com.google.api.services.genomics.model.ReferenceSet 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: 2016-05-27 16:00:31 UTC)
* on 2016-07-28 at 21:58:52 UTC
* Modify at your own risk.
*/
package com.google.api.services.genomics.model;
/**
* A reference set is a set of references which typically comprise a reference assembly for a
* species, such as `GRCh38` which is representative of the human genome. A reference set defines a
* common coordinate space for comparing reference-aligned experimental data. A reference set
* contains 1 or more references. For more genomics resource definitions, see [Fundamentals of
* Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* 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 ReferenceSet extends com.google.api.client.json.GenericJson {
/**
* Public id of this reference set, such as `GRCh37`.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.String assemblyId;
/**
* Free text description of this reference set.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.String description;
/**
* The server-generated reference set ID, unique across all reference sets.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.String id;
/**
* Order-independent MD5 checksum which identifies this reference set. The checksum is computed by
* sorting all lower case hexidecimal string `reference.md5checksum` (for all reference in this
* set) in ascending lexicographic order, concatenating, and taking the MD5 of that value. The
* resulting value is represented in lower case hexadecimal format.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.String md5checksum;
/**
* ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human) indicating the
* species which this reference set is intended to model. Note that contained references may
* specify a different `ncbiTaxonId`, as assemblies may contain reference sequences which do not
* belong to the modeled species, for example EBV in a human reference genome.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.Integer ncbiTaxonId;
/**
* The IDs of the reference objects that are part of this set. `Reference.md5checksum` must be
* unique within this set.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.util.List referenceIds;
/**
* All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version
* number, for example `NC_000001.11`.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.util.List sourceAccessions;
/**
* The URI from which the references were obtained.
* The value may be {@code null}.
*/
@com.google.api.client.util.Key
private java.lang.String sourceUri;
/**
* Public id of this reference set, such as `GRCh37`.
* @return value or {@code null} for none
*/
public java.lang.String getAssemblyId() {
return assemblyId;
}
/**
* Public id of this reference set, such as `GRCh37`.
* @param assemblyId assemblyId or {@code null} for none
*/
public ReferenceSet setAssemblyId(java.lang.String assemblyId) {
this.assemblyId = assemblyId;
return this;
}
/**
* Free text description of this reference set.
* @return value or {@code null} for none
*/
public java.lang.String getDescription() {
return description;
}
/**
* Free text description of this reference set.
* @param description description or {@code null} for none
*/
public ReferenceSet setDescription(java.lang.String description) {
this.description = description;
return this;
}
/**
* The server-generated reference set ID, unique across all reference sets.
* @return value or {@code null} for none
*/
public java.lang.String getId() {
return id;
}
/**
* The server-generated reference set ID, unique across all reference sets.
* @param id id or {@code null} for none
*/
public ReferenceSet setId(java.lang.String id) {
this.id = id;
return this;
}
/**
* Order-independent MD5 checksum which identifies this reference set. The checksum is computed by
* sorting all lower case hexidecimal string `reference.md5checksum` (for all reference in this
* set) in ascending lexicographic order, concatenating, and taking the MD5 of that value. The
* resulting value is represented in lower case hexadecimal format.
* @return value or {@code null} for none
*/
public java.lang.String getMd5checksum() {
return md5checksum;
}
/**
* Order-independent MD5 checksum which identifies this reference set. The checksum is computed by
* sorting all lower case hexidecimal string `reference.md5checksum` (for all reference in this
* set) in ascending lexicographic order, concatenating, and taking the MD5 of that value. The
* resulting value is represented in lower case hexadecimal format.
* @param md5checksum md5checksum or {@code null} for none
*/
public ReferenceSet setMd5checksum(java.lang.String md5checksum) {
this.md5checksum = md5checksum;
return this;
}
/**
* ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human) indicating the
* species which this reference set is intended to model. Note that contained references may
* specify a different `ncbiTaxonId`, as assemblies may contain reference sequences which do not
* belong to the modeled species, for example EBV in a human reference genome.
* @return value or {@code null} for none
*/
public java.lang.Integer getNcbiTaxonId() {
return ncbiTaxonId;
}
/**
* ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human) indicating the
* species which this reference set is intended to model. Note that contained references may
* specify a different `ncbiTaxonId`, as assemblies may contain reference sequences which do not
* belong to the modeled species, for example EBV in a human reference genome.
* @param ncbiTaxonId ncbiTaxonId or {@code null} for none
*/
public ReferenceSet setNcbiTaxonId(java.lang.Integer ncbiTaxonId) {
this.ncbiTaxonId = ncbiTaxonId;
return this;
}
/**
* The IDs of the reference objects that are part of this set. `Reference.md5checksum` must be
* unique within this set.
* @return value or {@code null} for none
*/
public java.util.List getReferenceIds() {
return referenceIds;
}
/**
* The IDs of the reference objects that are part of this set. `Reference.md5checksum` must be
* unique within this set.
* @param referenceIds referenceIds or {@code null} for none
*/
public ReferenceSet setReferenceIds(java.util.List referenceIds) {
this.referenceIds = referenceIds;
return this;
}
/**
* All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version
* number, for example `NC_000001.11`.
* @return value or {@code null} for none
*/
public java.util.List getSourceAccessions() {
return sourceAccessions;
}
/**
* All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version
* number, for example `NC_000001.11`.
* @param sourceAccessions sourceAccessions or {@code null} for none
*/
public ReferenceSet setSourceAccessions(java.util.List sourceAccessions) {
this.sourceAccessions = sourceAccessions;
return this;
}
/**
* The URI from which the references were obtained.
* @return value or {@code null} for none
*/
public java.lang.String getSourceUri() {
return sourceUri;
}
/**
* The URI from which the references were obtained.
* @param sourceUri sourceUri or {@code null} for none
*/
public ReferenceSet setSourceUri(java.lang.String sourceUri) {
this.sourceUri = sourceUri;
return this;
}
@Override
public ReferenceSet set(String fieldName, Object value) {
return (ReferenceSet) super.set(fieldName, value);
}
@Override
public ReferenceSet clone() {
return (ReferenceSet) super.clone();
}
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy