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- Bug fixes for general core bugs in 3.11.x will end 14 Nov 2022 (12 months plus 6 months extension).
- Bug fixes for security issues in 3.11.x will end 13 Nov 2023 (18 months plus 12 months extension).
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/lib/google/src/Google/Service/ -> Genomics.php (source)
Differences Between: [Versions 311 and 402] [Versions 311 and 403]
1 <?php 2 /* 3 * Copyright 2010 Google Inc. 4 * 5 * Licensed under the Apache License, Version 2.0 (the "License"); you may not 6 * use this file except in compliance with the License. You may obtain a copy of 7 * the License at 8 * 9 * http://www.apache.org/licenses/LICENSE-2.0 10 * 11 * Unless required by applicable law or agreed to in writing, software 12 * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT 13 * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the 14 * License for the specific language governing permissions and limitations under 15 * the License. 16 */ 17 18 /** 19 * Service definition for Genomics (v1). 20 * 21 * <p> 22 * An API to store, process, explore, and share DNA sequence reads, reference- 23 * based alignments, and variant calls.</p> 24 * 25 * <p> 26 * For more information about this service, see the API 27 * <a href="" target="_blank">Documentation</a> 28 * </p> 29 * 30 * @author Google, Inc. 31 */ 32 class Google_Service_Genomics extends Google_Service 33 { 34 /** View and manage your data in Google BigQuery. */ 35 const BIGQUERY = 36 "https://www.googleapis.com/auth/bigquery"; 37 /** View and manage your data across Google Cloud Platform services. */ 38 const CLOUD_PLATFORM = 39 "https://www.googleapis.com/auth/cloud-platform"; 40 /** Manage your data in Google Cloud Storage. */ 41 const DEVSTORAGE_READ_WRITE = 42 "https://www.googleapis.com/auth/devstorage.read_write"; 43 /** View and manage Genomics data. */ 44 const GENOMICS = 45 "https://www.googleapis.com/auth/genomics"; 46 /** View Genomics data. */ 47 const GENOMICS_READONLY = 48 "https://www.googleapis.com/auth/genomics.readonly"; 49 50 public $callsets; 51 public $datasets; 52 public $operations; 53 public $readgroupsets; 54 public $readgroupsets_coveragebuckets; 55 public $reads; 56 public $references; 57 public $references_bases; 58 public $referencesets; 59 public $variants; 60 public $variantsets; 61 62 63 /** 64 * Constructs the internal representation of the Genomics service. 65 * 66 * @param Google_Client $client 67 */ 68 public function __construct(Google_Client $client) 69 { 70 parent::__construct($client); 71 $this->rootUrl = 'https://genomics.googleapis.com/'; 72 $this->servicePath = ''; 73 $this->version = 'v1'; 74 $this->serviceName = 'genomics'; 75 76 $this->callsets = new Google_Service_Genomics_Callsets_Resource( 77 $this, 78 $this->serviceName, 79 'callsets', 80 array( 81 'methods' => array( 82 'create' => array( 83 'path' => 'v1/callsets', 84 'httpMethod' => 'POST', 85 'parameters' => array(), 86 ),'delete' => array( 87 'path' => 'v1/callsets/{callSetId}', 88 'httpMethod' => 'DELETE', 89 'parameters' => array( 90 'callSetId' => array( 91 'location' => 'path', 92 'type' => 'string', 93 'required' => true, 94 ), 95 ), 96 ),'get' => array( 97 'path' => 'v1/callsets/{callSetId}', 98 'httpMethod' => 'GET', 99 'parameters' => array( 100 'callSetId' => array( 101 'location' => 'path', 102 'type' => 'string', 103 'required' => true, 104 ), 105 ), 106 ),'patch' => array( 107 'path' => 'v1/callsets/{callSetId}', 108 'httpMethod' => 'PATCH', 109 'parameters' => array( 110 'callSetId' => array( 111 'location' => 'path', 112 'type' => 'string', 113 'required' => true, 114 ), 115 'updateMask' => array( 116 'location' => 'query', 117 'type' => 'string', 118 ), 119 ), 120 ),'search' => array( 121 'path' => 'v1/callsets/search', 122 'httpMethod' => 'POST', 123 'parameters' => array(), 124 ), 125 ) 126 ) 127 ); 128 $this->datasets = new Google_Service_Genomics_Datasets_Resource( 129 $this, 130 $this->serviceName, 131 'datasets', 132 array( 133 'methods' => array( 134 'create' => array( 135 'path' => 'v1/datasets', 136 'httpMethod' => 'POST', 137 'parameters' => array(), 138 ),'delete' => array( 139 'path' => 'v1/datasets/{datasetId}', 140 'httpMethod' => 'DELETE', 141 'parameters' => array( 142 'datasetId' => array( 143 'location' => 'path', 144 'type' => 'string', 145 'required' => true, 146 ), 147 ), 148 ),'get' => array( 149 'path' => 'v1/datasets/{datasetId}', 150 'httpMethod' => 'GET', 151 'parameters' => array( 152 'datasetId' => array( 153 'location' => 'path', 154 'type' => 'string', 155 'required' => true, 156 ), 157 ), 158 ),'getIamPolicy' => array( 159 'path' => 'v1/{+resource}:getIamPolicy', 160 'httpMethod' => 'POST', 161 'parameters' => array( 162 'resource' => array( 163 'location' => 'path', 164 'type' => 'string', 165 'required' => true, 166 ), 167 ), 168 ),'list' => array( 169 'path' => 'v1/datasets', 170 'httpMethod' => 'GET', 171 'parameters' => array( 172 'projectId' => array( 173 'location' => 'query', 174 'type' => 'string', 175 ), 176 'pageSize' => array( 177 'location' => 'query', 178 'type' => 'integer', 179 ), 180 'pageToken' => array( 181 'location' => 'query', 182 'type' => 'string', 183 ), 184 ), 185 ),'patch' => array( 186 'path' => 'v1/datasets/{datasetId}', 187 'httpMethod' => 'PATCH', 188 'parameters' => array( 189 'datasetId' => array( 190 'location' => 'path', 191 'type' => 'string', 192 'required' => true, 193 ), 194 'updateMask' => array( 195 'location' => 'query', 196 'type' => 'string', 197 ), 198 ), 199 ),'setIamPolicy' => array( 200 'path' => 'v1/{+resource}:setIamPolicy', 201 'httpMethod' => 'POST', 202 'parameters' => array( 203 'resource' => array( 204 'location' => 'path', 205 'type' => 'string', 206 'required' => true, 207 ), 208 ), 209 ),'testIamPermissions' => array( 210 'path' => 'v1/{+resource}:testIamPermissions', 211 'httpMethod' => 'POST', 212 'parameters' => array( 213 'resource' => array( 214 'location' => 'path', 215 'type' => 'string', 216 'required' => true, 217 ), 218 ), 219 ),'undelete' => array( 220 'path' => 'v1/datasets/{datasetId}:undelete', 221 'httpMethod' => 'POST', 222 'parameters' => array( 223 'datasetId' => array( 224 'location' => 'path', 225 'type' => 'string', 226 'required' => true, 227 ), 228 ), 229 ), 230 ) 231 ) 232 ); 233 $this->operations = new Google_Service_Genomics_Operations_Resource( 234 $this, 235 $this->serviceName, 236 'operations', 237 array( 238 'methods' => array( 239 'cancel' => array( 240 'path' => 'v1/{+name}:cancel', 241 'httpMethod' => 'POST', 242 'parameters' => array( 243 'name' => array( 244 'location' => 'path', 245 'type' => 'string', 246 'required' => true, 247 ), 248 ), 249 ),'delete' => array( 250 'path' => 'v1/{+name}', 251 'httpMethod' => 'DELETE', 252 'parameters' => array( 253 'name' => array( 254 'location' => 'path', 255 'type' => 'string', 256 'required' => true, 257 ), 258 ), 259 ),'get' => array( 260 'path' => 'v1/{+name}', 261 'httpMethod' => 'GET', 262 'parameters' => array( 263 'name' => array( 264 'location' => 'path', 265 'type' => 'string', 266 'required' => true, 267 ), 268 ), 269 ),'list' => array( 270 'path' => 'v1/{+name}', 271 'httpMethod' => 'GET', 272 'parameters' => array( 273 'name' => array( 274 'location' => 'path', 275 'type' => 'string', 276 'required' => true, 277 ), 278 'filter' => array( 279 'location' => 'query', 280 'type' => 'string', 281 ), 282 'pageToken' => array( 283 'location' => 'query', 284 'type' => 'string', 285 ), 286 'pageSize' => array( 287 'location' => 'query', 288 'type' => 'integer', 289 ), 290 ), 291 ), 292 ) 293 ) 294 ); 295 $this->readgroupsets = new Google_Service_Genomics_Readgroupsets_Resource( 296 $this, 297 $this->serviceName, 298 'readgroupsets', 299 array( 300 'methods' => array( 301 'delete' => array( 302 'path' => 'v1/readgroupsets/{readGroupSetId}', 303 'httpMethod' => 'DELETE', 304 'parameters' => array( 305 'readGroupSetId' => array( 306 'location' => 'path', 307 'type' => 'string', 308 'required' => true, 309 ), 310 ), 311 ),'export' => array( 312 'path' => 'v1/readgroupsets/{readGroupSetId}:export', 313 'httpMethod' => 'POST', 314 'parameters' => array( 315 'readGroupSetId' => array( 316 'location' => 'path', 317 'type' => 'string', 318 'required' => true, 319 ), 320 ), 321 ),'get' => array( 322 'path' => 'v1/readgroupsets/{readGroupSetId}', 323 'httpMethod' => 'GET', 324 'parameters' => array( 325 'readGroupSetId' => array( 326 'location' => 'path', 327 'type' => 'string', 328 'required' => true, 329 ), 330 ), 331 ),'import' => array( 332 'path' => 'v1/readgroupsets:import', 333 'httpMethod' => 'POST', 334 'parameters' => array(), 335 ),'patch' => array( 336 'path' => 'v1/readgroupsets/{readGroupSetId}', 337 'httpMethod' => 'PATCH', 338 'parameters' => array( 339 'readGroupSetId' => array( 340 'location' => 'path', 341 'type' => 'string', 342 'required' => true, 343 ), 344 'updateMask' => array( 345 'location' => 'query', 346 'type' => 'string', 347 ), 348 ), 349 ),'search' => array( 350 'path' => 'v1/readgroupsets/search', 351 'httpMethod' => 'POST', 352 'parameters' => array(), 353 ), 354 ) 355 ) 356 ); 357 $this->readgroupsets_coveragebuckets = new Google_Service_Genomics_ReadgroupsetsCoveragebuckets_Resource( 358 $this, 359 $this->serviceName, 360 'coveragebuckets', 361 array( 362 'methods' => array( 363 'list' => array( 364 'path' => 'v1/readgroupsets/{readGroupSetId}/coveragebuckets', 365 'httpMethod' => 'GET', 366 'parameters' => array( 367 'readGroupSetId' => array( 368 'location' => 'path', 369 'type' => 'string', 370 'required' => true, 371 ), 372 'end' => array( 373 'location' => 'query', 374 'type' => 'string', 375 ), 376 'pageSize' => array( 377 'location' => 'query', 378 'type' => 'integer', 379 ), 380 'start' => array( 381 'location' => 'query', 382 'type' => 'string', 383 ), 384 'pageToken' => array( 385 'location' => 'query', 386 'type' => 'string', 387 ), 388 'targetBucketWidth' => array( 389 'location' => 'query', 390 'type' => 'string', 391 ), 392 'referenceName' => array( 393 'location' => 'query', 394 'type' => 'string', 395 ), 396 ), 397 ), 398 ) 399 ) 400 ); 401 $this->reads = new Google_Service_Genomics_Reads_Resource( 402 $this, 403 $this->serviceName, 404 'reads', 405 array( 406 'methods' => array( 407 'search' => array( 408 'path' => 'v1/reads/search', 409 'httpMethod' => 'POST', 410 'parameters' => array(), 411 ), 412 ) 413 ) 414 ); 415 $this->references = new Google_Service_Genomics_References_Resource( 416 $this, 417 $this->serviceName, 418 'references', 419 array( 420 'methods' => array( 421 'get' => array( 422 'path' => 'v1/references/{referenceId}', 423 'httpMethod' => 'GET', 424 'parameters' => array( 425 'referenceId' => array( 426 'location' => 'path', 427 'type' => 'string', 428 'required' => true, 429 ), 430 ), 431 ),'search' => array( 432 'path' => 'v1/references/search', 433 'httpMethod' => 'POST', 434 'parameters' => array(), 435 ), 436 ) 437 ) 438 ); 439 $this->references_bases = new Google_Service_Genomics_ReferencesBases_Resource( 440 $this, 441 $this->serviceName, 442 'bases', 443 array( 444 'methods' => array( 445 'list' => array( 446 'path' => 'v1/references/{referenceId}/bases', 447 'httpMethod' => 'GET', 448 'parameters' => array( 449 'referenceId' => array( 450 'location' => 'path', 451 'type' => 'string', 452 'required' => true, 453 ), 454 'start' => array( 455 'location' => 'query', 456 'type' => 'string', 457 ), 458 'end' => array( 459 'location' => 'query', 460 'type' => 'string', 461 ), 462 'pageSize' => array( 463 'location' => 'query', 464 'type' => 'integer', 465 ), 466 'pageToken' => array( 467 'location' => 'query', 468 'type' => 'string', 469 ), 470 ), 471 ), 472 ) 473 ) 474 ); 475 $this->referencesets = new Google_Service_Genomics_Referencesets_Resource( 476 $this, 477 $this->serviceName, 478 'referencesets', 479 array( 480 'methods' => array( 481 'get' => array( 482 'path' => 'v1/referencesets/{referenceSetId}', 483 'httpMethod' => 'GET', 484 'parameters' => array( 485 'referenceSetId' => array( 486 'location' => 'path', 487 'type' => 'string', 488 'required' => true, 489 ), 490 ), 491 ),'search' => array( 492 'path' => 'v1/referencesets/search', 493 'httpMethod' => 'POST', 494 'parameters' => array(), 495 ), 496 ) 497 ) 498 ); 499 $this->variants = new Google_Service_Genomics_Variants_Resource( 500 $this, 501 $this->serviceName, 502 'variants', 503 array( 504 'methods' => array( 505 'create' => array( 506 'path' => 'v1/variants', 507 'httpMethod' => 'POST', 508 'parameters' => array(), 509 ),'delete' => array( 510 'path' => 'v1/variants/{variantId}', 511 'httpMethod' => 'DELETE', 512 'parameters' => array( 513 'variantId' => array( 514 'location' => 'path', 515 'type' => 'string', 516 'required' => true, 517 ), 518 ), 519 ),'get' => array( 520 'path' => 'v1/variants/{variantId}', 521 'httpMethod' => 'GET', 522 'parameters' => array( 523 'variantId' => array( 524 'location' => 'path', 525 'type' => 'string', 526 'required' => true, 527 ), 528 ), 529 ),'import' => array( 530 'path' => 'v1/variants:import', 531 'httpMethod' => 'POST', 532 'parameters' => array(), 533 ),'patch' => array( 534 'path' => 'v1/variants/{variantId}', 535 'httpMethod' => 'PATCH', 536 'parameters' => array( 537 'variantId' => array( 538 'location' => 'path', 539 'type' => 'string', 540 'required' => true, 541 ), 542 'updateMask' => array( 543 'location' => 'query', 544 'type' => 'string', 545 ), 546 ), 547 ),'search' => array( 548 'path' => 'v1/variants/search', 549 'httpMethod' => 'POST', 550 'parameters' => array(), 551 ), 552 ) 553 ) 554 ); 555 $this->variantsets = new Google_Service_Genomics_Variantsets_Resource( 556 $this, 557 $this->serviceName, 558 'variantsets', 559 array( 560 'methods' => array( 561 'create' => array( 562 'path' => 'v1/variantsets', 563 'httpMethod' => 'POST', 564 'parameters' => array(), 565 ),'delete' => array( 566 'path' => 'v1/variantsets/{variantSetId}', 567 'httpMethod' => 'DELETE', 568 'parameters' => array( 569 'variantSetId' => array( 570 'location' => 'path', 571 'type' => 'string', 572 'required' => true, 573 ), 574 ), 575 ),'export' => array( 576 'path' => 'v1/variantsets/{variantSetId}:export', 577 'httpMethod' => 'POST', 578 'parameters' => array( 579 'variantSetId' => array( 580 'location' => 'path', 581 'type' => 'string', 582 'required' => true, 583 ), 584 ), 585 ),'get' => array( 586 'path' => 'v1/variantsets/{variantSetId}', 587 'httpMethod' => 'GET', 588 'parameters' => array( 589 'variantSetId' => array( 590 'location' => 'path', 591 'type' => 'string', 592 'required' => true, 593 ), 594 ), 595 ),'patch' => array( 596 'path' => 'v1/variantsets/{variantSetId}', 597 'httpMethod' => 'PATCH', 598 'parameters' => array( 599 'variantSetId' => array( 600 'location' => 'path', 601 'type' => 'string', 602 'required' => true, 603 ), 604 'updateMask' => array( 605 'location' => 'query', 606 'type' => 'string', 607 ), 608 ), 609 ),'search' => array( 610 'path' => 'v1/variantsets/search', 611 'httpMethod' => 'POST', 612 'parameters' => array(), 613 ), 614 ) 615 ) 616 ); 617 } 618 } 619 620 621 /** 622 * The "callsets" collection of methods. 623 * Typical usage is: 624 * <code> 625 * $genomicsService = new Google_Service_Genomics(...); 626 * $callsets = $genomicsService->callsets; 627 * </code> 628 */ 629 class Google_Service_Genomics_Callsets_Resource extends Google_Service_Resource 630 { 631 632 /** 633 * Creates a new call set. (callsets.create) 634 * 635 * @param Google_CallSet $postBody 636 * @param array $optParams Optional parameters. 637 * @return Google_Service_Genomics_CallSet 638 */ 639 public function create(Google_Service_Genomics_CallSet $postBody, $optParams = array()) 640 { 641 $params = array('postBody' => $postBody); 642 $params = array_merge($params, $optParams); 643 return $this->call('create', array($params), "Google_Service_Genomics_CallSet"); 644 } 645 646 /** 647 * Deletes a call set. (callsets.delete) 648 * 649 * @param string $callSetId The ID of the call set to be deleted. 650 * @param array $optParams Optional parameters. 651 * @return Google_Service_Genomics_Empty 652 */ 653 public function delete($callSetId, $optParams = array()) 654 { 655 $params = array('callSetId' => $callSetId); 656 $params = array_merge($params, $optParams); 657 return $this->call('delete', array($params), "Google_Service_Genomics_Empty"); 658 } 659 660 /** 661 * Gets a call set by ID. (callsets.get) 662 * 663 * @param string $callSetId The ID of the call set. 664 * @param array $optParams Optional parameters. 665 * @return Google_Service_Genomics_CallSet 666 */ 667 public function get($callSetId, $optParams = array()) 668 { 669 $params = array('callSetId' => $callSetId); 670 $params = array_merge($params, $optParams); 671 return $this->call('get', array($params), "Google_Service_Genomics_CallSet"); 672 } 673 674 /** 675 * Updates a call set. This method supports patch semantics. (callsets.patch) 676 * 677 * @param string $callSetId The ID of the call set to be updated. 678 * @param Google_CallSet $postBody 679 * @param array $optParams Optional parameters. 680 * 681 * @opt_param string updateMask An optional mask specifying which fields to 682 * update. At this time, the only mutable field is name. The only acceptable 683 * value is "name". If unspecified, all mutable fields will be updated. 684 * @return Google_Service_Genomics_CallSet 685 */ 686 public function patch($callSetId, Google_Service_Genomics_CallSet $postBody, $optParams = array()) 687 { 688 $params = array('callSetId' => $callSetId, 'postBody' => $postBody); 689 $params = array_merge($params, $optParams); 690 return $this->call('patch', array($params), "Google_Service_Genomics_CallSet"); 691 } 692 693 /** 694 * Gets a list of call sets matching the criteria. Implements [GlobalAllianceApi 695 * .searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resour 696 * ces/avro/variantmethods.avdl#L178). (callsets.search) 697 * 698 * @param Google_SearchCallSetsRequest $postBody 699 * @param array $optParams Optional parameters. 700 * @return Google_Service_Genomics_SearchCallSetsResponse 701 */ 702 public function search(Google_Service_Genomics_SearchCallSetsRequest $postBody, $optParams = array()) 703 { 704 $params = array('postBody' => $postBody); 705 $params = array_merge($params, $optParams); 706 return $this->call('search', array($params), "Google_Service_Genomics_SearchCallSetsResponse"); 707 } 708 } 709 710 /** 711 * The "datasets" collection of methods. 712 * Typical usage is: 713 * <code> 714 * $genomicsService = new Google_Service_Genomics(...); 715 * $datasets = $genomicsService->datasets; 716 * </code> 717 */ 718 class Google_Service_Genomics_Datasets_Resource extends Google_Service_Resource 719 { 720 721 /** 722 * Creates a new dataset. (datasets.create) 723 * 724 * @param Google_Dataset $postBody 725 * @param array $optParams Optional parameters. 726 * @return Google_Service_Genomics_Dataset 727 */ 728 public function create(Google_Service_Genomics_Dataset $postBody, $optParams = array()) 729 { 730 $params = array('postBody' => $postBody); 731 $params = array_merge($params, $optParams); 732 return $this->call('create', array($params), "Google_Service_Genomics_Dataset"); 733 } 734 735 /** 736 * Deletes a dataset. (datasets.delete) 737 * 738 * @param string $datasetId The ID of the dataset to be deleted. 739 * @param array $optParams Optional parameters. 740 * @return Google_Service_Genomics_Empty 741 */ 742 public function delete($datasetId, $optParams = array()) 743 { 744 $params = array('datasetId' => $datasetId); 745 $params = array_merge($params, $optParams); 746 return $this->call('delete', array($params), "Google_Service_Genomics_Empty"); 747 } 748 749 /** 750 * Gets a dataset by ID. (datasets.get) 751 * 752 * @param string $datasetId The ID of the dataset. 753 * @param array $optParams Optional parameters. 754 * @return Google_Service_Genomics_Dataset 755 */ 756 public function get($datasetId, $optParams = array()) 757 { 758 $params = array('datasetId' => $datasetId); 759 $params = array_merge($params, $optParams); 760 return $this->call('get', array($params), "Google_Service_Genomics_Dataset"); 761 } 762 763 /** 764 * Gets the access control policy for the dataset. Is empty if the policy or the 765 * resource does not exist. See Getting a Policy for more information. 766 * (datasets.getIamPolicy) 767 * 768 * @param string $resource REQUIRED: The resource for which policy is being 769 * specified. Format is `datasets/`. 770 * @param Google_GetIamPolicyRequest $postBody 771 * @param array $optParams Optional parameters. 772 * @return Google_Service_Genomics_Policy 773 */ 774 public function getIamPolicy($resource, Google_Service_Genomics_GetIamPolicyRequest $postBody, $optParams = array()) 775 { 776 $params = array('resource' => $resource, 'postBody' => $postBody); 777 $params = array_merge($params, $optParams); 778 return $this->call('getIamPolicy', array($params), "Google_Service_Genomics_Policy"); 779 } 780 781 /** 782 * Lists datasets within a project. (datasets.listDatasets) 783 * 784 * @param array $optParams Optional parameters. 785 * 786 * @opt_param string projectId Required. The project to list datasets for. 787 * @opt_param int pageSize The maximum number of results returned by this 788 * request. If unspecified, defaults to 50. The maximum value is 1024. 789 * @opt_param string pageToken The continuation token, which is used to page 790 * through large result sets. To get the next page of results, set this 791 * parameter to the value of `nextPageToken` from the previous response. 792 * @return Google_Service_Genomics_ListDatasetsResponse 793 */ 794 public function listDatasets($optParams = array()) 795 { 796 $params = array(); 797 $params = array_merge($params, $optParams); 798 return $this->call('list', array($params), "Google_Service_Genomics_ListDatasetsResponse"); 799 } 800 801 /** 802 * Updates a dataset. This method supports patch semantics. (datasets.patch) 803 * 804 * @param string $datasetId The ID of the dataset to be updated. 805 * @param Google_Dataset $postBody 806 * @param array $optParams Optional parameters. 807 * 808 * @opt_param string updateMask An optional mask specifying which fields to 809 * update. At this time, the only mutable field is name. The only acceptable 810 * value is "name". If unspecified, all mutable fields will be updated. 811 * @return Google_Service_Genomics_Dataset 812 */ 813 public function patch($datasetId, Google_Service_Genomics_Dataset $postBody, $optParams = array()) 814 { 815 $params = array('datasetId' => $datasetId, 'postBody' => $postBody); 816 $params = array_merge($params, $optParams); 817 return $this->call('patch', array($params), "Google_Service_Genomics_Dataset"); 818 } 819 820 /** 821 * Sets the access control policy on the specified dataset. Replaces any 822 * existing policy. See Setting a Policy for more information. 823 * (datasets.setIamPolicy) 824 * 825 * @param string $resource REQUIRED: The resource for which policy is being 826 * specified. Format is `datasets/`. 827 * @param Google_SetIamPolicyRequest $postBody 828 * @param array $optParams Optional parameters. 829 * @return Google_Service_Genomics_Policy 830 */ 831 public function setIamPolicy($resource, Google_Service_Genomics_SetIamPolicyRequest $postBody, $optParams = array()) 832 { 833 $params = array('resource' => $resource, 'postBody' => $postBody); 834 $params = array_merge($params, $optParams); 835 return $this->call('setIamPolicy', array($params), "Google_Service_Genomics_Policy"); 836 } 837 838 /** 839 * Returns permissions that a caller has on the specified resource. See Testing 840 * Permissions for more information. (datasets.testIamPermissions) 841 * 842 * @param string $resource REQUIRED: The resource for which policy is being 843 * specified. Format is `datasets/`. 844 * @param Google_TestIamPermissionsRequest $postBody 845 * @param array $optParams Optional parameters. 846 * @return Google_Service_Genomics_TestIamPermissionsResponse 847 */ 848 public function testIamPermissions($resource, Google_Service_Genomics_TestIamPermissionsRequest $postBody, $optParams = array()) 849 { 850 $params = array('resource' => $resource, 'postBody' => $postBody); 851 $params = array_merge($params, $optParams); 852 return $this->call('testIamPermissions', array($params), "Google_Service_Genomics_TestIamPermissionsResponse"); 853 } 854 855 /** 856 * Undeletes a dataset by restoring a dataset which was deleted via this API. 857 * This operation is only possible for a week after the deletion occurred. 858 * (datasets.undelete) 859 * 860 * @param string $datasetId The ID of the dataset to be undeleted. 861 * @param Google_UndeleteDatasetRequest $postBody 862 * @param array $optParams Optional parameters. 863 * @return Google_Service_Genomics_Dataset 864 */ 865 public function undelete($datasetId, Google_Service_Genomics_UndeleteDatasetRequest $postBody, $optParams = array()) 866 { 867 $params = array('datasetId' => $datasetId, 'postBody' => $postBody); 868 $params = array_merge($params, $optParams); 869 return $this->call('undelete', array($params), "Google_Service_Genomics_Dataset"); 870 } 871 } 872 873 /** 874 * The "operations" collection of methods. 875 * Typical usage is: 876 * <code> 877 * $genomicsService = new Google_Service_Genomics(...); 878 * $operations = $genomicsService->operations; 879 * </code> 880 */ 881 class Google_Service_Genomics_Operations_Resource extends Google_Service_Resource 882 { 883 884 /** 885 * Starts asynchronous cancellation on a long-running operation. The server 886 * makes a best effort to cancel the operation, but success is not guaranteed. 887 * Clients may use Operations.GetOperation or Operations.ListOperations to check 888 * whether the cancellation succeeded or the operation completed despite 889 * cancellation. (operations.cancel) 890 * 891 * @param string $name The name of the operation resource to be cancelled. 892 * @param Google_CancelOperationRequest $postBody 893 * @param array $optParams Optional parameters. 894 * @return Google_Service_Genomics_Empty 895 */ 896 public function cancel($name, Google_Service_Genomics_CancelOperationRequest $postBody, $optParams = array()) 897 { 898 $params = array('name' => $name, 'postBody' => $postBody); 899 $params = array_merge($params, $optParams); 900 return $this->call('cancel', array($params), "Google_Service_Genomics_Empty"); 901 } 902 903 /** 904 * This method is not implemented. To cancel an operation, please use 905 * Operations.CancelOperation. (operations.delete) 906 * 907 * @param string $name The name of the operation resource to be deleted. 908 * @param array $optParams Optional parameters. 909 * @return Google_Service_Genomics_Empty 910 */ 911 public function delete($name, $optParams = array()) 912 { 913 $params = array('name' => $name); 914 $params = array_merge($params, $optParams); 915 return $this->call('delete', array($params), "Google_Service_Genomics_Empty"); 916 } 917 918 /** 919 * Gets the latest state of a long-running operation. Clients can use this 920 * method to poll the operation result at intervals as recommended by the API 921 * service. (operations.get) 922 * 923 * @param string $name The name of the operation resource. 924 * @param array $optParams Optional parameters. 925 * @return Google_Service_Genomics_Operation 926 */ 927 public function get($name, $optParams = array()) 928 { 929 $params = array('name' => $name); 930 $params = array_merge($params, $optParams); 931 return $this->call('get', array($params), "Google_Service_Genomics_Operation"); 932 } 933 934 /** 935 * Lists operations that match the specified filter in the request. 936 * (operations.listOperations) 937 * 938 * @param string $name The name of the operation collection. 939 * @param array $optParams Optional parameters. 940 * 941 * @opt_param string filter A string for filtering Operations. The following 942 * filter fields are supported: * projectId: Required. Corresponds to 943 * OperationMetadata.projectId. * createTime: The time this job was created, in 944 * seconds from the [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use 945 * `>=` and/or `= 1432140000` * `projectId = my-project AND createTime >= 946 * 1432140000 AND createTime <= 1432150000 AND status = RUNNING` 947 * @opt_param string pageToken The standard list page token. 948 * @opt_param int pageSize The maximum number of results to return. If 949 * unspecified, defaults to 256. The maximum value is 2048. 950 * @return Google_Service_Genomics_ListOperationsResponse 951 */ 952 public function listOperations($name, $optParams = array()) 953 { 954 $params = array('name' => $name); 955 $params = array_merge($params, $optParams); 956 return $this->call('list', array($params), "Google_Service_Genomics_ListOperationsResponse"); 957 } 958 } 959 960 /** 961 * The "readgroupsets" collection of methods. 962 * Typical usage is: 963 * <code> 964 * $genomicsService = new Google_Service_Genomics(...); 965 * $readgroupsets = $genomicsService->readgroupsets; 966 * </code> 967 */ 968 class Google_Service_Genomics_Readgroupsets_Resource extends Google_Service_Resource 969 { 970 971 /** 972 * Deletes a read group set. (readgroupsets.delete) 973 * 974 * @param string $readGroupSetId The ID of the read group set to be deleted. The 975 * caller must have WRITE permissions to the dataset associated with this read 976 * group set. 977 * @param array $optParams Optional parameters. 978 * @return Google_Service_Genomics_Empty 979 */ 980 public function delete($readGroupSetId, $optParams = array()) 981 { 982 $params = array('readGroupSetId' => $readGroupSetId); 983 $params = array_merge($params, $optParams); 984 return $this->call('delete', array($params), "Google_Service_Genomics_Empty"); 985 } 986 987 /** 988 * Exports a read group set to a BAM file in Google Cloud Storage. Note that 989 * currently there may be some differences between exported BAM files and the 990 * original BAM file at the time of import. See 991 * [ImportReadGroupSets](google.genomics.v1.ReadServiceV1.ImportReadGroupSets) 992 * for caveats. (readgroupsets.export) 993 * 994 * @param string $readGroupSetId Required. The ID of the read group set to 995 * export. 996 * @param Google_ExportReadGroupSetRequest $postBody 997 * @param array $optParams Optional parameters. 998 * @return Google_Service_Genomics_Operation 999 */ 1000 public function export($readGroupSetId, Google_Service_Genomics_ExportReadGroupSetRequest $postBody, $optParams = array()) 1001 { 1002 $params = array('readGroupSetId' => $readGroupSetId, 'postBody' => $postBody); 1003 $params = array_merge($params, $optParams); 1004 return $this->call('export', array($params), "Google_Service_Genomics_Operation"); 1005 } 1006 1007 /** 1008 * Gets a read group set by ID. (readgroupsets.get) 1009 * 1010 * @param string $readGroupSetId The ID of the read group set. 1011 * @param array $optParams Optional parameters. 1012 * @return Google_Service_Genomics_ReadGroupSet 1013 */ 1014 public function get($readGroupSetId, $optParams = array()) 1015 { 1016 $params = array('readGroupSetId' => $readGroupSetId); 1017 $params = array_merge($params, $optParams); 1018 return $this->call('get', array($params), "Google_Service_Genomics_ReadGroupSet"); 1019 } 1020 1021 /** 1022 * Creates read group sets by asynchronously importing the provided information. 1023 * The caller must have WRITE permissions to the dataset. ## Notes on 1024 * [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import - Tags will be 1025 * converted to strings - tag types are not preserved - Comments (`@CO`) in the 1026 * input file header will not be preserved - Original header order of references 1027 * (`@SQ`) will not be preserved - Any reverse stranded unmapped reads will be 1028 * reverse complemented, and their qualities (and "BQ" tag, if any) will be 1029 * reversed - Unmapped reads will be stripped of positional information 1030 * (reference name and position) (readgroupsets.import) 1031 * 1032 * @param Google_ImportReadGroupSetsRequest $postBody 1033 * @param array $optParams Optional parameters. 1034 * @return Google_Service_Genomics_Operation 1035 */ 1036 public function import(Google_Service_Genomics_ImportReadGroupSetsRequest $postBody, $optParams = array()) 1037 { 1038 $params = array('postBody' => $postBody); 1039 $params = array_merge($params, $optParams); 1040 return $this->call('import', array($params), "Google_Service_Genomics_Operation"); 1041 } 1042 1043 /** 1044 * Updates a read group set. This method supports patch semantics. 1045 * (readgroupsets.patch) 1046 * 1047 * @param string $readGroupSetId The ID of the read group set to be updated. The 1048 * caller must have WRITE permissions to the dataset associated with this read 1049 * group set. 1050 * @param Google_ReadGroupSet $postBody 1051 * @param array $optParams Optional parameters. 1052 * 1053 * @opt_param string updateMask An optional mask specifying which fields to 1054 * update. At this time, mutable fields are referenceSetId and name. Acceptable 1055 * values are "referenceSetId" and "name". If unspecified, all mutable fields 1056 * will be updated. 1057 * @return Google_Service_Genomics_ReadGroupSet 1058 */ 1059 public function patch($readGroupSetId, Google_Service_Genomics_ReadGroupSet $postBody, $optParams = array()) 1060 { 1061 $params = array('readGroupSetId' => $readGroupSetId, 'postBody' => $postBody); 1062 $params = array_merge($params, $optParams); 1063 return $this->call('patch', array($params), "Google_Service_Genomics_ReadGroupSet"); 1064 } 1065 1066 /** 1067 * Searches for read group sets matching the criteria. Implements [GlobalAllianc 1068 * eApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/ma 1069 * in/resources/avro/readmethods.avdl#L135). (readgroupsets.search) 1070 * 1071 * @param Google_SearchReadGroupSetsRequest $postBody 1072 * @param array $optParams Optional parameters. 1073 * @return Google_Service_Genomics_SearchReadGroupSetsResponse 1074 */ 1075 public function search(Google_Service_Genomics_SearchReadGroupSetsRequest $postBody, $optParams = array()) 1076 { 1077 $params = array('postBody' => $postBody); 1078 $params = array_merge($params, $optParams); 1079 return $this->call('search', array($params), "Google_Service_Genomics_SearchReadGroupSetsResponse"); 1080 } 1081 } 1082 1083 /** 1084 * The "coveragebuckets" collection of methods. 1085 * Typical usage is: 1086 * <code> 1087 * $genomicsService = new Google_Service_Genomics(...); 1088 * $coveragebuckets = $genomicsService->coveragebuckets; 1089 * </code> 1090 */ 1091 class Google_Service_Genomics_ReadgroupsetsCoveragebuckets_Resource extends Google_Service_Resource 1092 { 1093 1094 /** 1095 * Lists fixed width coverage buckets for a read group set, each of which 1096 * correspond to a range of a reference sequence. Each bucket summarizes 1097 * coverage information across its corresponding genomic range. Coverage is 1098 * defined as the number of reads which are aligned to a given base in the 1099 * reference sequence. Coverage buckets are available at several precomputed 1100 * bucket widths, enabling retrieval of various coverage 'zoom levels'. The 1101 * caller must have READ permissions for the target read group set. 1102 * (coveragebuckets.listReadgroupsetsCoveragebuckets) 1103 * 1104 * @param string $readGroupSetId Required. The ID of the read group set over 1105 * which coverage is requested. 1106 * @param array $optParams Optional parameters. 1107 * 1108 * @opt_param string end The end position of the range on the reference, 0-based 1109 * exclusive. If specified, `referenceName` must also be specified. If unset or 1110 * 0, defaults to the length of the reference. 1111 * @opt_param int pageSize The maximum number of results to return in a single 1112 * page. If unspecified, defaults to 1024. The maximum value is 2048. 1113 * @opt_param string start The start position of the range on the reference, 1114 * 0-based inclusive. If specified, `referenceName` must also be specified. 1115 * Defaults to 0. 1116 * @opt_param string pageToken The continuation token, which is used to page 1117 * through large result sets. To get the next page of results, set this 1118 * parameter to the value of `nextPageToken` from the previous response. 1119 * @opt_param string targetBucketWidth The desired width of each reported 1120 * coverage bucket in base pairs. This will be rounded down to the nearest 1121 * precomputed bucket width; the value of which is returned as `bucketWidth` in 1122 * the response. Defaults to infinity (each bucket spans an entire reference 1123 * sequence) or the length of the target range, if specified. The smallest 1124 * precomputed `bucketWidth` is currently 2048 base pairs; this is subject to 1125 * change. 1126 * @opt_param string referenceName The name of the reference to query, within 1127 * the reference set associated with this query. Optional. 1128 * @return Google_Service_Genomics_ListCoverageBucketsResponse 1129 */ 1130 public function listReadgroupsetsCoveragebuckets($readGroupSetId, $optParams = array()) 1131 { 1132 $params = array('readGroupSetId' => $readGroupSetId); 1133 $params = array_merge($params, $optParams); 1134 return $this->call('list', array($params), "Google_Service_Genomics_ListCoverageBucketsResponse"); 1135 } 1136 } 1137 1138 /** 1139 * The "reads" collection of methods. 1140 * Typical usage is: 1141 * <code> 1142 * $genomicsService = new Google_Service_Genomics(...); 1143 * $reads = $genomicsService->reads; 1144 * </code> 1145 */ 1146 class Google_Service_Genomics_Reads_Resource extends Google_Service_Resource 1147 { 1148 1149 /** 1150 * Gets a list of reads for one or more read group sets. Reads search operates 1151 * over a genomic coordinate space of reference sequence & position defined over 1152 * the reference sequences to which the requested read group sets are aligned. 1153 * If a target positional range is specified, search returns all reads whose 1154 * alignment to the reference genome overlap the range. A query which specifies 1155 * only read group set IDs yields all reads in those read group sets, including 1156 * unmapped reads. All reads returned (including reads on subsequent pages) are 1157 * ordered by genomic coordinate (reference sequence & position). Reads with 1158 * equivalent genomic coordinates are returned in a deterministic order. 1159 * Implements [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/b 1160 * lob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85). (reads.search) 1161 * 1162 * @param Google_SearchReadsRequest $postBody 1163 * @param array $optParams Optional parameters. 1164 * @return Google_Service_Genomics_SearchReadsResponse 1165 */ 1166 public function search(Google_Service_Genomics_SearchReadsRequest $postBody, $optParams = array()) 1167 { 1168 $params = array('postBody' => $postBody); 1169 $params = array_merge($params, $optParams); 1170 return $this->call('search', array($params), "Google_Service_Genomics_SearchReadsResponse"); 1171 } 1172 } 1173 1174 /** 1175 * The "references" collection of methods. 1176 * Typical usage is: 1177 * <code> 1178 * $genomicsService = new Google_Service_Genomics(...); 1179 * $references = $genomicsService->references; 1180 * </code> 1181 */ 1182 class Google_Service_Genomics_References_Resource extends Google_Service_Resource 1183 { 1184 1185 /** 1186 * Gets a reference. Implements [GlobalAllianceApi.getReference](https://github. 1187 * com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L 1188 * 158). (references.get) 1189 * 1190 * @param string $referenceId The ID of the reference. 1191 * @param array $optParams Optional parameters. 1192 * @return Google_Service_Genomics_Reference 1193 */ 1194 public function get($referenceId, $optParams = array()) 1195 { 1196 $params = array('referenceId' => $referenceId); 1197 $params = array_merge($params, $optParams); 1198 return $this->call('get', array($params), "Google_Service_Genomics_Reference"); 1199 } 1200 1201 /** 1202 * Searches for references which match the given criteria. Implements [GlobalAll 1203 * ianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/m 1204 * ain/resources/avro/referencemethods.avdl#L146). (references.search) 1205 * 1206 * @param Google_SearchReferencesRequest $postBody 1207 * @param array $optParams Optional parameters. 1208 * @return Google_Service_Genomics_SearchReferencesResponse 1209 */ 1210 public function search(Google_Service_Genomics_SearchReferencesRequest $postBody, $optParams = array()) 1211 { 1212 $params = array('postBody' => $postBody); 1213 $params = array_merge($params, $optParams); 1214 return $this->call('search', array($params), "Google_Service_Genomics_SearchReferencesResponse"); 1215 } 1216 } 1217 1218 /** 1219 * The "bases" collection of methods. 1220 * Typical usage is: 1221 * <code> 1222 * $genomicsService = new Google_Service_Genomics(...); 1223 * $bases = $genomicsService->bases; 1224 * </code> 1225 */ 1226 class Google_Service_Genomics_ReferencesBases_Resource extends Google_Service_Resource 1227 { 1228 1229 /** 1230 * Lists the bases in a reference, optionally restricted to a range. Implements 1231 * [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v 1232 * 0.5.1/src/main/resources/avro/referencemethods.avdl#L221). 1233 * (bases.listReferencesBases) 1234 * 1235 * @param string $referenceId The ID of the reference. 1236 * @param array $optParams Optional parameters. 1237 * 1238 * @opt_param string start The start position (0-based) of this query. Defaults 1239 * to 0. 1240 * @opt_param string end The end position (0-based, exclusive) of this query. 1241 * Defaults to the length of this reference. 1242 * @opt_param int pageSize Specifies the maximum number of bases to return in a 1243 * single page. 1244 * @opt_param string pageToken The continuation token, which is used to page 1245 * through large result sets. To get the next page of results, set this 1246 * parameter to the value of `nextPageToken` from the previous response. 1247 * @return Google_Service_Genomics_ListBasesResponse 1248 */ 1249 public function listReferencesBases($referenceId, $optParams = array()) 1250 { 1251 $params = array('referenceId' => $referenceId); 1252 $params = array_merge($params, $optParams); 1253 return $this->call('list', array($params), "Google_Service_Genomics_ListBasesResponse"); 1254 } 1255 } 1256 1257 /** 1258 * The "referencesets" collection of methods. 1259 * Typical usage is: 1260 * <code> 1261 * $genomicsService = new Google_Service_Genomics(...); 1262 * $referencesets = $genomicsService->referencesets; 1263 * </code> 1264 */ 1265 class Google_Service_Genomics_Referencesets_Resource extends Google_Service_Resource 1266 { 1267 1268 /** 1269 * Gets a reference set. Implements [GlobalAllianceApi.getReferenceSet](https:// 1270 * github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods 1271 * .avdl#L83). (referencesets.get) 1272 * 1273 * @param string $referenceSetId The ID of the reference set. 1274 * @param array $optParams Optional parameters. 1275 * @return Google_Service_Genomics_ReferenceSet 1276 */ 1277 public function get($referenceSetId, $optParams = array()) 1278 { 1279 $params = array('referenceSetId' => $referenceSetId); 1280 $params = array_merge($params, $optParams); 1281 return $this->call('get', array($params), "Google_Service_Genomics_ReferenceSet"); 1282 } 1283 1284 /** 1285 * Searches for reference sets which match the given criteria. Implements [Globa 1286 * lAllianceApi.searchReferenceSets](http://ga4gh.org/documentation/api/v0.5.1/g 1287 * a4gh_api.html#/schema/org.ga4gh.searchReferenceSets). (referencesets.search) 1288 * 1289 * @param Google_SearchReferenceSetsRequest $postBody 1290 * @param array $optParams Optional parameters. 1291 * @return Google_Service_Genomics_SearchReferenceSetsResponse 1292 */ 1293 public function search(Google_Service_Genomics_SearchReferenceSetsRequest $postBody, $optParams = array()) 1294 { 1295 $params = array('postBody' => $postBody); 1296 $params = array_merge($params, $optParams); 1297 return $this->call('search', array($params), "Google_Service_Genomics_SearchReferenceSetsResponse"); 1298 } 1299 } 1300 1301 /** 1302 * The "variants" collection of methods. 1303 * Typical usage is: 1304 * <code> 1305 * $genomicsService = new Google_Service_Genomics(...); 1306 * $variants = $genomicsService->variants; 1307 * </code> 1308 */ 1309 class Google_Service_Genomics_Variants_Resource extends Google_Service_Resource 1310 { 1311 1312 /** 1313 * Creates a new variant. (variants.create) 1314 * 1315 * @param Google_Variant $postBody 1316 * @param array $optParams Optional parameters. 1317 * @return Google_Service_Genomics_Variant 1318 */ 1319 public function create(Google_Service_Genomics_Variant $postBody, $optParams = array()) 1320 { 1321 $params = array('postBody' => $postBody); 1322 $params = array_merge($params, $optParams); 1323 return $this->call('create', array($params), "Google_Service_Genomics_Variant"); 1324 } 1325 1326 /** 1327 * Deletes a variant. (variants.delete) 1328 * 1329 * @param string $variantId The ID of the variant to be deleted. 1330 * @param array $optParams Optional parameters. 1331 * @return Google_Service_Genomics_Empty 1332 */ 1333 public function delete($variantId, $optParams = array()) 1334 { 1335 $params = array('variantId' => $variantId); 1336 $params = array_merge($params, $optParams); 1337 return $this->call('delete', array($params), "Google_Service_Genomics_Empty"); 1338 } 1339 1340 /** 1341 * Gets a variant by ID. (variants.get) 1342 * 1343 * @param string $variantId The ID of the variant. 1344 * @param array $optParams Optional parameters. 1345 * @return Google_Service_Genomics_Variant 1346 */ 1347 public function get($variantId, $optParams = array()) 1348 { 1349 $params = array('variantId' => $variantId); 1350 $params = array_merge($params, $optParams); 1351 return $this->call('get', array($params), "Google_Service_Genomics_Variant"); 1352 } 1353 1354 /** 1355 * Creates variant data by asynchronously importing the provided information. 1356 * The variants for import will be merged with any existing variant that matches 1357 * its reference sequence, start, end, reference bases, and alternative bases. 1358 * If no such variant exists, a new one will be created. When variants are 1359 * merged, the call information from the new variant is added to the existing 1360 * variant, and other fields (such as key/value pairs) are discarded. In 1361 * particular, this means for merged VCF variants that have conflicting INFO 1362 * fields, some data will be arbitrarily discarded. As a special case, for 1363 * single-sample VCF files, QUAL and FILTER fields will be moved to the call 1364 * level; these are sometimes interpreted in a call-specific context. Imported 1365 * VCF headers are appended to the metadata already in a variant set. 1366 * (variants.import) 1367 * 1368 * @param Google_ImportVariantsRequest $postBody 1369 * @param array $optParams Optional parameters. 1370 * @return Google_Service_Genomics_Operation 1371 */ 1372 public function import(Google_Service_Genomics_ImportVariantsRequest $postBody, $optParams = array()) 1373 { 1374 $params = array('postBody' => $postBody); 1375 $params = array_merge($params, $optParams); 1376 return $this->call('import', array($params), "Google_Service_Genomics_Operation"); 1377 } 1378 1379 /** 1380 * Updates a variant. This method supports patch semantics. Returns the modified 1381 * variant without its calls. (variants.patch) 1382 * 1383 * @param string $variantId The ID of the variant to be updated. 1384 * @param Google_Variant $postBody 1385 * @param array $optParams Optional parameters. 1386 * 1387 * @opt_param string updateMask An optional mask specifying which fields to 1388 * update. At this time, mutable fields are names and info. Acceptable values 1389 * are "names" and "info". If unspecified, all mutable fields will be updated. 1390 * @return Google_Service_Genomics_Variant 1391 */ 1392 public function patch($variantId, Google_Service_Genomics_Variant $postBody, $optParams = array()) 1393 { 1394 $params = array('variantId' => $variantId, 'postBody' => $postBody); 1395 $params = array_merge($params, $optParams); 1396 return $this->call('patch', array($params), "Google_Service_Genomics_Variant"); 1397 } 1398 1399 /** 1400 * Gets a list of variants matching the criteria. Implements [GlobalAllianceApi. 1401 * searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resourc 1402 * es/avro/variantmethods.avdl#L126). (variants.search) 1403 * 1404 * @param Google_SearchVariantsRequest $postBody 1405 * @param array $optParams Optional parameters. 1406 * @return Google_Service_Genomics_SearchVariantsResponse 1407 */ 1408 public function search(Google_Service_Genomics_SearchVariantsRequest $postBody, $optParams = array()) 1409 { 1410 $params = array('postBody' => $postBody); 1411 $params = array_merge($params, $optParams); 1412 return $this->call('search', array($params), "Google_Service_Genomics_SearchVariantsResponse"); 1413 } 1414 } 1415 1416 /** 1417 * The "variantsets" collection of methods. 1418 * Typical usage is: 1419 * <code> 1420 * $genomicsService = new Google_Service_Genomics(...); 1421 * $variantsets = $genomicsService->variantsets; 1422 * </code> 1423 */ 1424 class Google_Service_Genomics_Variantsets_Resource extends Google_Service_Resource 1425 { 1426 1427 /** 1428 * Creates a new variant set. The provided variant set must have a valid 1429 * `datasetId` set - all other fields are optional. Note that the `id` field 1430 * will be ignored, as this is assigned by the server. (variantsets.create) 1431 * 1432 * @param Google_VariantSet $postBody 1433 * @param array $optParams Optional parameters. 1434 * @return Google_Service_Genomics_VariantSet 1435 */ 1436 public function create(Google_Service_Genomics_VariantSet $postBody, $optParams = array()) 1437 { 1438 $params = array('postBody' => $postBody); 1439 $params = array_merge($params, $optParams); 1440 return $this->call('create', array($params), "Google_Service_Genomics_VariantSet"); 1441 } 1442 1443 /** 1444 * Deletes the contents of a variant set. The variant set object is not deleted. 1445 * (variantsets.delete) 1446 * 1447 * @param string $variantSetId The ID of the variant set to be deleted. 1448 * @param array $optParams Optional parameters. 1449 * @return Google_Service_Genomics_Empty 1450 */ 1451 public function delete($variantSetId, $optParams = array()) 1452 { 1453 $params = array('variantSetId' => $variantSetId); 1454 $params = array_merge($params, $optParams); 1455 return $this->call('delete', array($params), "Google_Service_Genomics_Empty"); 1456 } 1457 1458 /** 1459 * Exports variant set data to an external destination. (variantsets.export) 1460 * 1461 * @param string $variantSetId Required. The ID of the variant set that contains 1462 * variant data which should be exported. The caller must have READ access to 1463 * this variant set. 1464 * @param Google_ExportVariantSetRequest $postBody 1465 * @param array $optParams Optional parameters. 1466 * @return Google_Service_Genomics_Operation 1467 */ 1468 public function export($variantSetId, Google_Service_Genomics_ExportVariantSetRequest $postBody, $optParams = array()) 1469 { 1470 $params = array('variantSetId' => $variantSetId, 'postBody' => $postBody); 1471 $params = array_merge($params, $optParams); 1472 return $this->call('export', array($params), "Google_Service_Genomics_Operation"); 1473 } 1474 1475 /** 1476 * Gets a variant set by ID. (variantsets.get) 1477 * 1478 * @param string $variantSetId Required. The ID of the variant set. 1479 * @param array $optParams Optional parameters. 1480 * @return Google_Service_Genomics_VariantSet 1481 */ 1482 public function get($variantSetId, $optParams = array()) 1483 { 1484 $params = array('variantSetId' => $variantSetId); 1485 $params = array_merge($params, $optParams); 1486 return $this->call('get', array($params), "Google_Service_Genomics_VariantSet"); 1487 } 1488 1489 /** 1490 * Updates a variant set. This method supports patch semantics. 1491 * (variantsets.patch) 1492 * 1493 * @param string $variantSetId The ID of the variant to be updated (must already 1494 * exist). 1495 * @param Google_VariantSet $postBody 1496 * @param array $optParams Optional parameters. 1497 * 1498 * @opt_param string updateMask An optional mask specifying which fields to 1499 * update. At this time, the only mutable field is metadata. The only acceptable 1500 * value is "metadata". If unspecified, all mutable fields will be updated. 1501 * @return Google_Service_Genomics_VariantSet 1502 */ 1503 public function patch($variantSetId, Google_Service_Genomics_VariantSet $postBody, $optParams = array()) 1504 { 1505 $params = array('variantSetId' => $variantSetId, 'postBody' => $postBody); 1506 $params = array_merge($params, $optParams); 1507 return $this->call('patch', array($params), "Google_Service_Genomics_VariantSet"); 1508 } 1509 1510 /** 1511 * Returns a list of all variant sets matching search criteria. Implements [Glob 1512 * alAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1 1513 * /src/main/resources/avro/variantmethods.avdl#L49). (variantsets.search) 1514 * 1515 * @param Google_SearchVariantSetsRequest $postBody 1516 * @param array $optParams Optional parameters. 1517 * @return Google_Service_Genomics_SearchVariantSetsResponse 1518 */ 1519 public function search(Google_Service_Genomics_SearchVariantSetsRequest $postBody, $optParams = array()) 1520 { 1521 $params = array('postBody' => $postBody); 1522 $params = array_merge($params, $optParams); 1523 return $this->call('search', array($params), "Google_Service_Genomics_SearchVariantSetsResponse"); 1524 } 1525 } 1526 1527 1528 1529 1530 class Google_Service_Genomics_Binding extends Google_Collection 1531 { 1532 protected $collection_key = 'members'; 1533 protected $internal_gapi_mappings = array( 1534 ); 1535 public $members; 1536 public $role; 1537 1538 1539 public function setMembers($members) 1540 { 1541 $this->members = $members; 1542 } 1543 public function getMembers() 1544 { 1545 return $this->members; 1546 } 1547 public function setRole($role) 1548 { 1549 $this->role = $role; 1550 } 1551 public function getRole() 1552 { 1553 return $this->role; 1554 } 1555 } 1556 1557 class Google_Service_Genomics_CallSet extends Google_Collection 1558 { 1559 protected $collection_key = 'variantSetIds'; 1560 protected $internal_gapi_mappings = array( 1561 ); 1562 public $created; 1563 public $id; 1564 public $info; 1565 public $name; 1566 public $sampleId; 1567 public $variantSetIds; 1568 1569 1570 public function setCreated($created) 1571 { 1572 $this->created = $created; 1573 } 1574 public function getCreated() 1575 { 1576 return $this->created; 1577 } 1578 public function setId($id) 1579 { 1580 $this->id = $id; 1581 } 1582 public function getId() 1583 { 1584 return $this->id; 1585 } 1586 public function setInfo($info) 1587 { 1588 $this->info = $info; 1589 } 1590 public function getInfo() 1591 { 1592 return $this->info; 1593 } 1594 public function setName($name) 1595 { 1596 $this->name = $name; 1597 } 1598 public function getName() 1599 { 1600 return $this->name; 1601 } 1602 public function setSampleId($sampleId) 1603 { 1604 $this->sampleId = $sampleId; 1605 } 1606 public function getSampleId() 1607 { 1608 return $this->sampleId; 1609 } 1610 public function setVariantSetIds($variantSetIds) 1611 { 1612 $this->variantSetIds = $variantSetIds; 1613 } 1614 public function getVariantSetIds() 1615 { 1616 return $this->variantSetIds; 1617 } 1618 } 1619 1620 class Google_Service_Genomics_CallSetInfo extends Google_Model 1621 { 1622 } 1623 1624 class Google_Service_Genomics_CancelOperationRequest extends Google_Model 1625 { 1626 } 1627 1628 class Google_Service_Genomics_CigarUnit extends Google_Model 1629 { 1630 protected $internal_gapi_mappings = array( 1631 ); 1632 public $operation; 1633 public $operationLength; 1634 public $referenceSequence; 1635 1636 1637 public function setOperation($operation) 1638 { 1639 $this->operation = $operation; 1640 } 1641 public function getOperation() 1642 { 1643 return $this->operation; 1644 } 1645 public function setOperationLength($operationLength) 1646 { 1647 $this->operationLength = $operationLength; 1648 } 1649 public function getOperationLength() 1650 { 1651 return $this->operationLength; 1652 } 1653 public function setReferenceSequence($referenceSequence) 1654 { 1655 $this->referenceSequence = $referenceSequence; 1656 } 1657 public function getReferenceSequence() 1658 { 1659 return $this->referenceSequence; 1660 } 1661 } 1662 1663 class Google_Service_Genomics_CoverageBucket extends Google_Model 1664 { 1665 protected $internal_gapi_mappings = array( 1666 ); 1667 public $meanCoverage; 1668 protected $rangeType = 'Google_Service_Genomics_Range'; 1669 protected $rangeDataType = ''; 1670 1671 1672 public function setMeanCoverage($meanCoverage) 1673 { 1674 $this->meanCoverage = $meanCoverage; 1675 } 1676 public function getMeanCoverage() 1677 { 1678 return $this->meanCoverage; 1679 } 1680 public function setRange(Google_Service_Genomics_Range $range) 1681 { 1682 $this->range = $range; 1683 } 1684 public function getRange() 1685 { 1686 return $this->range; 1687 } 1688 } 1689 1690 class Google_Service_Genomics_Dataset extends Google_Model 1691 { 1692 protected $internal_gapi_mappings = array( 1693 ); 1694 public $createTime; 1695 public $id; 1696 public $name; 1697 public $projectId; 1698 1699 1700 public function setCreateTime($createTime) 1701 { 1702 $this->createTime = $createTime; 1703 } 1704 public function getCreateTime() 1705 { 1706 return $this->createTime; 1707 } 1708 public function setId($id) 1709 { 1710 $this->id = $id; 1711 } 1712 public function getId() 1713 { 1714 return $this->id; 1715 } 1716 public function setName($name) 1717 { 1718 $this->name = $name; 1719 } 1720 public function getName() 1721 { 1722 return $this->name; 1723 } 1724 public function setProjectId($projectId) 1725 { 1726 $this->projectId = $projectId; 1727 } 1728 public function getProjectId() 1729 { 1730 return $this->projectId; 1731 } 1732 } 1733 1734 class Google_Service_Genomics_Empty extends Google_Model 1735 { 1736 } 1737 1738 class Google_Service_Genomics_Experiment extends Google_Model 1739 { 1740 protected $internal_gapi_mappings = array( 1741 ); 1742 public $instrumentModel; 1743 public $libraryId; 1744 public $platformUnit; 1745 public $sequencingCenter; 1746 1747 1748 public function setInstrumentModel($instrumentModel) 1749 { 1750 $this->instrumentModel = $instrumentModel; 1751 } 1752 public function getInstrumentModel() 1753 { 1754 return $this->instrumentModel; 1755 } 1756 public function setLibraryId($libraryId) 1757 { 1758 $this->libraryId = $libraryId; 1759 } 1760 public function getLibraryId() 1761 { 1762 return $this->libraryId; 1763 } 1764 public function setPlatformUnit($platformUnit) 1765 { 1766 $this->platformUnit = $platformUnit; 1767 } 1768 public function getPlatformUnit() 1769 { 1770 return $this->platformUnit; 1771 } 1772 public function setSequencingCenter($sequencingCenter) 1773 { 1774 $this->sequencingCenter = $sequencingCenter; 1775 } 1776 public function getSequencingCenter() 1777 { 1778 return $this->sequencingCenter; 1779 } 1780 } 1781 1782 class Google_Service_Genomics_ExportReadGroupSetRequest extends Google_Collection 1783 { 1784 protected $collection_key = 'referenceNames'; 1785 protected $internal_gapi_mappings = array( 1786 ); 1787 public $exportUri; 1788 public $projectId; 1789 public $referenceNames; 1790 1791 1792 public function setExportUri($exportUri) 1793 { 1794 $this->exportUri = $exportUri; 1795 } 1796 public function getExportUri() 1797 { 1798 return $this->exportUri; 1799 } 1800 public function setProjectId($projectId) 1801 { 1802 $this->projectId = $projectId; 1803 } 1804 public function getProjectId() 1805 { 1806 return $this->projectId; 1807 } 1808 public function setReferenceNames($referenceNames) 1809 { 1810 $this->referenceNames = $referenceNames; 1811 } 1812 public function getReferenceNames() 1813 { 1814 return $this->referenceNames; 1815 } 1816 } 1817 1818 class Google_Service_Genomics_ExportVariantSetRequest extends Google_Collection 1819 { 1820 protected $collection_key = 'callSetIds'; 1821 protected $internal_gapi_mappings = array( 1822 ); 1823 public $bigqueryDataset; 1824 public $bigqueryTable; 1825 public $callSetIds; 1826 public $format; 1827 public $projectId; 1828 1829 1830 public function setBigqueryDataset($bigqueryDataset) 1831 { 1832 $this->bigqueryDataset = $bigqueryDataset; 1833 } 1834 public function getBigqueryDataset() 1835 { 1836 return $this->bigqueryDataset; 1837 } 1838 public function setBigqueryTable($bigqueryTable) 1839 { 1840 $this->bigqueryTable = $bigqueryTable; 1841 } 1842 public function getBigqueryTable() 1843 { 1844 return $this->bigqueryTable; 1845 } 1846 public function setCallSetIds($callSetIds) 1847 { 1848 $this->callSetIds = $callSetIds; 1849 } 1850 public function getCallSetIds() 1851 { 1852 return $this->callSetIds; 1853 } 1854 public function setFormat($format) 1855 { 1856 $this->format = $format; 1857 } 1858 public function getFormat() 1859 { 1860 return $this->format; 1861 } 1862 public function setProjectId($projectId) 1863 { 1864 $this->projectId = $projectId; 1865 } 1866 public function getProjectId() 1867 { 1868 return $this->projectId; 1869 } 1870 } 1871 1872 class Google_Service_Genomics_GetIamPolicyRequest extends Google_Model 1873 { 1874 } 1875 1876 class Google_Service_Genomics_ImportReadGroupSetsRequest extends Google_Collection 1877 { 1878 protected $collection_key = 'sourceUris'; 1879 protected $internal_gapi_mappings = array( 1880 ); 1881 public $datasetId; 1882 public $partitionStrategy; 1883 public $referenceSetId; 1884 public $sourceUris; 1885 1886 1887 public function setDatasetId($datasetId) 1888 { 1889 $this->datasetId = $datasetId; 1890 } 1891 public function getDatasetId() 1892 { 1893 return $this->datasetId; 1894 } 1895 public function setPartitionStrategy($partitionStrategy) 1896 { 1897 $this->partitionStrategy = $partitionStrategy; 1898 } 1899 public function getPartitionStrategy() 1900 { 1901 return $this->partitionStrategy; 1902 } 1903 public function setReferenceSetId($referenceSetId) 1904 { 1905 $this->referenceSetId = $referenceSetId; 1906 } 1907 public function getReferenceSetId() 1908 { 1909 return $this->referenceSetId; 1910 } 1911 public function setSourceUris($sourceUris) 1912 { 1913 $this->sourceUris = $sourceUris; 1914 } 1915 public function getSourceUris() 1916 { 1917 return $this->sourceUris; 1918 } 1919 } 1920 1921 class Google_Service_Genomics_ImportReadGroupSetsResponse extends Google_Collection 1922 { 1923 protected $collection_key = 'readGroupSetIds'; 1924 protected $internal_gapi_mappings = array( 1925 ); 1926 public $readGroupSetIds; 1927 1928 1929 public function setReadGroupSetIds($readGroupSetIds) 1930 { 1931 $this->readGroupSetIds = $readGroupSetIds; 1932 } 1933 public function getReadGroupSetIds() 1934 { 1935 return $this->readGroupSetIds; 1936 } 1937 } 1938 1939 class Google_Service_Genomics_ImportVariantsRequest extends Google_Collection 1940 { 1941 protected $collection_key = 'sourceUris'; 1942 protected $internal_gapi_mappings = array( 1943 ); 1944 public $format; 1945 public $normalizeReferenceNames; 1946 public $sourceUris; 1947 public $variantSetId; 1948 1949 1950 public function setFormat($format) 1951 { 1952 $this->format = $format; 1953 } 1954 public function getFormat() 1955 { 1956 return $this->format; 1957 } 1958 public function setNormalizeReferenceNames($normalizeReferenceNames) 1959 { 1960 $this->normalizeReferenceNames = $normalizeReferenceNames; 1961 } 1962 public function getNormalizeReferenceNames() 1963 { 1964 return $this->normalizeReferenceNames; 1965 } 1966 public function setSourceUris($sourceUris) 1967 { 1968 $this->sourceUris = $sourceUris; 1969 } 1970 public function getSourceUris() 1971 { 1972 return $this->sourceUris; 1973 } 1974 public function setVariantSetId($variantSetId) 1975 { 1976 $this->variantSetId = $variantSetId; 1977 } 1978 public function getVariantSetId() 1979 { 1980 return $this->variantSetId; 1981 } 1982 } 1983 1984 class Google_Service_Genomics_ImportVariantsResponse extends Google_Collection 1985 { 1986 protected $collection_key = 'callSetIds'; 1987 protected $internal_gapi_mappings = array( 1988 ); 1989 public $callSetIds; 1990 1991 1992 public function setCallSetIds($callSetIds) 1993 { 1994 $this->callSetIds = $callSetIds; 1995 } 1996 public function getCallSetIds() 1997 { 1998 return $this->callSetIds; 1999 } 2000 } 2001 2002 class Google_Service_Genomics_LinearAlignment extends Google_Collection 2003 { 2004 protected $collection_key = 'cigar'; 2005 protected $internal_gapi_mappings = array( 2006 ); 2007 protected $cigarType = 'Google_Service_Genomics_CigarUnit'; 2008 protected $cigarDataType = 'array'; 2009 public $mappingQuality; 2010 protected $positionType = 'Google_Service_Genomics_Position'; 2011 protected $positionDataType = ''; 2012 2013 2014 public function setCigar($cigar) 2015 { 2016 $this->cigar = $cigar; 2017 } 2018 public function getCigar() 2019 { 2020 return $this->cigar; 2021 } 2022 public function setMappingQuality($mappingQuality) 2023 { 2024 $this->mappingQuality = $mappingQuality; 2025 } 2026 public function getMappingQuality() 2027 { 2028 return $this->mappingQuality; 2029 } 2030 public function setPosition(Google_Service_Genomics_Position $position) 2031 { 2032 $this->position = $position; 2033 } 2034 public function getPosition() 2035 { 2036 return $this->position; 2037 } 2038 } 2039 2040 class Google_Service_Genomics_ListBasesResponse extends Google_Model 2041 { 2042 protected $internal_gapi_mappings = array( 2043 ); 2044 public $nextPageToken; 2045 public $offset; 2046 public $sequence; 2047 2048 2049 public function setNextPageToken($nextPageToken) 2050 { 2051 $this->nextPageToken = $nextPageToken; 2052 } 2053 public function getNextPageToken() 2054 { 2055 return $this->nextPageToken; 2056 } 2057 public function setOffset($offset) 2058 { 2059 $this->offset = $offset; 2060 } 2061 public function getOffset() 2062 { 2063 return $this->offset; 2064 } 2065 public function setSequence($sequence) 2066 { 2067 $this->sequence = $sequence; 2068 } 2069 public function getSequence() 2070 { 2071 return $this->sequence; 2072 } 2073 } 2074 2075 class Google_Service_Genomics_ListCoverageBucketsResponse extends Google_Collection 2076 { 2077 protected $collection_key = 'coverageBuckets'; 2078 protected $internal_gapi_mappings = array( 2079 ); 2080 public $bucketWidth; 2081 protected $coverageBucketsType = 'Google_Service_Genomics_CoverageBucket'; 2082 protected $coverageBucketsDataType = 'array'; 2083 public $nextPageToken; 2084 2085 2086 public function setBucketWidth($bucketWidth) 2087 { 2088 $this->bucketWidth = $bucketWidth; 2089 } 2090 public function getBucketWidth() 2091 { 2092 return $this->bucketWidth; 2093 } 2094 public function setCoverageBuckets($coverageBuckets) 2095 { 2096 $this->coverageBuckets = $coverageBuckets; 2097 } 2098 public function getCoverageBuckets() 2099 { 2100 return $this->coverageBuckets; 2101 } 2102 public function setNextPageToken($nextPageToken) 2103 { 2104 $this->nextPageToken = $nextPageToken; 2105 } 2106 public function getNextPageToken() 2107 { 2108 return $this->nextPageToken; 2109 } 2110 } 2111 2112 class Google_Service_Genomics_ListDatasetsResponse extends Google_Collection 2113 { 2114 protected $collection_key = 'datasets'; 2115 protected $internal_gapi_mappings = array( 2116 ); 2117 protected $datasetsType = 'Google_Service_Genomics_Dataset'; 2118 protected $datasetsDataType = 'array'; 2119 public $nextPageToken; 2120 2121 2122 public function setDatasets($datasets) 2123 { 2124 $this->datasets = $datasets; 2125 } 2126 public function getDatasets() 2127 { 2128 return $this->datasets; 2129 } 2130 public function setNextPageToken($nextPageToken) 2131 { 2132 $this->nextPageToken = $nextPageToken; 2133 } 2134 public function getNextPageToken() 2135 { 2136 return $this->nextPageToken; 2137 } 2138 } 2139 2140 class Google_Service_Genomics_ListOperationsResponse extends Google_Collection 2141 { 2142 protected $collection_key = 'operations'; 2143 protected $internal_gapi_mappings = array( 2144 ); 2145 public $nextPageToken; 2146 protected $operationsType = 'Google_Service_Genomics_Operation'; 2147 protected $operationsDataType = 'array'; 2148 2149 2150 public function setNextPageToken($nextPageToken) 2151 { 2152 $this->nextPageToken = $nextPageToken; 2153 } 2154 public function getNextPageToken() 2155 { 2156 return $this->nextPageToken; 2157 } 2158 public function setOperations($operations) 2159 { 2160 $this->operations = $operations; 2161 } 2162 public function getOperations() 2163 { 2164 return $this->operations; 2165 } 2166 } 2167 2168 class Google_Service_Genomics_Operation extends Google_Model 2169 { 2170 protected $internal_gapi_mappings = array( 2171 ); 2172 public $done; 2173 protected $errorType = 'Google_Service_Genomics_Status'; 2174 protected $errorDataType = ''; 2175 public $metadata; 2176 public $name; 2177 public $response; 2178 2179 2180 public function setDone($done) 2181 { 2182 $this->done = $done; 2183 } 2184 public function getDone() 2185 { 2186 return $this->done; 2187 } 2188 public function setError(Google_Service_Genomics_Status $error) 2189 { 2190 $this->error = $error; 2191 } 2192 public function getError() 2193 { 2194 return $this->error; 2195 } 2196 public function setMetadata($metadata) 2197 { 2198 $this->metadata = $metadata; 2199 } 2200 public function getMetadata() 2201 { 2202 return $this->metadata; 2203 } 2204 public function setName($name) 2205 { 2206 $this->name = $name; 2207 } 2208 public function getName() 2209 { 2210 return $this->name; 2211 } 2212 public function setResponse($response) 2213 { 2214 $this->response = $response; 2215 } 2216 public function getResponse() 2217 { 2218 return $this->response; 2219 } 2220 } 2221 2222 class Google_Service_Genomics_OperationEvent extends Google_Model 2223 { 2224 protected $internal_gapi_mappings = array( 2225 ); 2226 public $description; 2227 2228 2229 public function setDescription($description) 2230 { 2231 $this->description = $description; 2232 } 2233 public function getDescription() 2234 { 2235 return $this->description; 2236 } 2237 } 2238 2239 class Google_Service_Genomics_OperationMetadata extends Google_Collection 2240 { 2241 protected $collection_key = 'events'; 2242 protected $internal_gapi_mappings = array( 2243 ); 2244 public $createTime; 2245 protected $eventsType = 'Google_Service_Genomics_OperationEvent'; 2246 protected $eventsDataType = 'array'; 2247 public $projectId; 2248 public $request; 2249 2250 2251 public function setCreateTime($createTime) 2252 { 2253 $this->createTime = $createTime; 2254 } 2255 public function getCreateTime() 2256 { 2257 return $this->createTime; 2258 } 2259 public function setEvents($events) 2260 { 2261 $this->events = $events; 2262 } 2263 public function getEvents() 2264 { 2265 return $this->events; 2266 } 2267 public function setProjectId($projectId) 2268 { 2269 $this->projectId = $projectId; 2270 } 2271 public function getProjectId() 2272 { 2273 return $this->projectId; 2274 } 2275 public function setRequest($request) 2276 { 2277 $this->request = $request; 2278 } 2279 public function getRequest() 2280 { 2281 return $this->request; 2282 } 2283 } 2284 2285 class Google_Service_Genomics_OperationMetadataRequest extends Google_Model 2286 { 2287 } 2288 2289 class Google_Service_Genomics_OperationResponse extends Google_Model 2290 { 2291 } 2292 2293 class Google_Service_Genomics_Policy extends Google_Collection 2294 { 2295 protected $collection_key = 'bindings'; 2296 protected $internal_gapi_mappings = array( 2297 ); 2298 protected $bindingsType = 'Google_Service_Genomics_Binding'; 2299 protected $bindingsDataType = 'array'; 2300 public $etag; 2301 public $version; 2302 2303 2304 public function setBindings($bindings) 2305 { 2306 $this->bindings = $bindings; 2307 } 2308 public function getBindings() 2309 { 2310 return $this->bindings; 2311 } 2312 public function setEtag($etag) 2313 { 2314 $this->etag = $etag; 2315 } 2316 public function getEtag() 2317 { 2318 return $this->etag; 2319 } 2320 public function setVersion($version) 2321 { 2322 $this->version = $version; 2323 } 2324 public function getVersion() 2325 { 2326 return $this->version; 2327 } 2328 } 2329 2330 class Google_Service_Genomics_Position extends Google_Model 2331 { 2332 protected $internal_gapi_mappings = array( 2333 ); 2334 public $position; 2335 public $referenceName; 2336 public $reverseStrand; 2337 2338 2339 public function setPosition($position) 2340 { 2341 $this->position = $position; 2342 } 2343 public function getPosition() 2344 { 2345 return $this->position; 2346 } 2347 public function setReferenceName($referenceName) 2348 { 2349 $this->referenceName = $referenceName; 2350 } 2351 public function getReferenceName() 2352 { 2353 return $this->referenceName; 2354 } 2355 public function setReverseStrand($reverseStrand) 2356 { 2357 $this->reverseStrand = $reverseStrand; 2358 } 2359 public function getReverseStrand() 2360 { 2361 return $this->reverseStrand; 2362 } 2363 } 2364 2365 class Google_Service_Genomics_Program extends Google_Model 2366 { 2367 protected $internal_gapi_mappings = array( 2368 ); 2369 public $commandLine; 2370 public $id; 2371 public $name; 2372 public $prevProgramId; 2373 public $version; 2374 2375 2376 public function setCommandLine($commandLine) 2377 { 2378 $this->commandLine = $commandLine; 2379 } 2380 public function getCommandLine() 2381 { 2382 return $this->commandLine; 2383 } 2384 public function setId($id) 2385 { 2386 $this->id = $id; 2387 } 2388 public function getId() 2389 { 2390 return $this->id; 2391 } 2392 public function setName($name) 2393 { 2394 $this->name = $name; 2395 } 2396 public function getName() 2397 { 2398 return $this->name; 2399 } 2400 public function setPrevProgramId($prevProgramId) 2401 { 2402 $this->prevProgramId = $prevProgramId; 2403 } 2404 public function getPrevProgramId() 2405 { 2406 return $this->prevProgramId; 2407 } 2408 public function setVersion($version) 2409 { 2410 $this->version = $version; 2411 } 2412 public function getVersion() 2413 { 2414 return $this->version; 2415 } 2416 } 2417 2418 class Google_Service_Genomics_Range extends Google_Model 2419 { 2420 protected $internal_gapi_mappings = array( 2421 ); 2422 public $end; 2423 public $referenceName; 2424 public $start; 2425 2426 2427 public function setEnd($end) 2428 { 2429 $this->end = $end; 2430 } 2431 public function getEnd() 2432 { 2433 return $this->end; 2434 } 2435 public function setReferenceName($referenceName) 2436 { 2437 $this->referenceName = $referenceName; 2438 } 2439 public function getReferenceName() 2440 { 2441 return $this->referenceName; 2442 } 2443 public function setStart($start) 2444 { 2445 $this->start = $start; 2446 } 2447 public function getStart() 2448 { 2449 return $this->start; 2450 } 2451 } 2452 2453 class Google_Service_Genomics_Read extends Google_Collection 2454 { 2455 protected $collection_key = 'alignedQuality'; 2456 protected $internal_gapi_mappings = array( 2457 ); 2458 public $alignedQuality; 2459 public $alignedSequence; 2460 protected $alignmentType = 'Google_Service_Genomics_LinearAlignment'; 2461 protected $alignmentDataType = ''; 2462 public $duplicateFragment; 2463 public $failedVendorQualityChecks; 2464 public $fragmentLength; 2465 public $fragmentName; 2466 public $id; 2467 public $info; 2468 protected $nextMatePositionType = 'Google_Service_Genomics_Position'; 2469 protected $nextMatePositionDataType = ''; 2470 public $numberReads; 2471 public $properPlacement; 2472 public $readGroupId; 2473 public $readGroupSetId; 2474 public $readNumber; 2475 public $secondaryAlignment; 2476 public $supplementaryAlignment; 2477 2478 2479 public function setAlignedQuality($alignedQuality) 2480 { 2481 $this->alignedQuality = $alignedQuality; 2482 } 2483 public function getAlignedQuality() 2484 { 2485 return $this->alignedQuality; 2486 } 2487 public function setAlignedSequence($alignedSequence) 2488 { 2489 $this->alignedSequence = $alignedSequence; 2490 } 2491 public function getAlignedSequence() 2492 { 2493 return $this->alignedSequence; 2494 } 2495 public function setAlignment(Google_Service_Genomics_LinearAlignment $alignment) 2496 { 2497 $this->alignment = $alignment; 2498 } 2499 public function getAlignment() 2500 { 2501 return $this->alignment; 2502 } 2503 public function setDuplicateFragment($duplicateFragment) 2504 { 2505 $this->duplicateFragment = $duplicateFragment; 2506 } 2507 public function getDuplicateFragment() 2508 { 2509 return $this->duplicateFragment; 2510 } 2511 public function setFailedVendorQualityChecks($failedVendorQualityChecks) 2512 { 2513 $this->failedVendorQualityChecks = $failedVendorQualityChecks; 2514 } 2515 public function getFailedVendorQualityChecks() 2516 { 2517 return $this->failedVendorQualityChecks; 2518 } 2519 public function setFragmentLength($fragmentLength) 2520 { 2521 $this->fragmentLength = $fragmentLength; 2522 } 2523 public function getFragmentLength() 2524 { 2525 return $this->fragmentLength; 2526 } 2527 public function setFragmentName($fragmentName) 2528 { 2529 $this->fragmentName = $fragmentName; 2530 } 2531 public function getFragmentName() 2532 { 2533 return $this->fragmentName; 2534 } 2535 public function setId($id) 2536 { 2537 $this->id = $id; 2538 } 2539 public function getId() 2540 { 2541 return $this->id; 2542 } 2543 public function setInfo($info) 2544 { 2545 $this->info = $info; 2546 } 2547 public function getInfo() 2548 { 2549 return $this->info; 2550 } 2551 public function setNextMatePosition(Google_Service_Genomics_Position $nextMatePosition) 2552 { 2553 $this->nextMatePosition = $nextMatePosition; 2554 } 2555 public function getNextMatePosition() 2556 { 2557 return $this->nextMatePosition; 2558 } 2559 public function setNumberReads($numberReads) 2560 { 2561 $this->numberReads = $numberReads; 2562 } 2563 public function getNumberReads() 2564 { 2565 return $this->numberReads; 2566 } 2567 public function setProperPlacement($properPlacement) 2568 { 2569 $this->properPlacement = $properPlacement; 2570 } 2571 public function getProperPlacement() 2572 { 2573 return $this->properPlacement; 2574 } 2575 public function setReadGroupId($readGroupId) 2576 { 2577 $this->readGroupId = $readGroupId; 2578 } 2579 public function getReadGroupId() 2580 { 2581 return $this->readGroupId; 2582 } 2583 public function setReadGroupSetId($readGroupSetId) 2584 { 2585 $this->readGroupSetId = $readGroupSetId; 2586 } 2587 public function getReadGroupSetId() 2588 { 2589 return $this->readGroupSetId; 2590 } 2591 public function setReadNumber($readNumber) 2592 { 2593 $this->readNumber = $readNumber; 2594 } 2595 public function getReadNumber() 2596 { 2597 return $this->readNumber; 2598 } 2599 public function setSecondaryAlignment($secondaryAlignment) 2600 { 2601 $this->secondaryAlignment = $secondaryAlignment; 2602 } 2603 public function getSecondaryAlignment() 2604 { 2605 return $this->secondaryAlignment; 2606 } 2607 public function setSupplementaryAlignment($supplementaryAlignment) 2608 { 2609 $this->supplementaryAlignment = $supplementaryAlignment; 2610 } 2611 public function getSupplementaryAlignment() 2612 { 2613 return $this->supplementaryAlignment; 2614 } 2615 } 2616 2617 class Google_Service_Genomics_ReadGroup extends Google_Collection 2618 { 2619 protected $collection_key = 'programs'; 2620 protected $internal_gapi_mappings = array( 2621 ); 2622 public $datasetId; 2623 public $description; 2624 protected $experimentType = 'Google_Service_Genomics_Experiment'; 2625 protected $experimentDataType = ''; 2626 public $id; 2627 public $info; 2628 public $name; 2629 public $predictedInsertSize; 2630 protected $programsType = 'Google_Service_Genomics_Program'; 2631 protected $programsDataType = 'array'; 2632 public $referenceSetId; 2633 public $sampleId; 2634 2635 2636 public function setDatasetId($datasetId) 2637 { 2638 $this->datasetId = $datasetId; 2639 } 2640 public function getDatasetId() 2641 { 2642 return $this->datasetId; 2643 } 2644 public function setDescription($description) 2645 { 2646 $this->description = $description; 2647 } 2648 public function getDescription() 2649 { 2650 return $this->description; 2651 } 2652 public function setExperiment(Google_Service_Genomics_Experiment $experiment) 2653 { 2654 $this->experiment = $experiment; 2655 } 2656 public function getExperiment() 2657 { 2658 return $this->experiment; 2659 } 2660 public function setId($id) 2661 { 2662 $this->id = $id; 2663 } 2664 public function getId() 2665 { 2666 return $this->id; 2667 } 2668 public function setInfo($info) 2669 { 2670 $this->info = $info; 2671 } 2672 public function getInfo() 2673 { 2674 return $this->info; 2675 } 2676 public function setName($name) 2677 { 2678 $this->name = $name; 2679 } 2680 public function getName() 2681 { 2682 return $this->name; 2683 } 2684 public function setPredictedInsertSize($predictedInsertSize) 2685 { 2686 $this->predictedInsertSize = $predictedInsertSize; 2687 } 2688 public function getPredictedInsertSize() 2689 { 2690 return $this->predictedInsertSize; 2691 } 2692 public function setPrograms($programs) 2693 { 2694 $this->programs = $programs; 2695 } 2696 public function getPrograms() 2697 { 2698 return $this->programs; 2699 } 2700 public function setReferenceSetId($referenceSetId) 2701 { 2702 $this->referenceSetId = $referenceSetId; 2703 } 2704 public function getReferenceSetId() 2705 { 2706 return $this->referenceSetId; 2707 } 2708 public function setSampleId($sampleId) 2709 { 2710 $this->sampleId = $sampleId; 2711 } 2712 public function getSampleId() 2713 { 2714 return $this->sampleId; 2715 } 2716 } 2717 2718 class Google_Service_Genomics_ReadGroupInfo extends Google_Model 2719 { 2720 } 2721 2722 class Google_Service_Genomics_ReadGroupSet extends Google_Collection 2723 { 2724 protected $collection_key = 'readGroups'; 2725 protected $internal_gapi_mappings = array( 2726 ); 2727 public $datasetId; 2728 public $filename; 2729 public $id; 2730 public $info; 2731 public $name; 2732 protected $readGroupsType = 'Google_Service_Genomics_ReadGroup'; 2733 protected $readGroupsDataType = 'array'; 2734 public $referenceSetId; 2735 2736 2737 public function setDatasetId($datasetId) 2738 { 2739 $this->datasetId = $datasetId; 2740 } 2741 public function getDatasetId() 2742 { 2743 return $this->datasetId; 2744 } 2745 public function setFilename($filename) 2746 { 2747 $this->filename = $filename; 2748 } 2749 public function getFilename() 2750 { 2751 return $this->filename; 2752 } 2753 public function setId($id) 2754 { 2755 $this->id = $id; 2756 } 2757 public function getId() 2758 { 2759 return $this->id; 2760 } 2761 public function setInfo($info) 2762 { 2763 $this->info = $info; 2764 } 2765 public function getInfo() 2766 { 2767 return $this->info; 2768 } 2769 public function setName($name) 2770 { 2771 $this->name = $name; 2772 } 2773 public function getName() 2774 { 2775 return $this->name; 2776 } 2777 public function setReadGroups($readGroups) 2778 { 2779 $this->readGroups = $readGroups; 2780 } 2781 public function getReadGroups() 2782 { 2783 return $this->readGroups; 2784 } 2785 public function setReferenceSetId($referenceSetId) 2786 { 2787 $this->referenceSetId = $referenceSetId; 2788 } 2789 public function getReferenceSetId() 2790 { 2791 return $this->referenceSetId; 2792 } 2793 } 2794 2795 class Google_Service_Genomics_ReadGroupSetInfo extends Google_Model 2796 { 2797 } 2798 2799 class Google_Service_Genomics_ReadInfo extends Google_Model 2800 { 2801 } 2802 2803 class Google_Service_Genomics_Reference extends Google_Collection 2804 { 2805 protected $collection_key = 'sourceAccessions'; 2806 protected $internal_gapi_mappings = array( 2807 ); 2808 public $id; 2809 public $length; 2810 public $md5checksum; 2811 public $name; 2812 public $ncbiTaxonId; 2813 public $sourceAccessions; 2814 public $sourceUri; 2815 2816 2817 public function setId($id) 2818 { 2819 $this->id = $id; 2820 } 2821 public function getId() 2822 { 2823 return $this->id; 2824 } 2825 public function setLength($length) 2826 { 2827 $this->length = $length; 2828 } 2829 public function getLength() 2830 { 2831 return $this->length; 2832 } 2833 public function setMd5checksum($md5checksum) 2834 { 2835 $this->md5checksum = $md5checksum; 2836 } 2837 public function getMd5checksum() 2838 { 2839 return $this->md5checksum; 2840 } 2841 public function setName($name) 2842 { 2843 $this->name = $name; 2844 } 2845 public function getName() 2846 { 2847 return $this->name; 2848 } 2849 public function setNcbiTaxonId($ncbiTaxonId) 2850 { 2851 $this->ncbiTaxonId = $ncbiTaxonId; 2852 } 2853 public function getNcbiTaxonId() 2854 { 2855 return $this->ncbiTaxonId; 2856 } 2857 public function setSourceAccessions($sourceAccessions) 2858 { 2859 $this->sourceAccessions = $sourceAccessions; 2860 } 2861 public function getSourceAccessions() 2862 { 2863 return $this->sourceAccessions; 2864 } 2865 public function setSourceUri($sourceUri) 2866 { 2867 $this->sourceUri = $sourceUri; 2868 } 2869 public function getSourceUri() 2870 { 2871 return $this->sourceUri; 2872 } 2873 } 2874 2875 class Google_Service_Genomics_ReferenceBound extends Google_Model 2876 { 2877 protected $internal_gapi_mappings = array( 2878 ); 2879 public $referenceName; 2880 public $upperBound; 2881 2882 2883 public function setReferenceName($referenceName) 2884 { 2885 $this->referenceName = $referenceName; 2886 } 2887 public function getReferenceName() 2888 { 2889 return $this->referenceName; 2890 } 2891 public function setUpperBound($upperBound) 2892 { 2893 $this->upperBound = $upperBound; 2894 } 2895 public function getUpperBound() 2896 { 2897 return $this->upperBound; 2898 } 2899 } 2900 2901 class Google_Service_Genomics_ReferenceSet extends Google_Collection 2902 { 2903 protected $collection_key = 'sourceAccessions'; 2904 protected $internal_gapi_mappings = array( 2905 ); 2906 public $assemblyId; 2907 public $description; 2908 public $id; 2909 public $md5checksum; 2910 public $ncbiTaxonId; 2911 public $referenceIds; 2912 public $sourceAccessions; 2913 public $sourceUri; 2914 2915 2916 public function setAssemblyId($assemblyId) 2917 { 2918 $this->assemblyId = $assemblyId; 2919 } 2920 public function getAssemblyId() 2921 { 2922 return $this->assemblyId; 2923 } 2924 public function setDescription($description) 2925 { 2926 $this->description = $description; 2927 } 2928 public function getDescription() 2929 { 2930 return $this->description; 2931 } 2932 public function setId($id) 2933 { 2934 $this->id = $id; 2935 } 2936 public function getId() 2937 { 2938 return $this->id; 2939 } 2940 public function setMd5checksum($md5checksum) 2941 { 2942 $this->md5checksum = $md5checksum; 2943 } 2944 public function getMd5checksum() 2945 { 2946 return $this->md5checksum; 2947 } 2948 public function setNcbiTaxonId($ncbiTaxonId) 2949 { 2950 $this->ncbiTaxonId = $ncbiTaxonId; 2951 } 2952 public function getNcbiTaxonId() 2953 { 2954 return $this->ncbiTaxonId; 2955 } 2956 public function setReferenceIds($referenceIds) 2957 { 2958 $this->referenceIds = $referenceIds; 2959 } 2960 public function getReferenceIds() 2961 { 2962 return $this->referenceIds; 2963 } 2964 public function setSourceAccessions($sourceAccessions) 2965 { 2966 $this->sourceAccessions = $sourceAccessions; 2967 } 2968 public function getSourceAccessions() 2969 { 2970 return $this->sourceAccessions; 2971 } 2972 public function setSourceUri($sourceUri) 2973 { 2974 $this->sourceUri = $sourceUri; 2975 } 2976 public function getSourceUri() 2977 { 2978 return $this->sourceUri; 2979 } 2980 } 2981 2982 class Google_Service_Genomics_SearchCallSetsRequest extends Google_Collection 2983 { 2984 protected $collection_key = 'variantSetIds'; 2985 protected $internal_gapi_mappings = array( 2986 ); 2987 public $name; 2988 public $pageSize; 2989 public $pageToken; 2990 public $variantSetIds; 2991 2992 2993 public function setName($name) 2994 { 2995 $this->name = $name; 2996 } 2997 public function getName() 2998 { 2999 return $this->name; 3000 } 3001 public function setPageSize($pageSize) 3002 { 3003 $this->pageSize = $pageSize; 3004 } 3005 public function getPageSize() 3006 { 3007 return $this->pageSize; 3008 } 3009 public function setPageToken($pageToken) 3010 { 3011 $this->pageToken = $pageToken; 3012 } 3013 public function getPageToken() 3014 { 3015 return $this->pageToken; 3016 } 3017 public function setVariantSetIds($variantSetIds) 3018 { 3019 $this->variantSetIds = $variantSetIds; 3020 } 3021 public function getVariantSetIds() 3022 { 3023 return $this->variantSetIds; 3024 } 3025 } 3026 3027 class Google_Service_Genomics_SearchCallSetsResponse extends Google_Collection 3028 { 3029 protected $collection_key = 'callSets'; 3030 protected $internal_gapi_mappings = array( 3031 ); 3032 protected $callSetsType = 'Google_Service_Genomics_CallSet'; 3033 protected $callSetsDataType = 'array'; 3034 public $nextPageToken; 3035 3036 3037 public function setCallSets($callSets) 3038 { 3039 $this->callSets = $callSets; 3040 } 3041 public function getCallSets() 3042 { 3043 return $this->callSets; 3044 } 3045 public function setNextPageToken($nextPageToken) 3046 { 3047 $this->nextPageToken = $nextPageToken; 3048 } 3049 public function getNextPageToken() 3050 { 3051 return $this->nextPageToken; 3052 } 3053 } 3054 3055 class Google_Service_Genomics_SearchReadGroupSetsRequest extends Google_Collection 3056 { 3057 protected $collection_key = 'datasetIds'; 3058 protected $internal_gapi_mappings = array( 3059 ); 3060 public $datasetIds; 3061 public $name; 3062 public $pageSize; 3063 public $pageToken; 3064 3065 3066 public function setDatasetIds($datasetIds) 3067 { 3068 $this->datasetIds = $datasetIds; 3069 } 3070 public function getDatasetIds() 3071 { 3072 return $this->datasetIds; 3073 } 3074 public function setName($name) 3075 { 3076 $this->name = $name; 3077 } 3078 public function getName() 3079 { 3080 return $this->name; 3081 } 3082 public function setPageSize($pageSize) 3083 { 3084 $this->pageSize = $pageSize; 3085 } 3086 public function getPageSize() 3087 { 3088 return $this->pageSize; 3089 } 3090 public function setPageToken($pageToken) 3091 { 3092 $this->pageToken = $pageToken; 3093 } 3094 public function getPageToken() 3095 { 3096 return $this->pageToken; 3097 } 3098 } 3099 3100 class Google_Service_Genomics_SearchReadGroupSetsResponse extends Google_Collection 3101 { 3102 protected $collection_key = 'readGroupSets'; 3103 protected $internal_gapi_mappings = array( 3104 ); 3105 public $nextPageToken; 3106 protected $readGroupSetsType = 'Google_Service_Genomics_ReadGroupSet'; 3107 protected $readGroupSetsDataType = 'array'; 3108 3109 3110 public function setNextPageToken($nextPageToken) 3111 { 3112 $this->nextPageToken = $nextPageToken; 3113 } 3114 public function getNextPageToken() 3115 { 3116 return $this->nextPageToken; 3117 } 3118 public function setReadGroupSets($readGroupSets) 3119 { 3120 $this->readGroupSets = $readGroupSets; 3121 } 3122 public function getReadGroupSets() 3123 { 3124 return $this->readGroupSets; 3125 } 3126 } 3127 3128 class Google_Service_Genomics_SearchReadsRequest extends Google_Collection 3129 { 3130 protected $collection_key = 'readGroupSetIds'; 3131 protected $internal_gapi_mappings = array( 3132 ); 3133 public $end; 3134 public $pageSize; 3135 public $pageToken; 3136 public $readGroupIds; 3137 public $readGroupSetIds; 3138 public $referenceName; 3139 public $start; 3140 3141 3142 public function setEnd($end) 3143 { 3144 $this->end = $end; 3145 } 3146 public function getEnd() 3147 { 3148 return $this->end; 3149 } 3150 public function setPageSize($pageSize) 3151 { 3152 $this->pageSize = $pageSize; 3153 } 3154 public function getPageSize() 3155 { 3156 return $this->pageSize; 3157 } 3158 public function setPageToken($pageToken) 3159 { 3160 $this->pageToken = $pageToken; 3161 } 3162 public function getPageToken() 3163 { 3164 return $this->pageToken; 3165 } 3166 public function setReadGroupIds($readGroupIds) 3167 { 3168 $this->readGroupIds = $readGroupIds; 3169 } 3170 public function getReadGroupIds() 3171 { 3172 return $this->readGroupIds; 3173 } 3174 public function setReadGroupSetIds($readGroupSetIds) 3175 { 3176 $this->readGroupSetIds = $readGroupSetIds; 3177 } 3178 public function getReadGroupSetIds() 3179 { 3180 return $this->readGroupSetIds; 3181 } 3182 public function setReferenceName($referenceName) 3183 { 3184 $this->referenceName = $referenceName; 3185 } 3186 public function getReferenceName() 3187 { 3188 return $this->referenceName; 3189 } 3190 public function setStart($start) 3191 { 3192 $this->start = $start; 3193 } 3194 public function getStart() 3195 { 3196 return $this->start; 3197 } 3198 } 3199 3200 class Google_Service_Genomics_SearchReadsResponse extends Google_Collection 3201 { 3202 protected $collection_key = 'alignments'; 3203 protected $internal_gapi_mappings = array( 3204 ); 3205 protected $alignmentsType = 'Google_Service_Genomics_Read'; 3206 protected $alignmentsDataType = 'array'; 3207 public $nextPageToken; 3208 3209 3210 public function setAlignments($alignments) 3211 { 3212 $this->alignments = $alignments; 3213 } 3214 public function getAlignments() 3215 { 3216 return $this->alignments; 3217 } 3218 public function setNextPageToken($nextPageToken) 3219 { 3220 $this->nextPageToken = $nextPageToken; 3221 } 3222 public function getNextPageToken() 3223 { 3224 return $this->nextPageToken; 3225 } 3226 } 3227 3228 class Google_Service_Genomics_SearchReferenceSetsRequest extends Google_Collection 3229 { 3230 protected $collection_key = 'md5checksums'; 3231 protected $internal_gapi_mappings = array( 3232 ); 3233 public $accessions; 3234 public $assemblyId; 3235 public $md5checksums; 3236 public $pageSize; 3237 public $pageToken; 3238 3239 3240 public function setAccessions($accessions) 3241 { 3242 $this->accessions = $accessions; 3243 } 3244 public function getAccessions() 3245 { 3246 return $this->accessions; 3247 } 3248 public function setAssemblyId($assemblyId) 3249 { 3250 $this->assemblyId = $assemblyId; 3251 } 3252 public function getAssemblyId() 3253 { 3254 return $this->assemblyId; 3255 } 3256 public function setMd5checksums($md5checksums) 3257 { 3258 $this->md5checksums = $md5checksums; 3259 } 3260 public function getMd5checksums() 3261 { 3262 return $this->md5checksums; 3263 } 3264 public function setPageSize($pageSize) 3265 { 3266 $this->pageSize = $pageSize; 3267 } 3268 public function getPageSize() 3269 { 3270 return $this->pageSize; 3271 } 3272 public function setPageToken($pageToken) 3273 { 3274 $this->pageToken = $pageToken; 3275 } 3276 public function getPageToken() 3277 { 3278 return $this->pageToken; 3279 } 3280 } 3281 3282 class Google_Service_Genomics_SearchReferenceSetsResponse extends Google_Collection 3283 { 3284 protected $collection_key = 'referenceSets'; 3285 protected $internal_gapi_mappings = array( 3286 ); 3287 public $nextPageToken; 3288 protected $referenceSetsType = 'Google_Service_Genomics_ReferenceSet'; 3289 protected $referenceSetsDataType = 'array'; 3290 3291 3292 public function setNextPageToken($nextPageToken) 3293 { 3294 $this->nextPageToken = $nextPageToken; 3295 } 3296 public function getNextPageToken() 3297 { 3298 return $this->nextPageToken; 3299 } 3300 public function setReferenceSets($referenceSets) 3301 { 3302 $this->referenceSets = $referenceSets; 3303 } 3304 public function getReferenceSets() 3305 { 3306 return $this->referenceSets; 3307 } 3308 } 3309 3310 class Google_Service_Genomics_SearchReferencesRequest extends Google_Collection 3311 { 3312 protected $collection_key = 'md5checksums'; 3313 protected $internal_gapi_mappings = array( 3314 ); 3315 public $accessions; 3316 public $md5checksums; 3317 public $pageSize; 3318 public $pageToken; 3319 public $referenceSetId; 3320 3321 3322 public function setAccessions($accessions) 3323 { 3324 $this->accessions = $accessions; 3325 } 3326 public function getAccessions() 3327 { 3328 return $this->accessions; 3329 } 3330 public function setMd5checksums($md5checksums) 3331 { 3332 $this->md5checksums = $md5checksums; 3333 } 3334 public function getMd5checksums() 3335 { 3336 return $this->md5checksums; 3337 } 3338 public function setPageSize($pageSize) 3339 { 3340 $this->pageSize = $pageSize; 3341 } 3342 public function getPageSize() 3343 { 3344 return $this->pageSize; 3345 } 3346 public function setPageToken($pageToken) 3347 { 3348 $this->pageToken = $pageToken; 3349 } 3350 public function getPageToken() 3351 { 3352 return $this->pageToken; 3353 } 3354 public function setReferenceSetId($referenceSetId) 3355 { 3356 $this->referenceSetId = $referenceSetId; 3357 } 3358 public function getReferenceSetId() 3359 { 3360 return $this->referenceSetId; 3361 } 3362 } 3363 3364 class Google_Service_Genomics_SearchReferencesResponse extends Google_Collection 3365 { 3366 protected $collection_key = 'references'; 3367 protected $internal_gapi_mappings = array( 3368 ); 3369 public $nextPageToken; 3370 protected $referencesType = 'Google_Service_Genomics_Reference'; 3371 protected $referencesDataType = 'array'; 3372 3373 3374 public function setNextPageToken($nextPageToken) 3375 { 3376 $this->nextPageToken = $nextPageToken; 3377 } 3378 public function getNextPageToken() 3379 { 3380 return $this->nextPageToken; 3381 } 3382 public function setReferences($references) 3383 { 3384 $this->references = $references; 3385 } 3386 public function getReferences() 3387 { 3388 return $this->references; 3389 } 3390 } 3391 3392 class Google_Service_Genomics_SearchVariantSetsRequest extends Google_Collection 3393 { 3394 protected $collection_key = 'datasetIds'; 3395 protected $internal_gapi_mappings = array( 3396 ); 3397 public $datasetIds; 3398 public $pageSize; 3399 public $pageToken; 3400 3401 3402 public function setDatasetIds($datasetIds) 3403 { 3404 $this->datasetIds = $datasetIds; 3405 } 3406 public function getDatasetIds() 3407 { 3408 return $this->datasetIds; 3409 } 3410 public function setPageSize($pageSize) 3411 { 3412 $this->pageSize = $pageSize; 3413 } 3414 public function getPageSize() 3415 { 3416 return $this->pageSize; 3417 } 3418 public function setPageToken($pageToken) 3419 { 3420 $this->pageToken = $pageToken; 3421 } 3422 public function getPageToken() 3423 { 3424 return $this->pageToken; 3425 } 3426 } 3427 3428 class Google_Service_Genomics_SearchVariantSetsResponse extends Google_Collection 3429 { 3430 protected $collection_key = 'variantSets'; 3431 protected $internal_gapi_mappings = array( 3432 ); 3433 public $nextPageToken; 3434 protected $variantSetsType = 'Google_Service_Genomics_VariantSet'; 3435 protected $variantSetsDataType = 'array'; 3436 3437 3438 public function setNextPageToken($nextPageToken) 3439 { 3440 $this->nextPageToken = $nextPageToken; 3441 } 3442 public function getNextPageToken() 3443 { 3444 return $this->nextPageToken; 3445 } 3446 public function setVariantSets($variantSets) 3447 { 3448 $this->variantSets = $variantSets; 3449 } 3450 public function getVariantSets() 3451 { 3452 return $this->variantSets; 3453 } 3454 } 3455 3456 class Google_Service_Genomics_SearchVariantsRequest extends Google_Collection 3457 { 3458 protected $collection_key = 'variantSetIds'; 3459 protected $internal_gapi_mappings = array( 3460 ); 3461 public $callSetIds; 3462 public $end; 3463 public $maxCalls; 3464 public $pageSize; 3465 public $pageToken; 3466 public $referenceName; 3467 public $start; 3468 public $variantName; 3469 public $variantSetIds; 3470 3471 3472 public function setCallSetIds($callSetIds) 3473 { 3474 $this->callSetIds = $callSetIds; 3475 } 3476 public function getCallSetIds() 3477 { 3478 return $this->callSetIds; 3479 } 3480 public function setEnd($end) 3481 { 3482 $this->end = $end; 3483 } 3484 public function getEnd() 3485 { 3486 return $this->end; 3487 } 3488 public function setMaxCalls($maxCalls) 3489 { 3490 $this->maxCalls = $maxCalls; 3491 } 3492 public function getMaxCalls() 3493 { 3494 return $this->maxCalls; 3495 } 3496 public function setPageSize($pageSize) 3497 { 3498 $this->pageSize = $pageSize; 3499 } 3500 public function getPageSize() 3501 { 3502 return $this->pageSize; 3503 } 3504 public function setPageToken($pageToken) 3505 { 3506 $this->pageToken = $pageToken; 3507 } 3508 public function getPageToken() 3509 { 3510 return $this->pageToken; 3511 } 3512 public function setReferenceName($referenceName) 3513 { 3514 $this->referenceName = $referenceName; 3515 } 3516 public function getReferenceName() 3517 { 3518 return $this->referenceName; 3519 } 3520 public function setStart($start) 3521 { 3522 $this->start = $start; 3523 } 3524 public function getStart() 3525 { 3526 return $this->start; 3527 } 3528 public function setVariantName($variantName) 3529 { 3530 $this->variantName = $variantName; 3531 } 3532 public function getVariantName() 3533 { 3534 return $this->variantName; 3535 } 3536 public function setVariantSetIds($variantSetIds) 3537 { 3538 $this->variantSetIds = $variantSetIds; 3539 } 3540 public function getVariantSetIds() 3541 { 3542 return $this->variantSetIds; 3543 } 3544 } 3545 3546 class Google_Service_Genomics_SearchVariantsResponse extends Google_Collection 3547 { 3548 protected $collection_key = 'variants'; 3549 protected $internal_gapi_mappings = array( 3550 ); 3551 public $nextPageToken; 3552 protected $variantsType = 'Google_Service_Genomics_Variant'; 3553 protected $variantsDataType = 'array'; 3554 3555 3556 public function setNextPageToken($nextPageToken) 3557 { 3558 $this->nextPageToken = $nextPageToken; 3559 } 3560 public function getNextPageToken() 3561 { 3562 return $this->nextPageToken; 3563 } 3564 public function setVariants($variants) 3565 { 3566 $this->variants = $variants; 3567 } 3568 public function getVariants() 3569 { 3570 return $this->variants; 3571 } 3572 } 3573 3574 class Google_Service_Genomics_SetIamPolicyRequest extends Google_Model 3575 { 3576 protected $internal_gapi_mappings = array( 3577 ); 3578 protected $policyType = 'Google_Service_Genomics_Policy'; 3579 protected $policyDataType = ''; 3580 3581 3582 public function setPolicy(Google_Service_Genomics_Policy $policy) 3583 { 3584 $this->policy = $policy; 3585 } 3586 public function getPolicy() 3587 { 3588 return $this->policy; 3589 } 3590 } 3591 3592 class Google_Service_Genomics_Status extends Google_Collection 3593 { 3594 protected $collection_key = 'details'; 3595 protected $internal_gapi_mappings = array( 3596 ); 3597 public $code; 3598 public $details; 3599 public $message; 3600 3601 3602 public function setCode($code) 3603 { 3604 $this->code = $code; 3605 } 3606 public function getCode() 3607 { 3608 return $this->code; 3609 } 3610 public function setDetails($details) 3611 { 3612 $this->details = $details; 3613 } 3614 public function getDetails() 3615 { 3616 return $this->details; 3617 } 3618 public function setMessage($message) 3619 { 3620 $this->message = $message; 3621 } 3622 public function getMessage() 3623 { 3624 return $this->message; 3625 } 3626 } 3627 3628 class Google_Service_Genomics_StatusDetails extends Google_Model 3629 { 3630 } 3631 3632 class Google_Service_Genomics_TestIamPermissionsRequest extends Google_Collection 3633 { 3634 protected $collection_key = 'permissions'; 3635 protected $internal_gapi_mappings = array( 3636 ); 3637 public $permissions; 3638 3639 3640 public function setPermissions($permissions) 3641 { 3642 $this->permissions = $permissions; 3643 } 3644 public function getPermissions() 3645 { 3646 return $this->permissions; 3647 } 3648 } 3649 3650 class Google_Service_Genomics_TestIamPermissionsResponse extends Google_Collection 3651 { 3652 protected $collection_key = 'permissions'; 3653 protected $internal_gapi_mappings = array( 3654 ); 3655 public $permissions; 3656 3657 3658 public function setPermissions($permissions) 3659 { 3660 $this->permissions = $permissions; 3661 } 3662 public function getPermissions() 3663 { 3664 return $this->permissions; 3665 } 3666 } 3667 3668 class Google_Service_Genomics_UndeleteDatasetRequest extends Google_Model 3669 { 3670 } 3671 3672 class Google_Service_Genomics_Variant extends Google_Collection 3673 { 3674 protected $collection_key = 'names'; 3675 protected $internal_gapi_mappings = array( 3676 ); 3677 public $alternateBases; 3678 protected $callsType = 'Google_Service_Genomics_VariantCall'; 3679 protected $callsDataType = 'array'; 3680 public $created; 3681 public $end; 3682 public $filter; 3683 public $id; 3684 public $info; 3685 public $names; 3686 public $quality; 3687 public $referenceBases; 3688 public $referenceName; 3689 public $start; 3690 public $variantSetId; 3691 3692 3693 public function setAlternateBases($alternateBases) 3694 { 3695 $this->alternateBases = $alternateBases; 3696 } 3697 public function getAlternateBases() 3698 { 3699 return $this->alternateBases; 3700 } 3701 public function setCalls($calls) 3702 { 3703 $this->calls = $calls; 3704 } 3705 public function getCalls() 3706 { 3707 return $this->calls; 3708 } 3709 public function setCreated($created) 3710 { 3711 $this->created = $created; 3712 } 3713 public function getCreated() 3714 { 3715 return $this->created; 3716 } 3717 public function setEnd($end) 3718 { 3719 $this->end = $end; 3720 } 3721 public function getEnd() 3722 { 3723 return $this->end; 3724 } 3725 public function setFilter($filter) 3726 { 3727 $this->filter = $filter; 3728 } 3729 public function getFilter() 3730 { 3731 return $this->filter; 3732 } 3733 public function setId($id) 3734 { 3735 $this->id = $id; 3736 } 3737 public function getId() 3738 { 3739 return $this->id; 3740 } 3741 public function setInfo($info) 3742 { 3743 $this->info = $info; 3744 } 3745 public function getInfo() 3746 { 3747 return $this->info; 3748 } 3749 public function setNames($names) 3750 { 3751 $this->names = $names; 3752 } 3753 public function getNames() 3754 { 3755 return $this->names; 3756 } 3757 public function setQuality($quality) 3758 { 3759 $this->quality = $quality; 3760 } 3761 public function getQuality() 3762 { 3763 return $this->quality; 3764 } 3765 public function setReferenceBases($referenceBases) 3766 { 3767 $this->referenceBases = $referenceBases; 3768 } 3769 public function getReferenceBases() 3770 { 3771 return $this->referenceBases; 3772 } 3773 public function setReferenceName($referenceName) 3774 { 3775 $this->referenceName = $referenceName; 3776 } 3777 public function getReferenceName() 3778 { 3779 return $this->referenceName; 3780 } 3781 public function setStart($start) 3782 { 3783 $this->start = $start; 3784 } 3785 public function getStart() 3786 { 3787 return $this->start; 3788 } 3789 public function setVariantSetId($variantSetId) 3790 { 3791 $this->variantSetId = $variantSetId; 3792 } 3793 public function getVariantSetId() 3794 { 3795 return $this->variantSetId; 3796 } 3797 } 3798 3799 class Google_Service_Genomics_VariantCall extends Google_Collection 3800 { 3801 protected $collection_key = 'genotypeLikelihood'; 3802 protected $internal_gapi_mappings = array( 3803 ); 3804 public $callSetId; 3805 public $callSetName; 3806 public $genotype; 3807 public $genotypeLikelihood; 3808 public $info; 3809 public $phaseset; 3810 3811 3812 public function setCallSetId($callSetId) 3813 { 3814 $this->callSetId = $callSetId; 3815 } 3816 public function getCallSetId() 3817 { 3818 return $this->callSetId; 3819 } 3820 public function setCallSetName($callSetName) 3821 { 3822 $this->callSetName = $callSetName; 3823 } 3824 public function getCallSetName() 3825 { 3826 return $this->callSetName; 3827 } 3828 public function setGenotype($genotype) 3829 { 3830 $this->genotype = $genotype; 3831 } 3832 public function getGenotype() 3833 { 3834 return $this->genotype; 3835 } 3836 public function setGenotypeLikelihood($genotypeLikelihood) 3837 { 3838 $this->genotypeLikelihood = $genotypeLikelihood; 3839 } 3840 public function getGenotypeLikelihood() 3841 { 3842 return $this->genotypeLikelihood; 3843 } 3844 public function setInfo($info) 3845 { 3846 $this->info = $info; 3847 } 3848 public function getInfo() 3849 { 3850 return $this->info; 3851 } 3852 public function setPhaseset($phaseset) 3853 { 3854 $this->phaseset = $phaseset; 3855 } 3856 public function getPhaseset() 3857 { 3858 return $this->phaseset; 3859 } 3860 } 3861 3862 class Google_Service_Genomics_VariantCallInfo extends Google_Model 3863 { 3864 } 3865 3866 class Google_Service_Genomics_VariantInfo extends Google_Model 3867 { 3868 } 3869 3870 class Google_Service_Genomics_VariantSet extends Google_Collection 3871 { 3872 protected $collection_key = 'referenceBounds'; 3873 protected $internal_gapi_mappings = array( 3874 ); 3875 public $datasetId; 3876 public $id; 3877 protected $metadataType = 'Google_Service_Genomics_VariantSetMetadata'; 3878 protected $metadataDataType = 'array'; 3879 protected $referenceBoundsType = 'Google_Service_Genomics_ReferenceBound'; 3880 protected $referenceBoundsDataType = 'array'; 3881 3882 3883 public function setDatasetId($datasetId) 3884 { 3885 $this->datasetId = $datasetId; 3886 } 3887 public function getDatasetId() 3888 { 3889 return $this->datasetId; 3890 } 3891 public function setId($id) 3892 { 3893 $this->id = $id; 3894 } 3895 public function getId() 3896 { 3897 return $this->id; 3898 } 3899 public function setMetadata($metadata) 3900 { 3901 $this->metadata = $metadata; 3902 } 3903 public function getMetadata() 3904 { 3905 return $this->metadata; 3906 } 3907 public function setReferenceBounds($referenceBounds) 3908 { 3909 $this->referenceBounds = $referenceBounds; 3910 } 3911 public function getReferenceBounds() 3912 { 3913 return $this->referenceBounds; 3914 } 3915 } 3916 3917 class Google_Service_Genomics_VariantSetMetadata extends Google_Model 3918 { 3919 protected $internal_gapi_mappings = array( 3920 ); 3921 public $description; 3922 public $id; 3923 public $info; 3924 public $key; 3925 public $number; 3926 public $type; 3927 public $value; 3928 3929 3930 public function setDescription($description) 3931 { 3932 $this->description = $description; 3933 } 3934 public function getDescription() 3935 { 3936 return $this->description; 3937 } 3938 public function setId($id) 3939 { 3940 $this->id = $id; 3941 } 3942 public function getId() 3943 { 3944 return $this->id; 3945 } 3946 public function setInfo($info) 3947 { 3948 $this->info = $info; 3949 } 3950 public function getInfo() 3951 { 3952 return $this->info; 3953 } 3954 public function setKey($key) 3955 { 3956 $this->key = $key; 3957 } 3958 public function getKey() 3959 { 3960 return $this->key; 3961 } 3962 public function setNumber($number) 3963 { 3964 $this->number = $number; 3965 } 3966 public function getNumber() 3967 { 3968 return $this->number; 3969 } 3970 public function setType($type) 3971 { 3972 $this->type = $type; 3973 } 3974 public function getType() 3975 { 3976 return $this->type; 3977 } 3978 public function setValue($value) 3979 { 3980 $this->value = $value; 3981 } 3982 public function getValue() 3983 { 3984 return $this->value; 3985 } 3986 } 3987 3988 class Google_Service_Genomics_VariantSetMetadataInfo extends Google_Model 3989 { 3990 }
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