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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.gel.models.report.avro;
@SuppressWarnings("all")
@org.apache.avro.specific.AvroGenerated
public class Aneuploidy 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\":\"Aneuploidy\",\"namespace\":\"org.gel.models.report.avro\",\"fields\":[{\"name\":\"iscn\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"International System for Human Cytogenetic Nomenclature (.e.g: \\\"+14p+\\\", \\\"+t(13q21 q)\\\")\"},{\"name\":\"assembly\",\"type\":{\"type\":\"enum\",\"name\":\"Assembly\",\"doc\":\"The reference genome assembly\",\"symbols\":[\"GRCh38\",\"GRCh37\"]},\"doc\":\"The assembly\"},{\"name\":\"chromosome\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Chromosome involved in the aneuploidy\"},{\"name\":\"complete\",\"type\":\"boolean\",\"doc\":\"Wheter the aneuploidy is for the whole chromosme or just a fragment\"},{\"name\":\"coordinates\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"Coordinates\",\"fields\":[{\"name\":\"assembly\",\"type\":\"Assembly\",\"doc\":\"The assembly to which this variant corresponds\"},{\"name\":\"chromosome\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Chromosome without \\\"chr\\\" prefix (e.g. X rather than chrX)\"},{\"name\":\"start\",\"type\":\"int\",\"doc\":\"Start genomic position for variant (1-based)\"},{\"name\":\"end\",\"type\":\"int\",\"doc\":\"End genomic position for variant\"},{\"name\":\"ciStart\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"ConfidenceInterval\",\"fields\":[{\"name\":\"left\",\"type\":\"int\"},{\"name\":\"right\",\"type\":\"int\"}]}]},{\"name\":\"ciEnd\",\"type\":[\"null\",\"ConfidenceInterval\"]}]}],\"doc\":\"Coordinates can be specified to indicate the part of the chromosome affected\"},{\"name\":\"numberOfCopies\",\"type\":\"int\",\"doc\":\"Number of copies\"}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** International System for Human Cytogenetic Nomenclature (.e.g: "+14p+", "+t(13q21 q)") */
private java.lang.String iscn;
/** The assembly */
private org.gel.models.report.avro.Assembly assembly;
/** Chromosome involved in the aneuploidy */
private java.lang.String chromosome;
/** Wheter the aneuploidy is for the whole chromosme or just a fragment */
private boolean complete;
/** Coordinates can be specified to indicate the part of the chromosome affected */
private org.gel.models.report.avro.Coordinates coordinates;
/** Number of copies */
private int numberOfCopies;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public Aneuploidy() {}
/**
* All-args constructor.
*/
public Aneuploidy(java.lang.String iscn, org.gel.models.report.avro.Assembly assembly, java.lang.String chromosome, java.lang.Boolean complete, org.gel.models.report.avro.Coordinates coordinates, java.lang.Integer numberOfCopies) {
this.iscn = iscn;
this.assembly = assembly;
this.chromosome = chromosome;
this.complete = complete;
this.coordinates = coordinates;
this.numberOfCopies = numberOfCopies;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return iscn;
case 1: return assembly;
case 2: return chromosome;
case 3: return complete;
case 4: return coordinates;
case 5: return numberOfCopies;
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$) {
case 0: iscn = (java.lang.String)value$; break;
case 1: assembly = (org.gel.models.report.avro.Assembly)value$; break;
case 2: chromosome = (java.lang.String)value$; break;
case 3: complete = (java.lang.Boolean)value$; break;
case 4: coordinates = (org.gel.models.report.avro.Coordinates)value$; break;
case 5: numberOfCopies = (java.lang.Integer)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'iscn' field.
* International System for Human Cytogenetic Nomenclature (.e.g: "+14p+", "+t(13q21 q)") */
public java.lang.String getIscn() {
return iscn;
}
/**
* Sets the value of the 'iscn' field.
* International System for Human Cytogenetic Nomenclature (.e.g: "+14p+", "+t(13q21 q)") * @param value the value to set.
*/
public void setIscn(java.lang.String value) {
this.iscn = value;
}
/**
* Gets the value of the 'assembly' field.
* The assembly */
public org.gel.models.report.avro.Assembly getAssembly() {
return assembly;
}
/**
* Sets the value of the 'assembly' field.
* The assembly * @param value the value to set.
*/
public void setAssembly(org.gel.models.report.avro.Assembly value) {
this.assembly = value;
}
/**
* Gets the value of the 'chromosome' field.
* Chromosome involved in the aneuploidy */
public java.lang.String getChromosome() {
return chromosome;
}
/**
* Sets the value of the 'chromosome' field.
* Chromosome involved in the aneuploidy * @param value the value to set.
*/
public void setChromosome(java.lang.String value) {
this.chromosome = value;
}
/**
* Gets the value of the 'complete' field.
* Wheter the aneuploidy is for the whole chromosme or just a fragment */
public java.lang.Boolean getComplete() {
return complete;
}
/**
* Sets the value of the 'complete' field.
* Wheter the aneuploidy is for the whole chromosme or just a fragment * @param value the value to set.
*/
public void setComplete(java.lang.Boolean value) {
this.complete = value;
}
/**
* Gets the value of the 'coordinates' field.
* Coordinates can be specified to indicate the part of the chromosome affected */
public org.gel.models.report.avro.Coordinates getCoordinates() {
return coordinates;
}
/**
* Sets the value of the 'coordinates' field.
* Coordinates can be specified to indicate the part of the chromosome affected * @param value the value to set.
*/
public void setCoordinates(org.gel.models.report.avro.Coordinates value) {
this.coordinates = value;
}
/**
* Gets the value of the 'numberOfCopies' field.
* Number of copies */
public java.lang.Integer getNumberOfCopies() {
return numberOfCopies;
}
/**
* Sets the value of the 'numberOfCopies' field.
* Number of copies * @param value the value to set.
*/
public void setNumberOfCopies(java.lang.Integer value) {
this.numberOfCopies = value;
}
/** Creates a new Aneuploidy RecordBuilder */
public static org.gel.models.report.avro.Aneuploidy.Builder newBuilder() {
return new org.gel.models.report.avro.Aneuploidy.Builder();
}
/** Creates a new Aneuploidy RecordBuilder by copying an existing Builder */
public static org.gel.models.report.avro.Aneuploidy.Builder newBuilder(org.gel.models.report.avro.Aneuploidy.Builder other) {
return new org.gel.models.report.avro.Aneuploidy.Builder(other);
}
/** Creates a new Aneuploidy RecordBuilder by copying an existing Aneuploidy instance */
public static org.gel.models.report.avro.Aneuploidy.Builder newBuilder(org.gel.models.report.avro.Aneuploidy other) {
return new org.gel.models.report.avro.Aneuploidy.Builder(other);
}
/**
* RecordBuilder for Aneuploidy instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private java.lang.String iscn;
private org.gel.models.report.avro.Assembly assembly;
private java.lang.String chromosome;
private boolean complete;
private org.gel.models.report.avro.Coordinates coordinates;
private int numberOfCopies;
/** Creates a new Builder */
private Builder() {
super(org.gel.models.report.avro.Aneuploidy.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.gel.models.report.avro.Aneuploidy.Builder other) {
super(other);
if (isValidValue(fields()[0], other.iscn)) {
this.iscn = data().deepCopy(fields()[0].schema(), other.iscn);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.assembly)) {
this.assembly = data().deepCopy(fields()[1].schema(), other.assembly);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.chromosome)) {
this.chromosome = data().deepCopy(fields()[2].schema(), other.chromosome);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.complete)) {
this.complete = data().deepCopy(fields()[3].schema(), other.complete);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.coordinates)) {
this.coordinates = data().deepCopy(fields()[4].schema(), other.coordinates);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.numberOfCopies)) {
this.numberOfCopies = data().deepCopy(fields()[5].schema(), other.numberOfCopies);
fieldSetFlags()[5] = true;
}
}
/** Creates a Builder by copying an existing Aneuploidy instance */
private Builder(org.gel.models.report.avro.Aneuploidy other) {
super(org.gel.models.report.avro.Aneuploidy.SCHEMA$);
if (isValidValue(fields()[0], other.iscn)) {
this.iscn = data().deepCopy(fields()[0].schema(), other.iscn);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.assembly)) {
this.assembly = data().deepCopy(fields()[1].schema(), other.assembly);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.chromosome)) {
this.chromosome = data().deepCopy(fields()[2].schema(), other.chromosome);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.complete)) {
this.complete = data().deepCopy(fields()[3].schema(), other.complete);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.coordinates)) {
this.coordinates = data().deepCopy(fields()[4].schema(), other.coordinates);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.numberOfCopies)) {
this.numberOfCopies = data().deepCopy(fields()[5].schema(), other.numberOfCopies);
fieldSetFlags()[5] = true;
}
}
/** Gets the value of the 'iscn' field */
public java.lang.String getIscn() {
return iscn;
}
/** Sets the value of the 'iscn' field */
public org.gel.models.report.avro.Aneuploidy.Builder setIscn(java.lang.String value) {
validate(fields()[0], value);
this.iscn = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'iscn' field has been set */
public boolean hasIscn() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'iscn' field */
public org.gel.models.report.avro.Aneuploidy.Builder clearIscn() {
iscn = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'assembly' field */
public org.gel.models.report.avro.Assembly getAssembly() {
return assembly;
}
/** Sets the value of the 'assembly' field */
public org.gel.models.report.avro.Aneuploidy.Builder setAssembly(org.gel.models.report.avro.Assembly value) {
validate(fields()[1], value);
this.assembly = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'assembly' field has been set */
public boolean hasAssembly() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'assembly' field */
public org.gel.models.report.avro.Aneuploidy.Builder clearAssembly() {
assembly = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'chromosome' field */
public java.lang.String getChromosome() {
return chromosome;
}
/** Sets the value of the 'chromosome' field */
public org.gel.models.report.avro.Aneuploidy.Builder setChromosome(java.lang.String value) {
validate(fields()[2], value);
this.chromosome = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'chromosome' field has been set */
public boolean hasChromosome() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'chromosome' field */
public org.gel.models.report.avro.Aneuploidy.Builder clearChromosome() {
chromosome = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'complete' field */
public java.lang.Boolean getComplete() {
return complete;
}
/** Sets the value of the 'complete' field */
public org.gel.models.report.avro.Aneuploidy.Builder setComplete(boolean value) {
validate(fields()[3], value);
this.complete = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'complete' field has been set */
public boolean hasComplete() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'complete' field */
public org.gel.models.report.avro.Aneuploidy.Builder clearComplete() {
fieldSetFlags()[3] = false;
return this;
}
/** Gets the value of the 'coordinates' field */
public org.gel.models.report.avro.Coordinates getCoordinates() {
return coordinates;
}
/** Sets the value of the 'coordinates' field */
public org.gel.models.report.avro.Aneuploidy.Builder setCoordinates(org.gel.models.report.avro.Coordinates value) {
validate(fields()[4], value);
this.coordinates = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'coordinates' field has been set */
public boolean hasCoordinates() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'coordinates' field */
public org.gel.models.report.avro.Aneuploidy.Builder clearCoordinates() {
coordinates = null;
fieldSetFlags()[4] = false;
return this;
}
/** Gets the value of the 'numberOfCopies' field */
public java.lang.Integer getNumberOfCopies() {
return numberOfCopies;
}
/** Sets the value of the 'numberOfCopies' field */
public org.gel.models.report.avro.Aneuploidy.Builder setNumberOfCopies(int value) {
validate(fields()[5], value);
this.numberOfCopies = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'numberOfCopies' field has been set */
public boolean hasNumberOfCopies() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'numberOfCopies' field */
public org.gel.models.report.avro.Aneuploidy.Builder clearNumberOfCopies() {
fieldSetFlags()[5] = false;
return this;
}
@Override
public Aneuploidy build() {
try {
Aneuploidy record = new Aneuploidy();
record.iscn = fieldSetFlags()[0] ? this.iscn : (java.lang.String) defaultValue(fields()[0]);
record.assembly = fieldSetFlags()[1] ? this.assembly : (org.gel.models.report.avro.Assembly) defaultValue(fields()[1]);
record.chromosome = fieldSetFlags()[2] ? this.chromosome : (java.lang.String) defaultValue(fields()[2]);
record.complete = fieldSetFlags()[3] ? this.complete : (java.lang.Boolean) defaultValue(fields()[3]);
record.coordinates = fieldSetFlags()[4] ? this.coordinates : (org.gel.models.report.avro.Coordinates) defaultValue(fields()[4]);
record.numberOfCopies = fieldSetFlags()[5] ? this.numberOfCopies : (java.lang.Integer) defaultValue(fields()[5]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
