org.gel.models.report.avro.UniparentalDisomy Maven / Gradle / Ivy
/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.gel.models.report.avro;
@SuppressWarnings("all")
@org.apache.avro.specific.AvroGenerated
public class UniparentalDisomy 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\":\"UniparentalDisomy\",\"namespace\":\"org.gel.models.report.avro\",\"fields\":[{\"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 where two homologues were inherited from one parent\"},{\"name\":\"complete\",\"type\":[\"null\",\"boolean\"],\"doc\":\"indicates Whether the UPD event involves an entire chromosome or part of a chromosome\"},{\"name\":\"origin\",\"type\":{\"type\":\"enum\",\"name\":\"UniparentalDisomyOrigin\",\"symbols\":[\"paternal\",\"maternal\",\"unknown\"]},\"doc\":\"The parent who contributed two chromosomes was the mother (maternal) or the father (paternal)\"},{\"name\":\"uniparentalDisomyFragments\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"UniparentalDisomyFragment\",\"fields\":[{\"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\":\"uniparentalDisomyType\",\"type\":{\"type\":\"enum\",\"name\":\"UniparentalDisomyType\",\"symbols\":[\"isodisomy\",\"heterodisomy\",\"both\"]},\"doc\":\"indicates whether the UPD event involves `isodisomy`, `heterodisomy` or `both`\"}]}}],\"doc\":\"List of all of the UPD fragments for this UPD event\"},{\"name\":\"participantId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Participant affected by this UPD\"},{\"name\":\"uniparentalDisomyEvidences\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"UniparentalDisomyEvidences\",\"fields\":[{\"name\":\"ibds\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"IdentityByDescent\",\"fields\":[{\"name\":\"relatedSample\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},{\"name\":\"ibd0\",\"type\":\"float\"},{\"name\":\"ibd1\",\"type\":\"float\"},{\"name\":\"ibd2\",\"type\":\"float\"},{\"name\":\"pihat\",\"type\":\"float\"}]}}]}]}],\"doc\":\"Evidences for the UPD call\"}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** The assembly */
private org.gel.models.report.avro.Assembly assembly;
/** Chromosome where two homologues were inherited from one parent */
private java.lang.String chromosome;
/** indicates Whether the UPD event involves an entire chromosome or part of a chromosome */
private java.lang.Boolean complete;
/** The parent who contributed two chromosomes was the mother (maternal) or the father (paternal) */
private org.gel.models.report.avro.UniparentalDisomyOrigin origin;
/** List of all of the UPD fragments for this UPD event */
private java.util.List uniparentalDisomyFragments;
/** Participant affected by this UPD */
private java.lang.String participantId;
/** Evidences for the UPD call */
private org.gel.models.report.avro.UniparentalDisomyEvidences uniparentalDisomyEvidences;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public UniparentalDisomy() {}
/**
* All-args constructor.
*/
public UniparentalDisomy(org.gel.models.report.avro.Assembly assembly, java.lang.String chromosome, java.lang.Boolean complete, org.gel.models.report.avro.UniparentalDisomyOrigin origin, java.util.List uniparentalDisomyFragments, java.lang.String participantId, org.gel.models.report.avro.UniparentalDisomyEvidences uniparentalDisomyEvidences) {
this.assembly = assembly;
this.chromosome = chromosome;
this.complete = complete;
this.origin = origin;
this.uniparentalDisomyFragments = uniparentalDisomyFragments;
this.participantId = participantId;
this.uniparentalDisomyEvidences = uniparentalDisomyEvidences;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return assembly;
case 1: return chromosome;
case 2: return complete;
case 3: return origin;
case 4: return uniparentalDisomyFragments;
case 5: return participantId;
case 6: return uniparentalDisomyEvidences;
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$) {
case 0: assembly = (org.gel.models.report.avro.Assembly)value$; break;
case 1: chromosome = (java.lang.String)value$; break;
case 2: complete = (java.lang.Boolean)value$; break;
case 3: origin = (org.gel.models.report.avro.UniparentalDisomyOrigin)value$; break;
case 4: uniparentalDisomyFragments = (java.util.List)value$; break;
case 5: participantId = (java.lang.String)value$; break;
case 6: uniparentalDisomyEvidences = (org.gel.models.report.avro.UniparentalDisomyEvidences)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* 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 where two homologues were inherited from one parent */
public java.lang.String getChromosome() {
return chromosome;
}
/**
* Sets the value of the 'chromosome' field.
* Chromosome where two homologues were inherited from one parent * @param value the value to set.
*/
public void setChromosome(java.lang.String value) {
this.chromosome = value;
}
/**
* Gets the value of the 'complete' field.
* indicates Whether the UPD event involves an entire chromosome or part of a chromosome */
public java.lang.Boolean getComplete() {
return complete;
}
/**
* Sets the value of the 'complete' field.
* indicates Whether the UPD event involves an entire chromosome or part of a chromosome * @param value the value to set.
*/
public void setComplete(java.lang.Boolean value) {
this.complete = value;
}
/**
* Gets the value of the 'origin' field.
* The parent who contributed two chromosomes was the mother (maternal) or the father (paternal) */
public org.gel.models.report.avro.UniparentalDisomyOrigin getOrigin() {
return origin;
}
/**
* Sets the value of the 'origin' field.
* The parent who contributed two chromosomes was the mother (maternal) or the father (paternal) * @param value the value to set.
*/
public void setOrigin(org.gel.models.report.avro.UniparentalDisomyOrigin value) {
this.origin = value;
}
/**
* Gets the value of the 'uniparentalDisomyFragments' field.
* List of all of the UPD fragments for this UPD event */
public java.util.List getUniparentalDisomyFragments() {
return uniparentalDisomyFragments;
}
/**
* Sets the value of the 'uniparentalDisomyFragments' field.
* List of all of the UPD fragments for this UPD event * @param value the value to set.
*/
public void setUniparentalDisomyFragments(java.util.List value) {
this.uniparentalDisomyFragments = value;
}
/**
* Gets the value of the 'participantId' field.
* Participant affected by this UPD */
public java.lang.String getParticipantId() {
return participantId;
}
/**
* Sets the value of the 'participantId' field.
* Participant affected by this UPD * @param value the value to set.
*/
public void setParticipantId(java.lang.String value) {
this.participantId = value;
}
/**
* Gets the value of the 'uniparentalDisomyEvidences' field.
* Evidences for the UPD call */
public org.gel.models.report.avro.UniparentalDisomyEvidences getUniparentalDisomyEvidences() {
return uniparentalDisomyEvidences;
}
/**
* Sets the value of the 'uniparentalDisomyEvidences' field.
* Evidences for the UPD call * @param value the value to set.
*/
public void setUniparentalDisomyEvidences(org.gel.models.report.avro.UniparentalDisomyEvidences value) {
this.uniparentalDisomyEvidences = value;
}
/** Creates a new UniparentalDisomy RecordBuilder */
public static org.gel.models.report.avro.UniparentalDisomy.Builder newBuilder() {
return new org.gel.models.report.avro.UniparentalDisomy.Builder();
}
/** Creates a new UniparentalDisomy RecordBuilder by copying an existing Builder */
public static org.gel.models.report.avro.UniparentalDisomy.Builder newBuilder(org.gel.models.report.avro.UniparentalDisomy.Builder other) {
return new org.gel.models.report.avro.UniparentalDisomy.Builder(other);
}
/** Creates a new UniparentalDisomy RecordBuilder by copying an existing UniparentalDisomy instance */
public static org.gel.models.report.avro.UniparentalDisomy.Builder newBuilder(org.gel.models.report.avro.UniparentalDisomy other) {
return new org.gel.models.report.avro.UniparentalDisomy.Builder(other);
}
/**
* RecordBuilder for UniparentalDisomy instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private org.gel.models.report.avro.Assembly assembly;
private java.lang.String chromosome;
private java.lang.Boolean complete;
private org.gel.models.report.avro.UniparentalDisomyOrigin origin;
private java.util.List uniparentalDisomyFragments;
private java.lang.String participantId;
private org.gel.models.report.avro.UniparentalDisomyEvidences uniparentalDisomyEvidences;
/** Creates a new Builder */
private Builder() {
super(org.gel.models.report.avro.UniparentalDisomy.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.gel.models.report.avro.UniparentalDisomy.Builder other) {
super(other);
if (isValidValue(fields()[0], other.assembly)) {
this.assembly = data().deepCopy(fields()[0].schema(), other.assembly);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.chromosome)) {
this.chromosome = data().deepCopy(fields()[1].schema(), other.chromosome);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.complete)) {
this.complete = data().deepCopy(fields()[2].schema(), other.complete);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.origin)) {
this.origin = data().deepCopy(fields()[3].schema(), other.origin);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.uniparentalDisomyFragments)) {
this.uniparentalDisomyFragments = data().deepCopy(fields()[4].schema(), other.uniparentalDisomyFragments);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.participantId)) {
this.participantId = data().deepCopy(fields()[5].schema(), other.participantId);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.uniparentalDisomyEvidences)) {
this.uniparentalDisomyEvidences = data().deepCopy(fields()[6].schema(), other.uniparentalDisomyEvidences);
fieldSetFlags()[6] = true;
}
}
/** Creates a Builder by copying an existing UniparentalDisomy instance */
private Builder(org.gel.models.report.avro.UniparentalDisomy other) {
super(org.gel.models.report.avro.UniparentalDisomy.SCHEMA$);
if (isValidValue(fields()[0], other.assembly)) {
this.assembly = data().deepCopy(fields()[0].schema(), other.assembly);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.chromosome)) {
this.chromosome = data().deepCopy(fields()[1].schema(), other.chromosome);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.complete)) {
this.complete = data().deepCopy(fields()[2].schema(), other.complete);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.origin)) {
this.origin = data().deepCopy(fields()[3].schema(), other.origin);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.uniparentalDisomyFragments)) {
this.uniparentalDisomyFragments = data().deepCopy(fields()[4].schema(), other.uniparentalDisomyFragments);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.participantId)) {
this.participantId = data().deepCopy(fields()[5].schema(), other.participantId);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.uniparentalDisomyEvidences)) {
this.uniparentalDisomyEvidences = data().deepCopy(fields()[6].schema(), other.uniparentalDisomyEvidences);
fieldSetFlags()[6] = true;
}
}
/** 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.UniparentalDisomy.Builder setAssembly(org.gel.models.report.avro.Assembly value) {
validate(fields()[0], value);
this.assembly = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'assembly' field has been set */
public boolean hasAssembly() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'assembly' field */
public org.gel.models.report.avro.UniparentalDisomy.Builder clearAssembly() {
assembly = null;
fieldSetFlags()[0] = 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.UniparentalDisomy.Builder setChromosome(java.lang.String value) {
validate(fields()[1], value);
this.chromosome = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'chromosome' field has been set */
public boolean hasChromosome() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'chromosome' field */
public org.gel.models.report.avro.UniparentalDisomy.Builder clearChromosome() {
chromosome = null;
fieldSetFlags()[1] = 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.UniparentalDisomy.Builder setComplete(java.lang.Boolean value) {
validate(fields()[2], value);
this.complete = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'complete' field has been set */
public boolean hasComplete() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'complete' field */
public org.gel.models.report.avro.UniparentalDisomy.Builder clearComplete() {
complete = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'origin' field */
public org.gel.models.report.avro.UniparentalDisomyOrigin getOrigin() {
return origin;
}
/** Sets the value of the 'origin' field */
public org.gel.models.report.avro.UniparentalDisomy.Builder setOrigin(org.gel.models.report.avro.UniparentalDisomyOrigin value) {
validate(fields()[3], value);
this.origin = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'origin' field has been set */
public boolean hasOrigin() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'origin' field */
public org.gel.models.report.avro.UniparentalDisomy.Builder clearOrigin() {
origin = null;
fieldSetFlags()[3] = false;
return this;
}
/** Gets the value of the 'uniparentalDisomyFragments' field */
public java.util.List getUniparentalDisomyFragments() {
return uniparentalDisomyFragments;
}
/** Sets the value of the 'uniparentalDisomyFragments' field */
public org.gel.models.report.avro.UniparentalDisomy.Builder setUniparentalDisomyFragments(java.util.List value) {
validate(fields()[4], value);
this.uniparentalDisomyFragments = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'uniparentalDisomyFragments' field has been set */
public boolean hasUniparentalDisomyFragments() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'uniparentalDisomyFragments' field */
public org.gel.models.report.avro.UniparentalDisomy.Builder clearUniparentalDisomyFragments() {
uniparentalDisomyFragments = null;
fieldSetFlags()[4] = false;
return this;
}
/** Gets the value of the 'participantId' field */
public java.lang.String getParticipantId() {
return participantId;
}
/** Sets the value of the 'participantId' field */
public org.gel.models.report.avro.UniparentalDisomy.Builder setParticipantId(java.lang.String value) {
validate(fields()[5], value);
this.participantId = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'participantId' field has been set */
public boolean hasParticipantId() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'participantId' field */
public org.gel.models.report.avro.UniparentalDisomy.Builder clearParticipantId() {
participantId = null;
fieldSetFlags()[5] = false;
return this;
}
/** Gets the value of the 'uniparentalDisomyEvidences' field */
public org.gel.models.report.avro.UniparentalDisomyEvidences getUniparentalDisomyEvidences() {
return uniparentalDisomyEvidences;
}
/** Sets the value of the 'uniparentalDisomyEvidences' field */
public org.gel.models.report.avro.UniparentalDisomy.Builder setUniparentalDisomyEvidences(org.gel.models.report.avro.UniparentalDisomyEvidences value) {
validate(fields()[6], value);
this.uniparentalDisomyEvidences = value;
fieldSetFlags()[6] = true;
return this;
}
/** Checks whether the 'uniparentalDisomyEvidences' field has been set */
public boolean hasUniparentalDisomyEvidences() {
return fieldSetFlags()[6];
}
/** Clears the value of the 'uniparentalDisomyEvidences' field */
public org.gel.models.report.avro.UniparentalDisomy.Builder clearUniparentalDisomyEvidences() {
uniparentalDisomyEvidences = null;
fieldSetFlags()[6] = false;
return this;
}
@Override
public UniparentalDisomy build() {
try {
UniparentalDisomy record = new UniparentalDisomy();
record.assembly = fieldSetFlags()[0] ? this.assembly : (org.gel.models.report.avro.Assembly) defaultValue(fields()[0]);
record.chromosome = fieldSetFlags()[1] ? this.chromosome : (java.lang.String) defaultValue(fields()[1]);
record.complete = fieldSetFlags()[2] ? this.complete : (java.lang.Boolean) defaultValue(fields()[2]);
record.origin = fieldSetFlags()[3] ? this.origin : (org.gel.models.report.avro.UniparentalDisomyOrigin) defaultValue(fields()[3]);
record.uniparentalDisomyFragments = fieldSetFlags()[4] ? this.uniparentalDisomyFragments : (java.util.List) defaultValue(fields()[4]);
record.participantId = fieldSetFlags()[5] ? this.participantId : (java.lang.String) defaultValue(fields()[5]);
record.uniparentalDisomyEvidences = fieldSetFlags()[6] ? this.uniparentalDisomyEvidences : (org.gel.models.report.avro.UniparentalDisomyEvidences) defaultValue(fields()[6]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
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