org.opencb.biodata.models.variant.avro.GenomicFeature Maven / Gradle / Ivy
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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.opencb.biodata.models.variant.avro;
@SuppressWarnings("all")
/** The genomic feature */
@org.apache.avro.specific.AvroGenerated
public class GenomicFeature 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\":\"GenomicFeature\",\"namespace\":\"org.opencb.biodata.models.variant.avro\",\"doc\":\"The genomic feature\",\"fields\":[{\"name\":\"featureType\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"FeatureTypes\",\"doc\":\"The feature types\",\"symbols\":[\"regulatory_region\",\"gene\",\"transcript\",\"protein\"]}],\"doc\":\"Feature Type\"},{\"name\":\"ensemblId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Feature used, this should be a feature ID from Ensembl, (i.e, ENST00000544455)\"},{\"name\":\"xrefs\",\"type\":[\"null\",{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"}],\"doc\":\"Others IDs. Fields like the HGNC symbol if available should be added here\"}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** Feature Type */
private org.opencb.biodata.models.variant.avro.FeatureTypes featureType;
/** Feature used, this should be a feature ID from Ensembl, (i.e, ENST00000544455) */
private java.lang.String ensemblId;
/** Others IDs. Fields like the HGNC symbol if available should be added here */
private java.util.Map xrefs;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public GenomicFeature() {}
/**
* All-args constructor.
*/
public GenomicFeature(org.opencb.biodata.models.variant.avro.FeatureTypes featureType, java.lang.String ensemblId, java.util.Map xrefs) {
this.featureType = featureType;
this.ensemblId = ensemblId;
this.xrefs = xrefs;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return featureType;
case 1: return ensemblId;
case 2: return xrefs;
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$) {
case 0: featureType = (org.opencb.biodata.models.variant.avro.FeatureTypes)value$; break;
case 1: ensemblId = (java.lang.String)value$; break;
case 2: xrefs = (java.util.Map)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'featureType' field.
* Feature Type */
public org.opencb.biodata.models.variant.avro.FeatureTypes getFeatureType() {
return featureType;
}
/**
* Sets the value of the 'featureType' field.
* Feature Type * @param value the value to set.
*/
public void setFeatureType(org.opencb.biodata.models.variant.avro.FeatureTypes value) {
this.featureType = value;
}
/**
* Gets the value of the 'ensemblId' field.
* Feature used, this should be a feature ID from Ensembl, (i.e, ENST00000544455) */
public java.lang.String getEnsemblId() {
return ensemblId;
}
/**
* Sets the value of the 'ensemblId' field.
* Feature used, this should be a feature ID from Ensembl, (i.e, ENST00000544455) * @param value the value to set.
*/
public void setEnsemblId(java.lang.String value) {
this.ensemblId = value;
}
/**
* Gets the value of the 'xrefs' field.
* Others IDs. Fields like the HGNC symbol if available should be added here */
public java.util.Map getXrefs() {
return xrefs;
}
/**
* Sets the value of the 'xrefs' field.
* Others IDs. Fields like the HGNC symbol if available should be added here * @param value the value to set.
*/
public void setXrefs(java.util.Map value) {
this.xrefs = value;
}
/** Creates a new GenomicFeature RecordBuilder */
public static org.opencb.biodata.models.variant.avro.GenomicFeature.Builder newBuilder() {
return new org.opencb.biodata.models.variant.avro.GenomicFeature.Builder();
}
/** Creates a new GenomicFeature RecordBuilder by copying an existing Builder */
public static org.opencb.biodata.models.variant.avro.GenomicFeature.Builder newBuilder(org.opencb.biodata.models.variant.avro.GenomicFeature.Builder other) {
return new org.opencb.biodata.models.variant.avro.GenomicFeature.Builder(other);
}
/** Creates a new GenomicFeature RecordBuilder by copying an existing GenomicFeature instance */
public static org.opencb.biodata.models.variant.avro.GenomicFeature.Builder newBuilder(org.opencb.biodata.models.variant.avro.GenomicFeature other) {
return new org.opencb.biodata.models.variant.avro.GenomicFeature.Builder(other);
}
/**
* RecordBuilder for GenomicFeature instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private org.opencb.biodata.models.variant.avro.FeatureTypes featureType;
private java.lang.String ensemblId;
private java.util.Map xrefs;
/** Creates a new Builder */
private Builder() {
super(org.opencb.biodata.models.variant.avro.GenomicFeature.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.opencb.biodata.models.variant.avro.GenomicFeature.Builder other) {
super(other);
if (isValidValue(fields()[0], other.featureType)) {
this.featureType = data().deepCopy(fields()[0].schema(), other.featureType);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.ensemblId)) {
this.ensemblId = data().deepCopy(fields()[1].schema(), other.ensemblId);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.xrefs)) {
this.xrefs = data().deepCopy(fields()[2].schema(), other.xrefs);
fieldSetFlags()[2] = true;
}
}
/** Creates a Builder by copying an existing GenomicFeature instance */
private Builder(org.opencb.biodata.models.variant.avro.GenomicFeature other) {
super(org.opencb.biodata.models.variant.avro.GenomicFeature.SCHEMA$);
if (isValidValue(fields()[0], other.featureType)) {
this.featureType = data().deepCopy(fields()[0].schema(), other.featureType);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.ensemblId)) {
this.ensemblId = data().deepCopy(fields()[1].schema(), other.ensemblId);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.xrefs)) {
this.xrefs = data().deepCopy(fields()[2].schema(), other.xrefs);
fieldSetFlags()[2] = true;
}
}
/** Gets the value of the 'featureType' field */
public org.opencb.biodata.models.variant.avro.FeatureTypes getFeatureType() {
return featureType;
}
/** Sets the value of the 'featureType' field */
public org.opencb.biodata.models.variant.avro.GenomicFeature.Builder setFeatureType(org.opencb.biodata.models.variant.avro.FeatureTypes value) {
validate(fields()[0], value);
this.featureType = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'featureType' field has been set */
public boolean hasFeatureType() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'featureType' field */
public org.opencb.biodata.models.variant.avro.GenomicFeature.Builder clearFeatureType() {
featureType = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'ensemblId' field */
public java.lang.String getEnsemblId() {
return ensemblId;
}
/** Sets the value of the 'ensemblId' field */
public org.opencb.biodata.models.variant.avro.GenomicFeature.Builder setEnsemblId(java.lang.String value) {
validate(fields()[1], value);
this.ensemblId = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'ensemblId' field has been set */
public boolean hasEnsemblId() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'ensemblId' field */
public org.opencb.biodata.models.variant.avro.GenomicFeature.Builder clearEnsemblId() {
ensemblId = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'xrefs' field */
public java.util.Map getXrefs() {
return xrefs;
}
/** Sets the value of the 'xrefs' field */
public org.opencb.biodata.models.variant.avro.GenomicFeature.Builder setXrefs(java.util.Map value) {
validate(fields()[2], value);
this.xrefs = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'xrefs' field has been set */
public boolean hasXrefs() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'xrefs' field */
public org.opencb.biodata.models.variant.avro.GenomicFeature.Builder clearXrefs() {
xrefs = null;
fieldSetFlags()[2] = false;
return this;
}
@Override
public GenomicFeature build() {
try {
GenomicFeature record = new GenomicFeature();
record.featureType = fieldSetFlags()[0] ? this.featureType : (org.opencb.biodata.models.variant.avro.FeatureTypes) defaultValue(fields()[0]);
record.ensemblId = fieldSetFlags()[1] ? this.ensemblId : (java.lang.String) defaultValue(fields()[1]);
record.xrefs = fieldSetFlags()[2] ? this.xrefs : (java.util.Map) defaultValue(fields()[2]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
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