org.opencb.biodata.models.metadata.Individual Maven / Gradle / Ivy
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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.opencb.biodata.models.metadata;
@SuppressWarnings("all")
@org.apache.avro.specific.AvroGenerated
public class Individual 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\":\"Individual\",\"namespace\":\"org.opencb.biodata.models.metadata\",\"fields\":[{\"name\":\"id\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Individual identifier\"},{\"name\":\"family\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"default\":null},{\"name\":\"father\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"default\":null},{\"name\":\"mother\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"default\":null},{\"name\":\"sex\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"default\":null},{\"name\":\"phenotype\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"default\":null},{\"name\":\"samples\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"Sample\",\"fields\":[{\"name\":\"id\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Sample identifier\"},{\"name\":\"annotations\",\"type\":{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"},\"doc\":\"Sample annotations stored in a map of attributes according to the format:\\n attribute_name[:x] where x defines the attribute type, its valid values are:\\n n for numeric (i = integer, f = float)\\n s for string\\n b for boolean\\n\\n e.g. age:n, population:s, height:n, weight, risk factors, secondary conditions,...\",\"default\":{}}]}},\"default\":[]}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** Individual identifier */
private java.lang.String id;
private java.lang.String family;
private java.lang.String father;
private java.lang.String mother;
private java.lang.String sex;
private java.lang.String phenotype;
private java.util.List samples;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public Individual() {}
/**
* All-args constructor.
*/
public Individual(java.lang.String id, java.lang.String family, java.lang.String father, java.lang.String mother, java.lang.String sex, java.lang.String phenotype, java.util.List samples) {
this.id = id;
this.family = family;
this.father = father;
this.mother = mother;
this.sex = sex;
this.phenotype = phenotype;
this.samples = samples;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return id;
case 1: return family;
case 2: return father;
case 3: return mother;
case 4: return sex;
case 5: return phenotype;
case 6: return samples;
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$) {
case 0: id = (java.lang.String)value$; break;
case 1: family = (java.lang.String)value$; break;
case 2: father = (java.lang.String)value$; break;
case 3: mother = (java.lang.String)value$; break;
case 4: sex = (java.lang.String)value$; break;
case 5: phenotype = (java.lang.String)value$; break;
case 6: samples = (java.util.List)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'id' field.
* Individual identifier */
public java.lang.String getId() {
return id;
}
/**
* Sets the value of the 'id' field.
* Individual identifier * @param value the value to set.
*/
public void setId(java.lang.String value) {
this.id = value;
}
/**
* Gets the value of the 'family' field.
*/
public java.lang.String getFamily() {
return family;
}
/**
* Sets the value of the 'family' field.
* @param value the value to set.
*/
public void setFamily(java.lang.String value) {
this.family = value;
}
/**
* Gets the value of the 'father' field.
*/
public java.lang.String getFather() {
return father;
}
/**
* Sets the value of the 'father' field.
* @param value the value to set.
*/
public void setFather(java.lang.String value) {
this.father = value;
}
/**
* Gets the value of the 'mother' field.
*/
public java.lang.String getMother() {
return mother;
}
/**
* Sets the value of the 'mother' field.
* @param value the value to set.
*/
public void setMother(java.lang.String value) {
this.mother = value;
}
/**
* Gets the value of the 'sex' field.
*/
public java.lang.String getSex() {
return sex;
}
/**
* Sets the value of the 'sex' field.
* @param value the value to set.
*/
public void setSex(java.lang.String value) {
this.sex = value;
}
/**
* Gets the value of the 'phenotype' field.
*/
public java.lang.String getPhenotype() {
return phenotype;
}
/**
* Sets the value of the 'phenotype' field.
* @param value the value to set.
*/
public void setPhenotype(java.lang.String value) {
this.phenotype = value;
}
/**
* Gets the value of the 'samples' field.
*/
public java.util.List getSamples() {
return samples;
}
/**
* Sets the value of the 'samples' field.
* @param value the value to set.
*/
public void setSamples(java.util.List value) {
this.samples = value;
}
/** Creates a new Individual RecordBuilder */
public static org.opencb.biodata.models.metadata.Individual.Builder newBuilder() {
return new org.opencb.biodata.models.metadata.Individual.Builder();
}
/** Creates a new Individual RecordBuilder by copying an existing Builder */
public static org.opencb.biodata.models.metadata.Individual.Builder newBuilder(org.opencb.biodata.models.metadata.Individual.Builder other) {
return new org.opencb.biodata.models.metadata.Individual.Builder(other);
}
/** Creates a new Individual RecordBuilder by copying an existing Individual instance */
public static org.opencb.biodata.models.metadata.Individual.Builder newBuilder(org.opencb.biodata.models.metadata.Individual other) {
return new org.opencb.biodata.models.metadata.Individual.Builder(other);
}
/**
* RecordBuilder for Individual instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private java.lang.String id;
private java.lang.String family;
private java.lang.String father;
private java.lang.String mother;
private java.lang.String sex;
private java.lang.String phenotype;
private java.util.List samples;
/** Creates a new Builder */
private Builder() {
super(org.opencb.biodata.models.metadata.Individual.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.opencb.biodata.models.metadata.Individual.Builder other) {
super(other);
if (isValidValue(fields()[0], other.id)) {
this.id = data().deepCopy(fields()[0].schema(), other.id);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.family)) {
this.family = data().deepCopy(fields()[1].schema(), other.family);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.father)) {
this.father = data().deepCopy(fields()[2].schema(), other.father);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.mother)) {
this.mother = data().deepCopy(fields()[3].schema(), other.mother);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.sex)) {
this.sex = data().deepCopy(fields()[4].schema(), other.sex);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.phenotype)) {
this.phenotype = data().deepCopy(fields()[5].schema(), other.phenotype);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.samples)) {
this.samples = data().deepCopy(fields()[6].schema(), other.samples);
fieldSetFlags()[6] = true;
}
}
/** Creates a Builder by copying an existing Individual instance */
private Builder(org.opencb.biodata.models.metadata.Individual other) {
super(org.opencb.biodata.models.metadata.Individual.SCHEMA$);
if (isValidValue(fields()[0], other.id)) {
this.id = data().deepCopy(fields()[0].schema(), other.id);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.family)) {
this.family = data().deepCopy(fields()[1].schema(), other.family);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.father)) {
this.father = data().deepCopy(fields()[2].schema(), other.father);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.mother)) {
this.mother = data().deepCopy(fields()[3].schema(), other.mother);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.sex)) {
this.sex = data().deepCopy(fields()[4].schema(), other.sex);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.phenotype)) {
this.phenotype = data().deepCopy(fields()[5].schema(), other.phenotype);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.samples)) {
this.samples = data().deepCopy(fields()[6].schema(), other.samples);
fieldSetFlags()[6] = true;
}
}
/** Gets the value of the 'id' field */
public java.lang.String getId() {
return id;
}
/** Sets the value of the 'id' field */
public org.opencb.biodata.models.metadata.Individual.Builder setId(java.lang.String value) {
validate(fields()[0], value);
this.id = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'id' field has been set */
public boolean hasId() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'id' field */
public org.opencb.biodata.models.metadata.Individual.Builder clearId() {
id = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'family' field */
public java.lang.String getFamily() {
return family;
}
/** Sets the value of the 'family' field */
public org.opencb.biodata.models.metadata.Individual.Builder setFamily(java.lang.String value) {
validate(fields()[1], value);
this.family = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'family' field has been set */
public boolean hasFamily() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'family' field */
public org.opencb.biodata.models.metadata.Individual.Builder clearFamily() {
family = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'father' field */
public java.lang.String getFather() {
return father;
}
/** Sets the value of the 'father' field */
public org.opencb.biodata.models.metadata.Individual.Builder setFather(java.lang.String value) {
validate(fields()[2], value);
this.father = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'father' field has been set */
public boolean hasFather() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'father' field */
public org.opencb.biodata.models.metadata.Individual.Builder clearFather() {
father = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'mother' field */
public java.lang.String getMother() {
return mother;
}
/** Sets the value of the 'mother' field */
public org.opencb.biodata.models.metadata.Individual.Builder setMother(java.lang.String value) {
validate(fields()[3], value);
this.mother = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'mother' field has been set */
public boolean hasMother() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'mother' field */
public org.opencb.biodata.models.metadata.Individual.Builder clearMother() {
mother = null;
fieldSetFlags()[3] = false;
return this;
}
/** Gets the value of the 'sex' field */
public java.lang.String getSex() {
return sex;
}
/** Sets the value of the 'sex' field */
public org.opencb.biodata.models.metadata.Individual.Builder setSex(java.lang.String value) {
validate(fields()[4], value);
this.sex = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'sex' field has been set */
public boolean hasSex() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'sex' field */
public org.opencb.biodata.models.metadata.Individual.Builder clearSex() {
sex = null;
fieldSetFlags()[4] = false;
return this;
}
/** Gets the value of the 'phenotype' field */
public java.lang.String getPhenotype() {
return phenotype;
}
/** Sets the value of the 'phenotype' field */
public org.opencb.biodata.models.metadata.Individual.Builder setPhenotype(java.lang.String value) {
validate(fields()[5], value);
this.phenotype = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'phenotype' field has been set */
public boolean hasPhenotype() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'phenotype' field */
public org.opencb.biodata.models.metadata.Individual.Builder clearPhenotype() {
phenotype = null;
fieldSetFlags()[5] = false;
return this;
}
/** Gets the value of the 'samples' field */
public java.util.List getSamples() {
return samples;
}
/** Sets the value of the 'samples' field */
public org.opencb.biodata.models.metadata.Individual.Builder setSamples(java.util.List value) {
validate(fields()[6], value);
this.samples = value;
fieldSetFlags()[6] = true;
return this;
}
/** Checks whether the 'samples' field has been set */
public boolean hasSamples() {
return fieldSetFlags()[6];
}
/** Clears the value of the 'samples' field */
public org.opencb.biodata.models.metadata.Individual.Builder clearSamples() {
samples = null;
fieldSetFlags()[6] = false;
return this;
}
@Override
public Individual build() {
try {
Individual record = new Individual();
record.id = fieldSetFlags()[0] ? this.id : (java.lang.String) defaultValue(fields()[0]);
record.family = fieldSetFlags()[1] ? this.family : (java.lang.String) defaultValue(fields()[1]);
record.father = fieldSetFlags()[2] ? this.father : (java.lang.String) defaultValue(fields()[2]);
record.mother = fieldSetFlags()[3] ? this.mother : (java.lang.String) defaultValue(fields()[3]);
record.sex = fieldSetFlags()[4] ? this.sex : (java.lang.String) defaultValue(fields()[4]);
record.phenotype = fieldSetFlags()[5] ? this.phenotype : (java.lang.String) defaultValue(fields()[5]);
record.samples = fieldSetFlags()[6] ? this.samples : (java.util.List) defaultValue(fields()[6]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}