Coverage Report
File RestJobThread.java
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54% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| RestJobThread | 68 | 399 | 143 | ||
| RestJobThread.Stage | 70 | 0 | 0 | ||
| RestJobThread.AddDataTo | 552 | 0 | 0 |
Contributing tests
This file is covered by 1 test.
.
Source view
| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 7 | * Jalview is free software: you can redistribute it and/or | |
| 8 | * modify it under the terms of the GNU General Public License | |
| 9 | * as published by the Free Software Foundation, either version 3 | |
| 10 | * of the License, or (at your option) any later version. | |
| 11 | * | |
| 12 | * Jalview is distributed in the hope that it will be useful, but | |
| 13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
| 14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
| 15 | * PURPOSE. See the GNU General Public License for more details. | |
| 16 | * | |
| 17 | * You should have received a copy of the GNU General Public License | |
| 18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
| 19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
| 20 | */ | |
| 21 | package jalview.ws.rest; | |
| 22 | ||
| 23 | import java.util.Locale; | |
| 24 | ||
| 25 | import jalview.bin.Console; | |
| 26 | import jalview.datamodel.Alignment; | |
| 27 | import jalview.datamodel.AlignmentAnnotation; | |
| 28 | import jalview.datamodel.AlignmentI; | |
| 29 | import jalview.datamodel.AlignmentOrder; | |
| 30 | import jalview.datamodel.Annotation; | |
| 31 | import jalview.datamodel.HiddenColumns; | |
| 32 | import jalview.datamodel.SequenceGroup; | |
| 33 | import jalview.datamodel.SequenceI; | |
| 34 | import jalview.gui.AlignFrame; | |
| 35 | import jalview.gui.Desktop; | |
| 36 | import jalview.gui.PaintRefresher; | |
| 37 | import jalview.gui.WebserviceInfo; | |
| 38 | import jalview.io.NewickFile; | |
| 39 | import jalview.io.packed.JalviewDataset; | |
| 40 | import jalview.io.packed.JalviewDataset.AlignmentSet; | |
| 41 | import jalview.util.MessageManager; | |
| 42 | import jalview.ws.AWSThread; | |
| 43 | import jalview.ws.AWsJob; | |
| 44 | ||
| 45 | import java.awt.event.ActionEvent; | |
| 46 | import java.awt.event.ActionListener; | |
| 47 | import java.io.IOException; | |
| 48 | import java.util.ArrayList; | |
| 49 | import java.util.Hashtable; | |
| 50 | import java.util.List; | |
| 51 | import java.util.Map.Entry; | |
| 52 | ||
| 53 | import org.apache.axis.transport.http.HTTPConstants; | |
| 54 | import org.apache.http.Header; | |
| 55 | import org.apache.http.HttpEntity; | |
| 56 | import org.apache.http.HttpResponse; | |
| 57 | import org.apache.http.client.ClientProtocolException; | |
| 58 | import org.apache.http.client.methods.HttpGet; | |
| 59 | import org.apache.http.client.methods.HttpPost; | |
| 60 | import org.apache.http.client.methods.HttpRequestBase; | |
| 61 | import org.apache.http.entity.mime.HttpMultipartMode; | |
| 62 | import org.apache.http.entity.mime.MultipartEntity; | |
| 63 | import org.apache.http.impl.client.DefaultHttpClient; | |
| 64 | import org.apache.http.protocol.BasicHttpContext; | |
| 65 | import org.apache.http.protocol.HttpContext; | |
| 66 | import org.apache.http.util.EntityUtils; | |
| 67 | ||
| 68 | public class RestJobThread extends AWSThread | |
| 69 | { | |
| 70 | enum Stage | |
| 71 | { | |
| 72 | SUBMIT, POLL | |
| 73 | } | |
| 74 | ||
| 75 | protected RestClient restClient; | |
| 76 | ||
| 77 | 2 |  public RestJobThread(RestClient restClient) |
| 78 | { | |
| 79 | 2 | super(restClient.af, null, restClient._input, |
| 80 | restClient.service.postUrl); | |
| 81 | 2 | this.restClient = restClient; // may not be needed |
| 82 | // Test Code | |
| 83 | // minimal job - submit given input and parse result onto alignment as | |
| 84 | // annotation/whatever | |
| 85 | ||
| 86 | // look for tree data, etc. | |
| 87 | ||
| 88 | // for moment do following job type only | |
| 89 | // input=visiblealignment,groupsindex | |
| 90 | // ie one subjob using groups defined on alignment. | |
| 91 | 2 | if (!restClient.service.isHseparable()) |
| 92 | { | |
| 93 | 0 | jobs = new RestJob[1]; |
| 94 | 0 | jobs[0] = new RestJob(0, this, |
| 95 | restClient._input.getVisibleAlignment( | |
| 96 | restClient.service.getGapCharacter()), | |
| 97 | restClient._input.getVisibleContigs()); | |
| 98 | // need a function to get a range on a view/alignment and return both | |
| 99 | // annotation, groups and selection subsetted to just that region. | |
| 100 | ||
| 101 | } | |
| 102 | else | |
| 103 | { | |
| 104 | 2 | int[] viscontig = restClient._input.getVisibleContigs(); |
| 105 | 2 | AlignmentI[] viscontigals = restClient._input |
| 106 | .getVisibleContigAlignments( | |
| 107 | restClient.service.getGapCharacter()); | |
| 108 | 2 | if (viscontigals != null && viscontigals.length > 0) |
| 109 | { | |
| 110 | 2 | jobs = new RestJob[viscontigals.length]; |
| 111 | 4 | for (int j = 0; j < jobs.length; j++) |
| 112 | { | |
| 113 | 2 | int[] visc = new int[] { viscontig[j * 2], viscontig[j * 2 + 1] }; |
| 114 | 2 | if (j != 0) |
| 115 | { | |
| 116 | 0 | jobs[j] = new RestJob(j, this, viscontigals[j], visc); |
| 117 | } | |
| 118 | else | |
| 119 | { | |
| 120 | 2 | jobs[j] = new RestJob(0, this, viscontigals[j], visc); |
| 121 | } | |
| 122 | } | |
| 123 | } | |
| 124 | } | |
| 125 | // end Test Code | |
| 126 | /** | |
| 127 | * subjob types row based: per sequence in alignment/selected region { input | |
| 128 | * is one sequence or sequence ID } per alignment/selected region { input is | |
| 129 | * set of sequences, alignment, one or more sets of sequence IDs, | |
| 130 | */ | |
| 131 | ||
| 132 | 2 | if (!restClient.service.isHseparable()) |
| 133 | { | |
| 134 | ||
| 135 | // create a bunch of subjobs per visible contig to ensure result honours | |
| 136 | // hidden boundaries | |
| 137 | // TODO: determine if a 'soft' hSeperable property is needed - e.g. if | |
| 138 | // user does SS-pred on sequence with big hidden regions, its going to be | |
| 139 | // less reliable. | |
| 140 | } | |
| 141 | else | |
| 142 | { | |
| 143 | // create a single subjob for the visible/selected input | |
| 144 | ||
| 145 | } | |
| 146 | // TODO: decide if vSeperable exists: eg. column wide analysis where hidden | |
| 147 | // rows do not affect output - generally no analysis that generates | |
| 148 | // alignment annotation is vSeparable - | |
| 149 | } | |
| 150 | ||
| 151 | /** | |
| 152 | * create gui components for monitoring jobs | |
| 153 | * | |
| 154 | * @param webserviceInfo | |
| 155 | */ | |
| 156 | 0 | public void setWebServiceInfo(WebserviceInfo webserviceInfo) |
| 157 | { | |
| 158 | 0 | wsInfo = webserviceInfo; |
| 159 | 0 | for (int j = 0; j < jobs.length; j++) |
| 160 | { | |
| 161 | 0 | wsInfo.addJobPane(); |
| 162 | // Copy over any per job params | |
| 163 | 0 | if (jobs.length > 1) |
| 164 | { | |
| 165 | 0 | wsInfo.setProgressName("region " + jobs[j].getJobnum(), |
| 166 | jobs[j].getJobnum()); | |
| 167 | } | |
| 168 | else | |
| 169 | { | |
| 170 | 0 | wsInfo.setProgressText(jobs[j].getJobnum(), OutputHeader); |
| 171 | } | |
| 172 | } | |
| 173 | } | |
| 174 | ||
| 175 | 0 | private String getStage(Stage stg) |
| 176 | { | |
| 177 | 0 | if (stg == Stage.SUBMIT) |
| 178 | { | |
| 179 | 0 | return "submitting "; |
| 180 | } | |
| 181 | 0 | if (stg == Stage.POLL) |
| 182 | { | |
| 183 | 0 | return "checking status of "; |
| 184 | } | |
| 185 | ||
| 186 | 0 | return (" being confused about "); |
| 187 | } | |
| 188 | ||
| 189 | 0 | private void doPoll(RestJob rj) throws Exception |
| 190 | { | |
| 191 | 0 | String postUrl = rj.getPollUrl(); |
| 192 | 0 | doHttpReq(Stage.POLL, rj, postUrl); |
| 193 | } | |
| 194 | ||
| 195 | /** | |
| 196 | * construct the post and handle the response. | |
| 197 | * | |
| 198 | * @throws Exception | |
| 199 | */ | |
| 200 | 1 | public void doPost(RestJob rj) throws Exception |
| 201 | { | |
| 202 | 1 | String postUrl = rj.getPostUrl(); |
| 203 | 1 | doHttpReq(Stage.SUBMIT, rj, postUrl); |
| 204 | 1 | wsInfo.invalidate(); |
| 205 | } | |
| 206 | ||
| 207 | /** | |
| 208 | * do the HTTP request - and respond/set statuses appropriate to the current | |
| 209 | * stage. | |
| 210 | * | |
| 211 | * @param stg | |
| 212 | * @param rj | |
| 213 | * - provides any data needed for posting and used to record state | |
| 214 | * @param postUrl | |
| 215 | * - actual URL to post/get from | |
| 216 | * @throws Exception | |
| 217 | */ | |
| 218 | 1 | protected void doHttpReq(Stage stg, RestJob rj, String postUrl) |
| 219 | throws Exception | |
| 220 | { | |
| 221 | 1 | StringBuffer respText = new StringBuffer(); |
| 222 | // con.setContentHandlerFactory(new | |
| 223 | // jalview.ws.io.mime.HttpContentHandler()); | |
| 224 | 1 | HttpRequestBase request = null; |
| 225 | 1 | String messages = ""; |
| 226 | 1 | if (stg == Stage.SUBMIT) |
| 227 | { | |
| 228 | // Got this from | |
| 229 | // http://evgenyg.wordpress.com/2010/05/01/uploading-files-multipart-post-apache/ | |
| 230 | ||
| 231 | 1 | HttpPost htpost = new HttpPost(postUrl); |
| 232 | 1 | MultipartEntity postentity = new MultipartEntity( |
| 233 | HttpMultipartMode.STRICT); | |
| 234 | 1 | for (Entry<String, InputType> input : rj.getInputParams()) |
| 235 | { | |
| 236 | 2 | if (input.getValue().validFor(rj)) |
| 237 | { | |
| 238 | 2 | postentity.addPart(input.getKey(), |
| 239 | input.getValue().formatForInput(rj)); | |
| 240 | } | |
| 241 | else | |
| 242 | { | |
| 243 | 0 | messages += "Skipped an input (" + input.getKey() |
| 244 | + ") - Couldn't generate it from available data."; | |
| 245 | } | |
| 246 | } | |
| 247 | 1 | htpost.setEntity(postentity); |
| 248 | 1 | request = htpost; |
| 249 | } | |
| 250 | else | |
| 251 | { | |
| 252 | 0 | request = new HttpGet(postUrl); |
| 253 | } | |
| 254 | 1 | if (request != null) |
| 255 | { | |
| 256 | 1 | DefaultHttpClient httpclient = new DefaultHttpClient(); |
| 257 | ||
| 258 | 1 | HttpContext localContext = new BasicHttpContext(); |
| 259 | 1 | HttpResponse response = null; |
| 260 | 1 | try |
| 261 | { | |
| 262 | 1 | response = httpclient.execute(request); |
| 263 | } catch (ClientProtocolException he) | |
| 264 | { | |
| 265 | 0 | rj.statMessage = "Web Protocol Exception when " + getStage(stg) |
| 266 | + "Job. <br>Problematic url was <a href=\"" | |
| 267 | + request.getURI() + "\">" + request.getURI() | |
| 268 | + "</a><br>See Console output for details."; | |
| 269 | 0 | rj.setAllowedServerExceptions(0);// unrecoverable; |
| 270 | 0 | rj.error = true; |
| 271 | 0 | Console.fatal("Unexpected REST Job " + getStage(stg) |
| 272 | + "exception for URL " + rj.rsd.postUrl); | |
| 273 | 0 | throw (he); |
| 274 | } catch (IOException e) | |
| 275 | { | |
| 276 | 0 | rj.statMessage = "IO Exception when " + getStage(stg) |
| 277 | + "Job. <br>Problematic url was <a href=\"" | |
| 278 | + request.getURI() + "\">" + request.getURI() | |
| 279 | + "</a><br>See Console output for details."; | |
| 280 | 0 | Console.warn("IO Exception for REST Job " + getStage(stg) |
| 281 | + "exception for URL " + rj.rsd.postUrl); | |
| 282 | ||
| 283 | 0 | throw (e); |
| 284 | } | |
| 285 | 1 | switch (response.getStatusLine().getStatusCode()) |
| 286 | { | |
| 287 | 0 | case 200: |
| 288 | 0 | rj.running = false; |
| 289 | 0 | Console.debug("Processing result set."); |
| 290 | 0 | processResultSet(rj, response, request); |
| 291 | 0 | break; |
| 292 | 0 | case 202: |
| 293 | 0 | rj.statMessage = "<br>Job submitted successfully. Results available at this URL:\n" |
| 294 | + "<a href=" + rj.getJobId() + "\">" + rj.getJobId() | |
| 295 | + "</a><br>"; | |
| 296 | 0 | rj.running = true; |
| 297 | 0 | break; |
| 298 | 1 | case 302: |
| 299 | 1 | Header[] loc; |
| 300 | ? | if (!rj.isSubmitted() |
| 301 | && (loc = response | |
| 302 | .getHeaders(HTTPConstants.HEADER_LOCATION)) != null | |
| 303 | && loc.length > 0) | |
| 304 | { | |
| 305 | 1 | if (loc.length > 1) |
| 306 | { | |
| 307 | 0 | Console.warn("Ignoring additional " + (loc.length - 1) |
| 308 | + " location(s) provided in response header ( next one is '" | |
| 309 | + loc[1].getValue() + "' )"); | |
| 310 | } | |
| 311 | 1 | rj.setJobId(loc[0].getValue()); |
| 312 | 1 | rj.setSubmitted(true); |
| 313 | } | |
| 314 | 1 | completeStatus(rj, response); |
| 315 | 1 | break; |
| 316 | 0 | case 500: |
| 317 | // Failed. | |
| 318 | 0 | rj.setSubmitted(true); |
| 319 | 0 | rj.setAllowedServerExceptions(0); |
| 320 | 0 | rj.setSubjobComplete(true); |
| 321 | 0 | rj.error = true; |
| 322 | 0 | rj.running = false; |
| 323 | 0 | completeStatus(rj, response, |
| 324 | "" + getStage(stg) + "failed. Reason below:\n"); | |
| 325 | 0 | break; |
| 326 | 0 | default: |
| 327 | // Some other response. Probably need to pop up the content in a window. | |
| 328 | // TODO: deal with all other HTTP response codes from server. | |
| 329 | 0 | Console.warn("Unhandled response status when " + getStage(stg) |
| 330 | + "for " + postUrl + ": " + response.getStatusLine()); | |
| 331 | 0 | rj.error = true; |
| 332 | 0 | rj.setAllowedServerExceptions(0); |
| 333 | 0 | rj.setSubjobComplete(true); |
| 334 | 0 | rj.setSubmitted(true); |
| 335 | 0 | try |
| 336 | { | |
| 337 | 0 | completeStatus(rj, response, "" + getStage(stg) |
| 338 | + " resulted in an unexpected server response.<br/>Url concerned was <a href=\"" | |
| 339 | + request.getURI() + "\">" + request.getURI() | |
| 340 | + "</a><br/>Filtered response content below:<br/>"); | |
| 341 | } catch (IOException e) | |
| 342 | { | |
| 343 | 0 | Console.debug("IOException when consuming unhandled response", e); |
| 344 | } | |
| 345 | 0 | ; |
| 346 | } | |
| 347 | } | |
| 348 | } | |
| 349 | ||
| 350 | /** | |
| 351 | * job has completed. Something valid should be available from con | |
| 352 | * | |
| 353 | * @param rj | |
| 354 | * @param con | |
| 355 | * @param req | |
| 356 | * is a stateless request - expected to return the same data | |
| 357 | * regardless of how many times its called. | |
| 358 | */ | |
| 359 | 0 | private void processResultSet(RestJob rj, HttpResponse con, |
| 360 | HttpRequestBase req) | |
| 361 | { | |
| 362 | 0 | if (rj.statMessage == null) |
| 363 | { | |
| 364 | 0 | rj.statMessage = ""; |
| 365 | } | |
| 366 | 0 | rj.statMessage += "Job Complete.\n"; |
| 367 | 0 | try |
| 368 | { | |
| 369 | 0 | rj.resSet = new HttpResultSet(rj, con, req); |
| 370 | 0 | rj.gotresult = true; |
| 371 | } catch (IOException e) | |
| 372 | { | |
| 373 | 0 | rj.statMessage += "Couldn't parse results. Failed."; |
| 374 | 0 | rj.error = true; |
| 375 | 0 | rj.gotresult = false; |
| 376 | } | |
| 377 | } | |
| 378 | ||
| 379 | 1 | private void completeStatus(RestJob rj, HttpResponse con) |
| 380 | throws IOException | |
| 381 | { | |
| 382 | 1 | completeStatus(rj, con, null); |
| 383 | ||
| 384 | } | |
| 385 | ||
| 386 | 1 | private void completeStatus(RestJob rj, HttpResponse con, String prefix) |
| 387 | throws IOException | |
| 388 | { | |
| 389 | 1 | StringBuffer sb = new StringBuffer(); |
| 390 | 1 | if (prefix != null) |
| 391 | { | |
| 392 | 0 | sb.append(prefix); |
| 393 | } | |
| 394 | 1 | ; |
| 395 | 1 | if (rj.statMessage != null && rj.statMessage.length() > 0) |
| 396 | { | |
| 397 | 0 | sb.append(rj.statMessage); |
| 398 | } | |
| 399 | 1 | HttpEntity en = con.getEntity(); |
| 400 | /* | |
| 401 | * Just append the content as a string. | |
| 402 | */ | |
| 403 | 1 | String f; |
| 404 | 1 | StringBuffer content = new StringBuffer(f = EntityUtils.toString(en)); |
| 405 | 1 | f = f.toLowerCase(Locale.ROOT); |
| 406 | 1 | int body = f.indexOf("<body"); |
| 407 | 1 | if (body > -1) |
| 408 | { | |
| 409 | 0 | content.delete(0, f.indexOf(">", body) + 1); |
| 410 | } | |
| 411 | 1 | if (body > -1 && sb.length() > 0) |
| 412 | { | |
| 413 | 0 | sb.append("\n"); |
| 414 | 0 | content.insert(0, sb); |
| 415 | 0 | sb = null; |
| 416 | } | |
| 417 | 1 | f = null; |
| 418 | 1 | rj.statMessage = content.toString(); |
| 419 | } | |
| 420 | ||
| 421 | 0 | @Override |
| 422 | public void pollJob(AWsJob job) throws Exception | |
| 423 | { | |
| 424 | 0 | assert (job instanceof RestJob); |
| 425 | 0 | jalview.bin.Console.errPrintln("Debug RestJob: Polling Job"); |
| 426 | 0 | doPoll((RestJob) job); |
| 427 | } | |
| 428 | ||
| 429 | 1 | @Override |
| 430 | public void StartJob(AWsJob job) | |
| 431 | { | |
| 432 | 1 | assert (job instanceof RestJob); |
| 433 | 1 | try |
| 434 | { | |
| 435 | 1 | jalview.bin.Console.errPrintln("Debug RestJob: Posting Job"); |
| 436 | 1 | doPost((RestJob) job); |
| 437 | } catch (NoValidInputDataException erex) | |
| 438 | { | |
| 439 | 0 | job.setSubjobComplete(true); |
| 440 | 0 | job.setSubmitted(true); |
| 441 | 0 | ((RestJob) job).statMessage = "<br>It looks like there was a problem with the data sent to the service :<br>" |
| 442 | + erex.getMessage() + "\n"; | |
| 443 | 0 | ((RestJob) job).error = true; |
| 444 | ||
| 445 | } catch (Exception ex) | |
| 446 | { | |
| 447 | 1 | job.setSubjobComplete(true); |
| 448 | 1 | job.setAllowedServerExceptions(-1); |
| 449 | 1 | Console.error("Exception when trying to start Rest Job.", ex); |
| 450 | } | |
| 451 | } | |
| 452 | ||
| 453 | 0 | @Override |
| 454 | public void parseResult() | |
| 455 | { | |
| 456 | // crazy users will see this message | |
| 457 | // TODO: finish this! and remove the message below! | |
| 458 | 0 | Console.warn("Rest job result parser is currently INCOMPLETE!"); |
| 459 | 0 | int validres = 0; |
| 460 | 0 | for (RestJob rj : (RestJob[]) jobs) |
| 461 | { | |
| 462 | 0 | if (rj.hasResponse() && rj.resSet != null && rj.resSet.isValid()) |
| 463 | { | |
| 464 | 0 | String ln = null; |
| 465 | 0 | try |
| 466 | { | |
| 467 | 0 | Console.debug("Parsing data for job " + rj.getJobId()); |
| 468 | 0 | rj.parseResultSet(); |
| 469 | 0 | if (rj.hasResults()) |
| 470 | { | |
| 471 | 0 | validres++; |
| 472 | } | |
| 473 | 0 | Console.debug("Finished parsing data for job " + rj.getJobId()); |
| 474 | ||
| 475 | } catch (Error ex) | |
| 476 | { | |
| 477 | 0 | Console.warn( |
| 478 | "Failed to finish parsing data for job " + rj.getJobId()); | |
| 479 | 0 | ex.printStackTrace(); |
| 480 | } catch (Exception ex) | |
| 481 | { | |
| 482 | 0 | Console.warn( |
| 483 | "Failed to finish parsing data for job " + rj.getJobId()); | |
| 484 | 0 | ex.printStackTrace(); |
| 485 | } finally | |
| 486 | { | |
| 487 | 0 | rj.error = true; |
| 488 | 0 | rj.statMessage = "Error whilst parsing data for this job.<br>URL for job response is :<a href=\"" |
| 489 | + rj.resSet.getUrl() + "\">" + rj.resSet.getUrl() | |
| 490 | + "</a><br>"; | |
| 491 | } | |
| 492 | } | |
| 493 | } | |
| 494 | 0 | if (validres > 0) |
| 495 | { | |
| 496 | // add listeners and activate result display gui elements | |
| 497 | /** | |
| 498 | * decisions based on job result content + state of alignFrame that | |
| 499 | * originated the job: | |
| 500 | */ | |
| 501 | /* | |
| 502 | * 1. Can/Should this job automatically open a new window for results | |
| 503 | */ | |
| 504 | 0 | if (true) |
| 505 | { | |
| 506 | // preserver current jalview behaviour | |
| 507 | 0 | wsInfo.setViewResultsImmediatly(true); |
| 508 | } | |
| 509 | else | |
| 510 | { | |
| 511 | // realiseResults(true, true); | |
| 512 | } | |
| 513 | // otherwise, should automatically view results | |
| 514 | ||
| 515 | // TODO: check if at least one or more contexts are valid - if so, enable | |
| 516 | // gui | |
| 517 | 0 | wsInfo.showResultsNewFrame.addActionListener(new ActionListener() |
| 518 | { | |
| 519 | ||
| 520 | 0 | @Override |
| 521 | public void actionPerformed(ActionEvent e) | |
| 522 | { | |
| 523 | 0 | realiseResults(false); |
| 524 | } | |
| 525 | ||
| 526 | }); | |
| 527 | 0 | wsInfo.mergeResults.addActionListener(new ActionListener() |
| 528 | { | |
| 529 | ||
| 530 | 0 | @Override |
| 531 | public void actionPerformed(ActionEvent e) | |
| 532 | { | |
| 533 | 0 | realiseResults(true); |
| 534 | } | |
| 535 | ||
| 536 | }); | |
| 537 | ||
| 538 | 0 | wsInfo.setResultsReady(); |
| 539 | } | |
| 540 | else | |
| 541 | { | |
| 542 | // tell the user nothing was returned. | |
| 543 | 0 | wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR); |
| 544 | 0 | wsInfo.setFinishedNoResults(); |
| 545 | } | |
| 546 | } | |
| 547 | ||
| 548 | /** | |
| 549 | * instructions for whether to create new alignment view on current alignment | |
| 550 | * set, add to current set, or create new alignFrame | |
| 551 | */ | |
| 552 | private enum AddDataTo | |
| 553 | { | |
| 554 | /** | |
| 555 | * add annotation, trees etc to current view | |
| 556 | */ | |
| 557 | currentView, | |
| 558 | /** | |
| 559 | * create a new view derived from current view and add data to that | |
| 560 | */ | |
| 561 | newView, | |
| 562 | /** | |
| 563 | * create a new alignment frame for the result set and add annotation to | |
| 564 | * that. | |
| 565 | */ | |
| 566 | newAlignment | |
| 567 | }; | |
| 568 | ||
| 569 | 0 | public void realiseResults(boolean merge) |
| 570 | { | |
| 571 | /* | |
| 572 | * 2. Should the job modify the parent alignment frame/view(s) (if they | |
| 573 | * still exist and the alignment hasn't been edited) in order to display new | |
| 574 | * annotation/features. | |
| 575 | */ | |
| 576 | /** | |
| 577 | * alignment panels derived from each alignment set returned by service. | |
| 578 | */ | |
| 579 | 0 | ArrayList<jalview.gui.AlignmentPanel> destPanels = new ArrayList<jalview.gui.AlignmentPanel>(); |
| 580 | /** | |
| 581 | * list of instructions for how to process each distinct alignment set | |
| 582 | * returned by the job set | |
| 583 | */ | |
| 584 | 0 | ArrayList<AddDataTo> resultDest = new ArrayList<AddDataTo>(); |
| 585 | /** | |
| 586 | * when false, zeroth pane is panel derived from input deta. | |
| 587 | */ | |
| 588 | 0 | boolean newAlignment = false; |
| 589 | /** | |
| 590 | * gap character to be used for alignment reconstruction | |
| 591 | */ | |
| 592 | 0 | char gapCharacter = restClient.av.getGapCharacter(); |
| 593 | // Now, iterate over all alignment sets returned from all jobs: | |
| 594 | // first inspect jobs and collate results data in order to count alignments | |
| 595 | // and other results | |
| 596 | // then assemble results from decomposed (v followed by h-separated) jobs | |
| 597 | // finally, new views and alignments will be created and displayed as | |
| 598 | // necessary. | |
| 599 | 0 | boolean hsepjobs = restClient.service.isHseparable(); |
| 600 | 0 | boolean vsepjobs = restClient.service.isVseparable(); |
| 601 | // total number of distinct alignment sets generated by job set. | |
| 602 | 0 | int numAlSets = 0, als = 0; |
| 603 | 0 | List<AlignmentI> destAls = new ArrayList<AlignmentI>(); |
| 604 | 0 | List<jalview.datamodel.HiddenColumns> destColsel = new ArrayList<jalview.datamodel.HiddenColumns>(); |
| 605 | 0 | List<List<NewickFile>> trees = new ArrayList<List<NewickFile>>(); |
| 606 | ||
| 607 | 0 | do |
| 608 | { | |
| 609 | // Step 1. | |
| 610 | // iterate over each alignment set returned from each subjob. Treating | |
| 611 | // each one returned in parallel with others. | |
| 612 | // Result collation arrays | |
| 613 | ||
| 614 | /** | |
| 615 | * mapping between index of sequence in alignment that was submitted to | |
| 616 | * server and index of sequence in the input alignment | |
| 617 | */ | |
| 618 | 0 | int[][] ordermap = new int[jobs.length][]; |
| 619 | 0 | SequenceI[][] rseqs = new SequenceI[jobs.length][]; |
| 620 | 0 | AlignmentOrder[] orders = new AlignmentOrder[jobs.length]; |
| 621 | 0 | AlignmentAnnotation[][] alan = new AlignmentAnnotation[jobs.length][]; |
| 622 | 0 | SequenceGroup[][] sgrp = new SequenceGroup[jobs.length][]; |
| 623 | // Now collect all data for alignment Set als from job array | |
| 624 | 0 | for (int j = 0; j < jobs.length; j++) |
| 625 | { | |
| 626 | 0 | RestJob rj = (RestJob) jobs[j]; |
| 627 | 0 | if (rj.hasResults()) |
| 628 | { | |
| 629 | 0 | JalviewDataset rset = rj.context; |
| 630 | 0 | if (rset.hasAlignments()) |
| 631 | { | |
| 632 | 0 | if (numAlSets < rset.getAl().size()) |
| 633 | { | |
| 634 | 0 | numAlSets = rset.getAl().size(); |
| 635 | } | |
| 636 | 0 | if (als < rset.getAl().size() |
| 637 | && rset.getAl().get(als).isModified()) | |
| 638 | { | |
| 639 | // Collate result data | |
| 640 | // TODO: decide if all alignmentI should be collected rather than | |
| 641 | // specific alignment data containers | |
| 642 | // for moment, we just extract content, but this means any | |
| 643 | // alignment properties may be lost. | |
| 644 | 0 | AlignmentSet alset = rset.getAl().get(als); |
| 645 | 0 | alan[j] = alset.al.getAlignmentAnnotation(); |
| 646 | 0 | if (alset.al.getGroups() != null) |
| 647 | { | |
| 648 | 0 | sgrp[j] = new SequenceGroup[alset.al.getGroups().size()]; |
| 649 | 0 | alset.al.getGroups().toArray(sgrp[j]); |
| 650 | } | |
| 651 | else | |
| 652 | { | |
| 653 | 0 | sgrp[j] = null; |
| 654 | } | |
| 655 | 0 | orders[j] = new AlignmentOrder(alset.al); |
| 656 | 0 | rseqs[j] = alset.al.getSequencesArray(); |
| 657 | 0 | ordermap[j] = rj.getOrderMap(); |
| 658 | // if (rj.isInputUniquified()) { | |
| 659 | // jalview.analysis.AlignmentSorter.recoverOrder(rseqs[als]); | |
| 660 | // } | |
| 661 | ||
| 662 | 0 | if (alset.trees != null) |
| 663 | { | |
| 664 | 0 | trees.add(new ArrayList<NewickFile>(alset.trees)); |
| 665 | } | |
| 666 | else | |
| 667 | { | |
| 668 | 0 | trees.add(new ArrayList<NewickFile>()); |
| 669 | } | |
| 670 | } | |
| 671 | } | |
| 672 | } | |
| 673 | } | |
| 674 | // Now aggregate and present results from this frame of alignment data. | |
| 675 | 0 | int nvertsep = 0, nvertseps = 1; |
| 676 | 0 | if (vsepjobs) |
| 677 | { | |
| 678 | // Jobs relate to different rows of input alignment. | |
| 679 | // Jobs are subdivided by rows before columns, | |
| 680 | // so there will now be a number of subjobs according tohsep for each | |
| 681 | // vertsep | |
| 682 | // TODO: get vertical separation intervals for each job and set | |
| 683 | // nvertseps | |
| 684 | // TODO: merge data from each group/sequence onto whole | |
| 685 | // alignment | |
| 686 | } | |
| 687 | /** | |
| 688 | * index into rest jobs subdivided vertically | |
| 689 | */ | |
| 690 | 0 | int vrestjob = 0; |
| 691 | // Destination alignments for all result data. | |
| 692 | 0 | ArrayList<SequenceGroup> visgrps = new ArrayList<SequenceGroup>(); |
| 693 | 0 | Hashtable<String, SequenceGroup> groupNames = new Hashtable<String, SequenceGroup>(); |
| 694 | 0 | ArrayList<AlignmentAnnotation> visAlAn = null; |
| 695 | 0 | for (nvertsep = 0; nvertsep < nvertseps; nvertsep++) |
| 696 | { | |
| 697 | // TODO: set scope w.r.t. original alignment view for vertical | |
| 698 | // separation. | |
| 699 | { | |
| 700 | // results for a job exclude hidden columns of input data, so map | |
| 701 | // back on to all visible regions | |
| 702 | /** | |
| 703 | * rest job result we are working with | |
| 704 | */ | |
| 705 | 0 | int nrj = vrestjob; |
| 706 | ||
| 707 | 0 | RestJob rj = (RestJob) jobs[nrj]; |
| 708 | 0 | int contigs[] = input.getVisibleContigs(); |
| 709 | 0 | AlignmentI destAl = null; |
| 710 | 0 | jalview.datamodel.HiddenColumns destHCs = null; |
| 711 | // Resolve destAl for this data. | |
| 712 | 0 | if (als == 0 && rj.isInputContextModified()) |
| 713 | { | |
| 714 | // special case: transfer features, annotation, groups, etc, | |
| 715 | // from input | |
| 716 | // context to align panel derived from input data | |
| 717 | 0 | if (destAls.size() > als) |
| 718 | { | |
| 719 | 0 | destAl = destAls.get(als); |
| 720 | } | |
| 721 | else | |
| 722 | { | |
| 723 | 0 | if (!restClient.isAlignmentModified() && merge) |
| 724 | { | |
| 725 | 0 | destAl = restClient.av.getAlignment(); |
| 726 | 0 | destHCs = restClient.av.getAlignment().getHiddenColumns(); |
| 727 | 0 | resultDest.add(restClient.isShowResultsInNewView() |
| 728 | ? AddDataTo.newView | |
| 729 | : AddDataTo.currentView); | |
| 730 | 0 | destPanels.add(restClient.recoverAlignPanelForView()); |
| 731 | } | |
| 732 | else | |
| 733 | { | |
| 734 | 0 | newAlignment = true; |
| 735 | // recreate the input alignment data | |
| 736 | 0 | Object[] idat = input |
| 737 | .getAlignmentAndHiddenColumns(gapCharacter); | |
| 738 | 0 | destAl = new Alignment((SequenceI[]) idat[0]); |
| 739 | 0 | destHCs = (HiddenColumns) idat[1]; |
| 740 | 0 | resultDest.add(AddDataTo.newAlignment); |
| 741 | // but do not add to the alignment panel list - since we need to | |
| 742 | // create a whole new alignFrame set. | |
| 743 | } | |
| 744 | 0 | destAls.add(destAl); |
| 745 | 0 | destColsel.add(destHCs); |
| 746 | } | |
| 747 | } | |
| 748 | else | |
| 749 | { | |
| 750 | // alignment(s) returned by service is to be re-integrated and | |
| 751 | // displayed | |
| 752 | 0 | if (destAls.size() > als) |
| 753 | { | |
| 754 | 0 | if (!vsepjobs) |
| 755 | { | |
| 756 | // TODO: decide if multiple multiple alignments returned by | |
| 757 | // non-vseparable services are allowed. | |
| 758 | 0 | Console.warn( |
| 759 | "dealing with multiple alignment products returned by non-vertically separable service."); | |
| 760 | } | |
| 761 | // recover reference to last alignment created for this rest frame | |
| 762 | // ready for extension | |
| 763 | 0 | destAl = destAls.get(als); |
| 764 | 0 | destHCs = destColsel.get(als); |
| 765 | } | |
| 766 | else | |
| 767 | { | |
| 768 | 0 | Object[] newview; |
| 769 | ||
| 770 | 0 | if (!hsepjobs) |
| 771 | { | |
| 772 | // single alignment for any job that gets mapped back on to | |
| 773 | // input data. Reconstruct by interleaving parts of returned | |
| 774 | // alignment with hidden parts of input data. | |
| 775 | 0 | SequenceI[][] nsq = splitSeqsOnVisibleContigs(rseqs[nrj], |
| 776 | contigs, gapCharacter); | |
| 777 | 0 | AlignmentOrder alo[] = new AlignmentOrder[nsq.length]; |
| 778 | 0 | for (int no = 0; no < alo.length; no++) |
| 779 | { | |
| 780 | 0 | alo[no] = new AlignmentOrder(orders[nrj].getOrder()); |
| 781 | } | |
| 782 | 0 | newview = input.getUpdatedView(nsq, orders, gapCharacter); |
| 783 | } | |
| 784 | else | |
| 785 | { | |
| 786 | // each job maps to a single visible contig, and all need to be | |
| 787 | // stitched back together. | |
| 788 | // reconstruct using sub-region based MSA alignment construction | |
| 789 | // mechanism | |
| 790 | 0 | newview = input.getUpdatedView(rseqs, orders, gapCharacter); |
| 791 | } | |
| 792 | 0 | destAl = new Alignment((SequenceI[]) newview[0]); |
| 793 | 0 | destHCs = (HiddenColumns) newview[1]; |
| 794 | 0 | newAlignment = true; |
| 795 | // TODO create alignment from result data with propagated | |
| 796 | // references. | |
| 797 | 0 | destAls.add(destAl); |
| 798 | 0 | destColsel.add(destHCs); |
| 799 | 0 | resultDest.add(AddDataTo.newAlignment); |
| 800 | 0 | throw new Error( |
| 801 | MessageManager.getString("error.implementation_error") | |
| 802 | + "TODO: "); | |
| 803 | } | |
| 804 | } | |
| 805 | /** | |
| 806 | * save initial job in this set in case alignment is h-separable | |
| 807 | */ | |
| 808 | 0 | int initnrj = nrj; |
| 809 | // Now add in groups | |
| 810 | 0 | for (int ncnt = 0; ncnt < contigs.length; ncnt += 2) |
| 811 | { | |
| 812 | 0 | if (!hsepjobs) |
| 813 | { | |
| 814 | // single alignment for any job that gets mapped back on to input | |
| 815 | // data. | |
| 816 | } | |
| 817 | else | |
| 818 | { | |
| 819 | // each job maps to a single visible contig, and all need to be | |
| 820 | // stitched back together. | |
| 821 | 0 | if (ncnt > 0) |
| 822 | { | |
| 823 | 0 | nrj++; |
| 824 | } | |
| 825 | // TODO: apply options for group merging and annotation merging. | |
| 826 | // If merging not supported, then either clear hashtables now or | |
| 827 | // use them to rename the new annotation/groups for each contig if | |
| 828 | // a conflict occurs. | |
| 829 | } | |
| 830 | 0 | if (sgrp[nrj] != null) |
| 831 | { | |
| 832 | 0 | for (SequenceGroup sg : sgrp[nrj]) |
| 833 | { | |
| 834 | 0 | boolean recovered = false; |
| 835 | 0 | SequenceGroup exsg = null; |
| 836 | 0 | if (sg.getName() != null) |
| 837 | { | |
| 838 | 0 | exsg = groupNames.get(sg.getName()); |
| 839 | } | |
| 840 | 0 | if (exsg == null) |
| 841 | { | |
| 842 | 0 | exsg = new SequenceGroup(sg); |
| 843 | 0 | groupNames.put(exsg.getName(), exsg); |
| 844 | 0 | visgrps.add(exsg); |
| 845 | 0 | exsg.setStartRes(sg.getStartRes() + contigs[ncnt]); |
| 846 | 0 | exsg.setEndRes(sg.getEndRes() + contigs[ncnt]); |
| 847 | } | |
| 848 | else | |
| 849 | { | |
| 850 | 0 | recovered = true; |
| 851 | } | |
| 852 | // now replace any references from the result set with | |
| 853 | // corresponding refs from alignment input set. | |
| 854 | ||
| 855 | // TODO: cope with recovering hidden sequences from | |
| 856 | // resultContext | |
| 857 | { | |
| 858 | 0 | for (SequenceI oseq : sg.getSequences(null)) |
| 859 | { | |
| 860 | 0 | SequenceI nseq = getNewSeq(oseq, rseqs[nrj], |
| 861 | ordermap[nrj], destAl); | |
| 862 | 0 | if (nseq != null) |
| 863 | { | |
| 864 | 0 | if (!recovered) |
| 865 | { | |
| 866 | 0 | exsg.deleteSequence(oseq, false); |
| 867 | } | |
| 868 | 0 | exsg.addSequence(nseq, false); |
| 869 | } | |
| 870 | else | |
| 871 | { | |
| 872 | 0 | Console.warn( |
| 873 | "Couldn't resolve original sequence for new sequence."); | |
| 874 | } | |
| 875 | } | |
| 876 | 0 | if (sg.hasSeqrep()) |
| 877 | { | |
| 878 | 0 | if (exsg.getSeqrep() == sg.getSeqrep()) |
| 879 | { | |
| 880 | // lift over sequence rep reference too | |
| 881 | 0 | SequenceI oseq = sg.getSeqrep(); |
| 882 | 0 | SequenceI nseq = getNewSeq(oseq, rseqs[nrj], |
| 883 | ordermap[nrj], destAl); | |
| 884 | 0 | if (nseq != null) |
| 885 | { | |
| 886 | 0 | exsg.setSeqrep(nseq); |
| 887 | } | |
| 888 | } | |
| 889 | } | |
| 890 | } | |
| 891 | 0 | if (recovered) |
| 892 | { | |
| 893 | // adjust boundaries of recovered group w.r.t. new group being | |
| 894 | // merged on to original alignment. | |
| 895 | 0 | int start = sg.getStartRes() + contigs[ncnt], |
| 896 | end = sg.getEndRes() + contigs[ncnt]; | |
| 897 | 0 | if (start < exsg.getStartRes()) |
| 898 | { | |
| 899 | 0 | exsg.setStartRes(start); |
| 900 | } | |
| 901 | 0 | if (end > exsg.getEndRes()) |
| 902 | { | |
| 903 | 0 | exsg.setEndRes(end); |
| 904 | } | |
| 905 | } | |
| 906 | } | |
| 907 | } | |
| 908 | } | |
| 909 | // reset job counter | |
| 910 | 0 | nrj = initnrj; |
| 911 | // and finally add in annotation and any trees for each job | |
| 912 | 0 | for (int ncnt = 0; ncnt < contigs.length; ncnt += 2) |
| 913 | { | |
| 914 | 0 | if (!hsepjobs) |
| 915 | { | |
| 916 | // single alignment for any job that gets mapped back on to input | |
| 917 | // data. | |
| 918 | } | |
| 919 | else | |
| 920 | { | |
| 921 | // each job maps to a single visible contig, and all need to be | |
| 922 | // stitched back together. | |
| 923 | 0 | if (ncnt > 0) |
| 924 | { | |
| 925 | 0 | nrj++; |
| 926 | } | |
| 927 | } | |
| 928 | ||
| 929 | // merge alignmentAnnotation into one row | |
| 930 | 0 | if (alan[nrj] != null) |
| 931 | { | |
| 932 | 0 | for (int an = 0; an < alan[nrj].length; an++) |
| 933 | { | |
| 934 | 0 | SequenceI sqass = null; |
| 935 | 0 | SequenceGroup grass = null; |
| 936 | 0 | if (alan[nrj][an].sequenceRef != null) |
| 937 | { | |
| 938 | // TODO: ensure this relocates sequence reference to local | |
| 939 | // context. | |
| 940 | 0 | sqass = getNewSeq(alan[nrj][an].sequenceRef, rseqs[nrj], |
| 941 | ordermap[nrj], destAl); | |
| 942 | } | |
| 943 | 0 | if (alan[nrj][an].groupRef != null) |
| 944 | { | |
| 945 | // TODO: verify relocate group reference to local context | |
| 946 | // works correctly | |
| 947 | 0 | grass = groupNames.get(alan[nrj][an].groupRef.getName()); |
| 948 | 0 | if (grass == null) |
| 949 | { | |
| 950 | 0 | Console.error( |
| 951 | "Couldn't relocate group referemce for group " | |
| 952 | + alan[nrj][an].groupRef.getName()); | |
| 953 | } | |
| 954 | } | |
| 955 | 0 | if (visAlAn == null) |
| 956 | { | |
| 957 | 0 | visAlAn = new ArrayList<AlignmentAnnotation>(); |
| 958 | } | |
| 959 | 0 | AlignmentAnnotation visan = null; |
| 960 | 0 | for (AlignmentAnnotation v : visAlAn) |
| 961 | { | |
| 962 | 0 | if (v.label != null |
| 963 | && v.label.equals(alan[nrj][an].label)) | |
| 964 | { | |
| 965 | 0 | visan = v; |
| 966 | } | |
| 967 | } | |
| 968 | 0 | if (visan == null) |
| 969 | { | |
| 970 | 0 | visan = new AlignmentAnnotation(alan[nrj][an]); |
| 971 | // copy annotations, and wipe out/update refs. | |
| 972 | 0 | visan.annotations = new Annotation[input.getWidth()]; |
| 973 | 0 | visan.groupRef = grass; |
| 974 | 0 | visan.sequenceRef = sqass; |
| 975 | 0 | visAlAn.add(visan); |
| 976 | } | |
| 977 | 0 | if (contigs[ncnt] |
| 978 | + alan[nrj][an].annotations.length > visan.annotations.length) | |
| 979 | { | |
| 980 | // increase width of annotation row | |
| 981 | 0 | Annotation[] newannv = new Annotation[contigs[ncnt] |
| 982 | + alan[nrj][an].annotations.length]; | |
| 983 | 0 | System.arraycopy(visan.annotations, 0, newannv, 0, |
| 984 | visan.annotations.length); | |
| 985 | 0 | visan.annotations = newannv; |
| 986 | } | |
| 987 | // now copy local annotation data into correct position | |
| 988 | 0 | System.arraycopy(alan[nrj][an].annotations, 0, |
| 989 | visan.annotations, contigs[ncnt], | |
| 990 | alan[nrj][an].annotations.length); | |
| 991 | ||
| 992 | } | |
| 993 | } | |
| 994 | // Trees | |
| 995 | 0 | if (trees.get(nrj).size() > 0) |
| 996 | { | |
| 997 | 0 | for (NewickFile nf : trees.get(nrj)) |
| 998 | { | |
| 999 | // TODO: process each newick file, lifting over sequence refs to | |
| 1000 | // current alignment, if necessary. | |
| 1001 | 0 | Console.error( |
| 1002 | "Tree recovery from restjob not yet implemented."); | |
| 1003 | } | |
| 1004 | } | |
| 1005 | } | |
| 1006 | } | |
| 1007 | } // end of vseps loops. | |
| 1008 | 0 | if (visAlAn != null) |
| 1009 | { | |
| 1010 | 0 | for (AlignmentAnnotation v : visAlAn) |
| 1011 | { | |
| 1012 | 0 | destAls.get(als).addAnnotation(v); |
| 1013 | } | |
| 1014 | } | |
| 1015 | 0 | if (visgrps != null) |
| 1016 | { | |
| 1017 | 0 | for (SequenceGroup sg : visgrps) |
| 1018 | { | |
| 1019 | 0 | destAls.get(als).addGroup(sg); |
| 1020 | } | |
| 1021 | } | |
| 1022 | 0 | } while (++als < numAlSets); |
| 1023 | // Finally, assemble each new alignment, and create new gui components to | |
| 1024 | // present it. | |
| 1025 | /** | |
| 1026 | * current AlignFrame where results will go. | |
| 1027 | */ | |
| 1028 | 0 | AlignFrame destaf = restClient.recoverAlignFrameForView(); |
| 1029 | /** | |
| 1030 | * current pane being worked with | |
| 1031 | */ | |
| 1032 | 0 | jalview.gui.AlignmentPanel destPanel = restClient |
| 1033 | .recoverAlignPanelForView(); | |
| 1034 | 0 | als = 0; |
| 1035 | 0 | for (AddDataTo action : resultDest) |
| 1036 | { | |
| 1037 | 0 | AlignmentI destal; |
| 1038 | 0 | HiddenColumns destcs; |
| 1039 | 0 | String alTitle = MessageManager |
| 1040 | .formatMessage("label.webservice_job_title_on", new String[] | |
| 1041 | { restClient.service.details.Action, | |
| 1042 | restClient.service.details.Name, restClient.viewTitle }); | |
| 1043 | 0 | switch (action) |
| 1044 | { | |
| 1045 | 0 | case newAlignment: |
| 1046 | 0 | destal = destAls.get(als); |
| 1047 | 0 | destcs = destColsel.get(als); |
| 1048 | 0 | destaf = new AlignFrame(destal, destcs, AlignFrame.DEFAULT_WIDTH, |
| 1049 | AlignFrame.DEFAULT_HEIGHT); | |
| 1050 | 0 | PaintRefresher.Refresh(destaf, |
| 1051 | destaf.getViewport().getSequenceSetId()); | |
| 1052 | // todo transfer any feature settings and colouring | |
| 1053 | /* | |
| 1054 | * destaf.getFeatureRenderer().transferSettings(this.featureSettings); | |
| 1055 | * // update orders if (alorders.size() > 0) { if (alorders.size() == 1) | |
| 1056 | * { af.addSortByOrderMenuItem(WebServiceName + " Ordering", | |
| 1057 | * (AlignmentOrder) alorders.get(0)); } else { // construct a | |
| 1058 | * non-redundant ordering set Vector names = new Vector(); for (int i = | |
| 1059 | * 0, l = alorders.size(); i < l; i++) { String orderName = new | |
| 1060 | * String(" Region " + i); int j = i + 1; | |
| 1061 | * | |
| 1062 | * while (j < l) { if (((AlignmentOrder) alorders.get(i)) | |
| 1063 | * .equals(((AlignmentOrder) alorders.get(j)))) { alorders.remove(j); | |
| 1064 | * l--; orderName += "," + j; } else { j++; } } | |
| 1065 | * | |
| 1066 | * if (i == 0 && j == 1) { names.add(new String("")); } else { | |
| 1067 | * names.add(orderName); } } for (int i = 0, l = alorders.size(); i < l; | |
| 1068 | * i++) { af.addSortByOrderMenuItem( WebServiceName + ((String) | |
| 1069 | * names.get(i)) + " Ordering", (AlignmentOrder) alorders.get(i)); } } } | |
| 1070 | */ | |
| 1071 | // TODO: modify this and previous alignment's title if many alignments | |
| 1072 | // have been returned. | |
| 1073 | 0 | Desktop.addInternalFrame(destaf, alTitle, AlignFrame.DEFAULT_WIDTH, |
| 1074 | AlignFrame.DEFAULT_HEIGHT); | |
| 1075 | ||
| 1076 | 0 | break; |
| 1077 | 0 | case newView: |
| 1078 | // TODO: determine title for view | |
| 1079 | 0 | break; |
| 1080 | 0 | case currentView: |
| 1081 | 0 | break; |
| 1082 | } | |
| 1083 | } | |
| 1084 | 0 | if (!newAlignment) |
| 1085 | { | |
| 1086 | 0 | if (restClient.isShowResultsInNewView()) |
| 1087 | { | |
| 1088 | // destPanel = destPanel.alignFrame.newView(false); | |
| 1089 | } | |
| 1090 | } | |
| 1091 | else | |
| 1092 | { | |
| 1093 | ||
| 1094 | } | |
| 1095 | /* | |
| 1096 | * if (als) // add the destination panel to frame zero of result panel set } | |
| 1097 | * } if (destPanels.size()==0) { AlignFrame af = new AlignFrame((AlignmentI) | |
| 1098 | * idat[0], (ColumnSelection) idat[1], AlignFrame.DEFAULT_WIDTH, | |
| 1099 | * AlignFrame.DEFAULT_HEIGHT); | |
| 1100 | * | |
| 1101 | * jalview.gui.Desktop.addInternalFrame(af, "Results for " + | |
| 1102 | * restClient.service.details.Name + " " + restClient.service.details.Action | |
| 1103 | * + " on " + restClient.af.getTitle(), AlignFrame.DEFAULT_WIDTH, | |
| 1104 | * AlignFrame.DEFAULT_HEIGHT); destPanel = af.alignPanel; // create totally | |
| 1105 | * new alignment from stashed data/results | |
| 1106 | */ | |
| 1107 | ||
| 1108 | /* | |
| 1109 | */ | |
| 1110 | ||
| 1111 | /** | |
| 1112 | * alignments. New alignments are added to dataset, and subsequently | |
| 1113 | * annotated/visualised accordingly. 1. New alignment frame created for new | |
| 1114 | * alignment. Decide if any vis settings should be inherited from old | |
| 1115 | * alignment frame (e.g. sequence ordering ?). 2. Subsequent data added to | |
| 1116 | * alignment as below: | |
| 1117 | */ | |
| 1118 | /** | |
| 1119 | * annotation update to original/newly created context alignment: 1. | |
| 1120 | * identify alignment where annotation is to be loaded onto. 2. Add | |
| 1121 | * annotation, excluding any duplicates. 3. Ensure annotation is visible on | |
| 1122 | * alignment - honouring ordering given by file. | |
| 1123 | */ | |
| 1124 | /** | |
| 1125 | * features updated to original or newly created context alignment: 1. | |
| 1126 | * Features are(or were already) added to dataset. 2. Feature settings | |
| 1127 | * modified to ensure all features are displayed - honouring any ordering | |
| 1128 | * given by result file. Consider merging action with the code used by the | |
| 1129 | * DAS fetcher to update alignment views with new info. | |
| 1130 | */ | |
| 1131 | /** | |
| 1132 | * Seq associated data files (PDB files). 1. locate seq association in | |
| 1133 | * current dataset/alignment context and add file as normal - keep handle of | |
| 1134 | * any created ref objects. 2. decide if new data should be displayed : PDB | |
| 1135 | * display: if alignment has PDB display already, should new pdb files be | |
| 1136 | * aligned to it ? | |
| 1137 | * | |
| 1138 | */ | |
| 1139 | // destPanel.adjustAnnotationHeight(); | |
| 1140 | ||
| 1141 | } | |
| 1142 | ||
| 1143 | /** | |
| 1144 | * split the given array of sequences into blocks of subsequences | |
| 1145 | * corresponding to each visible contig | |
| 1146 | * | |
| 1147 | * @param sequenceIs | |
| 1148 | * @param contigs | |
| 1149 | * @param gapChar | |
| 1150 | * padding character for ragged ends of visible contig region. | |
| 1151 | * @return | |
| 1152 | */ | |
| 1153 | 0 | private SequenceI[][] splitSeqsOnVisibleContigs(SequenceI[] sequenceIs, |
| 1154 | int[] contigs, char gapChar) | |
| 1155 | { | |
| 1156 | 0 | int nvc = contigs == null ? 1 : contigs.length / 2; |
| 1157 | 0 | SequenceI[][] blocks = new SequenceI[nvc][]; |
| 1158 | 0 | if (contigs == null) |
| 1159 | { | |
| 1160 | 0 | blocks[0] = new SequenceI[sequenceIs.length]; |
| 1161 | 0 | System.arraycopy(sequenceIs, 0, blocks[0], 0, sequenceIs.length); |
| 1162 | } | |
| 1163 | else | |
| 1164 | { | |
| 1165 | // deja vu - have I written this before ?? propagateGaps does this in a | |
| 1166 | // way | |
| 1167 | 0 | char[] gapset = null; |
| 1168 | 0 | int start = 0, width = 0; |
| 1169 | 0 | for (int c = 0; c < nvc; c++) |
| 1170 | { | |
| 1171 | 0 | width = contigs[c * 2 + 1] - contigs[c * 2] + 1; |
| 1172 | 0 | for (int s = 0; s < sequenceIs.length; s++) |
| 1173 | { | |
| 1174 | 0 | int end = sequenceIs[s].getLength(); |
| 1175 | 0 | if (start < end) |
| 1176 | { | |
| 1177 | 0 | if (start + width < end) |
| 1178 | { | |
| 1179 | 0 | blocks[c][s] = sequenceIs[s].getSubSequence(start, |
| 1180 | start + width); | |
| 1181 | } | |
| 1182 | else | |
| 1183 | { | |
| 1184 | 0 | blocks[c][s] = sequenceIs[s].getSubSequence(start, end); |
| 1185 | 0 | String sq = blocks[c][s].getSequenceAsString(); |
| 1186 | 0 | for (int n = start + width; n > end; n--) |
| 1187 | { | |
| 1188 | 0 | sq += gapChar; |
| 1189 | } | |
| 1190 | } | |
| 1191 | } | |
| 1192 | else | |
| 1193 | { | |
| 1194 | 0 | if (gapset == null || gapset.length < width) |
| 1195 | { | |
| 1196 | 0 | char ng[] = new char[width]; |
| 1197 | 0 | int gs = 0; |
| 1198 | 0 | if (gapset != null) |
| 1199 | { | |
| 1200 | 0 | System.arraycopy(gapset, 0, ng, 0, gs = gapset.length); |
| 1201 | } | |
| 1202 | 0 | while (gs < ng.length) |
| 1203 | { | |
| 1204 | 0 | ng[gs++] = gapChar; |
| 1205 | } | |
| 1206 | } | |
| 1207 | 0 | blocks[c][s] = sequenceIs[s].getSubSequence(end, end); |
| 1208 | 0 | blocks[c][s].setSequence(gapset.toString().substring(0, width)); |
| 1209 | } | |
| 1210 | } | |
| 1211 | 0 | if (c > 0) |
| 1212 | { | |
| 1213 | // adjust window for next visible segnment | |
| 1214 | 0 | start += contigs[c * 2 + 1] - contigs[c * 2]; |
| 1215 | } | |
| 1216 | } | |
| 1217 | } | |
| 1218 | 0 | return blocks; |
| 1219 | } | |
| 1220 | ||
| 1221 | /** | |
| 1222 | * recover corresponding sequence from original input data corresponding to | |
| 1223 | * sequence in a specific job's input data. | |
| 1224 | * | |
| 1225 | * @param oseq | |
| 1226 | * @param sequenceIs | |
| 1227 | * @param is | |
| 1228 | * @param destAl | |
| 1229 | * @return | |
| 1230 | */ | |
| 1231 | 0 | private SequenceI getNewSeq(SequenceI oseq, SequenceI[] sequenceIs, |
| 1232 | int[] is, AlignmentI destAl) | |
| 1233 | { | |
| 1234 | 0 | int p = 0; |
| 1235 | 0 | while (p < sequenceIs.length && sequenceIs[p] != oseq) |
| 1236 | { | |
| 1237 | 0 | p++; |
| 1238 | } | |
| 1239 | 0 | if (p < sequenceIs.length && p < destAl.getHeight()) |
| 1240 | { | |
| 1241 | 0 | return destAl.getSequenceAt(is[p]); |
| 1242 | } | |
| 1243 | 0 | return null; |
| 1244 | } | |
| 1245 | ||
| 1246 | /** | |
| 1247 | * | |
| 1248 | * @return true if the run method is safe to call | |
| 1249 | */ | |
| 1250 | 1 | public boolean isValid() |
| 1251 | { | |
| 1252 | 1 | ArrayList<String> _warnings = new ArrayList<String>(); |
| 1253 | 1 | boolean validt = true; |
| 1254 | 1 | if (jobs != null) |
| 1255 | { | |
| 1256 | 1 | for (RestJob rj : (RestJob[]) jobs) |
| 1257 | { | |
| 1258 | 1 | if (!rj.hasValidInput()) |
| 1259 | { | |
| 1260 | // invalid input for this job | |
| 1261 | 0 | jalview.bin.Console.errPrintln("Job " + rj.getJobnum() |
| 1262 | + " has invalid input. ( " + rj.getStatus() + ")"); | |
| 1263 | 0 | if (rj.hasStatus() && !_warnings.contains(rj.getStatus())) |
| 1264 | { | |
| 1265 | 0 | _warnings.add(rj.getStatus()); |
| 1266 | } | |
| 1267 | 0 | validt = false; |
| 1268 | } | |
| 1269 | } | |
| 1270 | } | |
| 1271 | 1 | if (!validt) |
| 1272 | { | |
| 1273 | 0 | warnings = ""; |
| 1274 | 0 | for (String st : _warnings) |
| 1275 | { | |
| 1276 | 0 | if (warnings.length() > 0) |
| 1277 | { | |
| 1278 | 0 | warnings += "\n"; |
| 1279 | } | |
| 1280 | 0 | warnings += st; |
| 1281 | ||
| 1282 | } | |
| 1283 | } | |
| 1284 | 1 | return validt; |
| 1285 | } | |
| 1286 | ||
| 1287 | protected String warnings; | |
| 1288 | ||
| 1289 | 0 | public boolean hasWarnings() |
| 1290 | { | |
| 1291 | // TODO Auto-generated method stub | |
| 1292 | 0 | return warnings != null && warnings.length() > 0; |
| 1293 | } | |
| 1294 | ||
| 1295 | /** | |
| 1296 | * get any informative messages about why the job thread couldn't start. | |
| 1297 | * | |
| 1298 | * @return | |
| 1299 | */ | |
| 1300 | 0 | public String getWarnings() |
| 1301 | { | |
| 1302 | 0 | return isValid() ? "Job can be started. No warnings." |
| 1303 | 0 | : hasWarnings() ? warnings : ""; |
| 1304 | } | |
| 1305 | ||
| 1306 | } |