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EBIAlfaFold | 69 | 170 | 82 |
1 | ||
2 | /* | |
3 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
4 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
5 | * | |
6 | * This file is part of Jalview. | |
7 | * | |
8 | * Jalview is free software: you can redistribute it and/or | |
9 | * modify it under the terms of the GNU General Public License | |
10 | * as published by the Free Software Foundation, either version 3 | |
11 | * of the License, or (at your option) any later version. | |
12 | * | |
13 | * Jalview is distributed in the hope that it will be useful, but | |
14 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
15 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
16 | * PURPOSE. See the GNU General Public License for more details. | |
17 | * | |
18 | * You should have received a copy of the GNU General Public License | |
19 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
20 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
21 | */ | |
22 | package jalview.ws.dbsources; | |
23 | ||
24 | import java.io.File; | |
25 | import java.io.FileInputStream; | |
26 | import java.io.FileNotFoundException; | |
27 | import java.io.IOException; | |
28 | import java.io.InputStream; | |
29 | import java.util.ArrayList; | |
30 | import java.util.Date; | |
31 | import java.util.HashMap; | |
32 | import java.util.List; | |
33 | import java.util.Map; | |
34 | ||
35 | import org.json.simple.JSONArray; | |
36 | import org.json.simple.JSONObject; | |
37 | import org.json.simple.parser.ParseException; | |
38 | ||
39 | import com.stevesoft.pat.Regex; | |
40 | ||
41 | import jalview.api.FeatureSettingsModelI; | |
42 | import jalview.bin.Console; | |
43 | import jalview.datamodel.AlignmentAnnotation; | |
44 | import jalview.datamodel.AlignmentI; | |
45 | import jalview.datamodel.ContactMatrixI; | |
46 | import jalview.datamodel.DBRefEntry; | |
47 | import jalview.datamodel.GroupSet; | |
48 | import jalview.datamodel.PDBEntry; | |
49 | import jalview.datamodel.SequenceFeature; | |
50 | import jalview.datamodel.SequenceI; | |
51 | import jalview.gui.Desktop; | |
52 | import jalview.io.DataSourceType; | |
53 | import jalview.io.FileFormat; | |
54 | import jalview.io.FileFormatI; | |
55 | import jalview.io.FormatAdapter; | |
56 | import jalview.io.PDBFeatureSettings; | |
57 | import jalview.structure.StructureImportSettings.TFType; | |
58 | import jalview.structure.StructureMapping; | |
59 | import jalview.structure.StructureSelectionManager; | |
60 | import jalview.util.MessageManager; | |
61 | import jalview.util.Platform; | |
62 | import jalview.ws.datamodel.alphafold.PAEContactMatrix; | |
63 | import jalview.ws.utils.UrlDownloadClient; | |
64 | ||
65 | /** | |
66 | * @author JimP | |
67 | * | |
68 | */ | |
69 | public class EBIAlfaFold extends EbiFileRetrievedProxy | |
70 | { | |
71 | private static final String SEPARATOR = "|"; | |
72 | ||
73 | private static final String COLON = ":"; | |
74 | ||
75 | private static final int PDB_ID_LENGTH = 4; | |
76 | ||
77 | private static String AF_VERSION = "3"; | |
78 | ||
79 | 0 | public EBIAlfaFold() |
80 | { | |
81 | 0 | super(); |
82 | } | |
83 | ||
84 | /* | |
85 | * (non-Javadoc) | |
86 | * | |
87 | * @see jalview.ws.DbSourceProxy#getAccessionSeparator() | |
88 | */ | |
89 | 0 | @Override |
90 | public String getAccessionSeparator() | |
91 | { | |
92 | 0 | return null; |
93 | } | |
94 | ||
95 | /* | |
96 | * (non-Javadoc) | |
97 | * | |
98 | * @see jalview.ws.DbSourceProxy#getAccessionValidator() | |
99 | */ | |
100 | 0 | @Override |
101 | public Regex getAccessionValidator() | |
102 | { | |
103 | 0 | Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)"); |
104 | 0 | validator.setIgnoreCase(true); |
105 | 0 | return validator; |
106 | } | |
107 | ||
108 | /* | |
109 | * (non-Javadoc) | |
110 | * | |
111 | * @see jalview.ws.DbSourceProxy#getDbSource() | |
112 | */ | |
113 | 0 | @Override |
114 | public String getDbSource() | |
115 | { | |
116 | 0 | return "ALPHAFOLD"; |
117 | } | |
118 | ||
119 | /* | |
120 | * (non-Javadoc) | |
121 | * | |
122 | * @see jalview.ws.DbSourceProxy#getDbVersion() | |
123 | */ | |
124 | 0 | @Override |
125 | public String getDbVersion() | |
126 | { | |
127 | 0 | return "1"; |
128 | } | |
129 | ||
130 | 0 | public static String getAlphaFoldCifDownloadUrl(String id, String vnum) |
131 | { | |
132 | 0 | if (vnum == null || vnum.length() == 0) |
133 | { | |
134 | 0 | vnum = AF_VERSION; |
135 | } | |
136 | 0 | return "https://alphafold.ebi.ac.uk/files/" + id + "-model_v" + vnum |
137 | + ".cif"; | |
138 | } | |
139 | ||
140 | 6 | public static String getAlphaFoldPaeDownloadUrl(String id, String vnum) |
141 | { | |
142 | 6 | if (vnum == null || vnum.length() == 0) |
143 | { | |
144 | 0 | vnum = AF_VERSION; |
145 | } | |
146 | 6 | return "https://alphafold.ebi.ac.uk/files/" + id |
147 | + "-predicted_aligned_error_v" + vnum + ".json"; | |
148 | } | |
149 | ||
150 | /* | |
151 | * (non-Javadoc) | |
152 | * | |
153 | * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[]) | |
154 | */ | |
155 | 0 | @Override |
156 | public AlignmentI getSequenceRecords(String queries) throws Exception | |
157 | { | |
158 | 0 | return getSequenceRecords(queries, null); |
159 | } | |
160 | ||
161 | 0 | public AlignmentI getSequenceRecords(String queries, String retrievalUrl) |
162 | throws Exception | |
163 | { | |
164 | 0 | AlignmentI pdbAlignment = null; |
165 | 0 | String chain = null; |
166 | 0 | String id = null; |
167 | 0 | if (queries.indexOf(COLON) > -1) |
168 | { | |
169 | 0 | chain = queries.substring(queries.indexOf(COLON) + 1); |
170 | 0 | id = queries.substring(0, queries.indexOf(COLON)); |
171 | } | |
172 | else | |
173 | { | |
174 | 0 | id = queries; |
175 | } | |
176 | ||
177 | 0 | if (!isValidReference(id)) |
178 | { | |
179 | 0 | jalview.bin.Console.errPrintln( |
180 | "(AFClient) Ignoring invalid alphafold query: '" + id + "'"); | |
181 | 0 | stopQuery(); |
182 | 0 | return null; |
183 | } | |
184 | 0 | String alphaFoldCif = getAlphaFoldCifDownloadUrl(id, AF_VERSION); |
185 | 0 | if (retrievalUrl != null) |
186 | { | |
187 | 0 | alphaFoldCif = retrievalUrl; |
188 | } | |
189 | ||
190 | 0 | try |
191 | { | |
192 | 0 | File tmpFile = File.createTempFile(id, ".cif"); |
193 | 0 | Console.debug("Retrieving structure file for " + id + " from " |
194 | + alphaFoldCif); | |
195 | 0 | UrlDownloadClient.download(alphaFoldCif, tmpFile); |
196 | ||
197 | // may not need this check ? | |
198 | 0 | file = tmpFile.getAbsolutePath(); |
199 | 0 | if (file == null) |
200 | { | |
201 | 0 | return null; |
202 | } | |
203 | // TODO Get the PAE file somewhere around here and remove from JmolParser | |
204 | ||
205 | 0 | pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile, |
206 | id, chain, getDbSource(), getDbVersion()); | |
207 | ||
208 | 0 | if (pdbAlignment == null || pdbAlignment.getHeight() < 1) |
209 | { | |
210 | 0 | throw new Exception(MessageManager.formatMessage( |
211 | "exception.no_pdb_records_for_chain", new String[] | |
212 | 0 | { id, ((chain == null) ? "' '" : chain) })); |
213 | } | |
214 | // done during structure retrieval | |
215 | // retrieve_AlphaFold_pAE(id, pdbAlignment, retrievalUrl); | |
216 | ||
217 | } catch (Exception ex) // Problem parsing PDB file | |
218 | { | |
219 | 0 | stopQuery(); |
220 | 0 | throw (ex); |
221 | } | |
222 | 0 | return pdbAlignment; |
223 | } | |
224 | ||
225 | /** | |
226 | * get an alphafold pAE for the given id and return the File object of the | |
227 | * downloaded (temp) file | |
228 | * | |
229 | * @param id | |
230 | * @param pdbAlignment | |
231 | * @param retrievalUrl | |
232 | * - URL of .mmcif from EBI-AlphaFold - will be used to generate the | |
233 | * pAE URL automatically | |
234 | * @throws IOException | |
235 | * @throws Exception | |
236 | */ | |
237 | 6 | public static File fetchAlphaFoldPAE(String id, String retrievalUrl) |
238 | throws IOException | |
239 | { | |
240 | // import PAE as contact matrix - assume this will work if there was a | |
241 | // model | |
242 | 6 | String paeURL = getAlphaFoldPaeDownloadUrl(id, AF_VERSION); |
243 | ||
244 | 6 | if (retrievalUrl != null) |
245 | { | |
246 | // manufacture the PAE url from a url like ...-model-vN.cif | |
247 | 0 | paeURL = retrievalUrl.replace("model", "predicted_aligned_error") |
248 | .replace(".cif", ".json"); | |
249 | } | |
250 | ||
251 | // check the cache | |
252 | 6 | File pae = paeDownloadCache.get(paeURL); |
253 | 6 | if (pae != null && pae.exists() && (new Date().getTime() |
254 | - pae.lastModified()) < PAE_CACHE_STALE_TIME) | |
255 | { | |
256 | 5 | Console.debug( |
257 | "Using existing file in PAE cache for '" + paeURL + "'"); | |
258 | 5 | return pae; |
259 | } | |
260 | ||
261 | 1 | try |
262 | { | |
263 | 1 | pae = File.createTempFile(id == null ? "af_pae" : id, "pae_json"); |
264 | } catch (IOException e) | |
265 | { | |
266 | 0 | e.printStackTrace(); |
267 | } | |
268 | 1 | Console.debug("Downloading pae from " + paeURL + " to " + pae.toString() |
269 | + ""); | |
270 | 1 | try |
271 | { | |
272 | 1 | UrlDownloadClient.download(paeURL, pae); |
273 | } catch (IOException e) | |
274 | { | |
275 | 0 | throw e; |
276 | } | |
277 | // cache and it if successful | |
278 | 1 | paeDownloadCache.put(paeURL, pae); |
279 | 1 | return pae; |
280 | } | |
281 | ||
282 | /** | |
283 | * get an alphafold pAE for the given id, and add it to sequence 0 in | |
284 | * pdbAlignment (assuming it came from structurefile parser). | |
285 | * | |
286 | * @param id | |
287 | * @param pdbAlignment | |
288 | * @param retrievalUrl | |
289 | * - URL of .mmcif from EBI-AlphaFold - will be used to generate the | |
290 | * pAE URL automatically | |
291 | * @throws IOException | |
292 | * @throws Exception | |
293 | */ | |
294 | 0 | public static void retrieve_AlphaFold_pAE(String id, |
295 | AlignmentI pdbAlignment, String retrievalUrl) throws IOException | |
296 | { | |
297 | 0 | File pae = fetchAlphaFoldPAE(id, retrievalUrl); |
298 | 0 | addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false, null); |
299 | } | |
300 | ||
301 | 42 | public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae, |
302 | int index, String id, boolean isStruct, boolean isStructId, | |
303 | String label) | |
304 | { | |
305 | 42 | FileInputStream paeInput = null; |
306 | 42 | try |
307 | { | |
308 | 42 | paeInput = new FileInputStream(pae); |
309 | } catch (FileNotFoundException e) | |
310 | { | |
311 | 0 | Console.error( |
312 | "Could not find pAE file '" + pae.getAbsolutePath() + "'", e); | |
313 | 0 | return; |
314 | } | |
315 | ||
316 | 42 | if (isStruct) |
317 | { | |
318 | // ###### WRITE A TEST for this bit of the logic addAlphaFoldPAE with | |
319 | // different params. | |
320 | 0 | StructureSelectionManager ssm = StructureSelectionManager |
321 | .getStructureSelectionManager(Desktop.instance); | |
322 | 0 | if (ssm != null) |
323 | { | |
324 | 0 | String structFilename = isStructId ? ssm.findFileForPDBId(id) : id; |
325 | 0 | addPAEToStructure(ssm, structFilename, pae, label); |
326 | } | |
327 | ||
328 | } | |
329 | else | |
330 | { | |
331 | // attach to sequence?! | |
332 | 42 | try |
333 | { | |
334 | 42 | if (!importPaeJSONAsContactMatrixToSequence(pdbAlignment, paeInput, |
335 | index, id, label)) | |
336 | { | |
337 | 0 | Console.warn("Could not import contact matrix from '" |
338 | + pae.getAbsolutePath() + "' to sequence."); | |
339 | } | |
340 | } catch (IOException e1) | |
341 | { | |
342 | 0 | Console.error("Error when importing pAE file '" |
343 | + pae.getAbsolutePath() + "'", e1); | |
344 | } catch (ParseException e2) | |
345 | { | |
346 | 0 | Console.error("Error when parsing pAE file '" |
347 | + pae.getAbsolutePath() + "'", e2); | |
348 | } | |
349 | } | |
350 | ||
351 | } | |
352 | ||
353 | 0 | public static void addPAEToStructure(StructureSelectionManager ssm, |
354 | String structFilename, File pae, String label) | |
355 | { | |
356 | 0 | FileInputStream paeInput = null; |
357 | 0 | try |
358 | { | |
359 | 0 | paeInput = new FileInputStream(pae); |
360 | } catch (FileNotFoundException e) | |
361 | { | |
362 | 0 | Console.error( |
363 | "Could not find pAE file '" + pae.getAbsolutePath() + "'", e); | |
364 | 0 | return; |
365 | } | |
366 | 0 | if (ssm == null) |
367 | { | |
368 | 0 | ssm = StructureSelectionManager |
369 | .getStructureSelectionManager(Desktop.instance); | |
370 | } | |
371 | 0 | if (ssm != null) |
372 | { | |
373 | 0 | StructureMapping[] smArray = ssm.getMapping(structFilename); |
374 | ||
375 | 0 | try |
376 | { | |
377 | 0 | if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput, |
378 | label)) | |
379 | { | |
380 | 0 | Console.warn("Could not import contact matrix from '" |
381 | + pae.getAbsolutePath() + "' to structure."); | |
382 | } | |
383 | } catch (IOException e1) | |
384 | { | |
385 | 0 | Console.error("Error when importing pAE file '" |
386 | + pae.getAbsolutePath() + "'", e1); | |
387 | } catch (ParseException e2) | |
388 | { | |
389 | 0 | Console.error("Error when parsing pAE file '" |
390 | + pae.getAbsolutePath() + "'", e2); | |
391 | } | |
392 | } | |
393 | } | |
394 | ||
395 | /** | |
396 | * parses the given pAE matrix and adds it to sequence 0 in the given | |
397 | * alignment | |
398 | * | |
399 | * @param pdbAlignment | |
400 | * @param pae_input | |
401 | * @return true if there was a pAE matrix added | |
402 | * @throws ParseException | |
403 | * @throws IOException | |
404 | * @throws Exception | |
405 | */ | |
406 | 42 | public static boolean importPaeJSONAsContactMatrixToSequence( |
407 | AlignmentI pdbAlignment, InputStream pae_input, int index, | |
408 | String seqId, String label) throws IOException, ParseException | |
409 | { | |
410 | 42 | SequenceI sequence = null; |
411 | 42 | if (seqId == null) |
412 | { | |
413 | 42 | int seqToGet = index > 0 ? index : 0; |
414 | 42 | sequence = pdbAlignment.getSequenceAt(seqToGet); |
415 | } | |
416 | 42 | if (sequence == null) |
417 | { | |
418 | 0 | SequenceI[] sequences = pdbAlignment.findSequenceMatch(seqId); |
419 | 0 | if (sequences == null || sequences.length < 1) |
420 | { | |
421 | 0 | Console.warn("Could not find sequence with id '" + seqId |
422 | + "' to attach pAE matrix to. Ignoring matrix."); | |
423 | 0 | return false; |
424 | } | |
425 | else | |
426 | { | |
427 | 0 | sequence = sequences[0]; // just use the first sequence with this seqId |
428 | } | |
429 | } | |
430 | 42 | if (sequence == null) |
431 | { | |
432 | 0 | return false; |
433 | } | |
434 | 42 | return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input, |
435 | sequence, label); | |
436 | } | |
437 | ||
438 | 42 | public static boolean importPaeJSONAsContactMatrixToSequence( |
439 | AlignmentI pdbAlignment, InputStream pae_input, | |
440 | SequenceI sequence, String label) | |
441 | throws IOException, ParseException | |
442 | { | |
443 | 42 | JSONObject paeDict = parseJSONtoPAEContactMatrix(pae_input); |
444 | 42 | if (paeDict == null) |
445 | { | |
446 | 0 | Console.debug("JSON file did not parse properly."); |
447 | 0 | return false; |
448 | } | |
449 | 42 | ContactMatrixI matrix = new PAEContactMatrix(sequence, |
450 | (Map<String, Object>) paeDict); | |
451 | ||
452 | 42 | AlignmentAnnotation cmannot = sequence.addContactList(matrix); |
453 | 42 | if (label != null) |
454 | 0 | cmannot.label = label; |
455 | 42 | pdbAlignment.addAnnotation(cmannot); |
456 | ||
457 | 42 | return true; |
458 | } | |
459 | ||
460 | 48 | public static JSONObject parseJSONtoPAEContactMatrix( |
461 | InputStream pae_input) throws IOException, ParseException | |
462 | { | |
463 | 48 | Object paeJson = Platform.parseJSON(pae_input); |
464 | 48 | JSONObject paeDict = null; |
465 | 48 | if (paeJson instanceof JSONObject) |
466 | { | |
467 | 15 | paeDict = (JSONObject) paeJson; |
468 | } | |
469 | 33 | else if (paeJson instanceof JSONArray) |
470 | { | |
471 | 33 | JSONArray jsonArray = (JSONArray) paeJson; |
472 | 33 | if (jsonArray.size() > 0) |
473 | 33 | paeDict = (JSONObject) jsonArray.get(0); |
474 | } | |
475 | ||
476 | 48 | return paeDict; |
477 | } | |
478 | ||
479 | // ###### TEST THIS | |
480 | 3 | public static boolean importPaeJSONAsContactMatrixToStructure( |
481 | StructureMapping[] smArray, InputStream paeInput, String label) | |
482 | throws IOException, ParseException | |
483 | { | |
484 | 3 | boolean someDone = false; |
485 | 3 | for (StructureMapping sm : smArray) |
486 | { | |
487 | 3 | boolean thisDone = importPaeJSONAsContactMatrixToStructure(sm, |
488 | paeInput, label); | |
489 | 3 | someDone |= thisDone; |
490 | } | |
491 | 3 | return someDone; |
492 | } | |
493 | ||
494 | 3 | public static boolean importPaeJSONAsContactMatrixToStructure( |
495 | StructureMapping sm, InputStream paeInput, String label) | |
496 | throws IOException, ParseException | |
497 | { | |
498 | 3 | JSONObject pae_obj = parseJSONtoPAEContactMatrix(paeInput); |
499 | 3 | if (pae_obj == null) |
500 | { | |
501 | 0 | Console.debug("JSON file did not parse properly."); |
502 | 0 | return false; |
503 | } | |
504 | ||
505 | 3 | SequenceI seq = sm.getSequence(); |
506 | 3 | ContactMatrixI matrix = new PAEContactMatrix(seq, |
507 | (Map<String, Object>) pae_obj); | |
508 | 3 | AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix); |
509 | /* this already happens in Sequence.addContactList() | |
510 | seq.addAlignmentAnnotation(cmannot); | |
511 | */ | |
512 | 3 | return true; |
513 | } | |
514 | ||
515 | /** | |
516 | * general purpose structure importer - designed to yield alignment useful for | |
517 | * transfer of annotation to associated sequences | |
518 | * | |
519 | * @param alphaFoldCif | |
520 | * @param tmpFile | |
521 | * @param id | |
522 | * @param chain | |
523 | * @param dbSource | |
524 | * @param dbVersion | |
525 | * @return | |
526 | * @throws Exception | |
527 | */ | |
528 | 0 | public static AlignmentI importDownloadedStructureFromUrl( |
529 | String alphaFoldCif, File tmpFile, String id, String chain, | |
530 | String dbSource, String dbVersion) throws Exception | |
531 | { | |
532 | 0 | String file = tmpFile.getAbsolutePath(); |
533 | // todo get rid of Type and use FileFormatI instead? | |
534 | 0 | FileFormatI fileFormat = FileFormat.MMCif; |
535 | 0 | TFType tempfacType = TFType.PLDDT; |
536 | 0 | AlignmentI pdbAlignment = new FormatAdapter().readFile(tmpFile, file, |
537 | DataSourceType.FILE, fileFormat, tempfacType); | |
538 | ||
539 | 0 | if (pdbAlignment != null) |
540 | { | |
541 | 0 | List<SequenceI> toremove = new ArrayList<SequenceI>(); |
542 | 0 | for (SequenceI pdbcs : pdbAlignment.getSequences()) |
543 | { | |
544 | 0 | String chid = null; |
545 | // Mapping map=null; | |
546 | 0 | for (PDBEntry pid : pdbcs.getAllPDBEntries()) |
547 | { | |
548 | 0 | if (pid.getFile() == file) |
549 | { | |
550 | 0 | chid = pid.getChainCode(); |
551 | } | |
552 | } | |
553 | 0 | if (chain == null || (chid != null && (chid.equals(chain) |
554 | || chid.trim().equals(chain.trim()) | |
555 | || (chain.trim().length() == 0 && chid.equals("_"))))) | |
556 | { | |
557 | // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant. | |
558 | // TODO: suggest simplify naming to 1qip|A as default name defined | |
559 | 0 | pdbcs.setName(id + SEPARATOR + pdbcs.getName()); |
560 | // Might need to add more metadata to the PDBEntry object | |
561 | // like below | |
562 | /* | |
563 | * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry | |
564 | * entry.setId(id); if (entry.getProperty() == null) | |
565 | * entry.setProperty(new Hashtable()); | |
566 | * entry.getProperty().put("chains", pdbchain.id + "=" + | |
567 | * sq.getStart() + "-" + sq.getEnd()); | |
568 | * sq.getDatasetSequence().addPDBId(entry); | |
569 | */ | |
570 | // Add PDB DB Refs | |
571 | // We make a DBRefEtntry because we have obtained the PDB file from | |
572 | // a | |
573 | // verifiable source | |
574 | // JBPNote - PDB DBRefEntry should also carry the chain and mapping | |
575 | // information | |
576 | 0 | if (dbSource != null) |
577 | { | |
578 | 0 | DBRefEntry dbentry = new DBRefEntry(dbSource, |
579 | ||
580 | 0 | dbVersion, (chid == null ? id : id + chid)); |
581 | // dbentry.setMap() | |
582 | 0 | pdbcs.addDBRef(dbentry); |
583 | // update any feature groups | |
584 | 0 | List<SequenceFeature> allsf = pdbcs.getFeatures() |
585 | .getAllFeatures(); | |
586 | 0 | List<SequenceFeature> newsf = new ArrayList<SequenceFeature>(); |
587 | 0 | if (allsf != null && allsf.size() > 0) |
588 | { | |
589 | 0 | for (SequenceFeature f : allsf) |
590 | { | |
591 | 0 | if (file.equals(f.getFeatureGroup())) |
592 | { | |
593 | 0 | f = new SequenceFeature(f, f.type, f.begin, f.end, id, |
594 | f.score); | |
595 | } | |
596 | 0 | newsf.add(f); |
597 | } | |
598 | 0 | pdbcs.setSequenceFeatures(newsf); |
599 | } | |
600 | } | |
601 | } | |
602 | else | |
603 | { | |
604 | // mark this sequence to be removed from the alignment | |
605 | // - since it's not from the right chain | |
606 | 0 | toremove.add(pdbcs); |
607 | } | |
608 | } | |
609 | // now remove marked sequences | |
610 | 0 | for (SequenceI pdbcs : toremove) |
611 | { | |
612 | 0 | pdbAlignment.deleteSequence(pdbcs); |
613 | 0 | if (pdbcs.getAnnotation() != null) |
614 | { | |
615 | 0 | for (AlignmentAnnotation aa : pdbcs.getAnnotation()) |
616 | { | |
617 | 0 | pdbAlignment.deleteAnnotation(aa); |
618 | } | |
619 | } | |
620 | } | |
621 | } | |
622 | 0 | return pdbAlignment; |
623 | } | |
624 | ||
625 | /* | |
626 | * (non-Javadoc) | |
627 | * | |
628 | * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String) | |
629 | */ | |
630 | 0 | @Override |
631 | public boolean isValidReference(String accession) | |
632 | { | |
633 | 0 | Regex r = getAccessionValidator(); |
634 | 0 | return r.search(accession.trim()); |
635 | } | |
636 | ||
637 | /** | |
638 | * human glyoxalase | |
639 | */ | |
640 | 0 | @Override |
641 | public String getTestQuery() | |
642 | { | |
643 | 0 | return "AF-O15552-F1"; |
644 | } | |
645 | ||
646 | 0 | @Override |
647 | public String getDbName() | |
648 | { | |
649 | 0 | return "ALPHAFOLD"; // getDbSource(); |
650 | } | |
651 | ||
652 | 0 | @Override |
653 | public int getTier() | |
654 | { | |
655 | 0 | return 0; |
656 | } | |
657 | ||
658 | /** | |
659 | * Returns a descriptor for suitable feature display settings with | |
660 | * <ul> | |
661 | * <li>ResNums or insertions features visible</li> | |
662 | * <li>insertions features coloured red</li> | |
663 | * <li>ResNum features coloured by label</li> | |
664 | * <li>Insertions displayed above (on top of) ResNums</li> | |
665 | * </ul> | |
666 | */ | |
667 | 0 | @Override |
668 | public FeatureSettingsModelI getFeatureColourScheme() | |
669 | { | |
670 | 0 | return new PDBFeatureSettings(); |
671 | } | |
672 | ||
673 | // days * 86400000 | |
674 | private static final long PAE_CACHE_STALE_TIME = 1 * 86400000; | |
675 | ||
676 | private static Map<String, File> paeDownloadCache = new HashMap<>(); | |
677 | ||
678 | } |