org.opencb.biodata.models.variant.avro.HeritableTrait Maven / Gradle / Ivy
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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.opencb.biodata.models.variant.avro;
@SuppressWarnings("all")
/** The entity representing a phenotype and its inheritance pattern. */
@org.apache.avro.specific.AvroGenerated
public class HeritableTrait 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\":\"HeritableTrait\",\"namespace\":\"org.opencb.biodata.models.variant.avro\",\"doc\":\"The entity representing a phenotype and its inheritance pattern.\",\"fields\":[{\"name\":\"trait\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The trait (e.g.: HPO term, MIM term, DO term etc.)\"},{\"name\":\"inheritanceMode\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"ModeOfInheritance\",\"doc\":\"An enumeration for the different mode of inheritances:\\n\\n* `monoallelic_not_imprinted`: MONOALLELIC, autosomal or pseudoautosomal, not imprinted\\n* `monoallelic_maternally_imprinted`: MONOALLELIC, autosomal or pseudoautosomal, maternally imprinted (paternal allele expressed)\\n* `monoallelic_paternally_imprinted`: MONOALLELIC, autosomal or pseudoautosomal, paternally imprinted (maternal allele expressed)\\n* `monoallelic`: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown\\n* `biallelic`: BIALLELIC, autosomal or pseudoautosomal\\n* `monoallelic_and_biallelic`: BOTH monoallelic and biallelic, autosomal or pseudoautosomal\\n* `monoallelic_and_more_severe_biallelic`: BOTH monoallelic and biallelic, autosomal or pseudoautosomal (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal\\n* `xlinked_biallelic`: X-LINKED: hemizygous mutation in males, biallelic mutations in females\\n* `xlinked_monoallelic`: X linked: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)\\n* `mitochondrial`: MITOCHONDRIAL\\n* `unknown`: Unknown\\n* `NA`: Not applicable\",\"symbols\":[\"monoallelic\",\"monoallelic_not_imprinted\",\"monoallelic_maternally_imprinted\",\"monoallelic_paternally_imprinted\",\"biallelic\",\"monoallelic_and_biallelic\",\"monoallelic_and_more_severe_biallelic\",\"xlinked_biallelic\",\"xlinked_monoallelic\",\"mitochondrial\",\"unknown\",\"NA\"]}],\"doc\":\"The mode of inheritance\"}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** The trait (e.g.: HPO term, MIM term, DO term etc.) */
private java.lang.String trait;
/** The mode of inheritance */
private org.opencb.biodata.models.variant.avro.ModeOfInheritance inheritanceMode;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public HeritableTrait() {}
/**
* All-args constructor.
*/
public HeritableTrait(java.lang.String trait, org.opencb.biodata.models.variant.avro.ModeOfInheritance inheritanceMode) {
this.trait = trait;
this.inheritanceMode = inheritanceMode;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return trait;
case 1: return inheritanceMode;
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$) {
case 0: trait = (java.lang.String)value$; break;
case 1: inheritanceMode = (org.opencb.biodata.models.variant.avro.ModeOfInheritance)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'trait' field.
* The trait (e.g.: HPO term, MIM term, DO term etc.) */
public java.lang.String getTrait() {
return trait;
}
/**
* Sets the value of the 'trait' field.
* The trait (e.g.: HPO term, MIM term, DO term etc.) * @param value the value to set.
*/
public void setTrait(java.lang.String value) {
this.trait = value;
}
/**
* Gets the value of the 'inheritanceMode' field.
* The mode of inheritance */
public org.opencb.biodata.models.variant.avro.ModeOfInheritance getInheritanceMode() {
return inheritanceMode;
}
/**
* Sets the value of the 'inheritanceMode' field.
* The mode of inheritance * @param value the value to set.
*/
public void setInheritanceMode(org.opencb.biodata.models.variant.avro.ModeOfInheritance value) {
this.inheritanceMode = value;
}
/** Creates a new HeritableTrait RecordBuilder */
public static org.opencb.biodata.models.variant.avro.HeritableTrait.Builder newBuilder() {
return new org.opencb.biodata.models.variant.avro.HeritableTrait.Builder();
}
/** Creates a new HeritableTrait RecordBuilder by copying an existing Builder */
public static org.opencb.biodata.models.variant.avro.HeritableTrait.Builder newBuilder(org.opencb.biodata.models.variant.avro.HeritableTrait.Builder other) {
return new org.opencb.biodata.models.variant.avro.HeritableTrait.Builder(other);
}
/** Creates a new HeritableTrait RecordBuilder by copying an existing HeritableTrait instance */
public static org.opencb.biodata.models.variant.avro.HeritableTrait.Builder newBuilder(org.opencb.biodata.models.variant.avro.HeritableTrait other) {
return new org.opencb.biodata.models.variant.avro.HeritableTrait.Builder(other);
}
/**
* RecordBuilder for HeritableTrait instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private java.lang.String trait;
private org.opencb.biodata.models.variant.avro.ModeOfInheritance inheritanceMode;
/** Creates a new Builder */
private Builder() {
super(org.opencb.biodata.models.variant.avro.HeritableTrait.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.opencb.biodata.models.variant.avro.HeritableTrait.Builder other) {
super(other);
if (isValidValue(fields()[0], other.trait)) {
this.trait = data().deepCopy(fields()[0].schema(), other.trait);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.inheritanceMode)) {
this.inheritanceMode = data().deepCopy(fields()[1].schema(), other.inheritanceMode);
fieldSetFlags()[1] = true;
}
}
/** Creates a Builder by copying an existing HeritableTrait instance */
private Builder(org.opencb.biodata.models.variant.avro.HeritableTrait other) {
super(org.opencb.biodata.models.variant.avro.HeritableTrait.SCHEMA$);
if (isValidValue(fields()[0], other.trait)) {
this.trait = data().deepCopy(fields()[0].schema(), other.trait);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.inheritanceMode)) {
this.inheritanceMode = data().deepCopy(fields()[1].schema(), other.inheritanceMode);
fieldSetFlags()[1] = true;
}
}
/** Gets the value of the 'trait' field */
public java.lang.String getTrait() {
return trait;
}
/** Sets the value of the 'trait' field */
public org.opencb.biodata.models.variant.avro.HeritableTrait.Builder setTrait(java.lang.String value) {
validate(fields()[0], value);
this.trait = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'trait' field has been set */
public boolean hasTrait() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'trait' field */
public org.opencb.biodata.models.variant.avro.HeritableTrait.Builder clearTrait() {
trait = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'inheritanceMode' field */
public org.opencb.biodata.models.variant.avro.ModeOfInheritance getInheritanceMode() {
return inheritanceMode;
}
/** Sets the value of the 'inheritanceMode' field */
public org.opencb.biodata.models.variant.avro.HeritableTrait.Builder setInheritanceMode(org.opencb.biodata.models.variant.avro.ModeOfInheritance value) {
validate(fields()[1], value);
this.inheritanceMode = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'inheritanceMode' field has been set */
public boolean hasInheritanceMode() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'inheritanceMode' field */
public org.opencb.biodata.models.variant.avro.HeritableTrait.Builder clearInheritanceMode() {
inheritanceMode = null;
fieldSetFlags()[1] = false;
return this;
}
@Override
public HeritableTrait build() {
try {
HeritableTrait record = new HeritableTrait();
record.trait = fieldSetFlags()[0] ? this.trait : (java.lang.String) defaultValue(fields()[0]);
record.inheritanceMode = fieldSetFlags()[1] ? this.inheritanceMode : (org.opencb.biodata.models.variant.avro.ModeOfInheritance) defaultValue(fields()[1]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}