com.google.api.services.genomics.model.Annotation 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;
/**
* An annotation describes a region of reference genome. The value of an annotation may be one of
* several canonical types, supplemented by arbitrary info tags. An annotation is not inherently
* associated with a specific sample or individual (though a client could choose to use annotations
* in this way). Example canonical annotation types are `GENE` and `VARIANT`.
*
* 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 Annotation extends com.google.api.client.json.GenericJson {
/**
* The annotation set to which this annotation belongs.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.String annotationSetId;
/**
* The end position of the range on the reference, 0-based exclusive.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key @com.google.api.client.json.JsonString
private java.lang.Long end;
/**
* The server-generated annotation ID, unique across all annotations.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.String id;
/**
* A map of additional read alignment 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;
/**
* The display name of this annotation.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.String name;
/**
* The ID of the Google Genomics reference associated with this range.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.String referenceId;
/**
* The display name corresponding to the reference specified by `referenceId`, for example `chr1`,
* `1`, or `chrX`.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.String referenceName;
/**
* Whether this range refers to the reverse strand, as opposed to the forward strand. Note that
* regardless of this field, the start/end position of the range always refer to the forward
* strand.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.Boolean reverseStrand;
/**
* The start position of the range on the reference, 0-based inclusive.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key @com.google.api.client.json.JsonString
private java.lang.Long start;
/**
* A transcript value represents the assertion that a particular region of the reference genome
* may be transcribed as RNA. An alternative splicing pattern would be represented as a separate
* transcript object. This field is only set for annotations of type `TRANSCRIPT`.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private Transcript transcript;
/**
* The data type for this annotation. Must match the containing annotation set's type.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.String type;
/**
* A variant annotation, which describes the effect of a variant on the genome, the coding
* sequence, and/or higher level consequences at the organism level e.g. pathogenicity. This field
* is only set for annotations of type `VARIANT`.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private VariantAnnotation variant;
/**
* The annotation set to which this annotation belongs.
* @return value or {@code null} for none
*/
public java.lang.String getAnnotationSetId() {
return annotationSetId;
}
/**
* The annotation set to which this annotation belongs.
* @param annotationSetId annotationSetId or {@code null} for none
*/
public Annotation setAnnotationSetId(java.lang.String annotationSetId) {
this.annotationSetId = annotationSetId;
return this;
}
/**
* The end position of the range on the reference, 0-based exclusive.
* @return value or {@code null} for none
*/
public java.lang.Long getEnd() {
return end;
}
/**
* The end position of the range on the reference, 0-based exclusive.
* @param end end or {@code null} for none
*/
public Annotation setEnd(java.lang.Long end) {
this.end = end;
return this;
}
/**
* The server-generated annotation ID, unique across all annotations.
* @return value or {@code null} for none
*/
public java.lang.String getId() {
return id;
}
/**
* The server-generated annotation ID, unique across all annotations.
* @param id id or {@code null} for none
*/
public Annotation setId(java.lang.String id) {
this.id = id;
return this;
}
/**
* A map of additional read alignment 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 read alignment 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 Annotation setInfo(java.util.Map> info) {
this.info = info;
return this;
}
/**
* The display name of this annotation.
* @return value or {@code null} for none
*/
public java.lang.String getName() {
return name;
}
/**
* The display name of this annotation.
* @param name name or {@code null} for none
*/
public Annotation setName(java.lang.String name) {
this.name = name;
return this;
}
/**
* The ID of the Google Genomics reference associated with this range.
* @return value or {@code null} for none
*/
public java.lang.String getReferenceId() {
return referenceId;
}
/**
* The ID of the Google Genomics reference associated with this range.
* @param referenceId referenceId or {@code null} for none
*/
public Annotation setReferenceId(java.lang.String referenceId) {
this.referenceId = referenceId;
return this;
}
/**
* The display name corresponding to the reference specified by `referenceId`, for example `chr1`,
* `1`, or `chrX`.
* @return value or {@code null} for none
*/
public java.lang.String getReferenceName() {
return referenceName;
}
/**
* The display name corresponding to the reference specified by `referenceId`, for example `chr1`,
* `1`, or `chrX`.
* @param referenceName referenceName or {@code null} for none
*/
public Annotation setReferenceName(java.lang.String referenceName) {
this.referenceName = referenceName;
return this;
}
/**
* Whether this range refers to the reverse strand, as opposed to the forward strand. Note that
* regardless of this field, the start/end position of the range always refer to the forward
* strand.
* @return value or {@code null} for none
*/
public java.lang.Boolean getReverseStrand() {
return reverseStrand;
}
/**
* Whether this range refers to the reverse strand, as opposed to the forward strand. Note that
* regardless of this field, the start/end position of the range always refer to the forward
* strand.
* @param reverseStrand reverseStrand or {@code null} for none
*/
public Annotation setReverseStrand(java.lang.Boolean reverseStrand) {
this.reverseStrand = reverseStrand;
return this;
}
/**
* The start position of the range on the reference, 0-based inclusive.
* @return value or {@code null} for none
*/
public java.lang.Long getStart() {
return start;
}
/**
* The start position of the range on the reference, 0-based inclusive.
* @param start start or {@code null} for none
*/
public Annotation setStart(java.lang.Long start) {
this.start = start;
return this;
}
/**
* A transcript value represents the assertion that a particular region of the reference genome
* may be transcribed as RNA. An alternative splicing pattern would be represented as a separate
* transcript object. This field is only set for annotations of type `TRANSCRIPT`.
* @return value or {@code null} for none
*/
public Transcript getTranscript() {
return transcript;
}
/**
* A transcript value represents the assertion that a particular region of the reference genome
* may be transcribed as RNA. An alternative splicing pattern would be represented as a separate
* transcript object. This field is only set for annotations of type `TRANSCRIPT`.
* @param transcript transcript or {@code null} for none
*/
public Annotation setTranscript(Transcript transcript) {
this.transcript = transcript;
return this;
}
/**
* The data type for this annotation. Must match the containing annotation set's type.
* @return value or {@code null} for none
*/
public java.lang.String getType() {
return type;
}
/**
* The data type for this annotation. Must match the containing annotation set's type.
* @param type type or {@code null} for none
*/
public Annotation setType(java.lang.String type) {
this.type = type;
return this;
}
/**
* A variant annotation, which describes the effect of a variant on the genome, the coding
* sequence, and/or higher level consequences at the organism level e.g. pathogenicity. This field
* is only set for annotations of type `VARIANT`.
* @return value or {@code null} for none
*/
public VariantAnnotation getVariant() {
return variant;
}
/**
* A variant annotation, which describes the effect of a variant on the genome, the coding
* sequence, and/or higher level consequences at the organism level e.g. pathogenicity. This field
* is only set for annotations of type `VARIANT`.
* @param variant variant or {@code null} for none
*/
public Annotation setVariant(VariantAnnotation variant) {
this.variant = variant;
return this;
}
@Override
public Annotation set(String fieldName, Object value) {
return (Annotation) super.set(fieldName, value);
}
@Override
public Annotation clone() {
return (Annotation) super.clone();
}
}
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