com.google.api.services.genomics.model.Variant Maven / Gradle / Ivy
/*
* Copyright 2010 Google Inc.
*
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except
* in compliance with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software distributed under the License
* is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express
* or implied. See the License for the specific language governing permissions and limitations under
* the License.
*/
/*
* This code was generated by https://github.com/google/apis-client-generator/
* (build: 2016-07-08 17:28:43 UTC)
* on 2016-10-05 at 01:24:23 UTC
* Modify at your own risk.
*/
package com.google.api.services.genomics.model;
/**
* A variant represents a change in DNA sequence relative to a reference sequence. For example, a
* variant could represent a SNP or an insertion. Variants belong to a variant set. For more
* genomics resource definitions, see [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Each of the calls on
* a variant represent a determination of genotype with respect to that variant. For example, a call
* might assign probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named
* NA12345. A call belongs to a call set, which contains related calls typically from one sample.
*
* This is the Java data model class that specifies how to parse/serialize into the JSON that is
* transmitted over HTTP when working with the Genomics API. For a detailed explanation see:
* https://developers.google.com/api-client-library/java/google-http-java-client/json
*
*
* @author Google, Inc.
*/
@SuppressWarnings("javadoc")
public final class Variant extends com.google.api.client.json.GenericJson {
/**
* The bases that appear instead of the reference bases.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.util.List alternateBases;
/**
* The variant calls for this particular variant. Each one represents the determination of
* genotype with respect to this variant.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.util.List calls;
/**
* The date this variant was created, in milliseconds from the epoch.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key @com.google.api.client.json.JsonString
private java.lang.Long created;
/**
* The end position (0-based) of this variant. This corresponds to the first base after the last
* base in the reference allele. So, the length of the reference allele is (end - start). This is
* useful for variants that don't explicitly give alternate bases, for example large deletions.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key @com.google.api.client.json.JsonString
private java.lang.Long end;
/**
* A list of filters (normally quality filters) this variant has failed. `PASS` indicates this
* variant has passed all filters.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.util.List filter;
/**
* The server-generated variant ID, unique across all variants.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.String id;
/**
* A map of additional variant information. This must be of the form map (string key mapping to a
* list of string values).
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.util.Map> info;
/**
* Names for the variant, for example a RefSNP ID.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.util.List names;
/**
* A measure of how likely this variant is to be real. A higher value is better.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.Double quality;
/**
* The reference bases for this variant. They start at the given position.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.String referenceBases;
/**
* The reference on which this variant occurs. (such as `chr20` or `X`)
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.String referenceName;
/**
* The position at which this variant occurs (0-based). This corresponds to the first base of the
* string of reference bases.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key @com.google.api.client.json.JsonString
private java.lang.Long start;
/**
* The ID of the variant set this variant belongs to.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.String variantSetId;
/**
* The bases that appear instead of the reference bases.
* @return value or {@code null} for none
*/
public java.util.List getAlternateBases() {
return alternateBases;
}
/**
* The bases that appear instead of the reference bases.
* @param alternateBases alternateBases or {@code null} for none
*/
public Variant setAlternateBases(java.util.List alternateBases) {
this.alternateBases = alternateBases;
return this;
}
/**
* The variant calls for this particular variant. Each one represents the determination of
* genotype with respect to this variant.
* @return value or {@code null} for none
*/
public java.util.List getCalls() {
return calls;
}
/**
* The variant calls for this particular variant. Each one represents the determination of
* genotype with respect to this variant.
* @param calls calls or {@code null} for none
*/
public Variant setCalls(java.util.List calls) {
this.calls = calls;
return this;
}
/**
* The date this variant was created, in milliseconds from the epoch.
* @return value or {@code null} for none
*/
public java.lang.Long getCreated() {
return created;
}
/**
* The date this variant was created, in milliseconds from the epoch.
* @param created created or {@code null} for none
*/
public Variant setCreated(java.lang.Long created) {
this.created = created;
return this;
}
/**
* The end position (0-based) of this variant. This corresponds to the first base after the last
* base in the reference allele. So, the length of the reference allele is (end - start). This is
* useful for variants that don't explicitly give alternate bases, for example large deletions.
* @return value or {@code null} for none
*/
public java.lang.Long getEnd() {
return end;
}
/**
* The end position (0-based) of this variant. This corresponds to the first base after the last
* base in the reference allele. So, the length of the reference allele is (end - start). This is
* useful for variants that don't explicitly give alternate bases, for example large deletions.
* @param end end or {@code null} for none
*/
public Variant setEnd(java.lang.Long end) {
this.end = end;
return this;
}
/**
* A list of filters (normally quality filters) this variant has failed. `PASS` indicates this
* variant has passed all filters.
* @return value or {@code null} for none
*/
public java.util.List getFilter() {
return filter;
}
/**
* A list of filters (normally quality filters) this variant has failed. `PASS` indicates this
* variant has passed all filters.
* @param filter filter or {@code null} for none
*/
public Variant setFilter(java.util.List filter) {
this.filter = filter;
return this;
}
/**
* The server-generated variant ID, unique across all variants.
* @return value or {@code null} for none
*/
public java.lang.String getId() {
return id;
}
/**
* The server-generated variant ID, unique across all variants.
* @param id id or {@code null} for none
*/
public Variant setId(java.lang.String id) {
this.id = id;
return this;
}
/**
* A map of additional variant information. This must be of the form map (string key mapping to a
* list of string values).
* @return value or {@code null} for none
*/
public java.util.Map> getInfo() {
return info;
}
/**
* A map of additional variant information. This must be of the form map (string key mapping to a
* list of string values).
* @param info info or {@code null} for none
*/
public Variant setInfo(java.util.Map> info) {
this.info = info;
return this;
}
/**
* Names for the variant, for example a RefSNP ID.
* @return value or {@code null} for none
*/
public java.util.List getNames() {
return names;
}
/**
* Names for the variant, for example a RefSNP ID.
* @param names names or {@code null} for none
*/
public Variant setNames(java.util.List names) {
this.names = names;
return this;
}
/**
* A measure of how likely this variant is to be real. A higher value is better.
* @return value or {@code null} for none
*/
public java.lang.Double getQuality() {
return quality;
}
/**
* A measure of how likely this variant is to be real. A higher value is better.
* @param quality quality or {@code null} for none
*/
public Variant setQuality(java.lang.Double quality) {
this.quality = quality;
return this;
}
/**
* The reference bases for this variant. They start at the given position.
* @return value or {@code null} for none
*/
public java.lang.String getReferenceBases() {
return referenceBases;
}
/**
* The reference bases for this variant. They start at the given position.
* @param referenceBases referenceBases or {@code null} for none
*/
public Variant setReferenceBases(java.lang.String referenceBases) {
this.referenceBases = referenceBases;
return this;
}
/**
* The reference on which this variant occurs. (such as `chr20` or `X`)
* @return value or {@code null} for none
*/
public java.lang.String getReferenceName() {
return referenceName;
}
/**
* The reference on which this variant occurs. (such as `chr20` or `X`)
* @param referenceName referenceName or {@code null} for none
*/
public Variant setReferenceName(java.lang.String referenceName) {
this.referenceName = referenceName;
return this;
}
/**
* The position at which this variant occurs (0-based). This corresponds to the first base of the
* string of reference bases.
* @return value or {@code null} for none
*/
public java.lang.Long getStart() {
return start;
}
/**
* The position at which this variant occurs (0-based). This corresponds to the first base of the
* string of reference bases.
* @param start start or {@code null} for none
*/
public Variant setStart(java.lang.Long start) {
this.start = start;
return this;
}
/**
* The ID of the variant set this variant belongs to.
* @return value or {@code null} for none
*/
public java.lang.String getVariantSetId() {
return variantSetId;
}
/**
* The ID of the variant set this variant belongs to.
* @param variantSetId variantSetId or {@code null} for none
*/
public Variant setVariantSetId(java.lang.String variantSetId) {
this.variantSetId = variantSetId;
return this;
}
@Override
public Variant set(String fieldName, Object value) {
return (Variant) super.set(fieldName, value);
}
@Override
public Variant clone() {
return (Variant) super.clone();
}
}
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