org.opencb.biodata.models.variant.avro.Breakend Maven / Gradle / Ivy
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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.opencb.biodata.models.variant.avro;
@SuppressWarnings("all")
@org.apache.avro.specific.AvroGenerated
public class Breakend 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\":\"Breakend\",\"namespace\":\"org.opencb.biodata.models.variant.avro\",\"fields\":[{\"name\":\"mate\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"BreakendMate\",\"fields\":[{\"name\":\"chromosome\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"position\",\"type\":[\"null\",\"int\"]},{\"name\":\"ciPositionLeft\",\"type\":[\"null\",\"int\"]},{\"name\":\"ciPositionRight\",\"type\":[\"null\",\"int\"]}]}]},{\"name\":\"orientation\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"BreakendOrientation\",\"doc\":\"* SE | (Start -> End) | s | t[p[ | piece extending to the right of p is joined after t\\n * SS | (Start -> Start) | s | t]p] | reverse comp piece extending left of p is joined after t\\n * ES | (End -> Start) | s | ]p]t | piece extending to the left of p is joined before t\\n * EE | (End -> End) | s | [p[t | reverse comp piece extending right of p is joined before t\",\"symbols\":[\"SE\",\"SS\",\"ES\",\"EE\"]}]},{\"name\":\"insSeq\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
private org.opencb.biodata.models.variant.avro.BreakendMate mate;
private org.opencb.biodata.models.variant.avro.BreakendOrientation orientation;
private java.lang.String insSeq;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public Breakend() {}
/**
* All-args constructor.
*/
public Breakend(org.opencb.biodata.models.variant.avro.BreakendMate mate, org.opencb.biodata.models.variant.avro.BreakendOrientation orientation, java.lang.String insSeq) {
this.mate = mate;
this.orientation = orientation;
this.insSeq = insSeq;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return mate;
case 1: return orientation;
case 2: return insSeq;
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$) {
case 0: mate = (org.opencb.biodata.models.variant.avro.BreakendMate)value$; break;
case 1: orientation = (org.opencb.biodata.models.variant.avro.BreakendOrientation)value$; break;
case 2: insSeq = (java.lang.String)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'mate' field.
*/
public org.opencb.biodata.models.variant.avro.BreakendMate getMate() {
return mate;
}
/**
* Sets the value of the 'mate' field.
* @param value the value to set.
*/
public void setMate(org.opencb.biodata.models.variant.avro.BreakendMate value) {
this.mate = value;
}
/**
* Gets the value of the 'orientation' field.
*/
public org.opencb.biodata.models.variant.avro.BreakendOrientation getOrientation() {
return orientation;
}
/**
* Sets the value of the 'orientation' field.
* @param value the value to set.
*/
public void setOrientation(org.opencb.biodata.models.variant.avro.BreakendOrientation value) {
this.orientation = value;
}
/**
* Gets the value of the 'insSeq' field.
*/
public java.lang.String getInsSeq() {
return insSeq;
}
/**
* Sets the value of the 'insSeq' field.
* @param value the value to set.
*/
public void setInsSeq(java.lang.String value) {
this.insSeq = value;
}
/** Creates a new Breakend RecordBuilder */
public static org.opencb.biodata.models.variant.avro.Breakend.Builder newBuilder() {
return new org.opencb.biodata.models.variant.avro.Breakend.Builder();
}
/** Creates a new Breakend RecordBuilder by copying an existing Builder */
public static org.opencb.biodata.models.variant.avro.Breakend.Builder newBuilder(org.opencb.biodata.models.variant.avro.Breakend.Builder other) {
return new org.opencb.biodata.models.variant.avro.Breakend.Builder(other);
}
/** Creates a new Breakend RecordBuilder by copying an existing Breakend instance */
public static org.opencb.biodata.models.variant.avro.Breakend.Builder newBuilder(org.opencb.biodata.models.variant.avro.Breakend other) {
return new org.opencb.biodata.models.variant.avro.Breakend.Builder(other);
}
/**
* RecordBuilder for Breakend instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private org.opencb.biodata.models.variant.avro.BreakendMate mate;
private org.opencb.biodata.models.variant.avro.BreakendOrientation orientation;
private java.lang.String insSeq;
/** Creates a new Builder */
private Builder() {
super(org.opencb.biodata.models.variant.avro.Breakend.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.opencb.biodata.models.variant.avro.Breakend.Builder other) {
super(other);
if (isValidValue(fields()[0], other.mate)) {
this.mate = data().deepCopy(fields()[0].schema(), other.mate);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.orientation)) {
this.orientation = data().deepCopy(fields()[1].schema(), other.orientation);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.insSeq)) {
this.insSeq = data().deepCopy(fields()[2].schema(), other.insSeq);
fieldSetFlags()[2] = true;
}
}
/** Creates a Builder by copying an existing Breakend instance */
private Builder(org.opencb.biodata.models.variant.avro.Breakend other) {
super(org.opencb.biodata.models.variant.avro.Breakend.SCHEMA$);
if (isValidValue(fields()[0], other.mate)) {
this.mate = data().deepCopy(fields()[0].schema(), other.mate);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.orientation)) {
this.orientation = data().deepCopy(fields()[1].schema(), other.orientation);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.insSeq)) {
this.insSeq = data().deepCopy(fields()[2].schema(), other.insSeq);
fieldSetFlags()[2] = true;
}
}
/** Gets the value of the 'mate' field */
public org.opencb.biodata.models.variant.avro.BreakendMate getMate() {
return mate;
}
/** Sets the value of the 'mate' field */
public org.opencb.biodata.models.variant.avro.Breakend.Builder setMate(org.opencb.biodata.models.variant.avro.BreakendMate value) {
validate(fields()[0], value);
this.mate = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'mate' field has been set */
public boolean hasMate() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'mate' field */
public org.opencb.biodata.models.variant.avro.Breakend.Builder clearMate() {
mate = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'orientation' field */
public org.opencb.biodata.models.variant.avro.BreakendOrientation getOrientation() {
return orientation;
}
/** Sets the value of the 'orientation' field */
public org.opencb.biodata.models.variant.avro.Breakend.Builder setOrientation(org.opencb.biodata.models.variant.avro.BreakendOrientation value) {
validate(fields()[1], value);
this.orientation = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'orientation' field has been set */
public boolean hasOrientation() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'orientation' field */
public org.opencb.biodata.models.variant.avro.Breakend.Builder clearOrientation() {
orientation = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'insSeq' field */
public java.lang.String getInsSeq() {
return insSeq;
}
/** Sets the value of the 'insSeq' field */
public org.opencb.biodata.models.variant.avro.Breakend.Builder setInsSeq(java.lang.String value) {
validate(fields()[2], value);
this.insSeq = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'insSeq' field has been set */
public boolean hasInsSeq() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'insSeq' field */
public org.opencb.biodata.models.variant.avro.Breakend.Builder clearInsSeq() {
insSeq = null;
fieldSetFlags()[2] = false;
return this;
}
@Override
public Breakend build() {
try {
Breakend record = new Breakend();
record.mate = fieldSetFlags()[0] ? this.mate : (org.opencb.biodata.models.variant.avro.BreakendMate) defaultValue(fields()[0]);
record.orientation = fieldSetFlags()[1] ? this.orientation : (org.opencb.biodata.models.variant.avro.BreakendOrientation) defaultValue(fields()[1]);
record.insSeq = fieldSetFlags()[2] ? this.insSeq : (java.lang.String) defaultValue(fields()[2]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}