Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.gel.models.report.avro;
@SuppressWarnings("all")
@org.apache.avro.specific.AvroGenerated
public class StructuralVariantDetails 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\":\"StructuralVariantDetails\",\"namespace\":\"org.gel.models.report.avro\",\"fields\":[{\"name\":\"variantType\",\"type\":{\"type\":\"enum\",\"name\":\"StructuralVariantType\",\"symbols\":[\"ins\",\"dup\",\"inv\",\"amplification\",\"deletion\",\"dup_tandem\",\"del_me\",\"ins_me\"]},\"doc\":\"Strctural variant type\"},{\"name\":\"structuralVariantCoordinates\",\"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\"]}]},\"doc\":\"Structural variant coordinates\"},{\"name\":\"numberOfCopies\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"NumberOfCopies\",\"fields\":[{\"name\":\"numberOfCopies\",\"type\":\"int\",\"doc\":\"Number of copies given by the caller in one of the allele\"},{\"name\":\"confidenceIntervalMaximum\",\"type\":[\"null\",\"int\"]},{\"name\":\"confidenceIntervalMinimum\",\"type\":[\"null\",\"int\"]}]}}],\"doc\":\"Number of copies (required for copy number variants)\"}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** Strctural variant type */
private org.gel.models.report.avro.StructuralVariantType variantType;
/** Structural variant coordinates */
private org.gel.models.report.avro.Coordinates structuralVariantCoordinates;
/** Number of copies (required for copy number variants) */
private java.util.List numberOfCopies;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public StructuralVariantDetails() {}
/**
* All-args constructor.
*/
public StructuralVariantDetails(org.gel.models.report.avro.StructuralVariantType variantType, org.gel.models.report.avro.Coordinates structuralVariantCoordinates, java.util.List numberOfCopies) {
this.variantType = variantType;
this.structuralVariantCoordinates = structuralVariantCoordinates;
this.numberOfCopies = numberOfCopies;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return variantType;
case 1: return structuralVariantCoordinates;
case 2: 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$) {
case 0: variantType = (org.gel.models.report.avro.StructuralVariantType)value$; break;
case 1: structuralVariantCoordinates = (org.gel.models.report.avro.Coordinates)value$; break;
case 2: numberOfCopies = (java.util.List)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'variantType' field.
* Strctural variant type */
public org.gel.models.report.avro.StructuralVariantType getVariantType() {
return variantType;
}
/**
* Sets the value of the 'variantType' field.
* Strctural variant type * @param value the value to set.
*/
public void setVariantType(org.gel.models.report.avro.StructuralVariantType value) {
this.variantType = value;
}
/**
* Gets the value of the 'structuralVariantCoordinates' field.
* Structural variant coordinates */
public org.gel.models.report.avro.Coordinates getStructuralVariantCoordinates() {
return structuralVariantCoordinates;
}
/**
* Sets the value of the 'structuralVariantCoordinates' field.
* Structural variant coordinates * @param value the value to set.
*/
public void setStructuralVariantCoordinates(org.gel.models.report.avro.Coordinates value) {
this.structuralVariantCoordinates = value;
}
/**
* Gets the value of the 'numberOfCopies' field.
* Number of copies (required for copy number variants) */
public java.util.List getNumberOfCopies() {
return numberOfCopies;
}
/**
* Sets the value of the 'numberOfCopies' field.
* Number of copies (required for copy number variants) * @param value the value to set.
*/
public void setNumberOfCopies(java.util.List value) {
this.numberOfCopies = value;
}
/** Creates a new StructuralVariantDetails RecordBuilder */
public static org.gel.models.report.avro.StructuralVariantDetails.Builder newBuilder() {
return new org.gel.models.report.avro.StructuralVariantDetails.Builder();
}
/** Creates a new StructuralVariantDetails RecordBuilder by copying an existing Builder */
public static org.gel.models.report.avro.StructuralVariantDetails.Builder newBuilder(org.gel.models.report.avro.StructuralVariantDetails.Builder other) {
return new org.gel.models.report.avro.StructuralVariantDetails.Builder(other);
}
/** Creates a new StructuralVariantDetails RecordBuilder by copying an existing StructuralVariantDetails instance */
public static org.gel.models.report.avro.StructuralVariantDetails.Builder newBuilder(org.gel.models.report.avro.StructuralVariantDetails other) {
return new org.gel.models.report.avro.StructuralVariantDetails.Builder(other);
}
/**
* RecordBuilder for StructuralVariantDetails instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private org.gel.models.report.avro.StructuralVariantType variantType;
private org.gel.models.report.avro.Coordinates structuralVariantCoordinates;
private java.util.List numberOfCopies;
/** Creates a new Builder */
private Builder() {
super(org.gel.models.report.avro.StructuralVariantDetails.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.gel.models.report.avro.StructuralVariantDetails.Builder other) {
super(other);
if (isValidValue(fields()[0], other.variantType)) {
this.variantType = data().deepCopy(fields()[0].schema(), other.variantType);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.structuralVariantCoordinates)) {
this.structuralVariantCoordinates = data().deepCopy(fields()[1].schema(), other.structuralVariantCoordinates);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.numberOfCopies)) {
this.numberOfCopies = data().deepCopy(fields()[2].schema(), other.numberOfCopies);
fieldSetFlags()[2] = true;
}
}
/** Creates a Builder by copying an existing StructuralVariantDetails instance */
private Builder(org.gel.models.report.avro.StructuralVariantDetails other) {
super(org.gel.models.report.avro.StructuralVariantDetails.SCHEMA$);
if (isValidValue(fields()[0], other.variantType)) {
this.variantType = data().deepCopy(fields()[0].schema(), other.variantType);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.structuralVariantCoordinates)) {
this.structuralVariantCoordinates = data().deepCopy(fields()[1].schema(), other.structuralVariantCoordinates);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.numberOfCopies)) {
this.numberOfCopies = data().deepCopy(fields()[2].schema(), other.numberOfCopies);
fieldSetFlags()[2] = true;
}
}
/** Gets the value of the 'variantType' field */
public org.gel.models.report.avro.StructuralVariantType getVariantType() {
return variantType;
}
/** Sets the value of the 'variantType' field */
public org.gel.models.report.avro.StructuralVariantDetails.Builder setVariantType(org.gel.models.report.avro.StructuralVariantType value) {
validate(fields()[0], value);
this.variantType = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'variantType' field has been set */
public boolean hasVariantType() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'variantType' field */
public org.gel.models.report.avro.StructuralVariantDetails.Builder clearVariantType() {
variantType = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'structuralVariantCoordinates' field */
public org.gel.models.report.avro.Coordinates getStructuralVariantCoordinates() {
return structuralVariantCoordinates;
}
/** Sets the value of the 'structuralVariantCoordinates' field */
public org.gel.models.report.avro.StructuralVariantDetails.Builder setStructuralVariantCoordinates(org.gel.models.report.avro.Coordinates value) {
validate(fields()[1], value);
this.structuralVariantCoordinates = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'structuralVariantCoordinates' field has been set */
public boolean hasStructuralVariantCoordinates() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'structuralVariantCoordinates' field */
public org.gel.models.report.avro.StructuralVariantDetails.Builder clearStructuralVariantCoordinates() {
structuralVariantCoordinates = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'numberOfCopies' field */
public java.util.List getNumberOfCopies() {
return numberOfCopies;
}
/** Sets the value of the 'numberOfCopies' field */
public org.gel.models.report.avro.StructuralVariantDetails.Builder setNumberOfCopies(java.util.List value) {
validate(fields()[2], value);
this.numberOfCopies = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'numberOfCopies' field has been set */
public boolean hasNumberOfCopies() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'numberOfCopies' field */
public org.gel.models.report.avro.StructuralVariantDetails.Builder clearNumberOfCopies() {
numberOfCopies = null;
fieldSetFlags()[2] = false;
return this;
}
@Override
public StructuralVariantDetails build() {
try {
StructuralVariantDetails record = new StructuralVariantDetails();
record.variantType = fieldSetFlags()[0] ? this.variantType : (org.gel.models.report.avro.StructuralVariantType) defaultValue(fields()[0]);
record.structuralVariantCoordinates = fieldSetFlags()[1] ? this.structuralVariantCoordinates : (org.gel.models.report.avro.Coordinates) defaultValue(fields()[1]);
record.numberOfCopies = fieldSetFlags()[2] ? this.numberOfCopies : (java.util.List) defaultValue(fields()[2]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
