Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
SequenceFetcher | 69 | 308 | 108 | ||
SequenceFetcher.StringPair | 71 | 7 | 6 |
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.gui; | |
22 | ||
23 | import java.awt.BorderLayout; | |
24 | import java.awt.Font; | |
25 | import java.awt.event.ActionEvent; | |
26 | import java.awt.event.ActionListener; | |
27 | import java.awt.event.KeyAdapter; | |
28 | import java.awt.event.KeyEvent; | |
29 | import java.util.ArrayList; | |
30 | import java.util.Arrays; | |
31 | import java.util.HashSet; | |
32 | import java.util.Iterator; | |
33 | import java.util.List; | |
34 | ||
35 | import javax.swing.JButton; | |
36 | import javax.swing.JCheckBox; | |
37 | import javax.swing.JComboBox; | |
38 | import javax.swing.JInternalFrame; | |
39 | import javax.swing.JLabel; | |
40 | import javax.swing.JPanel; | |
41 | import javax.swing.JScrollPane; | |
42 | import javax.swing.JTextArea; | |
43 | import javax.swing.SwingConstants; | |
44 | ||
45 | import jalview.api.FeatureSettingsModelI; | |
46 | import jalview.bin.Cache; | |
47 | import jalview.bin.Console; | |
48 | import jalview.datamodel.AlignmentI; | |
49 | import jalview.datamodel.DBRefEntry; | |
50 | import jalview.datamodel.SequenceI; | |
51 | import jalview.fts.core.GFTSPanel; | |
52 | import jalview.fts.service.pdb.PDBFTSPanel; | |
53 | import jalview.fts.service.threedbeacons.TDBeaconsFTSPanel; | |
54 | import jalview.fts.service.uniprot.UniprotFTSPanel; | |
55 | import jalview.io.FileFormatI; | |
56 | import jalview.io.gff.SequenceOntologyI; | |
57 | import jalview.util.DBRefUtils; | |
58 | import jalview.util.MessageManager; | |
59 | import jalview.util.Platform; | |
60 | import jalview.ws.seqfetcher.DbSourceProxy; | |
61 | ||
62 | /** | |
63 | * A panel where the use may choose a database source, and enter one or more | |
64 | * accessions, to retrieve entries from the database. | |
65 | * <p> | |
66 | * If the selected source is Uniprot or PDB, a free text search panel is opened | |
67 | * instead to perform the search and selection. | |
68 | */ | |
69 | public class SequenceFetcher extends JPanel implements Runnable | |
70 | { | |
71 | private class StringPair | |
72 | { | |
73 | private String key; | |
74 | ||
75 | private String display; | |
76 | ||
77 | 0 | public StringPair(String s1, String s2) |
78 | { | |
79 | 0 | key = s1; |
80 | 0 | display = s2; |
81 | } | |
82 | ||
83 | 0 | public StringPair(String s) |
84 | { | |
85 | 0 | this(s, s); |
86 | } | |
87 | ||
88 | 0 | public String getKey() |
89 | { | |
90 | 0 | return key; |
91 | } | |
92 | ||
93 | 0 | public String getDisplay() |
94 | { | |
95 | 0 | return display; |
96 | } | |
97 | ||
98 | 0 | @Override |
99 | public String toString() | |
100 | { | |
101 | 0 | return display; |
102 | } | |
103 | ||
104 | 0 | public boolean equals(StringPair other) |
105 | { | |
106 | 0 | return other.key == this.key; |
107 | } | |
108 | } | |
109 | ||
110 | private static jalview.ws.SequenceFetcher sfetch = null; | |
111 | ||
112 | JLabel exampleAccession; | |
113 | ||
114 | JComboBox<StringPair> database; | |
115 | ||
116 | JCheckBox replacePunctuation; | |
117 | ||
118 | JButton okBtn; | |
119 | ||
120 | JButton exampleBtn; | |
121 | ||
122 | JButton closeBtn; | |
123 | ||
124 | JButton backBtn; | |
125 | ||
126 | JTextArea textArea; | |
127 | ||
128 | JInternalFrame frame; | |
129 | ||
130 | IProgressIndicator guiWindow; | |
131 | ||
132 | AlignFrame alignFrame; | |
133 | ||
134 | GFTSPanel parentSearchPanel; | |
135 | ||
136 | IProgressIndicator progressIndicator; | |
137 | ||
138 | volatile boolean _isConstructing = false; | |
139 | ||
140 | /** | |
141 | * Returns the shared instance of the SequenceFetcher client | |
142 | * | |
143 | * @return | |
144 | */ | |
145 | 2694 | public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton() |
146 | { | |
147 | 2694 | if (sfetch == null) |
148 | { | |
149 | 6 | sfetch = new jalview.ws.SequenceFetcher(); |
150 | } | |
151 | 2694 | return sfetch; |
152 | } | |
153 | ||
154 | /** | |
155 | * Constructor given a client to receive any status or progress messages | |
156 | * (currently either the Desktop, or an AlignFrame panel) | |
157 | * | |
158 | * @param guiIndic | |
159 | */ | |
160 | 0 | public SequenceFetcher(IProgressIndicator guiIndic) |
161 | { | |
162 | 0 | this(guiIndic, null, null); |
163 | } | |
164 | ||
165 | /** | |
166 | * Constructor with specified database and accession(s) to retrieve | |
167 | * | |
168 | * @param guiIndic | |
169 | * @param selectedDb | |
170 | * @param queryString | |
171 | */ | |
172 | 0 | public SequenceFetcher(IProgressIndicator guiIndic, |
173 | final String selectedDb, final String queryString) | |
174 | { | |
175 | 0 | this.progressIndicator = guiIndic; |
176 | 0 | getSequenceFetcherSingleton(); |
177 | 0 | this.guiWindow = progressIndicator; |
178 | ||
179 | 0 | if (progressIndicator instanceof AlignFrame) |
180 | { | |
181 | 0 | alignFrame = (AlignFrame) progressIndicator; |
182 | } | |
183 | ||
184 | 0 | jbInit(selectedDb); |
185 | 0 | textArea.setText(queryString); |
186 | ||
187 | 0 | frame = new JInternalFrame(); |
188 | 0 | frame.setContentPane(this); |
189 | 0 | frame.setFrameIcon(null); |
190 | 0 | Desktop.addInternalFrame(frame, getFrameTitle(), true, 400, |
191 | 0 | Platform.isAMacAndNotJS() ? 240 : 180); |
192 | } | |
193 | ||
194 | 0 | private String getFrameTitle() |
195 | { | |
196 | 0 | return ((alignFrame == null) |
197 | ? MessageManager.getString("label.new_sequence_fetcher") | |
198 | : MessageManager | |
199 | .getString("label.additional_sequence_fetcher")); | |
200 | } | |
201 | ||
202 | 0 | private void jbInit(String selectedDb) |
203 | { | |
204 | 0 | this.setLayout(new BorderLayout()); |
205 | ||
206 | 0 | database = new JComboBox<>(); |
207 | 0 | database.setFont(JvSwingUtils.getLabelFont()); |
208 | 0 | StringPair instructionItem = new StringPair( |
209 | MessageManager.getString("action.select_ddbb")); | |
210 | 0 | database.setPrototypeDisplayValue(instructionItem); |
211 | 0 | String[] sources = new jalview.ws.SequenceFetcher().getSupportedDb(); |
212 | 0 | Arrays.sort(sources, String.CASE_INSENSITIVE_ORDER); |
213 | 0 | database.addItem(instructionItem); |
214 | 0 | for (String source : sources) |
215 | { | |
216 | 0 | List<DbSourceProxy> slist = sfetch.getSourceProxy(source); |
217 | 0 | if (slist.size() == 1 && slist.get(0) != null) |
218 | { | |
219 | 0 | database.addItem(new StringPair(source, slist.get(0).getDbName())); |
220 | } | |
221 | else | |
222 | { | |
223 | 0 | database.addItem(new StringPair(source)); |
224 | } | |
225 | } | |
226 | 0 | setDatabaseSelectedItem(selectedDb); |
227 | 0 | if (database.getSelectedIndex() == -1) |
228 | { | |
229 | 0 | database.setSelectedIndex(0); |
230 | } | |
231 | 0 | database.setMaximumRowCount(database.getItemCount()); |
232 | 0 | database.addActionListener(new ActionListener() |
233 | { | |
234 | 0 | @Override |
235 | public void actionPerformed(ActionEvent e) | |
236 | { | |
237 | 0 | String currentSelection = ((StringPair) database.getSelectedItem()) |
238 | .getKey(); | |
239 | 0 | updateExampleQuery(currentSelection); |
240 | ||
241 | 0 | if ("pdb".equalsIgnoreCase(currentSelection)) |
242 | { | |
243 | 0 | frame.dispose(); |
244 | 0 | new PDBFTSPanel(SequenceFetcher.this); |
245 | } | |
246 | 0 | else if ("uniprot".equalsIgnoreCase(currentSelection)) |
247 | { | |
248 | 0 | frame.dispose(); |
249 | 0 | new UniprotFTSPanel(SequenceFetcher.this); |
250 | } | |
251 | 0 | else if ("3d-beacons".equalsIgnoreCase(currentSelection)) |
252 | { | |
253 | 0 | frame.dispose(); |
254 | 0 | new TDBeaconsFTSPanel(SequenceFetcher.this); |
255 | } | |
256 | else | |
257 | { | |
258 | 0 | otherSourceAction(); |
259 | } | |
260 | } | |
261 | }); | |
262 | ||
263 | 0 | exampleAccession = new JLabel(""); |
264 | 0 | exampleAccession.setFont(new Font("Verdana", Font.BOLD, 11)); |
265 | 0 | JLabel jLabel1 = new JLabel(MessageManager |
266 | .getString("label.separate_multiple_accession_ids")); | |
267 | 0 | jLabel1.setFont(new Font("Verdana", Font.ITALIC, 11)); |
268 | 0 | jLabel1.setHorizontalAlignment(SwingConstants.LEFT); |
269 | ||
270 | 0 | replacePunctuation = new JCheckBox( |
271 | MessageManager.getString("label.replace_commas_semicolons")); | |
272 | 0 | replacePunctuation.setHorizontalAlignment(SwingConstants.LEFT); |
273 | 0 | replacePunctuation.setFont(new Font("Verdana", Font.ITALIC, 11)); |
274 | 0 | okBtn = new JButton(MessageManager.getString("action.ok")); |
275 | 0 | okBtn.addActionListener(new ActionListener() |
276 | { | |
277 | 0 | @Override |
278 | public void actionPerformed(ActionEvent e) | |
279 | { | |
280 | 0 | ok_actionPerformed(); |
281 | } | |
282 | }); | |
283 | 0 | JButton clear = new JButton(MessageManager.getString("action.clear")); |
284 | 0 | clear.addActionListener(new ActionListener() |
285 | { | |
286 | 0 | @Override |
287 | public void actionPerformed(ActionEvent e) | |
288 | { | |
289 | 0 | clear_actionPerformed(); |
290 | } | |
291 | }); | |
292 | ||
293 | 0 | exampleBtn = new JButton(MessageManager.getString("label.example")); |
294 | 0 | exampleBtn.addActionListener(new ActionListener() |
295 | { | |
296 | 0 | @Override |
297 | public void actionPerformed(ActionEvent e) | |
298 | { | |
299 | 0 | example_actionPerformed(); |
300 | } | |
301 | }); | |
302 | 0 | closeBtn = new JButton(MessageManager.getString("action.cancel")); |
303 | 0 | closeBtn.addActionListener(new ActionListener() |
304 | { | |
305 | 0 | @Override |
306 | public void actionPerformed(ActionEvent e) | |
307 | { | |
308 | 0 | close_actionPerformed(e); |
309 | } | |
310 | }); | |
311 | 0 | backBtn = new JButton(MessageManager.getString("action.back")); |
312 | 0 | backBtn.addActionListener(new ActionListener() |
313 | { | |
314 | 0 | @Override |
315 | public void actionPerformed(ActionEvent e) | |
316 | { | |
317 | 0 | parentSearchPanel.btn_back_ActionPerformed(); |
318 | } | |
319 | }); | |
320 | // back not visible unless embedded | |
321 | 0 | backBtn.setVisible(false); |
322 | ||
323 | 0 | textArea = new JTextArea(); |
324 | 0 | textArea.setFont(JvSwingUtils.getLabelFont()); |
325 | 0 | textArea.setLineWrap(true); |
326 | 0 | textArea.addKeyListener(new KeyAdapter() |
327 | { | |
328 | 0 | @Override |
329 | public void keyPressed(KeyEvent e) | |
330 | { | |
331 | 0 | if (e.getKeyCode() == KeyEvent.VK_ENTER) |
332 | { | |
333 | 0 | ok_actionPerformed(); |
334 | } | |
335 | } | |
336 | }); | |
337 | ||
338 | 0 | JPanel actionPanel = new JPanel(); |
339 | 0 | actionPanel.add(backBtn); |
340 | 0 | actionPanel.add(exampleBtn); |
341 | 0 | actionPanel.add(clear); |
342 | 0 | actionPanel.add(okBtn); |
343 | 0 | actionPanel.add(closeBtn); |
344 | ||
345 | 0 | JPanel databasePanel = new JPanel(); |
346 | 0 | databasePanel.setLayout(new BorderLayout()); |
347 | 0 | databasePanel.add(database, BorderLayout.NORTH); |
348 | 0 | databasePanel.add(exampleAccession, BorderLayout.CENTER); |
349 | 0 | JPanel jPanel2a = new JPanel(new BorderLayout()); |
350 | 0 | jPanel2a.add(jLabel1, BorderLayout.NORTH); |
351 | 0 | jPanel2a.add(replacePunctuation, BorderLayout.SOUTH); |
352 | 0 | databasePanel.add(jPanel2a, BorderLayout.SOUTH); |
353 | ||
354 | 0 | JPanel idsPanel = new JPanel(); |
355 | 0 | idsPanel.setLayout(new BorderLayout(0, 5)); |
356 | 0 | JScrollPane jScrollPane1 = new JScrollPane(); |
357 | 0 | jScrollPane1.getViewport().add(textArea); |
358 | 0 | idsPanel.add(jScrollPane1, BorderLayout.CENTER); |
359 | ||
360 | 0 | this.add(actionPanel, BorderLayout.SOUTH); |
361 | 0 | this.add(idsPanel, BorderLayout.CENTER); |
362 | 0 | this.add(databasePanel, BorderLayout.NORTH); |
363 | } | |
364 | ||
365 | 0 | private void setDatabaseSelectedItem(String db) |
366 | { | |
367 | 0 | for (int i = 0; i < database.getItemCount(); i++) |
368 | { | |
369 | 0 | StringPair sp = database.getItemAt(i); |
370 | 0 | if (sp != null && db != null && db.equals(sp.getKey())) |
371 | { | |
372 | 0 | database.setSelectedIndex(i); |
373 | 0 | return; |
374 | } | |
375 | } | |
376 | } | |
377 | ||
378 | /** | |
379 | * Answers a semi-colon-delimited string with the example query or queries for | |
380 | * the selected database | |
381 | * | |
382 | * @param db | |
383 | * @return | |
384 | */ | |
385 | 0 | protected String getExampleQueries(String db) |
386 | { | |
387 | 0 | StringBuilder sb = new StringBuilder(); |
388 | 0 | HashSet<String> hs = new HashSet<>(); |
389 | 0 | for (DbSourceProxy dbs : sfetch.getSourceProxy(db)) |
390 | { | |
391 | 0 | String tq = dbs.getTestQuery(); |
392 | 0 | if (hs.add(tq)) // not a duplicate source |
393 | { | |
394 | 0 | if (sb.length() > 0) |
395 | { | |
396 | 0 | sb.append(";"); |
397 | } | |
398 | 0 | sb.append(tq); |
399 | } | |
400 | } | |
401 | 0 | return sb.toString(); |
402 | } | |
403 | ||
404 | /** | |
405 | * Action on selecting a database other than Uniprot or PDB is to enable or | |
406 | * disable 'Replace commas', and await input in the query field | |
407 | */ | |
408 | 0 | protected void otherSourceAction() |
409 | { | |
410 | 0 | try |
411 | { | |
412 | 0 | String eq = exampleAccession.getText(); |
413 | // TODO this should be a property of the SequenceFetcher whether commas | |
414 | // are allowed in the IDs... | |
415 | ||
416 | 0 | boolean enablePunct = !(eq != null && eq.indexOf(",") > -1); |
417 | 0 | replacePunctuation.setEnabled(enablePunct); |
418 | ||
419 | } catch (Exception ex) | |
420 | { | |
421 | 0 | exampleAccession.setText(""); |
422 | 0 | replacePunctuation.setEnabled(true); |
423 | } | |
424 | 0 | repaint(); |
425 | } | |
426 | ||
427 | /** | |
428 | * Sets the text of the example query to incorporate the example accession | |
429 | * provided by the selected database source | |
430 | * | |
431 | * @param selectedDatabase | |
432 | * @return | |
433 | */ | |
434 | 0 | protected String updateExampleQuery(String selectedDatabase) |
435 | { | |
436 | 0 | String eq = getExampleQueries(selectedDatabase); |
437 | 0 | exampleAccession.setText(MessageManager |
438 | .formatMessage("label.example_query_param", new String[] | |
439 | { eq })); | |
440 | 0 | return eq; |
441 | } | |
442 | ||
443 | /** | |
444 | * Action on clicking the 'Example' button is to write the example accession | |
445 | * as the query text field value | |
446 | */ | |
447 | 0 | protected void example_actionPerformed() |
448 | { | |
449 | 0 | String eq = getExampleQueries( |
450 | ((StringPair) database.getSelectedItem()).getKey()); | |
451 | 0 | textArea.setText(eq); |
452 | 0 | repaint(); |
453 | } | |
454 | ||
455 | /** | |
456 | * Clears the query input field | |
457 | */ | |
458 | 0 | protected void clear_actionPerformed() |
459 | { | |
460 | 0 | textArea.setText(""); |
461 | 0 | repaint(); |
462 | } | |
463 | ||
464 | /** | |
465 | * Action on Close button is to close this frame, and also (if it is embedded | |
466 | * in a search panel) to close the search panel | |
467 | * | |
468 | * @param e | |
469 | */ | |
470 | 0 | protected void close_actionPerformed(ActionEvent e) |
471 | { | |
472 | 0 | try |
473 | { | |
474 | 0 | frame.setClosed(true); |
475 | 0 | if (parentSearchPanel != null) |
476 | { | |
477 | 0 | parentSearchPanel.btn_cancel_ActionPerformed(); |
478 | } | |
479 | } catch (Exception ex) | |
480 | { | |
481 | } | |
482 | } | |
483 | ||
484 | /** | |
485 | * Action on OK is to start the fetch for entered accession(s) | |
486 | */ | |
487 | 0 | public void ok_actionPerformed() |
488 | { | |
489 | /* | |
490 | * tidy inputs and check there is something to search for | |
491 | */ | |
492 | 0 | String t0 = textArea.getText(); |
493 | 0 | String text = t0.trim(); |
494 | 0 | if (replacePunctuation.isEnabled() && replacePunctuation.isSelected()) |
495 | { | |
496 | 0 | text = text.replace(",", ";"); |
497 | } | |
498 | 0 | text = text.replaceAll("(\\s|[; ])+", ";"); |
499 | 0 | if (!t0.equals(text)) |
500 | { | |
501 | 0 | textArea.setText(text); |
502 | } | |
503 | 0 | if (text.isEmpty()) |
504 | { | |
505 | // todo i18n | |
506 | 0 | showErrorMessage( |
507 | "Please enter a (semi-colon separated list of) database id(s)"); | |
508 | 0 | resetDialog(); |
509 | 0 | return; |
510 | } | |
511 | 0 | if (database.getSelectedIndex() == 0) |
512 | { | |
513 | // todo i18n | |
514 | 0 | showErrorMessage("Please choose a database"); |
515 | 0 | resetDialog(); |
516 | 0 | return; |
517 | } | |
518 | ||
519 | 0 | exampleBtn.setEnabled(false); |
520 | 0 | textArea.setEnabled(false); |
521 | 0 | okBtn.setEnabled(false); |
522 | 0 | closeBtn.setEnabled(false); |
523 | 0 | backBtn.setEnabled(false); |
524 | ||
525 | 0 | Thread worker = new Thread(this); |
526 | 0 | worker.start(); |
527 | } | |
528 | ||
529 | 0 | private void resetDialog() |
530 | { | |
531 | 0 | exampleBtn.setEnabled(true); |
532 | 0 | textArea.setEnabled(true); |
533 | 0 | okBtn.setEnabled(true); |
534 | 0 | closeBtn.setEnabled(true); |
535 | 0 | backBtn.setEnabled(parentSearchPanel != null); |
536 | } | |
537 | ||
538 | 0 | @Override |
539 | public void run() | |
540 | { | |
541 | 0 | boolean addToLast = false; |
542 | 0 | List<String> aresultq = new ArrayList<>(); |
543 | 0 | List<String> presultTitle = new ArrayList<>(); |
544 | 0 | List<AlignmentI> presult = new ArrayList<>(); |
545 | 0 | List<AlignmentI> aresult = new ArrayList<>(); |
546 | 0 | List<DbSourceProxy> sources = sfetch.getSourceProxy( |
547 | ((StringPair) database.getSelectedItem()).getKey()); | |
548 | 0 | Iterator<DbSourceProxy> proxies = sources.iterator(); |
549 | 0 | String[] qries = textArea.getText().trim().split(";"); |
550 | 0 | List<String> nextFetch = Arrays.asList(qries); |
551 | 0 | Iterator<String> en = Arrays.asList(new String[0]).iterator(); |
552 | 0 | int nqueries = qries.length; |
553 | ||
554 | 0 | FeatureSettingsModelI preferredFeatureColours = null; |
555 | 0 | while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0)) |
556 | { | |
557 | 0 | if (!en.hasNext() && nextFetch.size() > 0) |
558 | { | |
559 | 0 | en = nextFetch.iterator(); |
560 | 0 | nqueries = nextFetch.size(); |
561 | // save the remaining queries in the original array | |
562 | 0 | qries = nextFetch.toArray(new String[nqueries]); |
563 | 0 | nextFetch = new ArrayList<>(); |
564 | } | |
565 | ||
566 | 0 | DbSourceProxy proxy = proxies.next(); |
567 | 0 | try |
568 | { | |
569 | // update status | |
570 | 0 | guiWindow.setProgressBar(MessageManager.formatMessage( |
571 | "status.fetching_sequence_queries_from", new String[] | |
572 | { Integer.valueOf(nqueries).toString(), | |
573 | proxy.getDbName() }), | |
574 | Thread.currentThread().hashCode()); | |
575 | 0 | if (proxy.getMaximumQueryCount() == 1) |
576 | { | |
577 | /* | |
578 | * proxy only handles one accession id at a time | |
579 | */ | |
580 | 0 | while (en.hasNext()) |
581 | { | |
582 | 0 | String acc = en.next(); |
583 | 0 | if (!fetchSingleAccession(proxy, acc, aresultq, aresult)) |
584 | { | |
585 | 0 | nextFetch.add(acc); |
586 | } | |
587 | } | |
588 | } | |
589 | else | |
590 | { | |
591 | /* | |
592 | * proxy can fetch multiple accessions at one time | |
593 | */ | |
594 | 0 | fetchMultipleAccessions(proxy, en, aresultq, aresult, nextFetch); |
595 | } | |
596 | } catch (Exception e) | |
597 | { | |
598 | 0 | showErrorMessage("Error retrieving " + textArea.getText() + " from " |
599 | + ((StringPair) database.getSelectedItem()).getDisplay()); | |
600 | // error | |
601 | // +="Couldn't retrieve sequences from "+database.getSelectedItem(); | |
602 | 0 | jalview.bin.Console.errPrintln("Retrieval failed for source ='" |
603 | + ((StringPair) database.getSelectedItem()).getDisplay() | |
604 | + "' and query\n'" + textArea.getText() + "'\n"); | |
605 | 0 | e.printStackTrace(); |
606 | } catch (OutOfMemoryError e) | |
607 | { | |
608 | 0 | showErrorMessage("Out of Memory when retrieving " |
609 | + textArea.getText() + " from " | |
610 | + ((StringPair) database.getSelectedItem()).getDisplay() | |
611 | + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n"); | |
612 | 0 | e.printStackTrace(); |
613 | } catch (Error e) | |
614 | { | |
615 | 0 | showErrorMessage("Serious Error retrieving " + textArea.getText() |
616 | + " from " | |
617 | + ((StringPair) database.getSelectedItem()).getDisplay()); | |
618 | 0 | e.printStackTrace(); |
619 | } | |
620 | ||
621 | // Stack results ready for opening in alignment windows | |
622 | 0 | if (aresult != null && aresult.size() > 0) |
623 | { | |
624 | 0 | FeatureSettingsModelI proxyColourScheme = proxy |
625 | .getFeatureColourScheme(); | |
626 | 0 | if (proxyColourScheme != null) |
627 | { | |
628 | 0 | preferredFeatureColours = proxyColourScheme; |
629 | } | |
630 | ||
631 | 0 | AlignmentI ar = null; |
632 | 0 | if (proxy.isAlignmentSource()) |
633 | { | |
634 | 0 | addToLast = false; |
635 | // new window for each result | |
636 | 0 | while (aresult.size() > 0) |
637 | { | |
638 | 0 | presult.add(aresult.remove(0)); |
639 | 0 | presultTitle.add( |
640 | aresultq.remove(0) + " " + getDefaultRetrievalTitle()); | |
641 | } | |
642 | } | |
643 | else | |
644 | { | |
645 | 0 | String titl = null; |
646 | 0 | if (addToLast && presult.size() > 0) |
647 | { | |
648 | 0 | ar = presult.remove(presult.size() - 1); |
649 | 0 | titl = presultTitle.remove(presultTitle.size() - 1); |
650 | } | |
651 | // concatenate all results in one window | |
652 | 0 | while (aresult.size() > 0) |
653 | { | |
654 | 0 | if (ar == null) |
655 | { | |
656 | 0 | ar = aresult.remove(0); |
657 | } | |
658 | else | |
659 | { | |
660 | 0 | ar.append(aresult.remove(0)); |
661 | } | |
662 | } | |
663 | 0 | addToLast = true; |
664 | 0 | presult.add(ar); |
665 | 0 | presultTitle.add(titl); |
666 | } | |
667 | } | |
668 | 0 | guiWindow.setProgressBar( |
669 | MessageManager.getString("status.finshed_querying"), | |
670 | Thread.currentThread().hashCode()); | |
671 | } | |
672 | 0 | guiWindow |
673 | .setProgressBar( | |
674 | 0 | (presult.size() > 0) |
675 | ? MessageManager | |
676 | .getString("status.parsing_results") | |
677 | : MessageManager.getString("status.processing"), | |
678 | Thread.currentThread().hashCode()); | |
679 | // process results | |
680 | 0 | while (presult.size() > 0) |
681 | { | |
682 | 0 | parseResult(presult.remove(0), presultTitle.remove(0), null, |
683 | preferredFeatureColours); | |
684 | } | |
685 | // only remove visual delay after we finished parsing. | |
686 | 0 | guiWindow.setProgressBar(null, Thread.currentThread().hashCode()); |
687 | 0 | if (nextFetch.size() > 0) |
688 | { | |
689 | 0 | StringBuffer sb = new StringBuffer(); |
690 | 0 | sb.append("Didn't retrieve the following " |
691 | 0 | + (nextFetch.size() == 1 ? "query" |
692 | : nextFetch.size() + " queries") | |
693 | + ": \n"); | |
694 | 0 | int l = sb.length(), lr = 0; |
695 | 0 | for (String s : nextFetch) |
696 | { | |
697 | 0 | if (l != sb.length()) |
698 | { | |
699 | 0 | sb.append("; "); |
700 | } | |
701 | 0 | if (lr - sb.length() > 40) |
702 | { | |
703 | 0 | sb.append("\n"); |
704 | } | |
705 | 0 | sb.append(s); |
706 | } | |
707 | 0 | showErrorMessage(sb.toString()); |
708 | } | |
709 | 0 | resetDialog(); |
710 | } | |
711 | ||
712 | /** | |
713 | * Tries to fetch one or more accession ids from the database proxy | |
714 | * | |
715 | * @param proxy | |
716 | * @param accessions | |
717 | * the queries to fetch | |
718 | * @param aresultq | |
719 | * a successful queries list to add to | |
720 | * @param aresult | |
721 | * a list of retrieved alignments to add to | |
722 | * @param nextFetch | |
723 | * failed queries are added to this list | |
724 | * @throws Exception | |
725 | */ | |
726 | 0 | void fetchMultipleAccessions(DbSourceProxy proxy, |
727 | Iterator<String> accessions, List<String> aresultq, | |
728 | List<AlignmentI> aresult, List<String> nextFetch) throws Exception | |
729 | { | |
730 | 0 | StringBuilder multiacc = new StringBuilder(); |
731 | 0 | List<String> tosend = new ArrayList<>(); |
732 | 0 | while (accessions.hasNext()) |
733 | { | |
734 | 0 | String nel = accessions.next(); |
735 | 0 | tosend.add(nel); |
736 | 0 | multiacc.append(nel); |
737 | 0 | if (accessions.hasNext()) |
738 | { | |
739 | 0 | multiacc.append(proxy.getAccessionSeparator()); |
740 | } | |
741 | } | |
742 | ||
743 | 0 | try |
744 | { | |
745 | 0 | String query = multiacc.toString(); |
746 | 0 | AlignmentI rslt = proxy.getSequenceRecords(query); |
747 | 0 | if (rslt == null || rslt.getHeight() == 0) |
748 | { | |
749 | // no results - pass on all queries to next source | |
750 | 0 | nextFetch.addAll(tosend); |
751 | } | |
752 | else | |
753 | { | |
754 | 0 | aresultq.add(query); |
755 | 0 | aresult.add(rslt); |
756 | 0 | if (tosend.size() > 1) |
757 | { | |
758 | 0 | checkResultForQueries(rslt, tosend, nextFetch, proxy); |
759 | } | |
760 | } | |
761 | } catch (OutOfMemoryError oome) | |
762 | { | |
763 | 0 | new OOMWarning("fetching " + multiacc + " from " |
764 | + ((StringPair) database.getSelectedItem()).getDisplay(), | |
765 | oome, this); | |
766 | } | |
767 | } | |
768 | ||
769 | /** | |
770 | * Query for a single accession id via the database proxy | |
771 | * | |
772 | * @param proxy | |
773 | * @param accession | |
774 | * @param aresultq | |
775 | * a list of successful queries to add to | |
776 | * @param aresult | |
777 | * a list of retrieved alignments to add to | |
778 | * @return true if the fetch was successful, else false | |
779 | */ | |
780 | 0 | boolean fetchSingleAccession(DbSourceProxy proxy, String accession, |
781 | List<String> aresultq, List<AlignmentI> aresult) | |
782 | { | |
783 | 0 | boolean success = false; |
784 | 0 | try |
785 | { | |
786 | 0 | if (aresult != null) |
787 | { | |
788 | 0 | try |
789 | { | |
790 | // give the server a chance to breathe | |
791 | 0 | Thread.sleep(5); |
792 | } catch (Exception e) | |
793 | { | |
794 | // | |
795 | } | |
796 | } | |
797 | ||
798 | 0 | AlignmentI indres = null; |
799 | 0 | try |
800 | { | |
801 | 0 | indres = proxy.getSequenceRecords(accession); |
802 | } catch (OutOfMemoryError oome) | |
803 | { | |
804 | 0 | new OOMWarning( |
805 | "fetching " + accession + " from " + proxy.getDbName(), | |
806 | oome, this); | |
807 | } | |
808 | 0 | if (indres != null) |
809 | { | |
810 | 0 | aresultq.add(accession); |
811 | 0 | aresult.add(indres); |
812 | 0 | success = true; |
813 | } | |
814 | } catch (Exception e) | |
815 | { | |
816 | 0 | Console.info("Error retrieving " + accession + " from " |
817 | + proxy.getDbName(), e); | |
818 | } | |
819 | 0 | return success; |
820 | } | |
821 | ||
822 | /** | |
823 | * Checks which of the queries were successfully retrieved by searching the | |
824 | * DBRefs of the retrieved sequences for a match. Any not found are added to | |
825 | * the 'nextFetch' list. | |
826 | * | |
827 | * @param rslt | |
828 | * @param queries | |
829 | * @param nextFetch | |
830 | * @param proxy | |
831 | */ | |
832 | 0 | void checkResultForQueries(AlignmentI rslt, List<String> queries, |
833 | List<String> nextFetch, DbSourceProxy proxy) | |
834 | { | |
835 | 0 | SequenceI[] rs = rslt.getSequencesArray(); |
836 | ||
837 | 0 | for (String q : queries) |
838 | { | |
839 | // BH 2019.01.25 dbr is never used. | |
840 | // DBRefEntry dbr = new DBRefEntry(); | |
841 | // dbr.setSource(proxy.getDbSource()); | |
842 | // dbr.setVersion(null); | |
843 | 0 | String accId = proxy.getAccessionIdFromQuery(q); |
844 | // dbr.setAccessionId(accId); | |
845 | 0 | boolean rfound = false; |
846 | 0 | for (int r = 0, nr = rs.length; r < nr; r++) |
847 | { | |
848 | 0 | if (rs[r] != null) |
849 | { | |
850 | 0 | List<DBRefEntry> found = DBRefUtils.searchRefs(rs[r].getDBRefs(), |
851 | accId); | |
852 | 0 | if (!found.isEmpty()) |
853 | { | |
854 | 0 | rfound = true; |
855 | 0 | break; |
856 | } | |
857 | } | |
858 | } | |
859 | 0 | if (!rfound) |
860 | { | |
861 | 0 | nextFetch.add(q); |
862 | } | |
863 | } | |
864 | } | |
865 | ||
866 | /** | |
867 | * | |
868 | * @return a standard title for any results retrieved using the currently | |
869 | * selected source and settings | |
870 | */ | |
871 | 0 | public String getDefaultRetrievalTitle() |
872 | { | |
873 | 0 | return "Retrieved from " |
874 | + ((StringPair) database.getSelectedItem()).getDisplay(); | |
875 | } | |
876 | ||
877 | /** | |
878 | * constructs an alignment frame given the data and metadata | |
879 | * | |
880 | * @param al | |
881 | * @param title | |
882 | * @param currentFileFormat | |
883 | * @param preferredFeatureColours | |
884 | * @return the alignment | |
885 | */ | |
886 | 0 | public AlignmentI parseResult(AlignmentI al, String title, |
887 | FileFormatI currentFileFormat, | |
888 | FeatureSettingsModelI preferredFeatureColours) | |
889 | { | |
890 | ||
891 | 0 | if (al != null && al.getHeight() > 0) |
892 | { | |
893 | 0 | if (title == null) |
894 | { | |
895 | 0 | title = getDefaultRetrievalTitle(); |
896 | } | |
897 | 0 | if (alignFrame == null) |
898 | { | |
899 | 0 | AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, |
900 | AlignFrame.DEFAULT_HEIGHT); | |
901 | 0 | if (currentFileFormat != null) |
902 | { | |
903 | 0 | af.currentFileFormat = currentFileFormat; |
904 | } | |
905 | ||
906 | 0 | List<SequenceI> alsqs = al.getSequences(); |
907 | 0 | synchronized (alsqs) |
908 | { | |
909 | 0 | for (SequenceI sq : alsqs) |
910 | { | |
911 | 0 | if (sq.getFeatures().hasFeatures()) |
912 | { | |
913 | 0 | af.setShowSeqFeatures(true); |
914 | 0 | break; |
915 | } | |
916 | } | |
917 | } | |
918 | ||
919 | 0 | af.getViewport().applyFeaturesStyle(preferredFeatureColours); |
920 | 0 | if (Cache.getDefault("HIDE_INTRONS", true)) |
921 | { | |
922 | 0 | af.hideFeatureColumns(SequenceOntologyI.EXON, false); |
923 | } | |
924 | 0 | Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH, |
925 | AlignFrame.DEFAULT_HEIGHT); | |
926 | ||
927 | 0 | af.setStatus(MessageManager |
928 | .getString("label.successfully_pasted_alignment_file")); | |
929 | ||
930 | 0 | try |
931 | { | |
932 | 0 | af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false)); |
933 | } catch (Exception ex) | |
934 | { | |
935 | } | |
936 | } | |
937 | else | |
938 | { | |
939 | 0 | alignFrame.viewport.addAlignment(al, title); |
940 | } | |
941 | } | |
942 | 0 | return al; |
943 | } | |
944 | ||
945 | 0 | void showErrorMessage(final String error) |
946 | { | |
947 | 0 | resetDialog(); |
948 | 0 | javax.swing.SwingUtilities.invokeLater(new Runnable() |
949 | { | |
950 | 0 | @Override |
951 | public void run() | |
952 | { | |
953 | 0 | JvOptionPane.showInternalMessageDialog(Desktop.desktop, error, |
954 | MessageManager.getString("label.error_retrieving_data"), | |
955 | JvOptionPane.WARNING_MESSAGE); | |
956 | } | |
957 | }); | |
958 | } | |
959 | ||
960 | 0 | public IProgressIndicator getProgressIndicator() |
961 | { | |
962 | 0 | return progressIndicator; |
963 | } | |
964 | ||
965 | 0 | public void setProgressIndicator(IProgressIndicator progressIndicator) |
966 | { | |
967 | 0 | this.progressIndicator = progressIndicator; |
968 | } | |
969 | ||
970 | /** | |
971 | * Hide this panel (on clicking the database button to open the database | |
972 | * chooser) | |
973 | */ | |
974 | 0 | void hidePanel() |
975 | { | |
976 | 0 | frame.setVisible(false); |
977 | } | |
978 | ||
979 | 0 | public void setQuery(String ids) |
980 | { | |
981 | 0 | textArea.setText(ids); |
982 | } | |
983 | ||
984 | /** | |
985 | * Called to modify the search panel for embedding as an alternative tab of a | |
986 | * free text search panel. The database choice list is hidden (since the | |
987 | * choice has been made), and a Back button is made visible (which reopens the | |
988 | * Sequence Fetcher panel). | |
989 | * | |
990 | * @param parentPanel | |
991 | */ | |
992 | 0 | public void embedIn(GFTSPanel parentPanel) |
993 | { | |
994 | 0 | database.setVisible(false); |
995 | 0 | backBtn.setVisible(true); |
996 | 0 | parentSearchPanel = parentPanel; |
997 | } | |
998 | } |