5397 lines
138 KiB
PHP
5397 lines
138 KiB
PHP
<?php
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/*
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* Copyright 2010 Google Inc.
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*
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* Licensed under the Apache License, Version 2.0 (the "License"); you may not
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* use this file except in compliance with the License. You may obtain a copy of
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* the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
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* WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
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* License for the specific language governing permissions and limitations under
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* the License.
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*/
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/**
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* Service definition for Genomics (v1beta2).
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*
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* <p>
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* Provides access to Genomics data.</p>
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*
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* <p>
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* For more information about this service, see the API
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* <a href="https://developers.google.com/genomics/v1beta2/reference" target="_blank">Documentation</a>
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* </p>
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*
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* @author Google, Inc.
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*/
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class Google_Service_Genomics extends Google_Service
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{
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/** View and manage your data in Google BigQuery. */
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const BIGQUERY =
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"https://www.googleapis.com/auth/bigquery";
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/** Manage your data in Google Cloud Storage. */
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const DEVSTORAGE_READ_WRITE =
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"https://www.googleapis.com/auth/devstorage.read_write";
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/** View and manage Genomics data. */
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const GENOMICS =
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"https://www.googleapis.com/auth/genomics";
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/** View Genomics data. */
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const GENOMICS_READONLY =
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"https://www.googleapis.com/auth/genomics.readonly";
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public $annotationSets;
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public $annotations;
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public $callsets;
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public $datasets;
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public $experimental_jobs;
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public $jobs;
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public $readgroupsets;
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public $readgroupsets_coveragebuckets;
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public $reads;
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public $references;
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public $references_bases;
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public $referencesets;
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public $variants;
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public $variantsets;
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/**
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* Constructs the internal representation of the Genomics service.
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*
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* @param Google_Client $client
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*/
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public function __construct(Google_Client $client)
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{
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parent::__construct($client);
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$this->servicePath = 'genomics/v1beta2/';
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$this->version = 'v1beta2';
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$this->serviceName = 'genomics';
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$this->annotationSets = new Google_Service_Genomics_AnnotationSets_Resource(
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$this,
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$this->serviceName,
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'annotationSets',
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array(
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'methods' => array(
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'create' => array(
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'path' => 'annotationSets',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'delete' => array(
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'path' => 'annotationSets/{annotationSetId}',
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'httpMethod' => 'DELETE',
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'parameters' => array(
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'annotationSetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'get' => array(
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'path' => 'annotationSets/{annotationSetId}',
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'httpMethod' => 'GET',
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'parameters' => array(
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'annotationSetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'patch' => array(
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'path' => 'annotationSets/{annotationSetId}',
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'httpMethod' => 'PATCH',
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'parameters' => array(
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'annotationSetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'search' => array(
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'path' => 'annotationSets/search',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'update' => array(
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'path' => 'annotationSets/{annotationSetId}',
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'httpMethod' => 'PUT',
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'parameters' => array(
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'annotationSetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),
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)
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)
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);
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$this->annotations = new Google_Service_Genomics_Annotations_Resource(
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$this,
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$this->serviceName,
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'annotations',
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array(
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'methods' => array(
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'batchCreate' => array(
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'path' => 'annotations:batchCreate',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'create' => array(
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'path' => 'annotations',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'delete' => array(
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'path' => 'annotations/{annotationId}',
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'httpMethod' => 'DELETE',
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'parameters' => array(
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'annotationId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'get' => array(
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'path' => 'annotations/{annotationId}',
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'httpMethod' => 'GET',
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'parameters' => array(
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'annotationId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'patch' => array(
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'path' => 'annotations/{annotationId}',
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'httpMethod' => 'PATCH',
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'parameters' => array(
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'annotationId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'search' => array(
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'path' => 'annotations/search',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'update' => array(
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'path' => 'annotations/{annotationId}',
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'httpMethod' => 'PUT',
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'parameters' => array(
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'annotationId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),
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)
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)
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);
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$this->callsets = new Google_Service_Genomics_Callsets_Resource(
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$this,
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$this->serviceName,
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'callsets',
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array(
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'methods' => array(
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'create' => array(
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'path' => 'callsets',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'delete' => array(
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'path' => 'callsets/{callSetId}',
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'httpMethod' => 'DELETE',
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'parameters' => array(
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'callSetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'get' => array(
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'path' => 'callsets/{callSetId}',
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'httpMethod' => 'GET',
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'parameters' => array(
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'callSetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'patch' => array(
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'path' => 'callsets/{callSetId}',
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'httpMethod' => 'PATCH',
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'parameters' => array(
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'callSetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'search' => array(
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'path' => 'callsets/search',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'update' => array(
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'path' => 'callsets/{callSetId}',
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'httpMethod' => 'PUT',
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'parameters' => array(
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'callSetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),
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)
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)
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);
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$this->datasets = new Google_Service_Genomics_Datasets_Resource(
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$this,
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$this->serviceName,
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'datasets',
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array(
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'methods' => array(
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'create' => array(
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'path' => 'datasets',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'delete' => array(
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'path' => 'datasets/{datasetId}',
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'httpMethod' => 'DELETE',
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'parameters' => array(
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'datasetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'get' => array(
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'path' => 'datasets/{datasetId}',
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'httpMethod' => 'GET',
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'parameters' => array(
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'datasetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'list' => array(
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'path' => 'datasets',
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'httpMethod' => 'GET',
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'parameters' => array(
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'pageToken' => array(
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'location' => 'query',
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'type' => 'string',
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),
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'projectNumber' => array(
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'location' => 'query',
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'type' => 'string',
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),
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'pageSize' => array(
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'location' => 'query',
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'type' => 'integer',
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),
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),
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),'patch' => array(
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'path' => 'datasets/{datasetId}',
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'httpMethod' => 'PATCH',
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'parameters' => array(
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'datasetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'undelete' => array(
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'path' => 'datasets/{datasetId}/undelete',
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'httpMethod' => 'POST',
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'parameters' => array(
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'datasetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'update' => array(
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'path' => 'datasets/{datasetId}',
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'httpMethod' => 'PUT',
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'parameters' => array(
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'datasetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),
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)
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)
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);
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$this->experimental_jobs = new Google_Service_Genomics_ExperimentalJobs_Resource(
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$this,
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$this->serviceName,
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'jobs',
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array(
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'methods' => array(
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'create' => array(
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'path' => 'experimental/jobs/create',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),
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)
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)
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);
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$this->jobs = new Google_Service_Genomics_Jobs_Resource(
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$this,
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$this->serviceName,
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'jobs',
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array(
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'methods' => array(
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'cancel' => array(
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'path' => 'jobs/{jobId}/cancel',
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'httpMethod' => 'POST',
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'parameters' => array(
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|
'jobId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'get' => array(
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'path' => 'jobs/{jobId}',
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'httpMethod' => 'GET',
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'parameters' => array(
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'jobId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'search' => array(
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'path' => 'jobs/search',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),
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)
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)
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);
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$this->readgroupsets = new Google_Service_Genomics_Readgroupsets_Resource(
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$this,
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$this->serviceName,
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'readgroupsets',
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array(
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'methods' => array(
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'align' => array(
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'path' => 'readgroupsets/align',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'call' => array(
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'path' => 'readgroupsets/call',
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'httpMethod' => 'POST',
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|
'parameters' => array(),
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|
),'delete' => array(
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'path' => 'readgroupsets/{readGroupSetId}',
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'httpMethod' => 'DELETE',
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|
'parameters' => array(
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|
'readGroupSetId' => array(
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'location' => 'path',
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|
'type' => 'string',
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'required' => true,
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),
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),
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),'export' => array(
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'path' => 'readgroupsets/export',
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'httpMethod' => 'POST',
|
|
'parameters' => array(),
|
|
),'get' => array(
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'path' => 'readgroupsets/{readGroupSetId}',
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|
'httpMethod' => 'GET',
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|
'parameters' => array(
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|
'readGroupSetId' => array(
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|
'location' => 'path',
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|
'type' => 'string',
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|
'required' => true,
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),
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),
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),'import' => array(
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'path' => 'readgroupsets/import',
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'httpMethod' => 'POST',
|
|
'parameters' => array(),
|
|
),'patch' => array(
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|
'path' => 'readgroupsets/{readGroupSetId}',
|
|
'httpMethod' => 'PATCH',
|
|
'parameters' => array(
|
|
'readGroupSetId' => array(
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|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
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|
),
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),
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|
),'search' => array(
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|
'path' => 'readgroupsets/search',
|
|
'httpMethod' => 'POST',
|
|
'parameters' => array(),
|
|
),'update' => array(
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|
'path' => 'readgroupsets/{readGroupSetId}',
|
|
'httpMethod' => 'PUT',
|
|
'parameters' => array(
|
|
'readGroupSetId' => array(
|
|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
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),
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),
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),
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)
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)
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);
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$this->readgroupsets_coveragebuckets = new Google_Service_Genomics_ReadgroupsetsCoveragebuckets_Resource(
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$this,
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$this->serviceName,
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'coveragebuckets',
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array(
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'methods' => array(
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|
'list' => array(
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|
'path' => 'readgroupsets/{readGroupSetId}/coveragebuckets',
|
|
'httpMethod' => 'GET',
|
|
'parameters' => array(
|
|
'readGroupSetId' => array(
|
|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
|
|
),
|
|
'pageSize' => array(
|
|
'location' => 'query',
|
|
'type' => 'integer',
|
|
),
|
|
'range.start' => array(
|
|
'location' => 'query',
|
|
'type' => 'string',
|
|
),
|
|
'range.end' => array(
|
|
'location' => 'query',
|
|
'type' => 'string',
|
|
),
|
|
'range.referenceName' => array(
|
|
'location' => 'query',
|
|
'type' => 'string',
|
|
),
|
|
'pageToken' => array(
|
|
'location' => 'query',
|
|
'type' => 'string',
|
|
),
|
|
'targetBucketWidth' => array(
|
|
'location' => 'query',
|
|
'type' => 'string',
|
|
),
|
|
),
|
|
),
|
|
)
|
|
)
|
|
);
|
|
$this->reads = new Google_Service_Genomics_Reads_Resource(
|
|
$this,
|
|
$this->serviceName,
|
|
'reads',
|
|
array(
|
|
'methods' => array(
|
|
'search' => array(
|
|
'path' => 'reads/search',
|
|
'httpMethod' => 'POST',
|
|
'parameters' => array(),
|
|
),
|
|
)
|
|
)
|
|
);
|
|
$this->references = new Google_Service_Genomics_References_Resource(
|
|
$this,
|
|
$this->serviceName,
|
|
'references',
|
|
array(
|
|
'methods' => array(
|
|
'get' => array(
|
|
'path' => 'references/{referenceId}',
|
|
'httpMethod' => 'GET',
|
|
'parameters' => array(
|
|
'referenceId' => array(
|
|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
|
|
),
|
|
),
|
|
),'search' => array(
|
|
'path' => 'references/search',
|
|
'httpMethod' => 'POST',
|
|
'parameters' => array(),
|
|
),
|
|
)
|
|
)
|
|
);
|
|
$this->references_bases = new Google_Service_Genomics_ReferencesBases_Resource(
|
|
$this,
|
|
$this->serviceName,
|
|
'bases',
|
|
array(
|
|
'methods' => array(
|
|
'list' => array(
|
|
'path' => 'references/{referenceId}/bases',
|
|
'httpMethod' => 'GET',
|
|
'parameters' => array(
|
|
'referenceId' => array(
|
|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
|
|
),
|
|
'pageToken' => array(
|
|
'location' => 'query',
|
|
'type' => 'string',
|
|
),
|
|
'end' => array(
|
|
'location' => 'query',
|
|
'type' => 'string',
|
|
),
|
|
'pageSize' => array(
|
|
'location' => 'query',
|
|
'type' => 'integer',
|
|
),
|
|
'start' => array(
|
|
'location' => 'query',
|
|
'type' => 'string',
|
|
),
|
|
),
|
|
),
|
|
)
|
|
)
|
|
);
|
|
$this->referencesets = new Google_Service_Genomics_Referencesets_Resource(
|
|
$this,
|
|
$this->serviceName,
|
|
'referencesets',
|
|
array(
|
|
'methods' => array(
|
|
'get' => array(
|
|
'path' => 'referencesets/{referenceSetId}',
|
|
'httpMethod' => 'GET',
|
|
'parameters' => array(
|
|
'referenceSetId' => array(
|
|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
|
|
),
|
|
),
|
|
),'search' => array(
|
|
'path' => 'referencesets/search',
|
|
'httpMethod' => 'POST',
|
|
'parameters' => array(),
|
|
),
|
|
)
|
|
)
|
|
);
|
|
$this->variants = new Google_Service_Genomics_Variants_Resource(
|
|
$this,
|
|
$this->serviceName,
|
|
'variants',
|
|
array(
|
|
'methods' => array(
|
|
'create' => array(
|
|
'path' => 'variants',
|
|
'httpMethod' => 'POST',
|
|
'parameters' => array(),
|
|
),'delete' => array(
|
|
'path' => 'variants/{variantId}',
|
|
'httpMethod' => 'DELETE',
|
|
'parameters' => array(
|
|
'variantId' => array(
|
|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
|
|
),
|
|
),
|
|
),'get' => array(
|
|
'path' => 'variants/{variantId}',
|
|
'httpMethod' => 'GET',
|
|
'parameters' => array(
|
|
'variantId' => array(
|
|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
|
|
),
|
|
),
|
|
),'search' => array(
|
|
'path' => 'variants/search',
|
|
'httpMethod' => 'POST',
|
|
'parameters' => array(),
|
|
),'update' => array(
|
|
'path' => 'variants/{variantId}',
|
|
'httpMethod' => 'PUT',
|
|
'parameters' => array(
|
|
'variantId' => array(
|
|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
|
|
),
|
|
),
|
|
),
|
|
)
|
|
)
|
|
);
|
|
$this->variantsets = new Google_Service_Genomics_Variantsets_Resource(
|
|
$this,
|
|
$this->serviceName,
|
|
'variantsets',
|
|
array(
|
|
'methods' => array(
|
|
'delete' => array(
|
|
'path' => 'variantsets/{variantSetId}',
|
|
'httpMethod' => 'DELETE',
|
|
'parameters' => array(
|
|
'variantSetId' => array(
|
|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
|
|
),
|
|
),
|
|
),'export' => array(
|
|
'path' => 'variantsets/{variantSetId}/export',
|
|
'httpMethod' => 'POST',
|
|
'parameters' => array(
|
|
'variantSetId' => array(
|
|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
|
|
),
|
|
),
|
|
),'get' => array(
|
|
'path' => 'variantsets/{variantSetId}',
|
|
'httpMethod' => 'GET',
|
|
'parameters' => array(
|
|
'variantSetId' => array(
|
|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
|
|
),
|
|
),
|
|
),'importVariants' => array(
|
|
'path' => 'variantsets/{variantSetId}/importVariants',
|
|
'httpMethod' => 'POST',
|
|
'parameters' => array(
|
|
'variantSetId' => array(
|
|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
|
|
),
|
|
),
|
|
),'mergeVariants' => array(
|
|
'path' => 'variantsets/{variantSetId}/mergeVariants',
|
|
'httpMethod' => 'POST',
|
|
'parameters' => array(
|
|
'variantSetId' => array(
|
|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
|
|
),
|
|
),
|
|
),'patch' => array(
|
|
'path' => 'variantsets/{variantSetId}',
|
|
'httpMethod' => 'PATCH',
|
|
'parameters' => array(
|
|
'variantSetId' => array(
|
|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
|
|
),
|
|
),
|
|
),'search' => array(
|
|
'path' => 'variantsets/search',
|
|
'httpMethod' => 'POST',
|
|
'parameters' => array(),
|
|
),'update' => array(
|
|
'path' => 'variantsets/{variantSetId}',
|
|
'httpMethod' => 'PUT',
|
|
'parameters' => array(
|
|
'variantSetId' => array(
|
|
'location' => 'path',
|
|
'type' => 'string',
|
|
'required' => true,
|
|
),
|
|
),
|
|
),
|
|
)
|
|
)
|
|
);
|
|
}
|
|
}
|
|
|
|
|
|
/**
|
|
* The "annotationSets" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $annotationSets = $genomicsService->annotationSets;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_AnnotationSets_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Creates a new annotation set. Caller must have WRITE permission for the
|
|
* associated dataset. (annotationSets.create)
|
|
*
|
|
* @param Google_AnnotationSet $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_AnnotationSet
|
|
*/
|
|
public function create(Google_Service_Genomics_AnnotationSet $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('create', array($params), "Google_Service_Genomics_AnnotationSet");
|
|
}
|
|
|
|
/**
|
|
* Deletes an annotation set. Caller must have WRITE permission for the
|
|
* associated annotation set. (annotationSets.delete)
|
|
*
|
|
* @param string $annotationSetId The ID of the annotation set to be deleted.
|
|
* @param array $optParams Optional parameters.
|
|
*/
|
|
public function delete($annotationSetId, $optParams = array())
|
|
{
|
|
$params = array('annotationSetId' => $annotationSetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('delete', array($params));
|
|
}
|
|
|
|
/**
|
|
* Gets an annotation set. Caller must have READ permission for the associated
|
|
* dataset. (annotationSets.get)
|
|
*
|
|
* @param string $annotationSetId The ID of the annotation set to be retrieved.
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_AnnotationSet
|
|
*/
|
|
public function get($annotationSetId, $optParams = array())
|
|
{
|
|
$params = array('annotationSetId' => $annotationSetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('get', array($params), "Google_Service_Genomics_AnnotationSet");
|
|
}
|
|
|
|
/**
|
|
* Updates an annotation set. The update must respect all mutability
|
|
* restrictions and other invariants described on the annotation set resource.
|
|
* Caller must have WRITE permission for the associated dataset. This method
|
|
* supports patch semantics. (annotationSets.patch)
|
|
*
|
|
* @param string $annotationSetId The ID of the annotation set to be updated.
|
|
* @param Google_AnnotationSet $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_AnnotationSet
|
|
*/
|
|
public function patch($annotationSetId, Google_Service_Genomics_AnnotationSet $postBody, $optParams = array())
|
|
{
|
|
$params = array('annotationSetId' => $annotationSetId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('patch', array($params), "Google_Service_Genomics_AnnotationSet");
|
|
}
|
|
|
|
/**
|
|
* Searches for annotation sets which match the given criteria. Results are
|
|
* returned in a deterministic order. Caller must have READ permission for the
|
|
* queried datasets. (annotationSets.search)
|
|
*
|
|
* @param Google_SearchAnnotationSetsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_SearchAnnotationSetsResponse
|
|
*/
|
|
public function search(Google_Service_Genomics_SearchAnnotationSetsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('search', array($params), "Google_Service_Genomics_SearchAnnotationSetsResponse");
|
|
}
|
|
|
|
/**
|
|
* Updates an annotation set. The update must respect all mutability
|
|
* restrictions and other invariants described on the annotation set resource.
|
|
* Caller must have WRITE permission for the associated dataset.
|
|
* (annotationSets.update)
|
|
*
|
|
* @param string $annotationSetId The ID of the annotation set to be updated.
|
|
* @param Google_AnnotationSet $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_AnnotationSet
|
|
*/
|
|
public function update($annotationSetId, Google_Service_Genomics_AnnotationSet $postBody, $optParams = array())
|
|
{
|
|
$params = array('annotationSetId' => $annotationSetId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('update', array($params), "Google_Service_Genomics_AnnotationSet");
|
|
}
|
|
}
|
|
|
|
/**
|
|
* The "annotations" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $annotations = $genomicsService->annotations;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_Annotations_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Creates one or more new annotations atomically. All annotations must belong
|
|
* to the same annotation set. Caller must have WRITE permission for this
|
|
* annotation set. For optimal performance, batch positionally adjacent
|
|
* annotations together.
|
|
*
|
|
* If the request has a systemic issue, such as an attempt to write to an
|
|
* inaccessible annotation set, the entire RPC will fail accordingly. For lesser
|
|
* data issues, when possible an error will be isolated to the corresponding
|
|
* batch entry in the response; the remaining well formed annotations will be
|
|
* created normally. (annotations.batchCreate)
|
|
*
|
|
* @param Google_BatchCreateAnnotationsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_BatchAnnotationsResponse
|
|
*/
|
|
public function batchCreate(Google_Service_Genomics_BatchCreateAnnotationsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('batchCreate', array($params), "Google_Service_Genomics_BatchAnnotationsResponse");
|
|
}
|
|
|
|
/**
|
|
* Creates a new annotation. Caller must have WRITE permission for the
|
|
* associated annotation set. (annotations.create)
|
|
*
|
|
* @param Google_Annotation $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Annotation
|
|
*/
|
|
public function create(Google_Service_Genomics_Annotation $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('create', array($params), "Google_Service_Genomics_Annotation");
|
|
}
|
|
|
|
/**
|
|
* Deletes an annotation. Caller must have WRITE permission for the associated
|
|
* annotation set. (annotations.delete)
|
|
*
|
|
* @param string $annotationId The ID of the annotation set to be deleted.
|
|
* @param array $optParams Optional parameters.
|
|
*/
|
|
public function delete($annotationId, $optParams = array())
|
|
{
|
|
$params = array('annotationId' => $annotationId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('delete', array($params));
|
|
}
|
|
|
|
/**
|
|
* Gets an annotation. Caller must have READ permission for the associated
|
|
* annotation set. (annotations.get)
|
|
*
|
|
* @param string $annotationId The ID of the annotation set to be retrieved.
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Annotation
|
|
*/
|
|
public function get($annotationId, $optParams = array())
|
|
{
|
|
$params = array('annotationId' => $annotationId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('get', array($params), "Google_Service_Genomics_Annotation");
|
|
}
|
|
|
|
/**
|
|
* Updates an annotation. The update must respect all mutability restrictions
|
|
* and other invariants described on the annotation resource. Caller must have
|
|
* WRITE permission for the associated dataset. This method supports patch
|
|
* semantics. (annotations.patch)
|
|
*
|
|
* @param string $annotationId The ID of the annotation set to be updated.
|
|
* @param Google_Annotation $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Annotation
|
|
*/
|
|
public function patch($annotationId, Google_Service_Genomics_Annotation $postBody, $optParams = array())
|
|
{
|
|
$params = array('annotationId' => $annotationId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('patch', array($params), "Google_Service_Genomics_Annotation");
|
|
}
|
|
|
|
/**
|
|
* Searches for annotations which match the given criteria. Results are returned
|
|
* ordered by start position. Annotations which have matching start positions
|
|
* are ordered deterministically. Caller must have READ permission for the
|
|
* queried annotation sets. (annotations.search)
|
|
*
|
|
* @param Google_SearchAnnotationsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_SearchAnnotationsResponse
|
|
*/
|
|
public function search(Google_Service_Genomics_SearchAnnotationsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('search', array($params), "Google_Service_Genomics_SearchAnnotationsResponse");
|
|
}
|
|
|
|
/**
|
|
* Updates an annotation. The update must respect all mutability restrictions
|
|
* and other invariants described on the annotation resource. Caller must have
|
|
* WRITE permission for the associated dataset. (annotations.update)
|
|
*
|
|
* @param string $annotationId The ID of the annotation set to be updated.
|
|
* @param Google_Annotation $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Annotation
|
|
*/
|
|
public function update($annotationId, Google_Service_Genomics_Annotation $postBody, $optParams = array())
|
|
{
|
|
$params = array('annotationId' => $annotationId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('update', array($params), "Google_Service_Genomics_Annotation");
|
|
}
|
|
}
|
|
|
|
/**
|
|
* The "callsets" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $callsets = $genomicsService->callsets;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_Callsets_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Creates a new call set. (callsets.create)
|
|
*
|
|
* @param Google_CallSet $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_CallSet
|
|
*/
|
|
public function create(Google_Service_Genomics_CallSet $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('create', array($params), "Google_Service_Genomics_CallSet");
|
|
}
|
|
|
|
/**
|
|
* Deletes a call set. (callsets.delete)
|
|
*
|
|
* @param string $callSetId The ID of the call set to be deleted.
|
|
* @param array $optParams Optional parameters.
|
|
*/
|
|
public function delete($callSetId, $optParams = array())
|
|
{
|
|
$params = array('callSetId' => $callSetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('delete', array($params));
|
|
}
|
|
|
|
/**
|
|
* Gets a call set by ID. (callsets.get)
|
|
*
|
|
* @param string $callSetId The ID of the call set.
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_CallSet
|
|
*/
|
|
public function get($callSetId, $optParams = array())
|
|
{
|
|
$params = array('callSetId' => $callSetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('get', array($params), "Google_Service_Genomics_CallSet");
|
|
}
|
|
|
|
/**
|
|
* Updates a call set. This method supports patch semantics. (callsets.patch)
|
|
*
|
|
* @param string $callSetId The ID of the call set to be updated.
|
|
* @param Google_CallSet $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_CallSet
|
|
*/
|
|
public function patch($callSetId, Google_Service_Genomics_CallSet $postBody, $optParams = array())
|
|
{
|
|
$params = array('callSetId' => $callSetId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('patch', array($params), "Google_Service_Genomics_CallSet");
|
|
}
|
|
|
|
/**
|
|
* Gets a list of call sets matching the criteria.
|
|
*
|
|
* Implements GlobalAllianceApi.searchCallSets. (callsets.search)
|
|
*
|
|
* @param Google_SearchCallSetsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_SearchCallSetsResponse
|
|
*/
|
|
public function search(Google_Service_Genomics_SearchCallSetsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('search', array($params), "Google_Service_Genomics_SearchCallSetsResponse");
|
|
}
|
|
|
|
/**
|
|
* Updates a call set. (callsets.update)
|
|
*
|
|
* @param string $callSetId The ID of the call set to be updated.
|
|
* @param Google_CallSet $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_CallSet
|
|
*/
|
|
public function update($callSetId, Google_Service_Genomics_CallSet $postBody, $optParams = array())
|
|
{
|
|
$params = array('callSetId' => $callSetId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('update', array($params), "Google_Service_Genomics_CallSet");
|
|
}
|
|
}
|
|
|
|
/**
|
|
* The "datasets" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $datasets = $genomicsService->datasets;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_Datasets_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Creates a new dataset. (datasets.create)
|
|
*
|
|
* @param Google_Dataset $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Dataset
|
|
*/
|
|
public function create(Google_Service_Genomics_Dataset $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('create', array($params), "Google_Service_Genomics_Dataset");
|
|
}
|
|
|
|
/**
|
|
* Deletes a dataset. (datasets.delete)
|
|
*
|
|
* @param string $datasetId The ID of the dataset to be deleted.
|
|
* @param array $optParams Optional parameters.
|
|
*/
|
|
public function delete($datasetId, $optParams = array())
|
|
{
|
|
$params = array('datasetId' => $datasetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('delete', array($params));
|
|
}
|
|
|
|
/**
|
|
* Gets a dataset by ID. (datasets.get)
|
|
*
|
|
* @param string $datasetId The ID of the dataset.
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Dataset
|
|
*/
|
|
public function get($datasetId, $optParams = array())
|
|
{
|
|
$params = array('datasetId' => $datasetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('get', array($params), "Google_Service_Genomics_Dataset");
|
|
}
|
|
|
|
/**
|
|
* Lists all datasets. (datasets.listDatasets)
|
|
*
|
|
* @param array $optParams Optional parameters.
|
|
*
|
|
* @opt_param string pageToken The continuation token, which is used to page
|
|
* through large result sets. To get the next page of results, set this
|
|
* parameter to the value of nextPageToken from the previous response.
|
|
* @opt_param string projectNumber The project to list datasets for.
|
|
* @opt_param int pageSize The maximum number of results returned by this
|
|
* request.
|
|
* @return Google_Service_Genomics_ListDatasetsResponse
|
|
*/
|
|
public function listDatasets($optParams = array())
|
|
{
|
|
$params = array();
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('list', array($params), "Google_Service_Genomics_ListDatasetsResponse");
|
|
}
|
|
|
|
/**
|
|
* Updates a dataset. This method supports patch semantics. (datasets.patch)
|
|
*
|
|
* @param string $datasetId The ID of the dataset to be updated.
|
|
* @param Google_Dataset $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Dataset
|
|
*/
|
|
public function patch($datasetId, Google_Service_Genomics_Dataset $postBody, $optParams = array())
|
|
{
|
|
$params = array('datasetId' => $datasetId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('patch', array($params), "Google_Service_Genomics_Dataset");
|
|
}
|
|
|
|
/**
|
|
* Undeletes a dataset by restoring a dataset which was deleted via this API.
|
|
* This operation is only possible for a week after the deletion occurred.
|
|
* (datasets.undelete)
|
|
*
|
|
* @param string $datasetId The ID of the dataset to be undeleted.
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Dataset
|
|
*/
|
|
public function undelete($datasetId, $optParams = array())
|
|
{
|
|
$params = array('datasetId' => $datasetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('undelete', array($params), "Google_Service_Genomics_Dataset");
|
|
}
|
|
|
|
/**
|
|
* Updates a dataset. (datasets.update)
|
|
*
|
|
* @param string $datasetId The ID of the dataset to be updated.
|
|
* @param Google_Dataset $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Dataset
|
|
*/
|
|
public function update($datasetId, Google_Service_Genomics_Dataset $postBody, $optParams = array())
|
|
{
|
|
$params = array('datasetId' => $datasetId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('update', array($params), "Google_Service_Genomics_Dataset");
|
|
}
|
|
}
|
|
|
|
/**
|
|
* The "experimental" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $experimental = $genomicsService->experimental;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_Experimental_Resource extends Google_Service_Resource
|
|
{
|
|
}
|
|
|
|
/**
|
|
* The "jobs" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $jobs = $genomicsService->jobs;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_ExperimentalJobs_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Creates and asynchronously runs an ad-hoc job. This is an experimental call
|
|
* and may be removed or changed at any time. (jobs.create)
|
|
*
|
|
* @param Google_ExperimentalCreateJobRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_ExperimentalCreateJobResponse
|
|
*/
|
|
public function create(Google_Service_Genomics_ExperimentalCreateJobRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('create', array($params), "Google_Service_Genomics_ExperimentalCreateJobResponse");
|
|
}
|
|
}
|
|
|
|
/**
|
|
* The "jobs" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $jobs = $genomicsService->jobs;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_Jobs_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Cancels a job by ID. Note that it is possible for partial results to be
|
|
* generated and stored for cancelled jobs. (jobs.cancel)
|
|
*
|
|
* @param string $jobId Required. The ID of the job.
|
|
* @param array $optParams Optional parameters.
|
|
*/
|
|
public function cancel($jobId, $optParams = array())
|
|
{
|
|
$params = array('jobId' => $jobId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('cancel', array($params));
|
|
}
|
|
|
|
/**
|
|
* Gets a job by ID. (jobs.get)
|
|
*
|
|
* @param string $jobId Required. The ID of the job.
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Job
|
|
*/
|
|
public function get($jobId, $optParams = array())
|
|
{
|
|
$params = array('jobId' => $jobId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('get', array($params), "Google_Service_Genomics_Job");
|
|
}
|
|
|
|
/**
|
|
* Gets a list of jobs matching the criteria. (jobs.search)
|
|
*
|
|
* @param Google_SearchJobsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_SearchJobsResponse
|
|
*/
|
|
public function search(Google_Service_Genomics_SearchJobsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('search', array($params), "Google_Service_Genomics_SearchJobsResponse");
|
|
}
|
|
}
|
|
|
|
/**
|
|
* The "readgroupsets" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $readgroupsets = $genomicsService->readgroupsets;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_Readgroupsets_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Aligns read data from existing read group sets or files from Google Cloud
|
|
* Storage. See the alignment and variant calling documentation for more
|
|
* details. (readgroupsets.align)
|
|
*
|
|
* @param Google_AlignReadGroupSetsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_AlignReadGroupSetsResponse
|
|
*/
|
|
public function align(Google_Service_Genomics_AlignReadGroupSetsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('align', array($params), "Google_Service_Genomics_AlignReadGroupSetsResponse");
|
|
}
|
|
|
|
/**
|
|
* Calls variants on read data from existing read group sets or files from
|
|
* Google Cloud Storage. See the alignment and variant calling documentation
|
|
* for more details. (readgroupsets.callReadgroupsets)
|
|
*
|
|
* @param Google_CallReadGroupSetsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_CallReadGroupSetsResponse
|
|
*/
|
|
public function callReadgroupsets(Google_Service_Genomics_CallReadGroupSetsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('call', array($params), "Google_Service_Genomics_CallReadGroupSetsResponse");
|
|
}
|
|
|
|
/**
|
|
* Deletes a read group set. (readgroupsets.delete)
|
|
*
|
|
* @param string $readGroupSetId The ID of the read group set to be deleted. The
|
|
* caller must have WRITE permissions to the dataset associated with this read
|
|
* group set.
|
|
* @param array $optParams Optional parameters.
|
|
*/
|
|
public function delete($readGroupSetId, $optParams = array())
|
|
{
|
|
$params = array('readGroupSetId' => $readGroupSetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('delete', array($params));
|
|
}
|
|
|
|
/**
|
|
* Exports read group sets to a BAM file in Google Cloud Storage.
|
|
*
|
|
* Note that currently there may be some differences between exported BAM files
|
|
* and the original BAM file at the time of import. In particular, comments in
|
|
* the input file header will not be preserved, some custom tags will be
|
|
* converted to strings, and original reference sequence order is not
|
|
* necessarily preserved. (readgroupsets.export)
|
|
*
|
|
* @param Google_ExportReadGroupSetsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_ExportReadGroupSetsResponse
|
|
*/
|
|
public function export(Google_Service_Genomics_ExportReadGroupSetsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('export', array($params), "Google_Service_Genomics_ExportReadGroupSetsResponse");
|
|
}
|
|
|
|
/**
|
|
* Gets a read group set by ID. (readgroupsets.get)
|
|
*
|
|
* @param string $readGroupSetId The ID of the read group set.
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_ReadGroupSet
|
|
*/
|
|
public function get($readGroupSetId, $optParams = array())
|
|
{
|
|
$params = array('readGroupSetId' => $readGroupSetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('get', array($params), "Google_Service_Genomics_ReadGroupSet");
|
|
}
|
|
|
|
/**
|
|
* Creates read group sets by asynchronously importing the provided information.
|
|
*
|
|
* Note that currently comments in the input file header are not imported and
|
|
* some custom tags will be converted to strings, rather than preserving tag
|
|
* types. The caller must have WRITE permissions to the dataset.
|
|
* (readgroupsets.import)
|
|
*
|
|
* @param Google_ImportReadGroupSetsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_ImportReadGroupSetsResponse
|
|
*/
|
|
public function import(Google_Service_Genomics_ImportReadGroupSetsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('import', array($params), "Google_Service_Genomics_ImportReadGroupSetsResponse");
|
|
}
|
|
|
|
/**
|
|
* Updates a read group set. This method supports patch semantics.
|
|
* (readgroupsets.patch)
|
|
*
|
|
* @param string $readGroupSetId The ID of the read group set to be updated. The
|
|
* caller must have WRITE permissions to the dataset associated with this read
|
|
* group set.
|
|
* @param Google_ReadGroupSet $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_ReadGroupSet
|
|
*/
|
|
public function patch($readGroupSetId, Google_Service_Genomics_ReadGroupSet $postBody, $optParams = array())
|
|
{
|
|
$params = array('readGroupSetId' => $readGroupSetId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('patch', array($params), "Google_Service_Genomics_ReadGroupSet");
|
|
}
|
|
|
|
/**
|
|
* Searches for read group sets matching the criteria.
|
|
*
|
|
* Implements GlobalAllianceApi.searchReadGroupSets. (readgroupsets.search)
|
|
*
|
|
* @param Google_SearchReadGroupSetsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_SearchReadGroupSetsResponse
|
|
*/
|
|
public function search(Google_Service_Genomics_SearchReadGroupSetsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('search', array($params), "Google_Service_Genomics_SearchReadGroupSetsResponse");
|
|
}
|
|
|
|
/**
|
|
* Updates a read group set. (readgroupsets.update)
|
|
*
|
|
* @param string $readGroupSetId The ID of the read group set to be updated. The
|
|
* caller must have WRITE permissions to the dataset associated with this read
|
|
* group set.
|
|
* @param Google_ReadGroupSet $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_ReadGroupSet
|
|
*/
|
|
public function update($readGroupSetId, Google_Service_Genomics_ReadGroupSet $postBody, $optParams = array())
|
|
{
|
|
$params = array('readGroupSetId' => $readGroupSetId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('update', array($params), "Google_Service_Genomics_ReadGroupSet");
|
|
}
|
|
}
|
|
|
|
/**
|
|
* The "coveragebuckets" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $coveragebuckets = $genomicsService->coveragebuckets;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_ReadgroupsetsCoveragebuckets_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Lists fixed width coverage buckets for a read group set, each of which
|
|
* correspond to a range of a reference sequence. Each bucket summarizes
|
|
* coverage information across its corresponding genomic range.
|
|
*
|
|
* Coverage is defined as the number of reads which are aligned to a given base
|
|
* in the reference sequence. Coverage buckets are available at several
|
|
* precomputed bucket widths, enabling retrieval of various coverage 'zoom
|
|
* levels'. The caller must have READ permissions for the target read group set.
|
|
* (coveragebuckets.listReadgroupsetsCoveragebuckets)
|
|
*
|
|
* @param string $readGroupSetId Required. The ID of the read group set over
|
|
* which coverage is requested.
|
|
* @param array $optParams Optional parameters.
|
|
*
|
|
* @opt_param int pageSize The maximum number of results to return in a single
|
|
* page. If unspecified, defaults to 1024. The maximum value is 2048.
|
|
* @opt_param string range.start The start position of the range on the
|
|
* reference, 0-based inclusive. If specified, referenceName must also be
|
|
* specified.
|
|
* @opt_param string range.end The end position of the range on the reference,
|
|
* 0-based exclusive. If specified, referenceName must also be specified.
|
|
* @opt_param string range.referenceName The reference sequence name, for
|
|
* example chr1, 1, or chrX.
|
|
* @opt_param string pageToken The continuation token, which is used to page
|
|
* through large result sets. To get the next page of results, set this
|
|
* parameter to the value of nextPageToken from the previous response.
|
|
* @opt_param string targetBucketWidth The desired width of each reported
|
|
* coverage bucket in base pairs. This will be rounded down to the nearest
|
|
* precomputed bucket width; the value of which is returned as bucketWidth in
|
|
* the response. Defaults to infinity (each bucket spans an entire reference
|
|
* sequence) or the length of the target range, if specified. The smallest
|
|
* precomputed bucketWidth is currently 2048 base pairs; this is subject to
|
|
* change.
|
|
* @return Google_Service_Genomics_ListCoverageBucketsResponse
|
|
*/
|
|
public function listReadgroupsetsCoveragebuckets($readGroupSetId, $optParams = array())
|
|
{
|
|
$params = array('readGroupSetId' => $readGroupSetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('list', array($params), "Google_Service_Genomics_ListCoverageBucketsResponse");
|
|
}
|
|
}
|
|
|
|
/**
|
|
* The "reads" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $reads = $genomicsService->reads;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_Reads_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Gets a list of reads for one or more read group sets. Reads search operates
|
|
* over a genomic coordinate space of reference sequence & position defined over
|
|
* the reference sequences to which the requested read group sets are aligned.
|
|
*
|
|
* If a target positional range is specified, search returns all reads whose
|
|
* alignment to the reference genome overlap the range. A query which specifies
|
|
* only read group set IDs yields all reads in those read group sets, including
|
|
* unmapped reads.
|
|
*
|
|
* All reads returned (including reads on subsequent pages) are ordered by
|
|
* genomic coordinate (reference sequence & position). Reads with equivalent
|
|
* genomic coordinates are returned in a deterministic order.
|
|
*
|
|
* Implements GlobalAllianceApi.searchReads. (reads.search)
|
|
*
|
|
* @param Google_SearchReadsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_SearchReadsResponse
|
|
*/
|
|
public function search(Google_Service_Genomics_SearchReadsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('search', array($params), "Google_Service_Genomics_SearchReadsResponse");
|
|
}
|
|
}
|
|
|
|
/**
|
|
* The "references" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $references = $genomicsService->references;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_References_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Gets a reference.
|
|
*
|
|
* Implements GlobalAllianceApi.getReference. (references.get)
|
|
*
|
|
* @param string $referenceId The ID of the reference.
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Reference
|
|
*/
|
|
public function get($referenceId, $optParams = array())
|
|
{
|
|
$params = array('referenceId' => $referenceId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('get', array($params), "Google_Service_Genomics_Reference");
|
|
}
|
|
|
|
/**
|
|
* Searches for references which match the given criteria.
|
|
*
|
|
* Implements GlobalAllianceApi.searchReferences. (references.search)
|
|
*
|
|
* @param Google_SearchReferencesRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_SearchReferencesResponse
|
|
*/
|
|
public function search(Google_Service_Genomics_SearchReferencesRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('search', array($params), "Google_Service_Genomics_SearchReferencesResponse");
|
|
}
|
|
}
|
|
|
|
/**
|
|
* The "bases" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $bases = $genomicsService->bases;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_ReferencesBases_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Lists the bases in a reference, optionally restricted to a range.
|
|
*
|
|
* Implements GlobalAllianceApi.getReferenceBases. (bases.listReferencesBases)
|
|
*
|
|
* @param string $referenceId The ID of the reference.
|
|
* @param array $optParams Optional parameters.
|
|
*
|
|
* @opt_param string pageToken The continuation token, which is used to page
|
|
* through large result sets. To get the next page of results, set this
|
|
* parameter to the value of nextPageToken from the previous response.
|
|
* @opt_param string end The end position (0-based, exclusive) of this query.
|
|
* Defaults to the length of this reference.
|
|
* @opt_param int pageSize Specifies the maximum number of bases to return in a
|
|
* single page.
|
|
* @opt_param string start The start position (0-based) of this query. Defaults
|
|
* to 0.
|
|
* @return Google_Service_Genomics_ListBasesResponse
|
|
*/
|
|
public function listReferencesBases($referenceId, $optParams = array())
|
|
{
|
|
$params = array('referenceId' => $referenceId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('list', array($params), "Google_Service_Genomics_ListBasesResponse");
|
|
}
|
|
}
|
|
|
|
/**
|
|
* The "referencesets" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $referencesets = $genomicsService->referencesets;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_Referencesets_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Gets a reference set.
|
|
*
|
|
* Implements GlobalAllianceApi.getReferenceSet. (referencesets.get)
|
|
*
|
|
* @param string $referenceSetId The ID of the reference set.
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_ReferenceSet
|
|
*/
|
|
public function get($referenceSetId, $optParams = array())
|
|
{
|
|
$params = array('referenceSetId' => $referenceSetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('get', array($params), "Google_Service_Genomics_ReferenceSet");
|
|
}
|
|
|
|
/**
|
|
* Searches for reference sets which match the given criteria.
|
|
*
|
|
* Implements GlobalAllianceApi.searchReferenceSets. (referencesets.search)
|
|
*
|
|
* @param Google_SearchReferenceSetsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_SearchReferenceSetsResponse
|
|
*/
|
|
public function search(Google_Service_Genomics_SearchReferenceSetsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('search', array($params), "Google_Service_Genomics_SearchReferenceSetsResponse");
|
|
}
|
|
}
|
|
|
|
/**
|
|
* The "variants" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $variants = $genomicsService->variants;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_Variants_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Creates a new variant. (variants.create)
|
|
*
|
|
* @param Google_Variant $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Variant
|
|
*/
|
|
public function create(Google_Service_Genomics_Variant $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('create', array($params), "Google_Service_Genomics_Variant");
|
|
}
|
|
|
|
/**
|
|
* Deletes a variant. (variants.delete)
|
|
*
|
|
* @param string $variantId The ID of the variant to be deleted.
|
|
* @param array $optParams Optional parameters.
|
|
*/
|
|
public function delete($variantId, $optParams = array())
|
|
{
|
|
$params = array('variantId' => $variantId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('delete', array($params));
|
|
}
|
|
|
|
/**
|
|
* Gets a variant by ID. (variants.get)
|
|
*
|
|
* @param string $variantId The ID of the variant.
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Variant
|
|
*/
|
|
public function get($variantId, $optParams = array())
|
|
{
|
|
$params = array('variantId' => $variantId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('get', array($params), "Google_Service_Genomics_Variant");
|
|
}
|
|
|
|
/**
|
|
* Gets a list of variants matching the criteria.
|
|
*
|
|
* Implements GlobalAllianceApi.searchVariants. (variants.search)
|
|
*
|
|
* @param Google_SearchVariantsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_SearchVariantsResponse
|
|
*/
|
|
public function search(Google_Service_Genomics_SearchVariantsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('search', array($params), "Google_Service_Genomics_SearchVariantsResponse");
|
|
}
|
|
|
|
/**
|
|
* Updates a variant's names and info fields. All other modifications are
|
|
* silently ignored. Returns the modified variant without its calls.
|
|
* (variants.update)
|
|
*
|
|
* @param string $variantId The ID of the variant to be updated.
|
|
* @param Google_Variant $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Variant
|
|
*/
|
|
public function update($variantId, Google_Service_Genomics_Variant $postBody, $optParams = array())
|
|
{
|
|
$params = array('variantId' => $variantId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('update', array($params), "Google_Service_Genomics_Variant");
|
|
}
|
|
}
|
|
|
|
/**
|
|
* The "variantsets" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $variantsets = $genomicsService->variantsets;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_Variantsets_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Deletes the contents of a variant set. The variant set object is not deleted.
|
|
* (variantsets.delete)
|
|
*
|
|
* @param string $variantSetId The ID of the variant set to be deleted.
|
|
* @param array $optParams Optional parameters.
|
|
*/
|
|
public function delete($variantSetId, $optParams = array())
|
|
{
|
|
$params = array('variantSetId' => $variantSetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('delete', array($params));
|
|
}
|
|
|
|
/**
|
|
* Exports variant set data to an external destination. (variantsets.export)
|
|
*
|
|
* @param string $variantSetId Required. The ID of the variant set that contains
|
|
* variant data which should be exported. The caller must have READ access to
|
|
* this variant set.
|
|
* @param Google_ExportVariantSetRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_ExportVariantSetResponse
|
|
*/
|
|
public function export($variantSetId, Google_Service_Genomics_ExportVariantSetRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('variantSetId' => $variantSetId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('export', array($params), "Google_Service_Genomics_ExportVariantSetResponse");
|
|
}
|
|
|
|
/**
|
|
* Gets a variant set by ID. (variantsets.get)
|
|
*
|
|
* @param string $variantSetId Required. The ID of the variant set.
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_VariantSet
|
|
*/
|
|
public function get($variantSetId, $optParams = array())
|
|
{
|
|
$params = array('variantSetId' => $variantSetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('get', array($params), "Google_Service_Genomics_VariantSet");
|
|
}
|
|
|
|
/**
|
|
* Creates variant data by asynchronously importing the provided information.
|
|
*
|
|
* The variants for import will be merged with any existing data and each other
|
|
* according to the behavior of mergeVariants. In particular, this means for
|
|
* merged VCF variants that have conflicting INFO fields, some data will be
|
|
* arbitrarily discarded. As a special case, for single-sample VCF files, QUAL
|
|
* and FILTER fields will be moved to the call level; these are sometimes
|
|
* interpreted in a call-specific context. Imported VCF headers are appended to
|
|
* the metadata already in a variant set. (variantsets.importVariants)
|
|
*
|
|
* @param string $variantSetId Required. The variant set to which variant data
|
|
* should be imported.
|
|
* @param Google_ImportVariantsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_ImportVariantsResponse
|
|
*/
|
|
public function importVariants($variantSetId, Google_Service_Genomics_ImportVariantsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('variantSetId' => $variantSetId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('importVariants', array($params), "Google_Service_Genomics_ImportVariantsResponse");
|
|
}
|
|
|
|
/**
|
|
* Merges the given variants with existing variants. Each variant will be merged
|
|
* with an existing variant that matches its reference sequence, start, end,
|
|
* reference bases, and alternative bases. If no such variant exists, a new one
|
|
* will be created.
|
|
*
|
|
* When variants are merged, the call information from the new variant is added
|
|
* to the existing variant, and other fields (such as key/value pairs) are
|
|
* discarded. (variantsets.mergeVariants)
|
|
*
|
|
* @param string $variantSetId The destination variant set.
|
|
* @param Google_MergeVariantsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
*/
|
|
public function mergeVariants($variantSetId, Google_Service_Genomics_MergeVariantsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('variantSetId' => $variantSetId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('mergeVariants', array($params));
|
|
}
|
|
|
|
/**
|
|
* Updates a variant set's metadata. All other modifications are silently
|
|
* ignored. This method supports patch semantics. (variantsets.patch)
|
|
*
|
|
* @param string $variantSetId The ID of the variant to be updated.
|
|
* @param Google_VariantSet $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_VariantSet
|
|
*/
|
|
public function patch($variantSetId, Google_Service_Genomics_VariantSet $postBody, $optParams = array())
|
|
{
|
|
$params = array('variantSetId' => $variantSetId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('patch', array($params), "Google_Service_Genomics_VariantSet");
|
|
}
|
|
|
|
/**
|
|
* Returns a list of all variant sets matching search criteria.
|
|
*
|
|
* Implements GlobalAllianceApi.searchVariantSets. (variantsets.search)
|
|
*
|
|
* @param Google_SearchVariantSetsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_SearchVariantSetsResponse
|
|
*/
|
|
public function search(Google_Service_Genomics_SearchVariantSetsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('search', array($params), "Google_Service_Genomics_SearchVariantSetsResponse");
|
|
}
|
|
|
|
/**
|
|
* Updates a variant set's metadata. All other modifications are silently
|
|
* ignored. (variantsets.update)
|
|
*
|
|
* @param string $variantSetId The ID of the variant to be updated.
|
|
* @param Google_VariantSet $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_VariantSet
|
|
*/
|
|
public function update($variantSetId, Google_Service_Genomics_VariantSet $postBody, $optParams = array())
|
|
{
|
|
$params = array('variantSetId' => $variantSetId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('update', array($params), "Google_Service_Genomics_VariantSet");
|
|
}
|
|
}
|
|
|
|
|
|
|
|
|
|
class Google_Service_Genomics_AlignReadGroupSetsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'bamSourceUris';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $bamSourceUris;
|
|
public $datasetId;
|
|
protected $interleavedFastqSourceType = 'Google_Service_Genomics_InterleavedFastqSource';
|
|
protected $interleavedFastqSourceDataType = '';
|
|
protected $pairedFastqSourceType = 'Google_Service_Genomics_PairedFastqSource';
|
|
protected $pairedFastqSourceDataType = '';
|
|
public $readGroupSetId;
|
|
|
|
|
|
public function setBamSourceUris($bamSourceUris)
|
|
{
|
|
$this->bamSourceUris = $bamSourceUris;
|
|
}
|
|
public function getBamSourceUris()
|
|
{
|
|
return $this->bamSourceUris;
|
|
}
|
|
public function setDatasetId($datasetId)
|
|
{
|
|
$this->datasetId = $datasetId;
|
|
}
|
|
public function getDatasetId()
|
|
{
|
|
return $this->datasetId;
|
|
}
|
|
public function setInterleavedFastqSource(Google_Service_Genomics_InterleavedFastqSource $interleavedFastqSource)
|
|
{
|
|
$this->interleavedFastqSource = $interleavedFastqSource;
|
|
}
|
|
public function getInterleavedFastqSource()
|
|
{
|
|
return $this->interleavedFastqSource;
|
|
}
|
|
public function setPairedFastqSource(Google_Service_Genomics_PairedFastqSource $pairedFastqSource)
|
|
{
|
|
$this->pairedFastqSource = $pairedFastqSource;
|
|
}
|
|
public function getPairedFastqSource()
|
|
{
|
|
return $this->pairedFastqSource;
|
|
}
|
|
public function setReadGroupSetId($readGroupSetId)
|
|
{
|
|
$this->readGroupSetId = $readGroupSetId;
|
|
}
|
|
public function getReadGroupSetId()
|
|
{
|
|
return $this->readGroupSetId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_AlignReadGroupSetsResponse extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $jobId;
|
|
|
|
|
|
public function setJobId($jobId)
|
|
{
|
|
$this->jobId = $jobId;
|
|
}
|
|
public function getJobId()
|
|
{
|
|
return $this->jobId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_Annotation extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $annotationSetId;
|
|
public $id;
|
|
public $info;
|
|
public $name;
|
|
protected $positionType = 'Google_Service_Genomics_RangePosition';
|
|
protected $positionDataType = '';
|
|
protected $transcriptType = 'Google_Service_Genomics_Transcript';
|
|
protected $transcriptDataType = '';
|
|
public $type;
|
|
protected $variantType = 'Google_Service_Genomics_VariantAnnotation';
|
|
protected $variantDataType = '';
|
|
|
|
|
|
public function setAnnotationSetId($annotationSetId)
|
|
{
|
|
$this->annotationSetId = $annotationSetId;
|
|
}
|
|
public function getAnnotationSetId()
|
|
{
|
|
return $this->annotationSetId;
|
|
}
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
public function setInfo($info)
|
|
{
|
|
$this->info = $info;
|
|
}
|
|
public function getInfo()
|
|
{
|
|
return $this->info;
|
|
}
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
public function setPosition(Google_Service_Genomics_RangePosition $position)
|
|
{
|
|
$this->position = $position;
|
|
}
|
|
public function getPosition()
|
|
{
|
|
return $this->position;
|
|
}
|
|
public function setTranscript(Google_Service_Genomics_Transcript $transcript)
|
|
{
|
|
$this->transcript = $transcript;
|
|
}
|
|
public function getTranscript()
|
|
{
|
|
return $this->transcript;
|
|
}
|
|
public function setType($type)
|
|
{
|
|
$this->type = $type;
|
|
}
|
|
public function getType()
|
|
{
|
|
return $this->type;
|
|
}
|
|
public function setVariant(Google_Service_Genomics_VariantAnnotation $variant)
|
|
{
|
|
$this->variant = $variant;
|
|
}
|
|
public function getVariant()
|
|
{
|
|
return $this->variant;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_AnnotationInfo extends Google_Model
|
|
{
|
|
}
|
|
|
|
class Google_Service_Genomics_AnnotationSet extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $datasetId;
|
|
public $id;
|
|
public $info;
|
|
public $name;
|
|
public $referenceSetId;
|
|
public $sourceUri;
|
|
public $type;
|
|
|
|
|
|
public function setDatasetId($datasetId)
|
|
{
|
|
$this->datasetId = $datasetId;
|
|
}
|
|
public function getDatasetId()
|
|
{
|
|
return $this->datasetId;
|
|
}
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
public function setInfo($info)
|
|
{
|
|
$this->info = $info;
|
|
}
|
|
public function getInfo()
|
|
{
|
|
return $this->info;
|
|
}
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
public function setReferenceSetId($referenceSetId)
|
|
{
|
|
$this->referenceSetId = $referenceSetId;
|
|
}
|
|
public function getReferenceSetId()
|
|
{
|
|
return $this->referenceSetId;
|
|
}
|
|
public function setSourceUri($sourceUri)
|
|
{
|
|
$this->sourceUri = $sourceUri;
|
|
}
|
|
public function getSourceUri()
|
|
{
|
|
return $this->sourceUri;
|
|
}
|
|
public function setType($type)
|
|
{
|
|
$this->type = $type;
|
|
}
|
|
public function getType()
|
|
{
|
|
return $this->type;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_AnnotationSetInfo extends Google_Model
|
|
{
|
|
}
|
|
|
|
class Google_Service_Genomics_BatchAnnotationsResponse extends Google_Collection
|
|
{
|
|
protected $collection_key = 'entries';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
protected $entriesType = 'Google_Service_Genomics_BatchAnnotationsResponseEntry';
|
|
protected $entriesDataType = 'array';
|
|
|
|
|
|
public function setEntries($entries)
|
|
{
|
|
$this->entries = $entries;
|
|
}
|
|
public function getEntries()
|
|
{
|
|
return $this->entries;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_BatchAnnotationsResponseEntry extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
protected $annotationType = 'Google_Service_Genomics_Annotation';
|
|
protected $annotationDataType = '';
|
|
protected $statusType = 'Google_Service_Genomics_BatchAnnotationsResponseEntryStatus';
|
|
protected $statusDataType = '';
|
|
|
|
|
|
public function setAnnotation(Google_Service_Genomics_Annotation $annotation)
|
|
{
|
|
$this->annotation = $annotation;
|
|
}
|
|
public function getAnnotation()
|
|
{
|
|
return $this->annotation;
|
|
}
|
|
public function setStatus(Google_Service_Genomics_BatchAnnotationsResponseEntryStatus $status)
|
|
{
|
|
$this->status = $status;
|
|
}
|
|
public function getStatus()
|
|
{
|
|
return $this->status;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_BatchAnnotationsResponseEntryStatus extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $code;
|
|
public $message;
|
|
|
|
|
|
public function setCode($code)
|
|
{
|
|
$this->code = $code;
|
|
}
|
|
public function getCode()
|
|
{
|
|
return $this->code;
|
|
}
|
|
public function setMessage($message)
|
|
{
|
|
$this->message = $message;
|
|
}
|
|
public function getMessage()
|
|
{
|
|
return $this->message;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_BatchCreateAnnotationsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'annotations';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
protected $annotationsType = 'Google_Service_Genomics_Annotation';
|
|
protected $annotationsDataType = 'array';
|
|
|
|
|
|
public function setAnnotations($annotations)
|
|
{
|
|
$this->annotations = $annotations;
|
|
}
|
|
public function getAnnotations()
|
|
{
|
|
return $this->annotations;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_CallReadGroupSetsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'sourceUris';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $datasetId;
|
|
public $readGroupSetId;
|
|
public $sourceUris;
|
|
|
|
|
|
public function setDatasetId($datasetId)
|
|
{
|
|
$this->datasetId = $datasetId;
|
|
}
|
|
public function getDatasetId()
|
|
{
|
|
return $this->datasetId;
|
|
}
|
|
public function setReadGroupSetId($readGroupSetId)
|
|
{
|
|
$this->readGroupSetId = $readGroupSetId;
|
|
}
|
|
public function getReadGroupSetId()
|
|
{
|
|
return $this->readGroupSetId;
|
|
}
|
|
public function setSourceUris($sourceUris)
|
|
{
|
|
$this->sourceUris = $sourceUris;
|
|
}
|
|
public function getSourceUris()
|
|
{
|
|
return $this->sourceUris;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_CallReadGroupSetsResponse extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $jobId;
|
|
|
|
|
|
public function setJobId($jobId)
|
|
{
|
|
$this->jobId = $jobId;
|
|
}
|
|
public function getJobId()
|
|
{
|
|
return $this->jobId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_CallSet extends Google_Collection
|
|
{
|
|
protected $collection_key = 'variantSetIds';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $created;
|
|
public $id;
|
|
public $info;
|
|
public $name;
|
|
public $sampleId;
|
|
public $variantSetIds;
|
|
|
|
|
|
public function setCreated($created)
|
|
{
|
|
$this->created = $created;
|
|
}
|
|
public function getCreated()
|
|
{
|
|
return $this->created;
|
|
}
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
public function setInfo($info)
|
|
{
|
|
$this->info = $info;
|
|
}
|
|
public function getInfo()
|
|
{
|
|
return $this->info;
|
|
}
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
public function setSampleId($sampleId)
|
|
{
|
|
$this->sampleId = $sampleId;
|
|
}
|
|
public function getSampleId()
|
|
{
|
|
return $this->sampleId;
|
|
}
|
|
public function setVariantSetIds($variantSetIds)
|
|
{
|
|
$this->variantSetIds = $variantSetIds;
|
|
}
|
|
public function getVariantSetIds()
|
|
{
|
|
return $this->variantSetIds;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_CallSetInfo extends Google_Model
|
|
{
|
|
}
|
|
|
|
class Google_Service_Genomics_CigarUnit extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $operation;
|
|
public $operationLength;
|
|
public $referenceSequence;
|
|
|
|
|
|
public function setOperation($operation)
|
|
{
|
|
$this->operation = $operation;
|
|
}
|
|
public function getOperation()
|
|
{
|
|
return $this->operation;
|
|
}
|
|
public function setOperationLength($operationLength)
|
|
{
|
|
$this->operationLength = $operationLength;
|
|
}
|
|
public function getOperationLength()
|
|
{
|
|
return $this->operationLength;
|
|
}
|
|
public function setReferenceSequence($referenceSequence)
|
|
{
|
|
$this->referenceSequence = $referenceSequence;
|
|
}
|
|
public function getReferenceSequence()
|
|
{
|
|
return $this->referenceSequence;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_CoverageBucket extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $meanCoverage;
|
|
protected $rangeType = 'Google_Service_Genomics_Range';
|
|
protected $rangeDataType = '';
|
|
|
|
|
|
public function setMeanCoverage($meanCoverage)
|
|
{
|
|
$this->meanCoverage = $meanCoverage;
|
|
}
|
|
public function getMeanCoverage()
|
|
{
|
|
return $this->meanCoverage;
|
|
}
|
|
public function setRange(Google_Service_Genomics_Range $range)
|
|
{
|
|
$this->range = $range;
|
|
}
|
|
public function getRange()
|
|
{
|
|
return $this->range;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_Dataset extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $id;
|
|
public $isPublic;
|
|
public $name;
|
|
public $projectNumber;
|
|
|
|
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
public function setIsPublic($isPublic)
|
|
{
|
|
$this->isPublic = $isPublic;
|
|
}
|
|
public function getIsPublic()
|
|
{
|
|
return $this->isPublic;
|
|
}
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
public function setProjectNumber($projectNumber)
|
|
{
|
|
$this->projectNumber = $projectNumber;
|
|
}
|
|
public function getProjectNumber()
|
|
{
|
|
return $this->projectNumber;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ExperimentalCreateJobRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'sourceUris';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $align;
|
|
public $callVariants;
|
|
public $gcsOutputPath;
|
|
public $pairedSourceUris;
|
|
public $projectNumber;
|
|
public $sourceUris;
|
|
|
|
|
|
public function setAlign($align)
|
|
{
|
|
$this->align = $align;
|
|
}
|
|
public function getAlign()
|
|
{
|
|
return $this->align;
|
|
}
|
|
public function setCallVariants($callVariants)
|
|
{
|
|
$this->callVariants = $callVariants;
|
|
}
|
|
public function getCallVariants()
|
|
{
|
|
return $this->callVariants;
|
|
}
|
|
public function setGcsOutputPath($gcsOutputPath)
|
|
{
|
|
$this->gcsOutputPath = $gcsOutputPath;
|
|
}
|
|
public function getGcsOutputPath()
|
|
{
|
|
return $this->gcsOutputPath;
|
|
}
|
|
public function setPairedSourceUris($pairedSourceUris)
|
|
{
|
|
$this->pairedSourceUris = $pairedSourceUris;
|
|
}
|
|
public function getPairedSourceUris()
|
|
{
|
|
return $this->pairedSourceUris;
|
|
}
|
|
public function setProjectNumber($projectNumber)
|
|
{
|
|
$this->projectNumber = $projectNumber;
|
|
}
|
|
public function getProjectNumber()
|
|
{
|
|
return $this->projectNumber;
|
|
}
|
|
public function setSourceUris($sourceUris)
|
|
{
|
|
$this->sourceUris = $sourceUris;
|
|
}
|
|
public function getSourceUris()
|
|
{
|
|
return $this->sourceUris;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ExperimentalCreateJobResponse extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $jobId;
|
|
|
|
|
|
public function setJobId($jobId)
|
|
{
|
|
$this->jobId = $jobId;
|
|
}
|
|
public function getJobId()
|
|
{
|
|
return $this->jobId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ExportReadGroupSetsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'referenceNames';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $exportUri;
|
|
public $projectNumber;
|
|
public $readGroupSetIds;
|
|
public $referenceNames;
|
|
|
|
|
|
public function setExportUri($exportUri)
|
|
{
|
|
$this->exportUri = $exportUri;
|
|
}
|
|
public function getExportUri()
|
|
{
|
|
return $this->exportUri;
|
|
}
|
|
public function setProjectNumber($projectNumber)
|
|
{
|
|
$this->projectNumber = $projectNumber;
|
|
}
|
|
public function getProjectNumber()
|
|
{
|
|
return $this->projectNumber;
|
|
}
|
|
public function setReadGroupSetIds($readGroupSetIds)
|
|
{
|
|
$this->readGroupSetIds = $readGroupSetIds;
|
|
}
|
|
public function getReadGroupSetIds()
|
|
{
|
|
return $this->readGroupSetIds;
|
|
}
|
|
public function setReferenceNames($referenceNames)
|
|
{
|
|
$this->referenceNames = $referenceNames;
|
|
}
|
|
public function getReferenceNames()
|
|
{
|
|
return $this->referenceNames;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ExportReadGroupSetsResponse extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $jobId;
|
|
|
|
|
|
public function setJobId($jobId)
|
|
{
|
|
$this->jobId = $jobId;
|
|
}
|
|
public function getJobId()
|
|
{
|
|
return $this->jobId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ExportVariantSetRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'callSetIds';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $bigqueryDataset;
|
|
public $bigqueryTable;
|
|
public $callSetIds;
|
|
public $format;
|
|
public $projectNumber;
|
|
|
|
|
|
public function setBigqueryDataset($bigqueryDataset)
|
|
{
|
|
$this->bigqueryDataset = $bigqueryDataset;
|
|
}
|
|
public function getBigqueryDataset()
|
|
{
|
|
return $this->bigqueryDataset;
|
|
}
|
|
public function setBigqueryTable($bigqueryTable)
|
|
{
|
|
$this->bigqueryTable = $bigqueryTable;
|
|
}
|
|
public function getBigqueryTable()
|
|
{
|
|
return $this->bigqueryTable;
|
|
}
|
|
public function setCallSetIds($callSetIds)
|
|
{
|
|
$this->callSetIds = $callSetIds;
|
|
}
|
|
public function getCallSetIds()
|
|
{
|
|
return $this->callSetIds;
|
|
}
|
|
public function setFormat($format)
|
|
{
|
|
$this->format = $format;
|
|
}
|
|
public function getFormat()
|
|
{
|
|
return $this->format;
|
|
}
|
|
public function setProjectNumber($projectNumber)
|
|
{
|
|
$this->projectNumber = $projectNumber;
|
|
}
|
|
public function getProjectNumber()
|
|
{
|
|
return $this->projectNumber;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ExportVariantSetResponse extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $jobId;
|
|
|
|
|
|
public function setJobId($jobId)
|
|
{
|
|
$this->jobId = $jobId;
|
|
}
|
|
public function getJobId()
|
|
{
|
|
return $this->jobId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ExternalId extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $id;
|
|
public $sourceName;
|
|
|
|
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
public function setSourceName($sourceName)
|
|
{
|
|
$this->sourceName = $sourceName;
|
|
}
|
|
public function getSourceName()
|
|
{
|
|
return $this->sourceName;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_FastqMetadata extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $libraryName;
|
|
public $platformName;
|
|
public $platformUnit;
|
|
public $readGroupName;
|
|
public $sampleName;
|
|
|
|
|
|
public function setLibraryName($libraryName)
|
|
{
|
|
$this->libraryName = $libraryName;
|
|
}
|
|
public function getLibraryName()
|
|
{
|
|
return $this->libraryName;
|
|
}
|
|
public function setPlatformName($platformName)
|
|
{
|
|
$this->platformName = $platformName;
|
|
}
|
|
public function getPlatformName()
|
|
{
|
|
return $this->platformName;
|
|
}
|
|
public function setPlatformUnit($platformUnit)
|
|
{
|
|
$this->platformUnit = $platformUnit;
|
|
}
|
|
public function getPlatformUnit()
|
|
{
|
|
return $this->platformUnit;
|
|
}
|
|
public function setReadGroupName($readGroupName)
|
|
{
|
|
$this->readGroupName = $readGroupName;
|
|
}
|
|
public function getReadGroupName()
|
|
{
|
|
return $this->readGroupName;
|
|
}
|
|
public function setSampleName($sampleName)
|
|
{
|
|
$this->sampleName = $sampleName;
|
|
}
|
|
public function getSampleName()
|
|
{
|
|
return $this->sampleName;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_GenomicsCall extends Google_Collection
|
|
{
|
|
protected $collection_key = 'genotypeLikelihood';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $callSetId;
|
|
public $callSetName;
|
|
public $genotype;
|
|
public $genotypeLikelihood;
|
|
public $info;
|
|
public $phaseset;
|
|
|
|
|
|
public function setCallSetId($callSetId)
|
|
{
|
|
$this->callSetId = $callSetId;
|
|
}
|
|
public function getCallSetId()
|
|
{
|
|
return $this->callSetId;
|
|
}
|
|
public function setCallSetName($callSetName)
|
|
{
|
|
$this->callSetName = $callSetName;
|
|
}
|
|
public function getCallSetName()
|
|
{
|
|
return $this->callSetName;
|
|
}
|
|
public function setGenotype($genotype)
|
|
{
|
|
$this->genotype = $genotype;
|
|
}
|
|
public function getGenotype()
|
|
{
|
|
return $this->genotype;
|
|
}
|
|
public function setGenotypeLikelihood($genotypeLikelihood)
|
|
{
|
|
$this->genotypeLikelihood = $genotypeLikelihood;
|
|
}
|
|
public function getGenotypeLikelihood()
|
|
{
|
|
return $this->genotypeLikelihood;
|
|
}
|
|
public function setInfo($info)
|
|
{
|
|
$this->info = $info;
|
|
}
|
|
public function getInfo()
|
|
{
|
|
return $this->info;
|
|
}
|
|
public function setPhaseset($phaseset)
|
|
{
|
|
$this->phaseset = $phaseset;
|
|
}
|
|
public function getPhaseset()
|
|
{
|
|
return $this->phaseset;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_GenomicsCallInfo extends Google_Model
|
|
{
|
|
}
|
|
|
|
class Google_Service_Genomics_ImportReadGroupSetsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'sourceUris';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $datasetId;
|
|
public $partitionStrategy;
|
|
public $referenceSetId;
|
|
public $sourceUris;
|
|
|
|
|
|
public function setDatasetId($datasetId)
|
|
{
|
|
$this->datasetId = $datasetId;
|
|
}
|
|
public function getDatasetId()
|
|
{
|
|
return $this->datasetId;
|
|
}
|
|
public function setPartitionStrategy($partitionStrategy)
|
|
{
|
|
$this->partitionStrategy = $partitionStrategy;
|
|
}
|
|
public function getPartitionStrategy()
|
|
{
|
|
return $this->partitionStrategy;
|
|
}
|
|
public function setReferenceSetId($referenceSetId)
|
|
{
|
|
$this->referenceSetId = $referenceSetId;
|
|
}
|
|
public function getReferenceSetId()
|
|
{
|
|
return $this->referenceSetId;
|
|
}
|
|
public function setSourceUris($sourceUris)
|
|
{
|
|
$this->sourceUris = $sourceUris;
|
|
}
|
|
public function getSourceUris()
|
|
{
|
|
return $this->sourceUris;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ImportReadGroupSetsResponse extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $jobId;
|
|
|
|
|
|
public function setJobId($jobId)
|
|
{
|
|
$this->jobId = $jobId;
|
|
}
|
|
public function getJobId()
|
|
{
|
|
return $this->jobId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ImportVariantsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'sourceUris';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $format;
|
|
public $sourceUris;
|
|
|
|
|
|
public function setFormat($format)
|
|
{
|
|
$this->format = $format;
|
|
}
|
|
public function getFormat()
|
|
{
|
|
return $this->format;
|
|
}
|
|
public function setSourceUris($sourceUris)
|
|
{
|
|
$this->sourceUris = $sourceUris;
|
|
}
|
|
public function getSourceUris()
|
|
{
|
|
return $this->sourceUris;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ImportVariantsResponse extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $jobId;
|
|
|
|
|
|
public function setJobId($jobId)
|
|
{
|
|
$this->jobId = $jobId;
|
|
}
|
|
public function getJobId()
|
|
{
|
|
return $this->jobId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_Int32Value extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $value;
|
|
|
|
|
|
public function setValue($value)
|
|
{
|
|
$this->value = $value;
|
|
}
|
|
public function getValue()
|
|
{
|
|
return $this->value;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_InterleavedFastqSource extends Google_Collection
|
|
{
|
|
protected $collection_key = 'sourceUris';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
protected $metadataType = 'Google_Service_Genomics_FastqMetadata';
|
|
protected $metadataDataType = '';
|
|
public $sourceUris;
|
|
|
|
|
|
public function setMetadata(Google_Service_Genomics_FastqMetadata $metadata)
|
|
{
|
|
$this->metadata = $metadata;
|
|
}
|
|
public function getMetadata()
|
|
{
|
|
return $this->metadata;
|
|
}
|
|
public function setSourceUris($sourceUris)
|
|
{
|
|
$this->sourceUris = $sourceUris;
|
|
}
|
|
public function getSourceUris()
|
|
{
|
|
return $this->sourceUris;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_Job extends Google_Collection
|
|
{
|
|
protected $collection_key = 'warnings';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $created;
|
|
public $detailedStatus;
|
|
public $errors;
|
|
public $id;
|
|
public $importedIds;
|
|
public $projectNumber;
|
|
protected $requestType = 'Google_Service_Genomics_JobRequest';
|
|
protected $requestDataType = '';
|
|
public $status;
|
|
public $warnings;
|
|
|
|
|
|
public function setCreated($created)
|
|
{
|
|
$this->created = $created;
|
|
}
|
|
public function getCreated()
|
|
{
|
|
return $this->created;
|
|
}
|
|
public function setDetailedStatus($detailedStatus)
|
|
{
|
|
$this->detailedStatus = $detailedStatus;
|
|
}
|
|
public function getDetailedStatus()
|
|
{
|
|
return $this->detailedStatus;
|
|
}
|
|
public function setErrors($errors)
|
|
{
|
|
$this->errors = $errors;
|
|
}
|
|
public function getErrors()
|
|
{
|
|
return $this->errors;
|
|
}
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
public function setImportedIds($importedIds)
|
|
{
|
|
$this->importedIds = $importedIds;
|
|
}
|
|
public function getImportedIds()
|
|
{
|
|
return $this->importedIds;
|
|
}
|
|
public function setProjectNumber($projectNumber)
|
|
{
|
|
$this->projectNumber = $projectNumber;
|
|
}
|
|
public function getProjectNumber()
|
|
{
|
|
return $this->projectNumber;
|
|
}
|
|
public function setRequest(Google_Service_Genomics_JobRequest $request)
|
|
{
|
|
$this->request = $request;
|
|
}
|
|
public function getRequest()
|
|
{
|
|
return $this->request;
|
|
}
|
|
public function setStatus($status)
|
|
{
|
|
$this->status = $status;
|
|
}
|
|
public function getStatus()
|
|
{
|
|
return $this->status;
|
|
}
|
|
public function setWarnings($warnings)
|
|
{
|
|
$this->warnings = $warnings;
|
|
}
|
|
public function getWarnings()
|
|
{
|
|
return $this->warnings;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_JobRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'source';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $destination;
|
|
public $source;
|
|
public $type;
|
|
|
|
|
|
public function setDestination($destination)
|
|
{
|
|
$this->destination = $destination;
|
|
}
|
|
public function getDestination()
|
|
{
|
|
return $this->destination;
|
|
}
|
|
public function setSource($source)
|
|
{
|
|
$this->source = $source;
|
|
}
|
|
public function getSource()
|
|
{
|
|
return $this->source;
|
|
}
|
|
public function setType($type)
|
|
{
|
|
$this->type = $type;
|
|
}
|
|
public function getType()
|
|
{
|
|
return $this->type;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_LinearAlignment extends Google_Collection
|
|
{
|
|
protected $collection_key = 'cigar';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
protected $cigarType = 'Google_Service_Genomics_CigarUnit';
|
|
protected $cigarDataType = 'array';
|
|
public $mappingQuality;
|
|
protected $positionType = 'Google_Service_Genomics_Position';
|
|
protected $positionDataType = '';
|
|
|
|
|
|
public function setCigar($cigar)
|
|
{
|
|
$this->cigar = $cigar;
|
|
}
|
|
public function getCigar()
|
|
{
|
|
return $this->cigar;
|
|
}
|
|
public function setMappingQuality($mappingQuality)
|
|
{
|
|
$this->mappingQuality = $mappingQuality;
|
|
}
|
|
public function getMappingQuality()
|
|
{
|
|
return $this->mappingQuality;
|
|
}
|
|
public function setPosition(Google_Service_Genomics_Position $position)
|
|
{
|
|
$this->position = $position;
|
|
}
|
|
public function getPosition()
|
|
{
|
|
return $this->position;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ListBasesResponse extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $nextPageToken;
|
|
public $offset;
|
|
public $sequence;
|
|
|
|
|
|
public function setNextPageToken($nextPageToken)
|
|
{
|
|
$this->nextPageToken = $nextPageToken;
|
|
}
|
|
public function getNextPageToken()
|
|
{
|
|
return $this->nextPageToken;
|
|
}
|
|
public function setOffset($offset)
|
|
{
|
|
$this->offset = $offset;
|
|
}
|
|
public function getOffset()
|
|
{
|
|
return $this->offset;
|
|
}
|
|
public function setSequence($sequence)
|
|
{
|
|
$this->sequence = $sequence;
|
|
}
|
|
public function getSequence()
|
|
{
|
|
return $this->sequence;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ListCoverageBucketsResponse extends Google_Collection
|
|
{
|
|
protected $collection_key = 'coverageBuckets';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $bucketWidth;
|
|
protected $coverageBucketsType = 'Google_Service_Genomics_CoverageBucket';
|
|
protected $coverageBucketsDataType = 'array';
|
|
public $nextPageToken;
|
|
|
|
|
|
public function setBucketWidth($bucketWidth)
|
|
{
|
|
$this->bucketWidth = $bucketWidth;
|
|
}
|
|
public function getBucketWidth()
|
|
{
|
|
return $this->bucketWidth;
|
|
}
|
|
public function setCoverageBuckets($coverageBuckets)
|
|
{
|
|
$this->coverageBuckets = $coverageBuckets;
|
|
}
|
|
public function getCoverageBuckets()
|
|
{
|
|
return $this->coverageBuckets;
|
|
}
|
|
public function setNextPageToken($nextPageToken)
|
|
{
|
|
$this->nextPageToken = $nextPageToken;
|
|
}
|
|
public function getNextPageToken()
|
|
{
|
|
return $this->nextPageToken;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ListDatasetsResponse extends Google_Collection
|
|
{
|
|
protected $collection_key = 'datasets';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
protected $datasetsType = 'Google_Service_Genomics_Dataset';
|
|
protected $datasetsDataType = 'array';
|
|
public $nextPageToken;
|
|
|
|
|
|
public function setDatasets($datasets)
|
|
{
|
|
$this->datasets = $datasets;
|
|
}
|
|
public function getDatasets()
|
|
{
|
|
return $this->datasets;
|
|
}
|
|
public function setNextPageToken($nextPageToken)
|
|
{
|
|
$this->nextPageToken = $nextPageToken;
|
|
}
|
|
public function getNextPageToken()
|
|
{
|
|
return $this->nextPageToken;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_MergeVariantsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'variants';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
protected $variantsType = 'Google_Service_Genomics_Variant';
|
|
protected $variantsDataType = 'array';
|
|
|
|
|
|
public function setVariants($variants)
|
|
{
|
|
$this->variants = $variants;
|
|
}
|
|
public function getVariants()
|
|
{
|
|
return $this->variants;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_Metadata extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $description;
|
|
public $id;
|
|
public $info;
|
|
public $key;
|
|
public $number;
|
|
public $type;
|
|
public $value;
|
|
|
|
|
|
public function setDescription($description)
|
|
{
|
|
$this->description = $description;
|
|
}
|
|
public function getDescription()
|
|
{
|
|
return $this->description;
|
|
}
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
public function setInfo($info)
|
|
{
|
|
$this->info = $info;
|
|
}
|
|
public function getInfo()
|
|
{
|
|
return $this->info;
|
|
}
|
|
public function setKey($key)
|
|
{
|
|
$this->key = $key;
|
|
}
|
|
public function getKey()
|
|
{
|
|
return $this->key;
|
|
}
|
|
public function setNumber($number)
|
|
{
|
|
$this->number = $number;
|
|
}
|
|
public function getNumber()
|
|
{
|
|
return $this->number;
|
|
}
|
|
public function setType($type)
|
|
{
|
|
$this->type = $type;
|
|
}
|
|
public function getType()
|
|
{
|
|
return $this->type;
|
|
}
|
|
public function setValue($value)
|
|
{
|
|
$this->value = $value;
|
|
}
|
|
public function getValue()
|
|
{
|
|
return $this->value;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_MetadataInfo extends Google_Model
|
|
{
|
|
}
|
|
|
|
class Google_Service_Genomics_PairedFastqSource extends Google_Collection
|
|
{
|
|
protected $collection_key = 'secondSourceUris';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $firstSourceUris;
|
|
protected $metadataType = 'Google_Service_Genomics_FastqMetadata';
|
|
protected $metadataDataType = '';
|
|
public $secondSourceUris;
|
|
|
|
|
|
public function setFirstSourceUris($firstSourceUris)
|
|
{
|
|
$this->firstSourceUris = $firstSourceUris;
|
|
}
|
|
public function getFirstSourceUris()
|
|
{
|
|
return $this->firstSourceUris;
|
|
}
|
|
public function setMetadata(Google_Service_Genomics_FastqMetadata $metadata)
|
|
{
|
|
$this->metadata = $metadata;
|
|
}
|
|
public function getMetadata()
|
|
{
|
|
return $this->metadata;
|
|
}
|
|
public function setSecondSourceUris($secondSourceUris)
|
|
{
|
|
$this->secondSourceUris = $secondSourceUris;
|
|
}
|
|
public function getSecondSourceUris()
|
|
{
|
|
return $this->secondSourceUris;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_Position extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $position;
|
|
public $referenceName;
|
|
public $reverseStrand;
|
|
|
|
|
|
public function setPosition($position)
|
|
{
|
|
$this->position = $position;
|
|
}
|
|
public function getPosition()
|
|
{
|
|
return $this->position;
|
|
}
|
|
public function setReferenceName($referenceName)
|
|
{
|
|
$this->referenceName = $referenceName;
|
|
}
|
|
public function getReferenceName()
|
|
{
|
|
return $this->referenceName;
|
|
}
|
|
public function setReverseStrand($reverseStrand)
|
|
{
|
|
$this->reverseStrand = $reverseStrand;
|
|
}
|
|
public function getReverseStrand()
|
|
{
|
|
return $this->reverseStrand;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_QueryRange extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $end;
|
|
public $referenceId;
|
|
public $referenceName;
|
|
public $start;
|
|
|
|
|
|
public function setEnd($end)
|
|
{
|
|
$this->end = $end;
|
|
}
|
|
public function getEnd()
|
|
{
|
|
return $this->end;
|
|
}
|
|
public function setReferenceId($referenceId)
|
|
{
|
|
$this->referenceId = $referenceId;
|
|
}
|
|
public function getReferenceId()
|
|
{
|
|
return $this->referenceId;
|
|
}
|
|
public function setReferenceName($referenceName)
|
|
{
|
|
$this->referenceName = $referenceName;
|
|
}
|
|
public function getReferenceName()
|
|
{
|
|
return $this->referenceName;
|
|
}
|
|
public function setStart($start)
|
|
{
|
|
$this->start = $start;
|
|
}
|
|
public function getStart()
|
|
{
|
|
return $this->start;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_Range extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $end;
|
|
public $referenceName;
|
|
public $start;
|
|
|
|
|
|
public function setEnd($end)
|
|
{
|
|
$this->end = $end;
|
|
}
|
|
public function getEnd()
|
|
{
|
|
return $this->end;
|
|
}
|
|
public function setReferenceName($referenceName)
|
|
{
|
|
$this->referenceName = $referenceName;
|
|
}
|
|
public function getReferenceName()
|
|
{
|
|
return $this->referenceName;
|
|
}
|
|
public function setStart($start)
|
|
{
|
|
$this->start = $start;
|
|
}
|
|
public function getStart()
|
|
{
|
|
return $this->start;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_RangePosition extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $end;
|
|
public $referenceId;
|
|
public $referenceName;
|
|
public $reverseStrand;
|
|
public $start;
|
|
|
|
|
|
public function setEnd($end)
|
|
{
|
|
$this->end = $end;
|
|
}
|
|
public function getEnd()
|
|
{
|
|
return $this->end;
|
|
}
|
|
public function setReferenceId($referenceId)
|
|
{
|
|
$this->referenceId = $referenceId;
|
|
}
|
|
public function getReferenceId()
|
|
{
|
|
return $this->referenceId;
|
|
}
|
|
public function setReferenceName($referenceName)
|
|
{
|
|
$this->referenceName = $referenceName;
|
|
}
|
|
public function getReferenceName()
|
|
{
|
|
return $this->referenceName;
|
|
}
|
|
public function setReverseStrand($reverseStrand)
|
|
{
|
|
$this->reverseStrand = $reverseStrand;
|
|
}
|
|
public function getReverseStrand()
|
|
{
|
|
return $this->reverseStrand;
|
|
}
|
|
public function setStart($start)
|
|
{
|
|
$this->start = $start;
|
|
}
|
|
public function getStart()
|
|
{
|
|
return $this->start;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_Read extends Google_Collection
|
|
{
|
|
protected $collection_key = 'alignedQuality';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $alignedQuality;
|
|
public $alignedSequence;
|
|
protected $alignmentType = 'Google_Service_Genomics_LinearAlignment';
|
|
protected $alignmentDataType = '';
|
|
public $duplicateFragment;
|
|
public $failedVendorQualityChecks;
|
|
public $fragmentLength;
|
|
public $fragmentName;
|
|
public $id;
|
|
public $info;
|
|
protected $nextMatePositionType = 'Google_Service_Genomics_Position';
|
|
protected $nextMatePositionDataType = '';
|
|
public $numberReads;
|
|
public $properPlacement;
|
|
public $readGroupId;
|
|
public $readGroupSetId;
|
|
public $readNumber;
|
|
public $secondaryAlignment;
|
|
public $supplementaryAlignment;
|
|
|
|
|
|
public function setAlignedQuality($alignedQuality)
|
|
{
|
|
$this->alignedQuality = $alignedQuality;
|
|
}
|
|
public function getAlignedQuality()
|
|
{
|
|
return $this->alignedQuality;
|
|
}
|
|
public function setAlignedSequence($alignedSequence)
|
|
{
|
|
$this->alignedSequence = $alignedSequence;
|
|
}
|
|
public function getAlignedSequence()
|
|
{
|
|
return $this->alignedSequence;
|
|
}
|
|
public function setAlignment(Google_Service_Genomics_LinearAlignment $alignment)
|
|
{
|
|
$this->alignment = $alignment;
|
|
}
|
|
public function getAlignment()
|
|
{
|
|
return $this->alignment;
|
|
}
|
|
public function setDuplicateFragment($duplicateFragment)
|
|
{
|
|
$this->duplicateFragment = $duplicateFragment;
|
|
}
|
|
public function getDuplicateFragment()
|
|
{
|
|
return $this->duplicateFragment;
|
|
}
|
|
public function setFailedVendorQualityChecks($failedVendorQualityChecks)
|
|
{
|
|
$this->failedVendorQualityChecks = $failedVendorQualityChecks;
|
|
}
|
|
public function getFailedVendorQualityChecks()
|
|
{
|
|
return $this->failedVendorQualityChecks;
|
|
}
|
|
public function setFragmentLength($fragmentLength)
|
|
{
|
|
$this->fragmentLength = $fragmentLength;
|
|
}
|
|
public function getFragmentLength()
|
|
{
|
|
return $this->fragmentLength;
|
|
}
|
|
public function setFragmentName($fragmentName)
|
|
{
|
|
$this->fragmentName = $fragmentName;
|
|
}
|
|
public function getFragmentName()
|
|
{
|
|
return $this->fragmentName;
|
|
}
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
public function setInfo($info)
|
|
{
|
|
$this->info = $info;
|
|
}
|
|
public function getInfo()
|
|
{
|
|
return $this->info;
|
|
}
|
|
public function setNextMatePosition(Google_Service_Genomics_Position $nextMatePosition)
|
|
{
|
|
$this->nextMatePosition = $nextMatePosition;
|
|
}
|
|
public function getNextMatePosition()
|
|
{
|
|
return $this->nextMatePosition;
|
|
}
|
|
public function setNumberReads($numberReads)
|
|
{
|
|
$this->numberReads = $numberReads;
|
|
}
|
|
public function getNumberReads()
|
|
{
|
|
return $this->numberReads;
|
|
}
|
|
public function setProperPlacement($properPlacement)
|
|
{
|
|
$this->properPlacement = $properPlacement;
|
|
}
|
|
public function getProperPlacement()
|
|
{
|
|
return $this->properPlacement;
|
|
}
|
|
public function setReadGroupId($readGroupId)
|
|
{
|
|
$this->readGroupId = $readGroupId;
|
|
}
|
|
public function getReadGroupId()
|
|
{
|
|
return $this->readGroupId;
|
|
}
|
|
public function setReadGroupSetId($readGroupSetId)
|
|
{
|
|
$this->readGroupSetId = $readGroupSetId;
|
|
}
|
|
public function getReadGroupSetId()
|
|
{
|
|
return $this->readGroupSetId;
|
|
}
|
|
public function setReadNumber($readNumber)
|
|
{
|
|
$this->readNumber = $readNumber;
|
|
}
|
|
public function getReadNumber()
|
|
{
|
|
return $this->readNumber;
|
|
}
|
|
public function setSecondaryAlignment($secondaryAlignment)
|
|
{
|
|
$this->secondaryAlignment = $secondaryAlignment;
|
|
}
|
|
public function getSecondaryAlignment()
|
|
{
|
|
return $this->secondaryAlignment;
|
|
}
|
|
public function setSupplementaryAlignment($supplementaryAlignment)
|
|
{
|
|
$this->supplementaryAlignment = $supplementaryAlignment;
|
|
}
|
|
public function getSupplementaryAlignment()
|
|
{
|
|
return $this->supplementaryAlignment;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ReadGroup extends Google_Collection
|
|
{
|
|
protected $collection_key = 'programs';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $datasetId;
|
|
public $description;
|
|
protected $experimentType = 'Google_Service_Genomics_ReadGroupExperiment';
|
|
protected $experimentDataType = '';
|
|
public $id;
|
|
public $info;
|
|
public $name;
|
|
public $predictedInsertSize;
|
|
protected $programsType = 'Google_Service_Genomics_ReadGroupProgram';
|
|
protected $programsDataType = 'array';
|
|
public $referenceSetId;
|
|
public $sampleId;
|
|
|
|
|
|
public function setDatasetId($datasetId)
|
|
{
|
|
$this->datasetId = $datasetId;
|
|
}
|
|
public function getDatasetId()
|
|
{
|
|
return $this->datasetId;
|
|
}
|
|
public function setDescription($description)
|
|
{
|
|
$this->description = $description;
|
|
}
|
|
public function getDescription()
|
|
{
|
|
return $this->description;
|
|
}
|
|
public function setExperiment(Google_Service_Genomics_ReadGroupExperiment $experiment)
|
|
{
|
|
$this->experiment = $experiment;
|
|
}
|
|
public function getExperiment()
|
|
{
|
|
return $this->experiment;
|
|
}
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
public function setInfo($info)
|
|
{
|
|
$this->info = $info;
|
|
}
|
|
public function getInfo()
|
|
{
|
|
return $this->info;
|
|
}
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
public function setPredictedInsertSize($predictedInsertSize)
|
|
{
|
|
$this->predictedInsertSize = $predictedInsertSize;
|
|
}
|
|
public function getPredictedInsertSize()
|
|
{
|
|
return $this->predictedInsertSize;
|
|
}
|
|
public function setPrograms($programs)
|
|
{
|
|
$this->programs = $programs;
|
|
}
|
|
public function getPrograms()
|
|
{
|
|
return $this->programs;
|
|
}
|
|
public function setReferenceSetId($referenceSetId)
|
|
{
|
|
$this->referenceSetId = $referenceSetId;
|
|
}
|
|
public function getReferenceSetId()
|
|
{
|
|
return $this->referenceSetId;
|
|
}
|
|
public function setSampleId($sampleId)
|
|
{
|
|
$this->sampleId = $sampleId;
|
|
}
|
|
public function getSampleId()
|
|
{
|
|
return $this->sampleId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ReadGroupExperiment extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $instrumentModel;
|
|
public $libraryId;
|
|
public $platformUnit;
|
|
public $sequencingCenter;
|
|
|
|
|
|
public function setInstrumentModel($instrumentModel)
|
|
{
|
|
$this->instrumentModel = $instrumentModel;
|
|
}
|
|
public function getInstrumentModel()
|
|
{
|
|
return $this->instrumentModel;
|
|
}
|
|
public function setLibraryId($libraryId)
|
|
{
|
|
$this->libraryId = $libraryId;
|
|
}
|
|
public function getLibraryId()
|
|
{
|
|
return $this->libraryId;
|
|
}
|
|
public function setPlatformUnit($platformUnit)
|
|
{
|
|
$this->platformUnit = $platformUnit;
|
|
}
|
|
public function getPlatformUnit()
|
|
{
|
|
return $this->platformUnit;
|
|
}
|
|
public function setSequencingCenter($sequencingCenter)
|
|
{
|
|
$this->sequencingCenter = $sequencingCenter;
|
|
}
|
|
public function getSequencingCenter()
|
|
{
|
|
return $this->sequencingCenter;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ReadGroupInfo extends Google_Model
|
|
{
|
|
}
|
|
|
|
class Google_Service_Genomics_ReadGroupProgram extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $commandLine;
|
|
public $id;
|
|
public $name;
|
|
public $prevProgramId;
|
|
public $version;
|
|
|
|
|
|
public function setCommandLine($commandLine)
|
|
{
|
|
$this->commandLine = $commandLine;
|
|
}
|
|
public function getCommandLine()
|
|
{
|
|
return $this->commandLine;
|
|
}
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
public function setPrevProgramId($prevProgramId)
|
|
{
|
|
$this->prevProgramId = $prevProgramId;
|
|
}
|
|
public function getPrevProgramId()
|
|
{
|
|
return $this->prevProgramId;
|
|
}
|
|
public function setVersion($version)
|
|
{
|
|
$this->version = $version;
|
|
}
|
|
public function getVersion()
|
|
{
|
|
return $this->version;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ReadGroupSet extends Google_Collection
|
|
{
|
|
protected $collection_key = 'readGroups';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $datasetId;
|
|
public $filename;
|
|
public $id;
|
|
public $info;
|
|
public $name;
|
|
protected $readGroupsType = 'Google_Service_Genomics_ReadGroup';
|
|
protected $readGroupsDataType = 'array';
|
|
public $referenceSetId;
|
|
|
|
|
|
public function setDatasetId($datasetId)
|
|
{
|
|
$this->datasetId = $datasetId;
|
|
}
|
|
public function getDatasetId()
|
|
{
|
|
return $this->datasetId;
|
|
}
|
|
public function setFilename($filename)
|
|
{
|
|
$this->filename = $filename;
|
|
}
|
|
public function getFilename()
|
|
{
|
|
return $this->filename;
|
|
}
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
public function setInfo($info)
|
|
{
|
|
$this->info = $info;
|
|
}
|
|
public function getInfo()
|
|
{
|
|
return $this->info;
|
|
}
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
public function setReadGroups($readGroups)
|
|
{
|
|
$this->readGroups = $readGroups;
|
|
}
|
|
public function getReadGroups()
|
|
{
|
|
return $this->readGroups;
|
|
}
|
|
public function setReferenceSetId($referenceSetId)
|
|
{
|
|
$this->referenceSetId = $referenceSetId;
|
|
}
|
|
public function getReferenceSetId()
|
|
{
|
|
return $this->referenceSetId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ReadGroupSetInfo extends Google_Model
|
|
{
|
|
}
|
|
|
|
class Google_Service_Genomics_ReadInfo extends Google_Model
|
|
{
|
|
}
|
|
|
|
class Google_Service_Genomics_Reference extends Google_Collection
|
|
{
|
|
protected $collection_key = 'sourceAccessions';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $id;
|
|
public $length;
|
|
public $md5checksum;
|
|
public $name;
|
|
public $ncbiTaxonId;
|
|
public $sourceAccessions;
|
|
public $sourceURI;
|
|
|
|
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
public function setLength($length)
|
|
{
|
|
$this->length = $length;
|
|
}
|
|
public function getLength()
|
|
{
|
|
return $this->length;
|
|
}
|
|
public function setMd5checksum($md5checksum)
|
|
{
|
|
$this->md5checksum = $md5checksum;
|
|
}
|
|
public function getMd5checksum()
|
|
{
|
|
return $this->md5checksum;
|
|
}
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
public function setNcbiTaxonId($ncbiTaxonId)
|
|
{
|
|
$this->ncbiTaxonId = $ncbiTaxonId;
|
|
}
|
|
public function getNcbiTaxonId()
|
|
{
|
|
return $this->ncbiTaxonId;
|
|
}
|
|
public function setSourceAccessions($sourceAccessions)
|
|
{
|
|
$this->sourceAccessions = $sourceAccessions;
|
|
}
|
|
public function getSourceAccessions()
|
|
{
|
|
return $this->sourceAccessions;
|
|
}
|
|
public function setSourceURI($sourceURI)
|
|
{
|
|
$this->sourceURI = $sourceURI;
|
|
}
|
|
public function getSourceURI()
|
|
{
|
|
return $this->sourceURI;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ReferenceBound extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $referenceName;
|
|
public $upperBound;
|
|
|
|
|
|
public function setReferenceName($referenceName)
|
|
{
|
|
$this->referenceName = $referenceName;
|
|
}
|
|
public function getReferenceName()
|
|
{
|
|
return $this->referenceName;
|
|
}
|
|
public function setUpperBound($upperBound)
|
|
{
|
|
$this->upperBound = $upperBound;
|
|
}
|
|
public function getUpperBound()
|
|
{
|
|
return $this->upperBound;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ReferenceSet extends Google_Collection
|
|
{
|
|
protected $collection_key = 'sourceAccessions';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $assemblyId;
|
|
public $description;
|
|
public $id;
|
|
public $md5checksum;
|
|
public $ncbiTaxonId;
|
|
public $referenceIds;
|
|
public $sourceAccessions;
|
|
public $sourceURI;
|
|
|
|
|
|
public function setAssemblyId($assemblyId)
|
|
{
|
|
$this->assemblyId = $assemblyId;
|
|
}
|
|
public function getAssemblyId()
|
|
{
|
|
return $this->assemblyId;
|
|
}
|
|
public function setDescription($description)
|
|
{
|
|
$this->description = $description;
|
|
}
|
|
public function getDescription()
|
|
{
|
|
return $this->description;
|
|
}
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
public function setMd5checksum($md5checksum)
|
|
{
|
|
$this->md5checksum = $md5checksum;
|
|
}
|
|
public function getMd5checksum()
|
|
{
|
|
return $this->md5checksum;
|
|
}
|
|
public function setNcbiTaxonId($ncbiTaxonId)
|
|
{
|
|
$this->ncbiTaxonId = $ncbiTaxonId;
|
|
}
|
|
public function getNcbiTaxonId()
|
|
{
|
|
return $this->ncbiTaxonId;
|
|
}
|
|
public function setReferenceIds($referenceIds)
|
|
{
|
|
$this->referenceIds = $referenceIds;
|
|
}
|
|
public function getReferenceIds()
|
|
{
|
|
return $this->referenceIds;
|
|
}
|
|
public function setSourceAccessions($sourceAccessions)
|
|
{
|
|
$this->sourceAccessions = $sourceAccessions;
|
|
}
|
|
public function getSourceAccessions()
|
|
{
|
|
return $this->sourceAccessions;
|
|
}
|
|
public function setSourceURI($sourceURI)
|
|
{
|
|
$this->sourceURI = $sourceURI;
|
|
}
|
|
public function getSourceURI()
|
|
{
|
|
return $this->sourceURI;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchAnnotationSetsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'types';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $datasetIds;
|
|
public $name;
|
|
public $pageSize;
|
|
public $pageToken;
|
|
public $referenceSetId;
|
|
public $types;
|
|
|
|
|
|
public function setDatasetIds($datasetIds)
|
|
{
|
|
$this->datasetIds = $datasetIds;
|
|
}
|
|
public function getDatasetIds()
|
|
{
|
|
return $this->datasetIds;
|
|
}
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
public function setPageSize($pageSize)
|
|
{
|
|
$this->pageSize = $pageSize;
|
|
}
|
|
public function getPageSize()
|
|
{
|
|
return $this->pageSize;
|
|
}
|
|
public function setPageToken($pageToken)
|
|
{
|
|
$this->pageToken = $pageToken;
|
|
}
|
|
public function getPageToken()
|
|
{
|
|
return $this->pageToken;
|
|
}
|
|
public function setReferenceSetId($referenceSetId)
|
|
{
|
|
$this->referenceSetId = $referenceSetId;
|
|
}
|
|
public function getReferenceSetId()
|
|
{
|
|
return $this->referenceSetId;
|
|
}
|
|
public function setTypes($types)
|
|
{
|
|
$this->types = $types;
|
|
}
|
|
public function getTypes()
|
|
{
|
|
return $this->types;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchAnnotationSetsResponse extends Google_Collection
|
|
{
|
|
protected $collection_key = 'annotationSets';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
protected $annotationSetsType = 'Google_Service_Genomics_AnnotationSet';
|
|
protected $annotationSetsDataType = 'array';
|
|
public $nextPageToken;
|
|
|
|
|
|
public function setAnnotationSets($annotationSets)
|
|
{
|
|
$this->annotationSets = $annotationSets;
|
|
}
|
|
public function getAnnotationSets()
|
|
{
|
|
return $this->annotationSets;
|
|
}
|
|
public function setNextPageToken($nextPageToken)
|
|
{
|
|
$this->nextPageToken = $nextPageToken;
|
|
}
|
|
public function getNextPageToken()
|
|
{
|
|
return $this->nextPageToken;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchAnnotationsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'annotationSetIds';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $annotationSetIds;
|
|
public $pageSize;
|
|
public $pageToken;
|
|
protected $rangeType = 'Google_Service_Genomics_QueryRange';
|
|
protected $rangeDataType = '';
|
|
|
|
|
|
public function setAnnotationSetIds($annotationSetIds)
|
|
{
|
|
$this->annotationSetIds = $annotationSetIds;
|
|
}
|
|
public function getAnnotationSetIds()
|
|
{
|
|
return $this->annotationSetIds;
|
|
}
|
|
public function setPageSize($pageSize)
|
|
{
|
|
$this->pageSize = $pageSize;
|
|
}
|
|
public function getPageSize()
|
|
{
|
|
return $this->pageSize;
|
|
}
|
|
public function setPageToken($pageToken)
|
|
{
|
|
$this->pageToken = $pageToken;
|
|
}
|
|
public function getPageToken()
|
|
{
|
|
return $this->pageToken;
|
|
}
|
|
public function setRange(Google_Service_Genomics_QueryRange $range)
|
|
{
|
|
$this->range = $range;
|
|
}
|
|
public function getRange()
|
|
{
|
|
return $this->range;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchAnnotationsResponse extends Google_Collection
|
|
{
|
|
protected $collection_key = 'annotations';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
protected $annotationsType = 'Google_Service_Genomics_Annotation';
|
|
protected $annotationsDataType = 'array';
|
|
public $nextPageToken;
|
|
|
|
|
|
public function setAnnotations($annotations)
|
|
{
|
|
$this->annotations = $annotations;
|
|
}
|
|
public function getAnnotations()
|
|
{
|
|
return $this->annotations;
|
|
}
|
|
public function setNextPageToken($nextPageToken)
|
|
{
|
|
$this->nextPageToken = $nextPageToken;
|
|
}
|
|
public function getNextPageToken()
|
|
{
|
|
return $this->nextPageToken;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchCallSetsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'variantSetIds';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $name;
|
|
public $pageSize;
|
|
public $pageToken;
|
|
public $variantSetIds;
|
|
|
|
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
public function setPageSize($pageSize)
|
|
{
|
|
$this->pageSize = $pageSize;
|
|
}
|
|
public function getPageSize()
|
|
{
|
|
return $this->pageSize;
|
|
}
|
|
public function setPageToken($pageToken)
|
|
{
|
|
$this->pageToken = $pageToken;
|
|
}
|
|
public function getPageToken()
|
|
{
|
|
return $this->pageToken;
|
|
}
|
|
public function setVariantSetIds($variantSetIds)
|
|
{
|
|
$this->variantSetIds = $variantSetIds;
|
|
}
|
|
public function getVariantSetIds()
|
|
{
|
|
return $this->variantSetIds;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchCallSetsResponse extends Google_Collection
|
|
{
|
|
protected $collection_key = 'callSets';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
protected $callSetsType = 'Google_Service_Genomics_CallSet';
|
|
protected $callSetsDataType = 'array';
|
|
public $nextPageToken;
|
|
|
|
|
|
public function setCallSets($callSets)
|
|
{
|
|
$this->callSets = $callSets;
|
|
}
|
|
public function getCallSets()
|
|
{
|
|
return $this->callSets;
|
|
}
|
|
public function setNextPageToken($nextPageToken)
|
|
{
|
|
$this->nextPageToken = $nextPageToken;
|
|
}
|
|
public function getNextPageToken()
|
|
{
|
|
return $this->nextPageToken;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchJobsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'status';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $createdAfter;
|
|
public $createdBefore;
|
|
public $pageSize;
|
|
public $pageToken;
|
|
public $projectNumber;
|
|
public $status;
|
|
|
|
|
|
public function setCreatedAfter($createdAfter)
|
|
{
|
|
$this->createdAfter = $createdAfter;
|
|
}
|
|
public function getCreatedAfter()
|
|
{
|
|
return $this->createdAfter;
|
|
}
|
|
public function setCreatedBefore($createdBefore)
|
|
{
|
|
$this->createdBefore = $createdBefore;
|
|
}
|
|
public function getCreatedBefore()
|
|
{
|
|
return $this->createdBefore;
|
|
}
|
|
public function setPageSize($pageSize)
|
|
{
|
|
$this->pageSize = $pageSize;
|
|
}
|
|
public function getPageSize()
|
|
{
|
|
return $this->pageSize;
|
|
}
|
|
public function setPageToken($pageToken)
|
|
{
|
|
$this->pageToken = $pageToken;
|
|
}
|
|
public function getPageToken()
|
|
{
|
|
return $this->pageToken;
|
|
}
|
|
public function setProjectNumber($projectNumber)
|
|
{
|
|
$this->projectNumber = $projectNumber;
|
|
}
|
|
public function getProjectNumber()
|
|
{
|
|
return $this->projectNumber;
|
|
}
|
|
public function setStatus($status)
|
|
{
|
|
$this->status = $status;
|
|
}
|
|
public function getStatus()
|
|
{
|
|
return $this->status;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchJobsResponse extends Google_Collection
|
|
{
|
|
protected $collection_key = 'jobs';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
protected $jobsType = 'Google_Service_Genomics_Job';
|
|
protected $jobsDataType = 'array';
|
|
public $nextPageToken;
|
|
|
|
|
|
public function setJobs($jobs)
|
|
{
|
|
$this->jobs = $jobs;
|
|
}
|
|
public function getJobs()
|
|
{
|
|
return $this->jobs;
|
|
}
|
|
public function setNextPageToken($nextPageToken)
|
|
{
|
|
$this->nextPageToken = $nextPageToken;
|
|
}
|
|
public function getNextPageToken()
|
|
{
|
|
return $this->nextPageToken;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchReadGroupSetsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'datasetIds';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $datasetIds;
|
|
public $name;
|
|
public $pageSize;
|
|
public $pageToken;
|
|
|
|
|
|
public function setDatasetIds($datasetIds)
|
|
{
|
|
$this->datasetIds = $datasetIds;
|
|
}
|
|
public function getDatasetIds()
|
|
{
|
|
return $this->datasetIds;
|
|
}
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
public function setPageSize($pageSize)
|
|
{
|
|
$this->pageSize = $pageSize;
|
|
}
|
|
public function getPageSize()
|
|
{
|
|
return $this->pageSize;
|
|
}
|
|
public function setPageToken($pageToken)
|
|
{
|
|
$this->pageToken = $pageToken;
|
|
}
|
|
public function getPageToken()
|
|
{
|
|
return $this->pageToken;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchReadGroupSetsResponse extends Google_Collection
|
|
{
|
|
protected $collection_key = 'readGroupSets';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $nextPageToken;
|
|
protected $readGroupSetsType = 'Google_Service_Genomics_ReadGroupSet';
|
|
protected $readGroupSetsDataType = 'array';
|
|
|
|
|
|
public function setNextPageToken($nextPageToken)
|
|
{
|
|
$this->nextPageToken = $nextPageToken;
|
|
}
|
|
public function getNextPageToken()
|
|
{
|
|
return $this->nextPageToken;
|
|
}
|
|
public function setReadGroupSets($readGroupSets)
|
|
{
|
|
$this->readGroupSets = $readGroupSets;
|
|
}
|
|
public function getReadGroupSets()
|
|
{
|
|
return $this->readGroupSets;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchReadsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'readGroupSetIds';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $end;
|
|
public $pageSize;
|
|
public $pageToken;
|
|
public $readGroupIds;
|
|
public $readGroupSetIds;
|
|
public $referenceName;
|
|
public $start;
|
|
|
|
|
|
public function setEnd($end)
|
|
{
|
|
$this->end = $end;
|
|
}
|
|
public function getEnd()
|
|
{
|
|
return $this->end;
|
|
}
|
|
public function setPageSize($pageSize)
|
|
{
|
|
$this->pageSize = $pageSize;
|
|
}
|
|
public function getPageSize()
|
|
{
|
|
return $this->pageSize;
|
|
}
|
|
public function setPageToken($pageToken)
|
|
{
|
|
$this->pageToken = $pageToken;
|
|
}
|
|
public function getPageToken()
|
|
{
|
|
return $this->pageToken;
|
|
}
|
|
public function setReadGroupIds($readGroupIds)
|
|
{
|
|
$this->readGroupIds = $readGroupIds;
|
|
}
|
|
public function getReadGroupIds()
|
|
{
|
|
return $this->readGroupIds;
|
|
}
|
|
public function setReadGroupSetIds($readGroupSetIds)
|
|
{
|
|
$this->readGroupSetIds = $readGroupSetIds;
|
|
}
|
|
public function getReadGroupSetIds()
|
|
{
|
|
return $this->readGroupSetIds;
|
|
}
|
|
public function setReferenceName($referenceName)
|
|
{
|
|
$this->referenceName = $referenceName;
|
|
}
|
|
public function getReferenceName()
|
|
{
|
|
return $this->referenceName;
|
|
}
|
|
public function setStart($start)
|
|
{
|
|
$this->start = $start;
|
|
}
|
|
public function getStart()
|
|
{
|
|
return $this->start;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchReadsResponse extends Google_Collection
|
|
{
|
|
protected $collection_key = 'alignments';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
protected $alignmentsType = 'Google_Service_Genomics_Read';
|
|
protected $alignmentsDataType = 'array';
|
|
public $nextPageToken;
|
|
|
|
|
|
public function setAlignments($alignments)
|
|
{
|
|
$this->alignments = $alignments;
|
|
}
|
|
public function getAlignments()
|
|
{
|
|
return $this->alignments;
|
|
}
|
|
public function setNextPageToken($nextPageToken)
|
|
{
|
|
$this->nextPageToken = $nextPageToken;
|
|
}
|
|
public function getNextPageToken()
|
|
{
|
|
return $this->nextPageToken;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchReferenceSetsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'md5checksums';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $accessions;
|
|
public $assemblyId;
|
|
public $md5checksums;
|
|
public $pageSize;
|
|
public $pageToken;
|
|
|
|
|
|
public function setAccessions($accessions)
|
|
{
|
|
$this->accessions = $accessions;
|
|
}
|
|
public function getAccessions()
|
|
{
|
|
return $this->accessions;
|
|
}
|
|
public function setAssemblyId($assemblyId)
|
|
{
|
|
$this->assemblyId = $assemblyId;
|
|
}
|
|
public function getAssemblyId()
|
|
{
|
|
return $this->assemblyId;
|
|
}
|
|
public function setMd5checksums($md5checksums)
|
|
{
|
|
$this->md5checksums = $md5checksums;
|
|
}
|
|
public function getMd5checksums()
|
|
{
|
|
return $this->md5checksums;
|
|
}
|
|
public function setPageSize($pageSize)
|
|
{
|
|
$this->pageSize = $pageSize;
|
|
}
|
|
public function getPageSize()
|
|
{
|
|
return $this->pageSize;
|
|
}
|
|
public function setPageToken($pageToken)
|
|
{
|
|
$this->pageToken = $pageToken;
|
|
}
|
|
public function getPageToken()
|
|
{
|
|
return $this->pageToken;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchReferenceSetsResponse extends Google_Collection
|
|
{
|
|
protected $collection_key = 'referenceSets';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $nextPageToken;
|
|
protected $referenceSetsType = 'Google_Service_Genomics_ReferenceSet';
|
|
protected $referenceSetsDataType = 'array';
|
|
|
|
|
|
public function setNextPageToken($nextPageToken)
|
|
{
|
|
$this->nextPageToken = $nextPageToken;
|
|
}
|
|
public function getNextPageToken()
|
|
{
|
|
return $this->nextPageToken;
|
|
}
|
|
public function setReferenceSets($referenceSets)
|
|
{
|
|
$this->referenceSets = $referenceSets;
|
|
}
|
|
public function getReferenceSets()
|
|
{
|
|
return $this->referenceSets;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchReferencesRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'md5checksums';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $accessions;
|
|
public $md5checksums;
|
|
public $pageSize;
|
|
public $pageToken;
|
|
public $referenceSetId;
|
|
|
|
|
|
public function setAccessions($accessions)
|
|
{
|
|
$this->accessions = $accessions;
|
|
}
|
|
public function getAccessions()
|
|
{
|
|
return $this->accessions;
|
|
}
|
|
public function setMd5checksums($md5checksums)
|
|
{
|
|
$this->md5checksums = $md5checksums;
|
|
}
|
|
public function getMd5checksums()
|
|
{
|
|
return $this->md5checksums;
|
|
}
|
|
public function setPageSize($pageSize)
|
|
{
|
|
$this->pageSize = $pageSize;
|
|
}
|
|
public function getPageSize()
|
|
{
|
|
return $this->pageSize;
|
|
}
|
|
public function setPageToken($pageToken)
|
|
{
|
|
$this->pageToken = $pageToken;
|
|
}
|
|
public function getPageToken()
|
|
{
|
|
return $this->pageToken;
|
|
}
|
|
public function setReferenceSetId($referenceSetId)
|
|
{
|
|
$this->referenceSetId = $referenceSetId;
|
|
}
|
|
public function getReferenceSetId()
|
|
{
|
|
return $this->referenceSetId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchReferencesResponse extends Google_Collection
|
|
{
|
|
protected $collection_key = 'references';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $nextPageToken;
|
|
protected $referencesType = 'Google_Service_Genomics_Reference';
|
|
protected $referencesDataType = 'array';
|
|
|
|
|
|
public function setNextPageToken($nextPageToken)
|
|
{
|
|
$this->nextPageToken = $nextPageToken;
|
|
}
|
|
public function getNextPageToken()
|
|
{
|
|
return $this->nextPageToken;
|
|
}
|
|
public function setReferences($references)
|
|
{
|
|
$this->references = $references;
|
|
}
|
|
public function getReferences()
|
|
{
|
|
return $this->references;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchVariantSetsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'datasetIds';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $datasetIds;
|
|
public $pageSize;
|
|
public $pageToken;
|
|
|
|
|
|
public function setDatasetIds($datasetIds)
|
|
{
|
|
$this->datasetIds = $datasetIds;
|
|
}
|
|
public function getDatasetIds()
|
|
{
|
|
return $this->datasetIds;
|
|
}
|
|
public function setPageSize($pageSize)
|
|
{
|
|
$this->pageSize = $pageSize;
|
|
}
|
|
public function getPageSize()
|
|
{
|
|
return $this->pageSize;
|
|
}
|
|
public function setPageToken($pageToken)
|
|
{
|
|
$this->pageToken = $pageToken;
|
|
}
|
|
public function getPageToken()
|
|
{
|
|
return $this->pageToken;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchVariantSetsResponse extends Google_Collection
|
|
{
|
|
protected $collection_key = 'variantSets';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $nextPageToken;
|
|
protected $variantSetsType = 'Google_Service_Genomics_VariantSet';
|
|
protected $variantSetsDataType = 'array';
|
|
|
|
|
|
public function setNextPageToken($nextPageToken)
|
|
{
|
|
$this->nextPageToken = $nextPageToken;
|
|
}
|
|
public function getNextPageToken()
|
|
{
|
|
return $this->nextPageToken;
|
|
}
|
|
public function setVariantSets($variantSets)
|
|
{
|
|
$this->variantSets = $variantSets;
|
|
}
|
|
public function getVariantSets()
|
|
{
|
|
return $this->variantSets;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchVariantsRequest extends Google_Collection
|
|
{
|
|
protected $collection_key = 'variantSetIds';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $callSetIds;
|
|
public $end;
|
|
public $maxCalls;
|
|
public $pageSize;
|
|
public $pageToken;
|
|
public $referenceName;
|
|
public $start;
|
|
public $variantName;
|
|
public $variantSetIds;
|
|
|
|
|
|
public function setCallSetIds($callSetIds)
|
|
{
|
|
$this->callSetIds = $callSetIds;
|
|
}
|
|
public function getCallSetIds()
|
|
{
|
|
return $this->callSetIds;
|
|
}
|
|
public function setEnd($end)
|
|
{
|
|
$this->end = $end;
|
|
}
|
|
public function getEnd()
|
|
{
|
|
return $this->end;
|
|
}
|
|
public function setMaxCalls($maxCalls)
|
|
{
|
|
$this->maxCalls = $maxCalls;
|
|
}
|
|
public function getMaxCalls()
|
|
{
|
|
return $this->maxCalls;
|
|
}
|
|
public function setPageSize($pageSize)
|
|
{
|
|
$this->pageSize = $pageSize;
|
|
}
|
|
public function getPageSize()
|
|
{
|
|
return $this->pageSize;
|
|
}
|
|
public function setPageToken($pageToken)
|
|
{
|
|
$this->pageToken = $pageToken;
|
|
}
|
|
public function getPageToken()
|
|
{
|
|
return $this->pageToken;
|
|
}
|
|
public function setReferenceName($referenceName)
|
|
{
|
|
$this->referenceName = $referenceName;
|
|
}
|
|
public function getReferenceName()
|
|
{
|
|
return $this->referenceName;
|
|
}
|
|
public function setStart($start)
|
|
{
|
|
$this->start = $start;
|
|
}
|
|
public function getStart()
|
|
{
|
|
return $this->start;
|
|
}
|
|
public function setVariantName($variantName)
|
|
{
|
|
$this->variantName = $variantName;
|
|
}
|
|
public function getVariantName()
|
|
{
|
|
return $this->variantName;
|
|
}
|
|
public function setVariantSetIds($variantSetIds)
|
|
{
|
|
$this->variantSetIds = $variantSetIds;
|
|
}
|
|
public function getVariantSetIds()
|
|
{
|
|
return $this->variantSetIds;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchVariantsResponse extends Google_Collection
|
|
{
|
|
protected $collection_key = 'variants';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $nextPageToken;
|
|
protected $variantsType = 'Google_Service_Genomics_Variant';
|
|
protected $variantsDataType = 'array';
|
|
|
|
|
|
public function setNextPageToken($nextPageToken)
|
|
{
|
|
$this->nextPageToken = $nextPageToken;
|
|
}
|
|
public function getNextPageToken()
|
|
{
|
|
return $this->nextPageToken;
|
|
}
|
|
public function setVariants($variants)
|
|
{
|
|
$this->variants = $variants;
|
|
}
|
|
public function getVariants()
|
|
{
|
|
return $this->variants;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_Transcript extends Google_Collection
|
|
{
|
|
protected $collection_key = 'exons';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
protected $codingSequenceType = 'Google_Service_Genomics_TranscriptCodingSequence';
|
|
protected $codingSequenceDataType = '';
|
|
protected $exonsType = 'Google_Service_Genomics_TranscriptExon';
|
|
protected $exonsDataType = 'array';
|
|
public $geneId;
|
|
|
|
|
|
public function setCodingSequence(Google_Service_Genomics_TranscriptCodingSequence $codingSequence)
|
|
{
|
|
$this->codingSequence = $codingSequence;
|
|
}
|
|
public function getCodingSequence()
|
|
{
|
|
return $this->codingSequence;
|
|
}
|
|
public function setExons($exons)
|
|
{
|
|
$this->exons = $exons;
|
|
}
|
|
public function getExons()
|
|
{
|
|
return $this->exons;
|
|
}
|
|
public function setGeneId($geneId)
|
|
{
|
|
$this->geneId = $geneId;
|
|
}
|
|
public function getGeneId()
|
|
{
|
|
return $this->geneId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_TranscriptCodingSequence extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $end;
|
|
public $start;
|
|
|
|
|
|
public function setEnd($end)
|
|
{
|
|
$this->end = $end;
|
|
}
|
|
public function getEnd()
|
|
{
|
|
return $this->end;
|
|
}
|
|
public function setStart($start)
|
|
{
|
|
$this->start = $start;
|
|
}
|
|
public function getStart()
|
|
{
|
|
return $this->start;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_TranscriptExon extends Google_Model
|
|
{
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $end;
|
|
protected $frameType = 'Google_Service_Genomics_Int32Value';
|
|
protected $frameDataType = '';
|
|
public $start;
|
|
|
|
|
|
public function setEnd($end)
|
|
{
|
|
$this->end = $end;
|
|
}
|
|
public function getEnd()
|
|
{
|
|
return $this->end;
|
|
}
|
|
public function setFrame(Google_Service_Genomics_Int32Value $frame)
|
|
{
|
|
$this->frame = $frame;
|
|
}
|
|
public function getFrame()
|
|
{
|
|
return $this->frame;
|
|
}
|
|
public function setStart($start)
|
|
{
|
|
$this->start = $start;
|
|
}
|
|
public function getStart()
|
|
{
|
|
return $this->start;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_Variant extends Google_Collection
|
|
{
|
|
protected $collection_key = 'names';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $alternateBases;
|
|
protected $callsType = 'Google_Service_Genomics_GenomicsCall';
|
|
protected $callsDataType = 'array';
|
|
public $created;
|
|
public $end;
|
|
public $filter;
|
|
public $id;
|
|
public $info;
|
|
public $names;
|
|
public $quality;
|
|
public $referenceBases;
|
|
public $referenceName;
|
|
public $start;
|
|
public $variantSetId;
|
|
|
|
|
|
public function setAlternateBases($alternateBases)
|
|
{
|
|
$this->alternateBases = $alternateBases;
|
|
}
|
|
public function getAlternateBases()
|
|
{
|
|
return $this->alternateBases;
|
|
}
|
|
public function setCalls($calls)
|
|
{
|
|
$this->calls = $calls;
|
|
}
|
|
public function getCalls()
|
|
{
|
|
return $this->calls;
|
|
}
|
|
public function setCreated($created)
|
|
{
|
|
$this->created = $created;
|
|
}
|
|
public function getCreated()
|
|
{
|
|
return $this->created;
|
|
}
|
|
public function setEnd($end)
|
|
{
|
|
$this->end = $end;
|
|
}
|
|
public function getEnd()
|
|
{
|
|
return $this->end;
|
|
}
|
|
public function setFilter($filter)
|
|
{
|
|
$this->filter = $filter;
|
|
}
|
|
public function getFilter()
|
|
{
|
|
return $this->filter;
|
|
}
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
public function setInfo($info)
|
|
{
|
|
$this->info = $info;
|
|
}
|
|
public function getInfo()
|
|
{
|
|
return $this->info;
|
|
}
|
|
public function setNames($names)
|
|
{
|
|
$this->names = $names;
|
|
}
|
|
public function getNames()
|
|
{
|
|
return $this->names;
|
|
}
|
|
public function setQuality($quality)
|
|
{
|
|
$this->quality = $quality;
|
|
}
|
|
public function getQuality()
|
|
{
|
|
return $this->quality;
|
|
}
|
|
public function setReferenceBases($referenceBases)
|
|
{
|
|
$this->referenceBases = $referenceBases;
|
|
}
|
|
public function getReferenceBases()
|
|
{
|
|
return $this->referenceBases;
|
|
}
|
|
public function setReferenceName($referenceName)
|
|
{
|
|
$this->referenceName = $referenceName;
|
|
}
|
|
public function getReferenceName()
|
|
{
|
|
return $this->referenceName;
|
|
}
|
|
public function setStart($start)
|
|
{
|
|
$this->start = $start;
|
|
}
|
|
public function getStart()
|
|
{
|
|
return $this->start;
|
|
}
|
|
public function setVariantSetId($variantSetId)
|
|
{
|
|
$this->variantSetId = $variantSetId;
|
|
}
|
|
public function getVariantSetId()
|
|
{
|
|
return $this->variantSetId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_VariantAnnotation extends Google_Collection
|
|
{
|
|
protected $collection_key = 'transcriptIds';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $alternateBases;
|
|
public $clinicalSignificance;
|
|
protected $conditionsType = 'Google_Service_Genomics_VariantAnnotationCondition';
|
|
protected $conditionsDataType = 'array';
|
|
public $effect;
|
|
public $geneId;
|
|
public $transcriptIds;
|
|
public $type;
|
|
|
|
|
|
public function setAlternateBases($alternateBases)
|
|
{
|
|
$this->alternateBases = $alternateBases;
|
|
}
|
|
public function getAlternateBases()
|
|
{
|
|
return $this->alternateBases;
|
|
}
|
|
public function setClinicalSignificance($clinicalSignificance)
|
|
{
|
|
$this->clinicalSignificance = $clinicalSignificance;
|
|
}
|
|
public function getClinicalSignificance()
|
|
{
|
|
return $this->clinicalSignificance;
|
|
}
|
|
public function setConditions($conditions)
|
|
{
|
|
$this->conditions = $conditions;
|
|
}
|
|
public function getConditions()
|
|
{
|
|
return $this->conditions;
|
|
}
|
|
public function setEffect($effect)
|
|
{
|
|
$this->effect = $effect;
|
|
}
|
|
public function getEffect()
|
|
{
|
|
return $this->effect;
|
|
}
|
|
public function setGeneId($geneId)
|
|
{
|
|
$this->geneId = $geneId;
|
|
}
|
|
public function getGeneId()
|
|
{
|
|
return $this->geneId;
|
|
}
|
|
public function setTranscriptIds($transcriptIds)
|
|
{
|
|
$this->transcriptIds = $transcriptIds;
|
|
}
|
|
public function getTranscriptIds()
|
|
{
|
|
return $this->transcriptIds;
|
|
}
|
|
public function setType($type)
|
|
{
|
|
$this->type = $type;
|
|
}
|
|
public function getType()
|
|
{
|
|
return $this->type;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_VariantAnnotationCondition extends Google_Collection
|
|
{
|
|
protected $collection_key = 'names';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $conceptId;
|
|
protected $externalIdsType = 'Google_Service_Genomics_ExternalId';
|
|
protected $externalIdsDataType = 'array';
|
|
public $names;
|
|
public $omimId;
|
|
|
|
|
|
public function setConceptId($conceptId)
|
|
{
|
|
$this->conceptId = $conceptId;
|
|
}
|
|
public function getConceptId()
|
|
{
|
|
return $this->conceptId;
|
|
}
|
|
public function setExternalIds($externalIds)
|
|
{
|
|
$this->externalIds = $externalIds;
|
|
}
|
|
public function getExternalIds()
|
|
{
|
|
return $this->externalIds;
|
|
}
|
|
public function setNames($names)
|
|
{
|
|
$this->names = $names;
|
|
}
|
|
public function getNames()
|
|
{
|
|
return $this->names;
|
|
}
|
|
public function setOmimId($omimId)
|
|
{
|
|
$this->omimId = $omimId;
|
|
}
|
|
public function getOmimId()
|
|
{
|
|
return $this->omimId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_VariantInfo extends Google_Model
|
|
{
|
|
}
|
|
|
|
class Google_Service_Genomics_VariantSet extends Google_Collection
|
|
{
|
|
protected $collection_key = 'referenceBounds';
|
|
protected $internal_gapi_mappings = array(
|
|
);
|
|
public $datasetId;
|
|
public $id;
|
|
protected $metadataType = 'Google_Service_Genomics_Metadata';
|
|
protected $metadataDataType = 'array';
|
|
protected $referenceBoundsType = 'Google_Service_Genomics_ReferenceBound';
|
|
protected $referenceBoundsDataType = 'array';
|
|
|
|
|
|
public function setDatasetId($datasetId)
|
|
{
|
|
$this->datasetId = $datasetId;
|
|
}
|
|
public function getDatasetId()
|
|
{
|
|
return $this->datasetId;
|
|
}
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
public function setMetadata($metadata)
|
|
{
|
|
$this->metadata = $metadata;
|
|
}
|
|
public function getMetadata()
|
|
{
|
|
return $this->metadata;
|
|
}
|
|
public function setReferenceBounds($referenceBounds)
|
|
{
|
|
$this->referenceBounds = $referenceBounds;
|
|
}
|
|
public function getReferenceBounds()
|
|
{
|
|
return $this->referenceBounds;
|
|
}
|
|
}
|