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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 Rearrangement 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\":\"Rearrangement\",\"namespace\":\"org.gel.models.report.avro\",\"fields\":[{\"name\":\"leftCoordinates\",\"type\":{\"type\":\"record\",\"name\":\"Coordinates\",\"fields\":[{\"name\":\"assembly\",\"type\":{\"type\":\"enum\",\"name\":\"Assembly\",\"doc\":\"The reference genome assembly\",\"symbols\":[\"GRCh38\",\"GRCh37\"]},\"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\"]}]}},{\"name\":\"rightCoordinates\",\"type\":\"Coordinates\"},{\"name\":\"orientation\",\"type\":{\"type\":\"enum\",\"name\":\"Orientation\",\"symbols\":[\"start_start\",\"start_end\",\"end_end\"]}},{\"name\":\"leftInsSeq\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"rightInsSeq\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
private org.gel.models.report.avro.Coordinates leftCoordinates;
private org.gel.models.report.avro.Coordinates rightCoordinates;
private org.gel.models.report.avro.Orientation orientation;
private java.lang.String leftInsSeq;
private java.lang.String rightInsSeq;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public Rearrangement() {}
/**
* All-args constructor.
*/
public Rearrangement(org.gel.models.report.avro.Coordinates leftCoordinates, org.gel.models.report.avro.Coordinates rightCoordinates, org.gel.models.report.avro.Orientation orientation, java.lang.String leftInsSeq, java.lang.String rightInsSeq) {
this.leftCoordinates = leftCoordinates;
this.rightCoordinates = rightCoordinates;
this.orientation = orientation;
this.leftInsSeq = leftInsSeq;
this.rightInsSeq = rightInsSeq;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return leftCoordinates;
case 1: return rightCoordinates;
case 2: return orientation;
case 3: return leftInsSeq;
case 4: return rightInsSeq;
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$) {
case 0: leftCoordinates = (org.gel.models.report.avro.Coordinates)value$; break;
case 1: rightCoordinates = (org.gel.models.report.avro.Coordinates)value$; break;
case 2: orientation = (org.gel.models.report.avro.Orientation)value$; break;
case 3: leftInsSeq = (java.lang.String)value$; break;
case 4: rightInsSeq = (java.lang.String)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'leftCoordinates' field.
*/
public org.gel.models.report.avro.Coordinates getLeftCoordinates() {
return leftCoordinates;
}
/**
* Sets the value of the 'leftCoordinates' field.
* @param value the value to set.
*/
public void setLeftCoordinates(org.gel.models.report.avro.Coordinates value) {
this.leftCoordinates = value;
}
/**
* Gets the value of the 'rightCoordinates' field.
*/
public org.gel.models.report.avro.Coordinates getRightCoordinates() {
return rightCoordinates;
}
/**
* Sets the value of the 'rightCoordinates' field.
* @param value the value to set.
*/
public void setRightCoordinates(org.gel.models.report.avro.Coordinates value) {
this.rightCoordinates = value;
}
/**
* Gets the value of the 'orientation' field.
*/
public org.gel.models.report.avro.Orientation getOrientation() {
return orientation;
}
/**
* Sets the value of the 'orientation' field.
* @param value the value to set.
*/
public void setOrientation(org.gel.models.report.avro.Orientation value) {
this.orientation = value;
}
/**
* Gets the value of the 'leftInsSeq' field.
*/
public java.lang.String getLeftInsSeq() {
return leftInsSeq;
}
/**
* Sets the value of the 'leftInsSeq' field.
* @param value the value to set.
*/
public void setLeftInsSeq(java.lang.String value) {
this.leftInsSeq = value;
}
/**
* Gets the value of the 'rightInsSeq' field.
*/
public java.lang.String getRightInsSeq() {
return rightInsSeq;
}
/**
* Sets the value of the 'rightInsSeq' field.
* @param value the value to set.
*/
public void setRightInsSeq(java.lang.String value) {
this.rightInsSeq = value;
}
/** Creates a new Rearrangement RecordBuilder */
public static org.gel.models.report.avro.Rearrangement.Builder newBuilder() {
return new org.gel.models.report.avro.Rearrangement.Builder();
}
/** Creates a new Rearrangement RecordBuilder by copying an existing Builder */
public static org.gel.models.report.avro.Rearrangement.Builder newBuilder(org.gel.models.report.avro.Rearrangement.Builder other) {
return new org.gel.models.report.avro.Rearrangement.Builder(other);
}
/** Creates a new Rearrangement RecordBuilder by copying an existing Rearrangement instance */
public static org.gel.models.report.avro.Rearrangement.Builder newBuilder(org.gel.models.report.avro.Rearrangement other) {
return new org.gel.models.report.avro.Rearrangement.Builder(other);
}
/**
* RecordBuilder for Rearrangement instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private org.gel.models.report.avro.Coordinates leftCoordinates;
private org.gel.models.report.avro.Coordinates rightCoordinates;
private org.gel.models.report.avro.Orientation orientation;
private java.lang.String leftInsSeq;
private java.lang.String rightInsSeq;
/** Creates a new Builder */
private Builder() {
super(org.gel.models.report.avro.Rearrangement.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.gel.models.report.avro.Rearrangement.Builder other) {
super(other);
if (isValidValue(fields()[0], other.leftCoordinates)) {
this.leftCoordinates = data().deepCopy(fields()[0].schema(), other.leftCoordinates);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.rightCoordinates)) {
this.rightCoordinates = data().deepCopy(fields()[1].schema(), other.rightCoordinates);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.orientation)) {
this.orientation = data().deepCopy(fields()[2].schema(), other.orientation);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.leftInsSeq)) {
this.leftInsSeq = data().deepCopy(fields()[3].schema(), other.leftInsSeq);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.rightInsSeq)) {
this.rightInsSeq = data().deepCopy(fields()[4].schema(), other.rightInsSeq);
fieldSetFlags()[4] = true;
}
}
/** Creates a Builder by copying an existing Rearrangement instance */
private Builder(org.gel.models.report.avro.Rearrangement other) {
super(org.gel.models.report.avro.Rearrangement.SCHEMA$);
if (isValidValue(fields()[0], other.leftCoordinates)) {
this.leftCoordinates = data().deepCopy(fields()[0].schema(), other.leftCoordinates);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.rightCoordinates)) {
this.rightCoordinates = data().deepCopy(fields()[1].schema(), other.rightCoordinates);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.orientation)) {
this.orientation = data().deepCopy(fields()[2].schema(), other.orientation);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.leftInsSeq)) {
this.leftInsSeq = data().deepCopy(fields()[3].schema(), other.leftInsSeq);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.rightInsSeq)) {
this.rightInsSeq = data().deepCopy(fields()[4].schema(), other.rightInsSeq);
fieldSetFlags()[4] = true;
}
}
/** Gets the value of the 'leftCoordinates' field */
public org.gel.models.report.avro.Coordinates getLeftCoordinates() {
return leftCoordinates;
}
/** Sets the value of the 'leftCoordinates' field */
public org.gel.models.report.avro.Rearrangement.Builder setLeftCoordinates(org.gel.models.report.avro.Coordinates value) {
validate(fields()[0], value);
this.leftCoordinates = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'leftCoordinates' field has been set */
public boolean hasLeftCoordinates() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'leftCoordinates' field */
public org.gel.models.report.avro.Rearrangement.Builder clearLeftCoordinates() {
leftCoordinates = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'rightCoordinates' field */
public org.gel.models.report.avro.Coordinates getRightCoordinates() {
return rightCoordinates;
}
/** Sets the value of the 'rightCoordinates' field */
public org.gel.models.report.avro.Rearrangement.Builder setRightCoordinates(org.gel.models.report.avro.Coordinates value) {
validate(fields()[1], value);
this.rightCoordinates = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'rightCoordinates' field has been set */
public boolean hasRightCoordinates() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'rightCoordinates' field */
public org.gel.models.report.avro.Rearrangement.Builder clearRightCoordinates() {
rightCoordinates = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'orientation' field */
public org.gel.models.report.avro.Orientation getOrientation() {
return orientation;
}
/** Sets the value of the 'orientation' field */
public org.gel.models.report.avro.Rearrangement.Builder setOrientation(org.gel.models.report.avro.Orientation value) {
validate(fields()[2], value);
this.orientation = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'orientation' field has been set */
public boolean hasOrientation() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'orientation' field */
public org.gel.models.report.avro.Rearrangement.Builder clearOrientation() {
orientation = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'leftInsSeq' field */
public java.lang.String getLeftInsSeq() {
return leftInsSeq;
}
/** Sets the value of the 'leftInsSeq' field */
public org.gel.models.report.avro.Rearrangement.Builder setLeftInsSeq(java.lang.String value) {
validate(fields()[3], value);
this.leftInsSeq = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'leftInsSeq' field has been set */
public boolean hasLeftInsSeq() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'leftInsSeq' field */
public org.gel.models.report.avro.Rearrangement.Builder clearLeftInsSeq() {
leftInsSeq = null;
fieldSetFlags()[3] = false;
return this;
}
/** Gets the value of the 'rightInsSeq' field */
public java.lang.String getRightInsSeq() {
return rightInsSeq;
}
/** Sets the value of the 'rightInsSeq' field */
public org.gel.models.report.avro.Rearrangement.Builder setRightInsSeq(java.lang.String value) {
validate(fields()[4], value);
this.rightInsSeq = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'rightInsSeq' field has been set */
public boolean hasRightInsSeq() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'rightInsSeq' field */
public org.gel.models.report.avro.Rearrangement.Builder clearRightInsSeq() {
rightInsSeq = null;
fieldSetFlags()[4] = false;
return this;
}
@Override
public Rearrangement build() {
try {
Rearrangement record = new Rearrangement();
record.leftCoordinates = fieldSetFlags()[0] ? this.leftCoordinates : (org.gel.models.report.avro.Coordinates) defaultValue(fields()[0]);
record.rightCoordinates = fieldSetFlags()[1] ? this.rightCoordinates : (org.gel.models.report.avro.Coordinates) defaultValue(fields()[1]);
record.orientation = fieldSetFlags()[2] ? this.orientation : (org.gel.models.report.avro.Orientation) defaultValue(fields()[2]);
record.leftInsSeq = fieldSetFlags()[3] ? this.leftInsSeq : (java.lang.String) defaultValue(fields()[3]);
record.rightInsSeq = fieldSetFlags()[4] ? this.rightInsSeq : (java.lang.String) defaultValue(fields()[4]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
