com.google.api.services.genomics.model.Transcript Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of google-api-services-genomics Show documentation
There is a newer version: v2alpha1-rev20220913-2.0.0
Show newest version
/*
 * 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 transcript represents the assertion that a particular region of the reference genome may be
 * transcribed as RNA.
 *
 *  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 Transcript extends com.google.api.client.json.GenericJson {

  /**
   * The range of the coding sequence for this transcript, if any. To determine the exact ranges of
   * coding sequence, intersect this range with those of the exons, if any. If there are any exons,
   * the codingSequence must start and end within them. Note that in some cases, the reference
   * genome will not exactly match the observed mRNA transcript e.g. due to variance in the source
   * genome from reference. In these cases, exon.frame will not necessarily match the expected
   * reference reading frame and coding exon reference bases cannot necessarily be concatenated to
   * produce the original transcript mRNA.
   * The value may be {@code null}.
   */
  @com.google.api.client.util.Key
  private CodingSequence codingSequence;

  /**
   * The exons that compose this transcript. This field should be unset for genomes where transcript
   * splicing does not occur, for example prokaryotes. Introns are regions of the transcript that
   * are not included in the spliced RNA product. Though not explicitly modeled here, intron ranges
   * can be deduced; all regions of this transcript that are not exons are introns. Exonic sequences
   * do not necessarily code for a translational product (amino acids). Only the regions of exons
   * bounded by the codingSequence correspond to coding DNA sequence. Exons are ordered by start
   * position and may not overlap.
   * The value may be {@code null}.
   */
  @com.google.api.client.util.Key
  private java.util.List exons;

  /**
   * The annotation ID of the gene from which this transcript is transcribed.
   * The value may be {@code null}.
   */
  @com.google.api.client.util.Key
  private java.lang.String geneId;

  /**
   * The range of the coding sequence for this transcript, if any. To determine the exact ranges of
   * coding sequence, intersect this range with those of the exons, if any. If there are any exons,
   * the codingSequence must start and end within them. Note that in some cases, the reference
   * genome will not exactly match the observed mRNA transcript e.g. due to variance in the source
   * genome from reference. In these cases, exon.frame will not necessarily match the expected
   * reference reading frame and coding exon reference bases cannot necessarily be concatenated to
   * produce the original transcript mRNA.
   * @return value or {@code null} for none
   */
  public CodingSequence getCodingSequence() {
    return codingSequence;
  }

  /**
   * The range of the coding sequence for this transcript, if any. To determine the exact ranges of
   * coding sequence, intersect this range with those of the exons, if any. If there are any exons,
   * the codingSequence must start and end within them. Note that in some cases, the reference
   * genome will not exactly match the observed mRNA transcript e.g. due to variance in the source
   * genome from reference. In these cases, exon.frame will not necessarily match the expected
   * reference reading frame and coding exon reference bases cannot necessarily be concatenated to
   * produce the original transcript mRNA.
   * @param codingSequence codingSequence or {@code null} for none
   */
  public Transcript setCodingSequence(CodingSequence codingSequence) {
    this.codingSequence = codingSequence;
    return this;
  }

  /**
   * The exons that compose this transcript. This field should be unset for genomes where transcript
   * splicing does not occur, for example prokaryotes. Introns are regions of the transcript that
   * are not included in the spliced RNA product. Though not explicitly modeled here, intron ranges
   * can be deduced; all regions of this transcript that are not exons are introns. Exonic sequences
   * do not necessarily code for a translational product (amino acids). Only the regions of exons
   * bounded by the codingSequence correspond to coding DNA sequence. Exons are ordered by start
   * position and may not overlap.
   * @return value or {@code null} for none
   */
  public java.util.List getExons() {
    return exons;
  }

  /**
   * The exons that compose this transcript. This field should be unset for genomes where transcript
   * splicing does not occur, for example prokaryotes. Introns are regions of the transcript that
   * are not included in the spliced RNA product. Though not explicitly modeled here, intron ranges
   * can be deduced; all regions of this transcript that are not exons are introns. Exonic sequences
   * do not necessarily code for a translational product (amino acids). Only the regions of exons
   * bounded by the codingSequence correspond to coding DNA sequence. Exons are ordered by start
   * position and may not overlap.
   * @param exons exons or {@code null} for none
   */
  public Transcript setExons(java.util.List exons) {
    this.exons = exons;
    return this;
  }

  /**
   * The annotation ID of the gene from which this transcript is transcribed.
   * @return value or {@code null} for none
   */
  public java.lang.String getGeneId() {
    return geneId;
  }

  /**
   * The annotation ID of the gene from which this transcript is transcribed.
   * @param geneId geneId or {@code null} for none
   */
  public Transcript setGeneId(java.lang.String geneId) {
    this.geneId = geneId;
    return this;
  }

  @Override
  public Transcript set(String fieldName, Object value) {
    return (Transcript) super.set(fieldName, value);
  }

  @Override
  public Transcript clone() {
    return (Transcript) super.clone();
  }

}