {
url = null;
fieldSetFlags()[6] = false;
return this;
}
/** Gets the value of the 'summary' field */
public java.lang.String getSummary() {
return summary;
}
/** Sets the value of the 'summary' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder setSummary(java.lang.String value) {
validate(fields()[7], value);
this.summary = value;
fieldSetFlags()[7] = true;
return this;
}
/** Checks whether the 'summary' field has been set */
public boolean hasSummary() {
return fieldSetFlags()[7];
}
/** Clears the value of the 'summary' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder clearSummary() {
summary = null;
fieldSetFlags()[7] = false;
return this;
}
/** Gets the value of the 'pubmed' field */
public java.util.List getPubmed() {
return pubmed;
}
/** Sets the value of the 'pubmed' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder setPubmed(java.util.List value) {
validate(fields()[8], value);
this.pubmed = value;
fieldSetFlags()[8] = true;
return this;
}
/** Checks whether the 'pubmed' field has been set */
public boolean hasPubmed() {
return fieldSetFlags()[8];
}
/** Clears the value of the 'pubmed' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder clearPubmed() {
pubmed = null;
fieldSetFlags()[8] = false;
return this;
}
/** Gets the value of the 'alleles' field */
public java.util.List getAlleles() {
return alleles;
}
/** Sets the value of the 'alleles' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder setAlleles(java.util.List value) {
validate(fields()[9], value);
this.alleles = value;
fieldSetFlags()[9] = true;
return this;
}
/** Checks whether the 'alleles' field has been set */
public boolean hasAlleles() {
return fieldSetFlags()[9];
}
/** Clears the value of the 'alleles' field */
public org.opencb.biodata.models.variant.avro.PharmacogenomicsClinicalAnnotation.Builder clearAlleles() {
alleles = null;
fieldSetFlags()[9] = false;
return this;
}
@Override
public PharmacogenomicsClinicalAnnotation build() {
try {
PharmacogenomicsClinicalAnnotation record = new PharmacogenomicsClinicalAnnotation();
record.variantId = fieldSetFlags()[0] ? this.variantId : (java.lang.String) defaultValue(fields()[0]);
record.geneNames = fieldSetFlags()[1] ? this.geneNames : (java.util.List) defaultValue(fields()[1]);
record.phenotypes = fieldSetFlags()[2] ? this.phenotypes : (java.util.List) defaultValue(fields()[2]);
record.phenotypeTypes = fieldSetFlags()[3] ? this.phenotypeTypes : (java.util.List) defaultValue(fields()[3]);
record.confidence = fieldSetFlags()[4] ? this.confidence : (java.lang.String) defaultValue(fields()[4]);
record.score = fieldSetFlags()[5] ? this.score : (java.lang.String) defaultValue(fields()[5]);
record.url = fieldSetFlags()[6] ? this.url : (java.lang.String) defaultValue(fields()[6]);
record.summary = fieldSetFlags()[7] ? this.summary : (java.lang.String) defaultValue(fields()[7]);
record.pubmed = fieldSetFlags()[8] ? this.pubmed : (java.util.List) defaultValue(fields()[8]);
record.alleles = fieldSetFlags()[9] ? this.alleles : (java.util.List) defaultValue(fields()[9]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
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