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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.opencb.biodata.models.variant.metadata;
@SuppressWarnings("all")
/** Variant File Header. Contains simple and complex metadata lines describing the content of the file.
This header matches with the VCF header.
A header may have multiple Simple or Complex lines with the same key */
@org.apache.avro.specific.AvroGenerated
public class VariantFileHeader 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\":\"VariantFileHeader\",\"namespace\":\"org.opencb.biodata.models.variant.metadata\",\"doc\":\"Variant File Header. Contains simple and complex metadata lines describing the content of the file.\\n This header matches with the VCF header.\\n A header may have multiple Simple or Complex lines with the same key\",\"fields\":[{\"name\":\"version\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},{\"name\":\"complexLines\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"VariantFileHeaderComplexLine\",\"fields\":[{\"name\":\"key\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Key of group of the Complex Header Line, e.g. INFO, FORMAT, FILTER, ALT, ...\"},{\"name\":\"id\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"ID or Name of the line\"},{\"name\":\"description\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The description\",\"default\":null},{\"name\":\"number\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Arity of the values associated with this metadata line.\\n Only present if the metadata line describes data fields, i.e. key == INFO or FORMAT\\n Accepted values:\\n - : The field has always this number of values.\\n - A: The field has one value per alternate allele.\\n - R: The field has one value for each possible allele, including the reference.\\n - G: The field has one value for each possible genotype\\n - .: The number of possible values varies, is unknown or unbounded.\",\"default\":null},{\"name\":\"type\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Type of the values associated with this metadata line.\\n Only present if the metadata line describes data fields, i.e. key == INFO or FORMAT\\n Accepted values:\\n - Integer\\n - Float\\n - String\\n - Character\\n - Flag\",\"default\":null},{\"name\":\"genericFields\",\"type\":{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"},\"doc\":\"Other optional fields\",\"default\":{}}]}},\"doc\":\"complex lines, e.g. INFO=\",\"default\":[]},{\"name\":\"simpleLines\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"VariantFileHeaderSimpleLine\",\"fields\":[{\"name\":\"key\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Key of group of the Simple Header Line, e.g. source, assembly, pedigreeDB, ...\"},{\"name\":\"value\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Value\"}]}},\"doc\":\"simple lines, e.g. fileDate=20090805\",\"default\":[]}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
private java.lang.String version;
/** complex lines, e.g. INFO= */
private java.util.List complexLines;
/** simple lines, e.g. fileDate=20090805 */
private java.util.List simpleLines;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public VariantFileHeader() {}
/**
* All-args constructor.
*/
public VariantFileHeader(java.lang.String version, java.util.List complexLines, java.util.List simpleLines) {
this.version = version;
this.complexLines = complexLines;
this.simpleLines = simpleLines;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return version;
case 1: return complexLines;
case 2: return simpleLines;
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$) {
case 0: version = (java.lang.String)value$; break;
case 1: complexLines = (java.util.List)value$; break;
case 2: simpleLines = (java.util.List)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'version' field.
*/
public java.lang.String getVersion() {
return version;
}
/**
* Sets the value of the 'version' field.
* @param value the value to set.
*/
public void setVersion(java.lang.String value) {
this.version = value;
}
/**
* Gets the value of the 'complexLines' field.
* complex lines, e.g. INFO= */
public java.util.List getComplexLines() {
return complexLines;
}
/**
* Sets the value of the 'complexLines' field.
* complex lines, e.g. INFO= * @param value the value to set.
*/
public void setComplexLines(java.util.List value) {
this.complexLines = value;
}
/**
* Gets the value of the 'simpleLines' field.
* simple lines, e.g. fileDate=20090805 */
public java.util.List getSimpleLines() {
return simpleLines;
}
/**
* Sets the value of the 'simpleLines' field.
* simple lines, e.g. fileDate=20090805 * @param value the value to set.
*/
public void setSimpleLines(java.util.List value) {
this.simpleLines = value;
}
/** Creates a new VariantFileHeader RecordBuilder */
public static org.opencb.biodata.models.variant.metadata.VariantFileHeader.Builder newBuilder() {
return new org.opencb.biodata.models.variant.metadata.VariantFileHeader.Builder();
}
/** Creates a new VariantFileHeader RecordBuilder by copying an existing Builder */
public static org.opencb.biodata.models.variant.metadata.VariantFileHeader.Builder newBuilder(org.opencb.biodata.models.variant.metadata.VariantFileHeader.Builder other) {
return new org.opencb.biodata.models.variant.metadata.VariantFileHeader.Builder(other);
}
/** Creates a new VariantFileHeader RecordBuilder by copying an existing VariantFileHeader instance */
public static org.opencb.biodata.models.variant.metadata.VariantFileHeader.Builder newBuilder(org.opencb.biodata.models.variant.metadata.VariantFileHeader other) {
return new org.opencb.biodata.models.variant.metadata.VariantFileHeader.Builder(other);
}
/**
* RecordBuilder for VariantFileHeader instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private java.lang.String version;
private java.util.List complexLines;
private java.util.List simpleLines;
/** Creates a new Builder */
private Builder() {
super(org.opencb.biodata.models.variant.metadata.VariantFileHeader.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.opencb.biodata.models.variant.metadata.VariantFileHeader.Builder other) {
super(other);
if (isValidValue(fields()[0], other.version)) {
this.version = data().deepCopy(fields()[0].schema(), other.version);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.complexLines)) {
this.complexLines = data().deepCopy(fields()[1].schema(), other.complexLines);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.simpleLines)) {
this.simpleLines = data().deepCopy(fields()[2].schema(), other.simpleLines);
fieldSetFlags()[2] = true;
}
}
/** Creates a Builder by copying an existing VariantFileHeader instance */
private Builder(org.opencb.biodata.models.variant.metadata.VariantFileHeader other) {
super(org.opencb.biodata.models.variant.metadata.VariantFileHeader.SCHEMA$);
if (isValidValue(fields()[0], other.version)) {
this.version = data().deepCopy(fields()[0].schema(), other.version);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.complexLines)) {
this.complexLines = data().deepCopy(fields()[1].schema(), other.complexLines);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.simpleLines)) {
this.simpleLines = data().deepCopy(fields()[2].schema(), other.simpleLines);
fieldSetFlags()[2] = true;
}
}
/** Gets the value of the 'version' field */
public java.lang.String getVersion() {
return version;
}
/** Sets the value of the 'version' field */
public org.opencb.biodata.models.variant.metadata.VariantFileHeader.Builder setVersion(java.lang.String value) {
validate(fields()[0], value);
this.version = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'version' field has been set */
public boolean hasVersion() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'version' field */
public org.opencb.biodata.models.variant.metadata.VariantFileHeader.Builder clearVersion() {
version = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'complexLines' field */
public java.util.List getComplexLines() {
return complexLines;
}
/** Sets the value of the 'complexLines' field */
public org.opencb.biodata.models.variant.metadata.VariantFileHeader.Builder setComplexLines(java.util.List value) {
validate(fields()[1], value);
this.complexLines = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'complexLines' field has been set */
public boolean hasComplexLines() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'complexLines' field */
public org.opencb.biodata.models.variant.metadata.VariantFileHeader.Builder clearComplexLines() {
complexLines = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'simpleLines' field */
public java.util.List getSimpleLines() {
return simpleLines;
}
/** Sets the value of the 'simpleLines' field */
public org.opencb.biodata.models.variant.metadata.VariantFileHeader.Builder setSimpleLines(java.util.List value) {
validate(fields()[2], value);
this.simpleLines = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'simpleLines' field has been set */
public boolean hasSimpleLines() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'simpleLines' field */
public org.opencb.biodata.models.variant.metadata.VariantFileHeader.Builder clearSimpleLines() {
simpleLines = null;
fieldSetFlags()[2] = false;
return this;
}
@Override
public VariantFileHeader build() {
try {
VariantFileHeader record = new VariantFileHeader();
record.version = fieldSetFlags()[0] ? this.version : (java.lang.String) defaultValue(fields()[0]);
record.complexLines = fieldSetFlags()[1] ? this.complexLines : (java.util.List) defaultValue(fields()[1]);
record.simpleLines = fieldSetFlags()[2] ? this.simpleLines : (java.util.List) defaultValue(fields()[2]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
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