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AAStructureBindingModel | 81 | 512 | 252 | ||
AAStructureBindingModel.SuperposeData | 88 | 2 | 1 |
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.structures.models; | |
22 | ||
23 | import java.awt.Color; | |
24 | import java.io.File; | |
25 | import java.io.IOException; | |
26 | import java.util.ArrayList; | |
27 | import java.util.Arrays; | |
28 | import java.util.BitSet; | |
29 | import java.util.Collections; | |
30 | import java.util.HashMap; | |
31 | import java.util.LinkedHashMap; | |
32 | import java.util.List; | |
33 | import java.util.Locale; | |
34 | import java.util.Map; | |
35 | ||
36 | import javax.swing.SwingUtilities; | |
37 | ||
38 | import jalview.api.AlignViewportI; | |
39 | import jalview.api.AlignmentViewPanel; | |
40 | import jalview.api.FeatureRenderer; | |
41 | import jalview.api.SequenceRenderer; | |
42 | import jalview.api.StructureSelectionManagerProvider; | |
43 | import jalview.api.structures.JalviewStructureDisplayI; | |
44 | import jalview.bin.Console; | |
45 | import jalview.datamodel.AlignmentI; | |
46 | import jalview.datamodel.ColumnSelection; | |
47 | import jalview.datamodel.HiddenColumns; | |
48 | import jalview.datamodel.MappedFeatures; | |
49 | import jalview.datamodel.PDBEntry; | |
50 | import jalview.datamodel.SequenceFeature; | |
51 | import jalview.datamodel.SequenceI; | |
52 | import jalview.ext.rbvi.chimera.JalviewChimeraBinding; | |
53 | import jalview.gui.AlignmentPanel; | |
54 | import jalview.gui.Desktop; | |
55 | import jalview.gui.StructureViewer.ViewerType; | |
56 | import jalview.io.DataSourceType; | |
57 | import jalview.io.StructureFile; | |
58 | import jalview.renderer.seqfeatures.FeatureColourFinder; | |
59 | import jalview.schemes.ColourSchemeI; | |
60 | import jalview.schemes.ResidueProperties; | |
61 | import jalview.structure.AtomSpec; | |
62 | import jalview.structure.AtomSpecModel; | |
63 | import jalview.structure.StructureCommandI; | |
64 | import jalview.structure.StructureCommandsI; | |
65 | import jalview.structure.StructureCommandsI.AtomSpecType; | |
66 | import jalview.structure.StructureListener; | |
67 | import jalview.structure.StructureMapping; | |
68 | import jalview.structure.StructureSelectionManager; | |
69 | import jalview.util.Comparison; | |
70 | import jalview.util.MessageManager; | |
71 | ||
72 | /** | |
73 | * | |
74 | * A base class to hold common function for 3D structure model binding. Initial | |
75 | * version created by refactoring JMol and Chimera binding models, but other | |
76 | * structure viewers could in principle be accommodated in future. | |
77 | * | |
78 | * @author gmcarstairs | |
79 | * | |
80 | */ | |
81 | public abstract class AAStructureBindingModel | |
82 | extends SequenceStructureBindingModel | |
83 | implements StructureListener, StructureSelectionManagerProvider | |
84 | { | |
85 | /** | |
86 | * Data bean class to simplify parameterisation in superposeStructures | |
87 | */ | |
88 | public static class SuperposeData | |
89 | { | |
90 | public String filename; | |
91 | ||
92 | public String pdbId; | |
93 | ||
94 | public String chain = ""; | |
95 | ||
96 | /** | |
97 | * is the mapped sequence not protein ? | |
98 | */ | |
99 | public boolean isRna; | |
100 | ||
101 | /* | |
102 | * The pdb residue number (if any) mapped to columns of the alignment | |
103 | */ | |
104 | public int[] pdbResNo; // or use SparseIntArray? | |
105 | ||
106 | public String modelId; | |
107 | ||
108 | /** | |
109 | * Constructor | |
110 | * | |
111 | * @param width | |
112 | * width of alignment (number of columns that may potentially | |
113 | * participate in superposition) | |
114 | * @param model | |
115 | * structure viewer model number | |
116 | */ | |
117 | 9 | public SuperposeData(int width, String model) |
118 | { | |
119 | 9 | pdbResNo = new int[width]; |
120 | 9 | modelId = model; |
121 | } | |
122 | } | |
123 | ||
124 | private static final int MIN_POS_TO_SUPERPOSE = 4; | |
125 | ||
126 | private static final String COLOURING_STRUCTURES = MessageManager | |
127 | .getString("status.colouring_structures"); | |
128 | ||
129 | /* | |
130 | * the Jalview panel through which the user interacts | |
131 | * with the structure viewer | |
132 | */ | |
133 | private JalviewStructureDisplayI viewer; | |
134 | ||
135 | /* | |
136 | * helper that generates command syntax | |
137 | */ | |
138 | private StructureCommandsI commandGenerator; | |
139 | ||
140 | private StructureSelectionManager ssm; | |
141 | ||
142 | /* | |
143 | * modelled chains, formatted as "pdbid:chainCode" | |
144 | */ | |
145 | private List<String> chainNames; | |
146 | ||
147 | /* | |
148 | * lookup of pdb file name by key "pdbid:chainCode" | |
149 | */ | |
150 | private Map<String, String> chainFile; | |
151 | ||
152 | /* | |
153 | * distinct PDB entries (pdb files) associated | |
154 | * with sequences | |
155 | */ | |
156 | private PDBEntry[] pdbEntry; | |
157 | ||
158 | /* | |
159 | * sequences mapped to each pdbentry | |
160 | */ | |
161 | private SequenceI[][] sequence; | |
162 | ||
163 | /* | |
164 | * array of target chains for sequences - tied to pdbentry and sequence[] | |
165 | */ | |
166 | private String[][] chains; | |
167 | ||
168 | /* | |
169 | * datasource protocol for access to PDBEntrylatest | |
170 | */ | |
171 | DataSourceType protocol = null; | |
172 | ||
173 | protected boolean colourBySequence = true; | |
174 | ||
175 | /** | |
176 | * true if all sequences appear to be nucleotide | |
177 | */ | |
178 | private boolean nucleotide; | |
179 | ||
180 | private boolean finishedInit = false; | |
181 | ||
182 | /** | |
183 | * current set of model filenames loaded in the viewer | |
184 | */ | |
185 | protected String[] modelFileNames = null; | |
186 | ||
187 | public String fileLoadingError; | |
188 | ||
189 | protected Thread externalViewerMonitor; | |
190 | ||
191 | /** | |
192 | * Constructor | |
193 | * | |
194 | * @param ssm | |
195 | * @param seqs | |
196 | */ | |
197 | 51 | public AAStructureBindingModel(StructureSelectionManager ssm, |
198 | SequenceI[][] seqs) | |
199 | { | |
200 | 51 | this.ssm = ssm; |
201 | 51 | this.sequence = seqs; |
202 | 51 | chainNames = new ArrayList<>(); |
203 | 51 | chainFile = new HashMap<>(); |
204 | } | |
205 | ||
206 | /** | |
207 | * Constructor | |
208 | * | |
209 | * @param ssm | |
210 | * @param pdbentry | |
211 | * @param sequenceIs | |
212 | * @param protocol | |
213 | */ | |
214 | 51 | public AAStructureBindingModel(StructureSelectionManager ssm, |
215 | PDBEntry[] pdbentry, SequenceI[][] sequenceIs, | |
216 | DataSourceType protocol) | |
217 | { | |
218 | 51 | this(ssm, sequenceIs); |
219 | 51 | this.nucleotide = Comparison.isNucleotide(sequenceIs); |
220 | 51 | this.pdbEntry = pdbentry; |
221 | 51 | this.protocol = protocol; |
222 | 51 | resolveChains(); |
223 | } | |
224 | ||
225 | 51 | private boolean resolveChains() |
226 | { | |
227 | /** | |
228 | * final count of chain mappings discovered | |
229 | */ | |
230 | 51 | int chainmaps = 0; |
231 | // JBPNote: JAL-2693 - this should be a list of chain mappings per | |
232 | // [pdbentry][sequence] | |
233 | 51 | String[][] newchains = new String[pdbEntry.length][]; |
234 | 51 | int pe = 0; |
235 | 51 | for (PDBEntry pdb : pdbEntry) |
236 | { | |
237 | 60 | SequenceI[] seqsForPdb = sequence[pe]; |
238 | 60 | if (seqsForPdb != null) |
239 | { | |
240 | 60 | newchains[pe] = new String[seqsForPdb.length]; |
241 | 60 | int se = 0; |
242 | 60 | for (SequenceI asq : seqsForPdb) |
243 | { | |
244 | 72 | String chain = (chains != null && chains[pe] != null) |
245 | ? chains[pe][se] | |
246 | : null; | |
247 | 72 | SequenceI sq = (asq.getDatasetSequence() == null) ? asq |
248 | : asq.getDatasetSequence(); | |
249 | 72 | if (sq.getAllPDBEntries() != null) |
250 | { | |
251 | 72 | for (PDBEntry pdbentry : sq.getAllPDBEntries()) |
252 | { | |
253 | 86 | if (pdb.getFile() != null && pdbentry.getFile() != null |
254 | && pdb.getFile().equals(pdbentry.getFile())) | |
255 | { | |
256 | 54 | String chaincode = pdbentry.getChainCode(); |
257 | 54 | if (chaincode != null && chaincode.length() > 0) |
258 | { | |
259 | 41 | chain = chaincode; |
260 | 41 | chainmaps++; |
261 | 41 | break; |
262 | } | |
263 | } | |
264 | } | |
265 | } | |
266 | 72 | newchains[pe][se] = chain; |
267 | 72 | se++; |
268 | } | |
269 | 60 | pe++; |
270 | } | |
271 | } | |
272 | ||
273 | 51 | chains = newchains; |
274 | 51 | return chainmaps > 0; |
275 | } | |
276 | ||
277 | 838 | public StructureSelectionManager getSsm() |
278 | { | |
279 | 838 | return ssm; |
280 | } | |
281 | ||
282 | /** | |
283 | * Returns the i'th PDBEntry (or null) | |
284 | * | |
285 | * @param i | |
286 | * @return | |
287 | */ | |
288 | 329 | public PDBEntry getPdbEntry(int i) |
289 | { | |
290 | 329 | return (pdbEntry != null && pdbEntry.length > i) ? pdbEntry[i] : null; |
291 | } | |
292 | ||
293 | /** | |
294 | * Answers true if this binding includes the given PDB id, else false | |
295 | * | |
296 | * @param pdbId | |
297 | * @return | |
298 | */ | |
299 | 1 | public boolean hasPdbId(String pdbId) |
300 | { | |
301 | 1 | if (pdbEntry != null) |
302 | { | |
303 | 1 | for (PDBEntry pdb : pdbEntry) |
304 | { | |
305 | 1 | if (pdb.getId().equals(pdbId)) |
306 | { | |
307 | 0 | return true; |
308 | } | |
309 | } | |
310 | } | |
311 | 1 | return false; |
312 | } | |
313 | ||
314 | /** | |
315 | * Returns the number of modelled PDB file entries. | |
316 | * | |
317 | * @return | |
318 | */ | |
319 | 536 | public int getPdbCount() |
320 | { | |
321 | 536 | return pdbEntry == null ? 0 : pdbEntry.length; |
322 | } | |
323 | ||
324 | 1105 | public SequenceI[][] getSequence() |
325 | { | |
326 | 1105 | return sequence; |
327 | } | |
328 | ||
329 | 535 | public String[][] getChains() |
330 | { | |
331 | 535 | return chains; |
332 | } | |
333 | ||
334 | 0 | public DataSourceType getProtocol() |
335 | { | |
336 | 0 | return protocol; |
337 | } | |
338 | ||
339 | // TODO may remove this if calling methods can be pulled up here | |
340 | 1 | protected void setPdbentry(PDBEntry[] pdbentry) |
341 | { | |
342 | 1 | this.pdbEntry = pdbentry; |
343 | } | |
344 | ||
345 | 1 | protected void setSequence(SequenceI[][] sequence) |
346 | { | |
347 | 1 | this.sequence = sequence; |
348 | } | |
349 | ||
350 | 1 | protected void setChains(String[][] chains) |
351 | { | |
352 | 1 | this.chains = chains; |
353 | } | |
354 | ||
355 | /** | |
356 | * Construct a title string for the viewer window based on the data Jalview | |
357 | * knows about | |
358 | * | |
359 | * @param viewerName | |
360 | * TODO | |
361 | * @param verbose | |
362 | * | |
363 | * @return | |
364 | */ | |
365 | 94 | public String getViewerTitle(String viewerName, boolean verbose) |
366 | { | |
367 | 94 | if (getSequence() == null || getSequence().length < 1 |
368 | || getPdbCount() < 1 || getSequence()[0].length < 1) | |
369 | { | |
370 | 0 | return ("Jalview " + viewerName + " Window"); |
371 | } | |
372 | // TODO: give a more informative title when multiple structures are | |
373 | // displayed. | |
374 | 94 | StringBuilder title = new StringBuilder(64); |
375 | 94 | final PDBEntry pdbe = getPdbEntry(0); |
376 | 94 | title.append(viewerName + " view for " + getSequence()[0][0].getName() |
377 | + ":" + pdbe.getId()); | |
378 | ||
379 | 94 | if (verbose) |
380 | { | |
381 | 94 | String method = (String) pdbe.getProperty("method"); |
382 | 94 | if (method != null) |
383 | { | |
384 | 0 | title.append(" Method: ").append(method); |
385 | } | |
386 | 94 | String chain = (String) pdbe.getProperty("chains"); |
387 | 94 | if (chain != null) |
388 | { | |
389 | 0 | title.append(" Chain:").append(chain); |
390 | } | |
391 | } | |
392 | 94 | return title.toString(); |
393 | } | |
394 | ||
395 | /** | |
396 | * Called by after closeViewer is called, to release any resources and | |
397 | * references so they can be garbage collected. Override if needed. | |
398 | */ | |
399 | 0 | protected void releaseUIResources() |
400 | { | |
401 | } | |
402 | ||
403 | 0 | @Override |
404 | public void releaseReferences(Object svl) | |
405 | { | |
406 | } | |
407 | ||
408 | 159 | public boolean isColourBySequence() |
409 | { | |
410 | 159 | return colourBySequence; |
411 | } | |
412 | ||
413 | /** | |
414 | * Called when the binding thinks the UI needs to be refreshed after a | |
415 | * structure viewer state change. This could be because structures were | |
416 | * loaded, or because an error has occurred. Default does nothing, override as | |
417 | * required. | |
418 | */ | |
419 | 0 | public void refreshGUI() |
420 | { | |
421 | } | |
422 | ||
423 | /** | |
424 | * Instruct the Jalview binding to update the pdbentries vector if necessary | |
425 | * prior to matching the jmol view's contents to the list of structure files | |
426 | * Jalview knows about. By default does nothing, override as required. | |
427 | */ | |
428 | 47 | public void refreshPdbEntries() |
429 | { | |
430 | } | |
431 | ||
432 | 102 | public void setColourBySequence(boolean colourBySequence) |
433 | { | |
434 | 102 | this.colourBySequence = colourBySequence; |
435 | } | |
436 | ||
437 | 78 | protected void addSequenceAndChain(int pe, SequenceI[] seq, |
438 | String[] tchain) | |
439 | { | |
440 | 78 | if (pe < 0 || pe >= getPdbCount()) |
441 | { | |
442 | 0 | throw new Error(MessageManager.formatMessage( |
443 | "error.implementation_error_no_pdbentry_from_index", | |
444 | new Object[] | |
445 | { Integer.valueOf(pe).toString() })); | |
446 | } | |
447 | 78 | final String nullChain = "TheNullChain"; |
448 | 78 | List<SequenceI> s = new ArrayList<>(); |
449 | 78 | List<String> c = new ArrayList<>(); |
450 | 78 | if (getChains() == null) |
451 | { | |
452 | 0 | setChains(new String[getPdbCount()][]); |
453 | } | |
454 | 78 | if (getSequence()[pe] != null) |
455 | { | |
456 | 189 | for (int i = 0; i < getSequence()[pe].length; i++) |
457 | { | |
458 | 112 | s.add(getSequence()[pe][i]); |
459 | 112 | if (getChains()[pe] != null) |
460 | { | |
461 | 110 | if (i < getChains()[pe].length) |
462 | { | |
463 | 110 | c.add(getChains()[pe][i]); |
464 | } | |
465 | else | |
466 | { | |
467 | 0 | c.add(nullChain); |
468 | } | |
469 | } | |
470 | else | |
471 | { | |
472 | 2 | if (tchain != null && tchain.length > 0) |
473 | { | |
474 | 0 | c.add(nullChain); |
475 | } | |
476 | } | |
477 | } | |
478 | } | |
479 | 191 | for (int i = 0; i < seq.length; i++) |
480 | { | |
481 | 113 | if (!s.contains(seq[i])) |
482 | { | |
483 | 1 | s.add(seq[i]); |
484 | 1 | if (tchain != null && i < tchain.length) |
485 | { | |
486 | 0 | c.add(tchain[i] == null ? nullChain : tchain[i]); |
487 | } | |
488 | } | |
489 | } | |
490 | 78 | SequenceI[] tmp = s.toArray(new SequenceI[s.size()]); |
491 | 78 | getSequence()[pe] = tmp; |
492 | 78 | if (c.size() > 0) |
493 | { | |
494 | 75 | String[] tch = c.toArray(new String[c.size()]); |
495 | 185 | for (int i = 0; i < tch.length; i++) |
496 | { | |
497 | 110 | if (tch[i] == nullChain) |
498 | { | |
499 | 0 | tch[i] = null; |
500 | } | |
501 | } | |
502 | 75 | getChains()[pe] = tch; |
503 | } | |
504 | else | |
505 | { | |
506 | 3 | getChains()[pe] = null; |
507 | } | |
508 | } | |
509 | ||
510 | /** | |
511 | * add structures and any known sequence associations | |
512 | * | |
513 | * @returns the pdb entries added to the current set. | |
514 | */ | |
515 | 1 | public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, |
516 | SequenceI[][] seq, String[][] chns) | |
517 | { | |
518 | 1 | List<PDBEntry> v = new ArrayList<>(); |
519 | 1 | List<int[]> rtn = new ArrayList<>(); |
520 | 2 | for (int i = 0; i < getPdbCount(); i++) |
521 | { | |
522 | 1 | v.add(getPdbEntry(i)); |
523 | } | |
524 | 2 | for (int i = 0; i < pdbe.length; i++) |
525 | { | |
526 | 1 | int r = v.indexOf(pdbe[i]); |
527 | 1 | if (r == -1 || r >= getPdbCount()) |
528 | { | |
529 | 1 | rtn.add(new int[] { v.size(), i }); |
530 | 1 | v.add(pdbe[i]); |
531 | } | |
532 | else | |
533 | { | |
534 | // just make sure the sequence/chain entries are all up to date | |
535 | 0 | addSequenceAndChain(r, seq[i], chns[i]); |
536 | } | |
537 | } | |
538 | 1 | pdbe = v.toArray(new PDBEntry[v.size()]); |
539 | 1 | setPdbentry(pdbe); |
540 | 1 | if (rtn.size() > 0) |
541 | { | |
542 | // expand the tied sequence[] and string[] arrays | |
543 | 1 | SequenceI[][] sqs = new SequenceI[getPdbCount()][]; |
544 | 1 | String[][] sch = new String[getPdbCount()][]; |
545 | 1 | System.arraycopy(getSequence(), 0, sqs, 0, getSequence().length); |
546 | 1 | System.arraycopy(getChains(), 0, sch, 0, this.getChains().length); |
547 | 1 | setSequence(sqs); |
548 | 1 | setChains(sch); |
549 | 1 | pdbe = new PDBEntry[rtn.size()]; |
550 | 2 | for (int r = 0; r < pdbe.length; r++) |
551 | { | |
552 | 1 | int[] stri = (rtn.get(r)); |
553 | // record the pdb file as a new addition | |
554 | 1 | pdbe[r] = getPdbEntry(stri[0]); |
555 | // and add the new sequence/chain entries | |
556 | 1 | addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]); |
557 | } | |
558 | } | |
559 | else | |
560 | { | |
561 | 0 | pdbe = null; |
562 | } | |
563 | 1 | return pdbe; |
564 | } | |
565 | ||
566 | /** | |
567 | * Add sequences to the pe'th pdbentry's sequence set. | |
568 | * | |
569 | * @param pe | |
570 | * @param seq | |
571 | */ | |
572 | 77 | public void addSequence(int pe, SequenceI[] seq) |
573 | { | |
574 | 77 | addSequenceAndChain(pe, seq, null); |
575 | } | |
576 | ||
577 | /** | |
578 | * add the given sequences to the mapping scope for the given pdb file handle | |
579 | * | |
580 | * @param pdbFile | |
581 | * - pdbFile identifier | |
582 | * @param seq | |
583 | * - set of sequences it can be mapped to | |
584 | */ | |
585 | 33 | public void addSequenceForStructFile(String pdbFile, SequenceI[] seq) |
586 | { | |
587 | 66 | for (int pe = 0; pe < getPdbCount(); pe++) |
588 | { | |
589 | 33 | if (getPdbEntry(pe).getFile().equals(pdbFile)) |
590 | { | |
591 | 28 | addSequence(pe, seq); |
592 | } | |
593 | } | |
594 | } | |
595 | ||
596 | @Override | |
597 | public abstract void highlightAtoms(List<AtomSpec> atoms); | |
598 | ||
599 | 0 | protected boolean isNucleotide() |
600 | { | |
601 | 0 | return this.nucleotide; |
602 | } | |
603 | ||
604 | /** | |
605 | * Returns a readable description of all mappings for the wrapped pdbfile to | |
606 | * any mapped sequences | |
607 | * | |
608 | * @param pdbfile | |
609 | * @param seqs | |
610 | * @return | |
611 | */ | |
612 | 0 | public String printMappings() |
613 | { | |
614 | 0 | if (pdbEntry == null) |
615 | { | |
616 | 0 | return ""; |
617 | } | |
618 | 0 | StringBuilder sb = new StringBuilder(128); |
619 | 0 | for (int pdbe = 0; pdbe < getPdbCount(); pdbe++) |
620 | { | |
621 | 0 | String pdbfile = getPdbEntry(pdbe).getFile(); |
622 | 0 | List<SequenceI> seqs = Arrays.asList(getSequence()[pdbe]); |
623 | 0 | sb.append(getSsm().printMappings(pdbfile, seqs)); |
624 | } | |
625 | 0 | return sb.toString(); |
626 | } | |
627 | ||
628 | /** | |
629 | * Returns the mapped structure position for a given aligned column of a given | |
630 | * sequence, or -1 if the column is gapped, beyond the end of the sequence, or | |
631 | * not mapped to structure. | |
632 | * | |
633 | * @param seq | |
634 | * @param alignedPos | |
635 | * @param mapping | |
636 | * @return | |
637 | */ | |
638 | 620 | protected int getMappedPosition(SequenceI seq, int alignedPos, |
639 | StructureMapping mapping) | |
640 | { | |
641 | 620 | if (alignedPos >= seq.getLength()) |
642 | { | |
643 | 1 | return -1; |
644 | } | |
645 | ||
646 | 619 | if (Comparison.isGap(seq.getCharAt(alignedPos))) |
647 | { | |
648 | 6 | return -1; |
649 | } | |
650 | 613 | int seqPos = seq.findPosition(alignedPos); |
651 | 613 | int pos = mapping.getPDBResNum(seqPos); |
652 | 613 | return pos; |
653 | } | |
654 | ||
655 | /** | |
656 | * Helper method to identify residues that can participate in a structure | |
657 | * superposition command. For each structure, identify a sequence in the | |
658 | * alignment which is mapped to the structure. Identify non-gapped columns in | |
659 | * the sequence which have a mapping to a residue in the structure. Returns | |
660 | * the index of the first structure that has a mapping to the alignment. | |
661 | * | |
662 | * @param alignment | |
663 | * the sequence alignment which is the basis of structure | |
664 | * superposition | |
665 | * @param matched | |
666 | * a BitSet, where bit j is set to indicate that every structure has | |
667 | * a mapped residue present in column j (so the column can | |
668 | * participate in structure alignment) | |
669 | * @param structures | |
670 | * an array of data beans corresponding to pdb file index | |
671 | * @return | |
672 | */ | |
673 | 3 | protected int findSuperposableResidues(AlignmentI alignment, |
674 | BitSet matched, | |
675 | AAStructureBindingModel.SuperposeData[] structures) | |
676 | { | |
677 | 3 | int refStructure = -1; |
678 | 3 | String[] files = getStructureFiles(); |
679 | 3 | if (files == null) |
680 | { | |
681 | 0 | return -1; |
682 | } | |
683 | 11 | for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) |
684 | { | |
685 | 8 | StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]); |
686 | 8 | int lastPos = -1; |
687 | ||
688 | /* | |
689 | * Find the first mapped sequence (if any) for this PDB entry which is in | |
690 | * the alignment | |
691 | */ | |
692 | 8 | final int seqCountForPdbFile = getSequence()[pdbfnum].length; |
693 | 16 | for (int s = 0; s < seqCountForPdbFile; s++) |
694 | { | |
695 | 8 | for (StructureMapping mapping : mappings) |
696 | { | |
697 | 8 | final SequenceI theSequence = getSequence()[pdbfnum][s]; |
698 | 8 | if (mapping.getSequence() == theSequence |
699 | && alignment.findIndex(theSequence) > -1) | |
700 | { | |
701 | 8 | if (refStructure < 0) |
702 | { | |
703 | 3 | refStructure = pdbfnum; |
704 | } | |
705 | 638 | for (int r = 0; r < alignment.getWidth(); r++) |
706 | { | |
707 | 630 | if (!matched.get(r)) |
708 | { | |
709 | 10 | continue; |
710 | } | |
711 | 620 | int pos = getMappedPosition(theSequence, r, mapping); |
712 | 620 | if (pos < 1 || pos == lastPos) |
713 | { | |
714 | 7 | matched.clear(r); |
715 | 7 | continue; |
716 | } | |
717 | 613 | lastPos = pos; |
718 | 613 | structures[pdbfnum].pdbResNo[r] = pos; |
719 | } | |
720 | 8 | String chain = mapping.getChain(); |
721 | 8 | if (chain != null && chain.trim().length() > 0) |
722 | { | |
723 | 8 | structures[pdbfnum].chain = chain; |
724 | } | |
725 | 8 | structures[pdbfnum].pdbId = mapping.getPdbId(); |
726 | 8 | structures[pdbfnum].isRna = !theSequence.isProtein(); |
727 | ||
728 | /* | |
729 | * move on to next pdb file (ignore sequences for other chains | |
730 | * for the same structure) | |
731 | */ | |
732 | 8 | s = seqCountForPdbFile; |
733 | 8 | break; // fixme break out of two loops here! |
734 | } | |
735 | } | |
736 | } | |
737 | } | |
738 | 3 | return refStructure; |
739 | } | |
740 | ||
741 | /** | |
742 | * Returns true if the structure viewer has loaded all of the files of | |
743 | * interest (identified by the file mapping having been set up), or false if | |
744 | * any are still not loaded after a timeout interval. | |
745 | * | |
746 | * @param files | |
747 | */ | |
748 | 1 | protected boolean waitForFileLoad(String[] files) |
749 | { | |
750 | /* | |
751 | * give up after 10 secs plus 1 sec per file | |
752 | */ | |
753 | 1 | long starttime = System.currentTimeMillis(); |
754 | 1 | long endTime = 10000 + 1000 * files.length + starttime; |
755 | 1 | String notLoaded = null; |
756 | ||
757 | 1 | boolean waiting = true; |
758 | 2 | while (waiting && System.currentTimeMillis() < endTime) |
759 | { | |
760 | 1 | waiting = false; |
761 | 1 | for (String file : files) |
762 | { | |
763 | 2 | notLoaded = file; |
764 | 2 | if (file == null) |
765 | { | |
766 | 0 | continue; |
767 | } | |
768 | 2 | try |
769 | { | |
770 | 2 | StructureMapping[] sm = getSsm().getMapping(file); |
771 | 2 | if (sm == null || sm.length == 0) |
772 | { | |
773 | 0 | waiting = true; |
774 | } | |
775 | } catch (Throwable x) | |
776 | { | |
777 | 0 | waiting = true; |
778 | } | |
779 | } | |
780 | } | |
781 | ||
782 | 1 | if (waiting) |
783 | { | |
784 | 0 | jalview.bin.Console.errPrintln( |
785 | "Timed out waiting for structure viewer to load file " | |
786 | + notLoaded); | |
787 | 0 | return false; |
788 | } | |
789 | 1 | return true; |
790 | } | |
791 | ||
792 | 0 | @Override |
793 | public boolean isListeningFor(SequenceI seq) | |
794 | { | |
795 | 0 | if (sequence != null) |
796 | { | |
797 | 0 | for (SequenceI[] seqs : sequence) |
798 | { | |
799 | 0 | if (seqs != null) |
800 | { | |
801 | 0 | for (SequenceI s : seqs) |
802 | { | |
803 | 0 | if (s == seq || (s.getDatasetSequence() != null |
804 | && s.getDatasetSequence() == seq.getDatasetSequence())) | |
805 | { | |
806 | 0 | return true; |
807 | } | |
808 | } | |
809 | } | |
810 | } | |
811 | } | |
812 | 0 | return false; |
813 | } | |
814 | ||
815 | 425 | public boolean isFinishedInit() |
816 | { | |
817 | 425 | return finishedInit; |
818 | } | |
819 | ||
820 | 90 | public void setFinishedInit(boolean fi) |
821 | { | |
822 | 90 | this.finishedInit = fi; |
823 | } | |
824 | ||
825 | /** | |
826 | * Returns a list of chains mapped in this viewer, formatted as | |
827 | * "pdbid:chainCode" | |
828 | * | |
829 | * @return | |
830 | */ | |
831 | 112 | public List<String> getChainNames() |
832 | { | |
833 | 112 | return chainNames; |
834 | } | |
835 | ||
836 | /** | |
837 | * Returns the Jalview panel hosting the structure viewer (if any) | |
838 | * | |
839 | * @return | |
840 | */ | |
841 | 2833 | public JalviewStructureDisplayI getViewer() |
842 | { | |
843 | 2833 | return viewer; |
844 | } | |
845 | ||
846 | 68 | public void setViewer(JalviewStructureDisplayI v) |
847 | { | |
848 | 68 | viewer = v; |
849 | } | |
850 | ||
851 | /** | |
852 | * Constructs and sends a command to align structures against a reference | |
853 | * structure, based on one or more sequence alignments. May optionally return | |
854 | * an error or warning message for the alignment command(s). | |
855 | * | |
856 | * @param alignWith | |
857 | * an array of one or more alignment views to process | |
858 | * @return | |
859 | */ | |
860 | 1 | public String superposeStructures(List<AlignmentViewPanel> alignWith) |
861 | { | |
862 | 1 | String error = ""; |
863 | 1 | String[] files = getStructureFiles(); |
864 | ||
865 | 1 | if (!waitForFileLoad(files)) |
866 | { | |
867 | 0 | return null; |
868 | } | |
869 | 1 | refreshPdbEntries(); |
870 | ||
871 | 1 | for (AlignmentViewPanel view : alignWith) |
872 | { | |
873 | 1 | AlignmentI alignment = view.getAlignment(); |
874 | 1 | HiddenColumns hiddenCols = alignment.getHiddenColumns(); |
875 | /* | |
876 | * 'matched' bit i will be set for visible alignment columns i where | |
877 | * all sequences have a residue with a mapping to their PDB structure | |
878 | */ | |
879 | 1 | final int width = alignment.getWidth(); |
880 | 1 | BitSet matched = new BitSet(); |
881 | 1 | ColumnSelection cs = view.getAlignViewport().getColumnSelection(); |
882 | // restrict to active column selection, if there is one | |
883 | 1 | if (cs != null && cs.hasSelectedColumns() |
884 | && cs.getSelected().size() >= 4) | |
885 | { | |
886 | 0 | for (int s : cs.getSelected()) |
887 | { | |
888 | 0 | matched.set(s); |
889 | } | |
890 | } | |
891 | else | |
892 | { | |
893 | 298 | for (int m = 0; m < width; m++) |
894 | { | |
895 | 297 | if (hiddenCols == null || hiddenCols.isVisible(m)) |
896 | { | |
897 | 297 | matched.set(m); |
898 | } | |
899 | } | |
900 | } | |
901 | 1 | AAStructureBindingModel.SuperposeData[] structures = new AAStructureBindingModel.SuperposeData[files.length]; |
902 | 3 | for (int f = 0; f < files.length; f++) |
903 | { | |
904 | 2 | structures[f] = new AAStructureBindingModel.SuperposeData(width, |
905 | getModelIdForFile(files[f])); | |
906 | } | |
907 | ||
908 | /* | |
909 | * Calculate the superposable alignment columns ('matched'), and the | |
910 | * corresponding structure residue positions (structures.pdbResNo) | |
911 | */ | |
912 | 1 | int refStructure = findSuperposableResidues(alignment, matched, |
913 | structures); | |
914 | ||
915 | /* | |
916 | * require at least 4 positions to be able to execute superposition | |
917 | */ | |
918 | 1 | int nmatched = matched.cardinality(); |
919 | 1 | if (nmatched < MIN_POS_TO_SUPERPOSE) |
920 | { | |
921 | 0 | String msg = MessageManager |
922 | .formatMessage("label.insufficient_residues", nmatched); | |
923 | 0 | error += view.getViewName() + ": " + msg + "; "; |
924 | 0 | continue; |
925 | } | |
926 | ||
927 | /* | |
928 | * get a model of the superposable residues in the reference structure | |
929 | */ | |
930 | 1 | AtomSpecModel refAtoms = getAtomSpec(structures[refStructure], |
931 | matched); | |
932 | ||
933 | /* | |
934 | * Show all as backbone before doing superposition(s) | |
935 | * (residues used for matching will be shown as ribbon) | |
936 | */ | |
937 | // todo better way to ensure synchronous than setting getReply true!! | |
938 | 1 | executeCommands(commandGenerator.showBackbone(), true, null); |
939 | ||
940 | 1 | AtomSpecType backbone = structures[refStructure].isRna |
941 | ? AtomSpecType.PHOSPHATE | |
942 | : AtomSpecType.ALPHA; | |
943 | 1 | List<AtomSpecModel> models = new ArrayList<AtomSpecModel>(); |
944 | 1 | models.add(refAtoms); |
945 | /* | |
946 | * superpose each (other) structure to the reference in turn | |
947 | */ | |
948 | 3 | for (int i = 0; i < structures.length; i++) |
949 | { | |
950 | 2 | if (i != refStructure) |
951 | { | |
952 | 1 | AtomSpecModel atomSpec = getAtomSpec(structures[i], matched); |
953 | 1 | List<StructureCommandI> commands = commandGenerator |
954 | .superposeStructures(refAtoms, atomSpec, backbone); | |
955 | 1 | List<String> replies = executeCommands(commands, true, null); |
956 | 1 | for (String reply : replies) |
957 | { | |
958 | // return this error (Chimera only) to the user | |
959 | 0 | if (reply.toLowerCase(Locale.ROOT) |
960 | .contains("unequal numbers of atoms")) | |
961 | { | |
962 | 0 | error += "; " + reply; |
963 | } | |
964 | } | |
965 | 1 | models.add(atomSpec); |
966 | } | |
967 | } | |
968 | 1 | List<StructureCommandI> finalView = commandGenerator |
969 | .centerViewOn(models); | |
970 | 1 | if (finalView != null && finalView.size() > 0) |
971 | { | |
972 | 1 | executeCommands(finalView, false, "Centered on Superposition"); |
973 | } | |
974 | } | |
975 | 1 | return error; |
976 | } | |
977 | ||
978 | 2 | private AtomSpecModel getAtomSpec( |
979 | AAStructureBindingModel.SuperposeData superposeData, | |
980 | BitSet matched) | |
981 | { | |
982 | 2 | AtomSpecModel model = new AtomSpecModel(); |
983 | 2 | int nextColumnMatch = matched.nextSetBit(0); |
984 | 594 | while (nextColumnMatch != -1) |
985 | { | |
986 | 592 | int pdbResNum = superposeData.pdbResNo[nextColumnMatch]; |
987 | 592 | model.addRange(superposeData.modelId, pdbResNum, pdbResNum, |
988 | superposeData.chain); | |
989 | 592 | nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1); |
990 | } | |
991 | ||
992 | 2 | return model; |
993 | } | |
994 | ||
995 | /** | |
996 | * returns the current sequenceRenderer that should be used to colour the | |
997 | * structures | |
998 | * | |
999 | * @param alignment | |
1000 | * | |
1001 | * @return | |
1002 | */ | |
1003 | public abstract SequenceRenderer getSequenceRenderer( | |
1004 | AlignmentViewPanel alignment); | |
1005 | ||
1006 | /** | |
1007 | * Sends a command to the structure viewer to colour each chain with a | |
1008 | * distinct colour (to the extent supported by the viewer) | |
1009 | */ | |
1010 | 0 | public void colourByChain() |
1011 | { | |
1012 | 0 | colourBySequence = false; |
1013 | ||
1014 | // TODO: JAL-628 colour chains distinctly across all visible models | |
1015 | ||
1016 | 0 | executeCommand(false, COLOURING_STRUCTURES, |
1017 | commandGenerator.colourByChain()); | |
1018 | } | |
1019 | ||
1020 | /** | |
1021 | * Sends a command to the structure viewer to colour each chain with a | |
1022 | * distinct colour (to the extent supported by the viewer) | |
1023 | */ | |
1024 | 0 | public void colourByCharge() |
1025 | { | |
1026 | 0 | colourBySequence = false; |
1027 | ||
1028 | 0 | executeCommands(commandGenerator.colourByCharge(), false, |
1029 | COLOURING_STRUCTURES); | |
1030 | } | |
1031 | ||
1032 | /** | |
1033 | * Sends a command to the structure to apply a colour scheme (defined in | |
1034 | * Jalview but not necessarily applied to the alignment), which defines a | |
1035 | * colour per residue letter. More complex schemes (e.g. that depend on | |
1036 | * consensus) cannot be used here and are ignored. | |
1037 | * | |
1038 | * @param cs | |
1039 | */ | |
1040 | 0 | public void colourByJalviewColourScheme(ColourSchemeI cs) |
1041 | { | |
1042 | 0 | colourBySequence = false; |
1043 | ||
1044 | 0 | if (cs == null || !cs.isSimple()) |
1045 | { | |
1046 | 0 | return; |
1047 | } | |
1048 | ||
1049 | /* | |
1050 | * build a map of {Residue3LetterCode, Color} | |
1051 | */ | |
1052 | 0 | Map<String, Color> colours = new HashMap<>(); |
1053 | 0 | List<String> residues = ResidueProperties.getResidues(isNucleotide(), |
1054 | false); | |
1055 | 0 | for (String resName : residues) |
1056 | { | |
1057 | 0 | char res = resName.length() == 3 |
1058 | ? ResidueProperties.getSingleCharacterCode(resName) | |
1059 | : resName.charAt(0); | |
1060 | 0 | Color colour = cs.findColour(res, 0, null, null, 0f); |
1061 | 0 | colours.put(resName, colour); |
1062 | } | |
1063 | ||
1064 | /* | |
1065 | * pass to the command constructor, and send the command | |
1066 | */ | |
1067 | 0 | List<StructureCommandI> cmd = commandGenerator |
1068 | .colourByResidues(colours); | |
1069 | 0 | executeCommands(cmd, false, COLOURING_STRUCTURES); |
1070 | } | |
1071 | ||
1072 | 0 | public void setBackgroundColour(Color col) |
1073 | { | |
1074 | 0 | StructureCommandI cmd = commandGenerator.setBackgroundColour(col); |
1075 | 0 | executeCommand(false, null, cmd); |
1076 | } | |
1077 | ||
1078 | /** | |
1079 | * Execute one structure viewer command. If {@code getReply} is true, may | |
1080 | * optionally return one or more reply messages, else returns null. | |
1081 | * | |
1082 | * @param cmd | |
1083 | * @param getReply | |
1084 | */ | |
1085 | protected abstract List<String> executeCommand(StructureCommandI cmd, | |
1086 | boolean getReply); | |
1087 | ||
1088 | /** | |
1089 | * Executes one or more structure viewer commands | |
1090 | * | |
1091 | * @param commands | |
1092 | * @param getReply | |
1093 | * @param msg | |
1094 | */ | |
1095 | 320 | public List<String> executeCommands(List<StructureCommandI> commands, |
1096 | boolean getReply, String msg) | |
1097 | { | |
1098 | 320 | return executeCommand(getReply, msg, |
1099 | commands.toArray(new StructureCommandI[commands.size()])); | |
1100 | } | |
1101 | ||
1102 | /** | |
1103 | * Executes one or more structure viewer commands, optionally returning the | |
1104 | * reply, and optionally showing a status message while the command is being | |
1105 | * executed. | |
1106 | * <p> | |
1107 | * If a reply is wanted, the execution is done synchronously (waits), | |
1108 | * otherwise it is done in a separate thread (doesn't wait). WARNING: if you | |
1109 | * are sending commands that need to execute before later calls to | |
1110 | * executeCommand (e.g. mouseovers, which clean up after previous ones) then | |
1111 | * set getReply true to ensure that commands are not executed out of order. | |
1112 | * | |
1113 | * @param getReply | |
1114 | * @param msg | |
1115 | * @param cmds | |
1116 | * @return | |
1117 | */ | |
1118 | 320 | protected List<String> executeCommand(boolean getReply, String msg, |
1119 | StructureCommandI... cmds) | |
1120 | { | |
1121 | 320 | JalviewStructureDisplayI theViewer = getViewer(); |
1122 | 320 | final long handle = msg == null ? 0 : theViewer.startProgressBar(msg); |
1123 | ||
1124 | 317 | if (getReply) |
1125 | { | |
1126 | /* | |
1127 | * execute and wait for reply | |
1128 | */ | |
1129 | 2 | List<String> response = new ArrayList<>(); |
1130 | 2 | try |
1131 | { | |
1132 | 2 | for (StructureCommandI cmd : cmds) |
1133 | { | |
1134 | 2 | List<String> replies = executeCommand(cmd, true); |
1135 | 2 | if (replies != null) |
1136 | { | |
1137 | 0 | response.addAll(replies); |
1138 | } | |
1139 | } | |
1140 | 2 | return response; |
1141 | } finally | |
1142 | { | |
1143 | 2 | if (msg != null) |
1144 | { | |
1145 | 0 | theViewer.stopProgressBar(null, handle); |
1146 | } | |
1147 | } | |
1148 | } | |
1149 | ||
1150 | /* | |
1151 | * fire and forget | |
1152 | */ | |
1153 | 315 | String threadName = msg == null ? "StructureCommand" : msg; |
1154 | 315 | new Thread(new Runnable() |
1155 | { | |
1156 | 315 | @Override |
1157 | public void run() | |
1158 | { | |
1159 | 315 | try |
1160 | { | |
1161 | 315 | for (StructureCommandI cmd : cmds) |
1162 | { | |
1163 | 305 | executeCommand(cmd, false); |
1164 | } | |
1165 | } finally | |
1166 | { | |
1167 | 315 | if (msg != null) |
1168 | { | |
1169 | 315 | SwingUtilities.invokeLater(new Runnable() |
1170 | { | |
1171 | 314 | @Override |
1172 | public void run() | |
1173 | { | |
1174 | 314 | theViewer.stopProgressBar(null, handle); |
1175 | } | |
1176 | }); | |
1177 | } | |
1178 | } | |
1179 | } | |
1180 | }, threadName).start(); | |
1181 | 315 | return null; |
1182 | } | |
1183 | ||
1184 | /** | |
1185 | * Colours any structures associated with sequences in the given alignment as | |
1186 | * coloured in the alignment view, provided colourBySequence is enabled | |
1187 | */ | |
1188 | 332 | public void colourBySequence(AlignmentViewPanel alignmentv) |
1189 | { | |
1190 | 332 | if (!colourBySequence || !isLoadingFinished() || getSsm() == null) |
1191 | { | |
1192 | 16 | return; |
1193 | } | |
1194 | 316 | Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, sequence, |
1195 | alignmentv); | |
1196 | ||
1197 | 307 | List<StructureCommandI> colourBySequenceCommands = commandGenerator |
1198 | .colourBySequence(colourMap); | |
1199 | 307 | executeCommands(colourBySequenceCommands, false, COLOURING_STRUCTURES); |
1200 | } | |
1201 | ||
1202 | /** | |
1203 | * Centre the display in the structure viewer | |
1204 | */ | |
1205 | 0 | public void focusView() |
1206 | { | |
1207 | 0 | executeCommand(false, null, commandGenerator.focusView()); |
1208 | } | |
1209 | ||
1210 | /** | |
1211 | * Generates and executes a command to show only specified chains in the | |
1212 | * structure viewer. The list of chains to show should contain entries | |
1213 | * formatted as "pdbid:chaincode". | |
1214 | * | |
1215 | * @param toShow | |
1216 | */ | |
1217 | 0 | public void showChains(List<String> toShow) |
1218 | { | |
1219 | // todo or reformat toShow list entries as modelNo:pdbId:chainCode ? | |
1220 | ||
1221 | /* | |
1222 | * Reformat the pdbid:chainCode values as modelNo:chainCode | |
1223 | * since this is what is needed to construct the viewer command | |
1224 | * todo: find a less messy way to do this | |
1225 | */ | |
1226 | 0 | List<String> showThese = new ArrayList<>(); |
1227 | 0 | for (String chainId : toShow) |
1228 | { | |
1229 | 0 | String[] tokens = chainId.split("\\:"); |
1230 | 0 | if (tokens.length == 2) |
1231 | { | |
1232 | 0 | String pdbFile = getFileForChain(chainId); |
1233 | 0 | String model = getModelIdForFile(pdbFile); |
1234 | 0 | showThese.add(model + ":" + tokens[1]); |
1235 | } | |
1236 | } | |
1237 | 0 | executeCommands(commandGenerator.showChains(showThese), false, null); |
1238 | } | |
1239 | ||
1240 | /** | |
1241 | * Answers the structure viewer's model id given a PDB file name. Returns an | |
1242 | * empty string if model id is not found. | |
1243 | * | |
1244 | * @param chainId | |
1245 | * @return | |
1246 | */ | |
1247 | protected abstract String getModelIdForFile(String chainId); | |
1248 | ||
1249 | 375 | public boolean hasFileLoadingError() |
1250 | { | |
1251 | 375 | return fileLoadingError != null && fileLoadingError.length() > 0; |
1252 | } | |
1253 | ||
1254 | /** | |
1255 | * Returns the FeatureRenderer for the given alignment view | |
1256 | * | |
1257 | * @param avp | |
1258 | * @return | |
1259 | */ | |
1260 | 43 | public FeatureRenderer getFeatureRenderer(AlignmentViewPanel avp) |
1261 | { | |
1262 | 43 | AlignmentViewPanel ap = (avp == null) ? getViewer().getAlignmentPanel() |
1263 | : avp; | |
1264 | 42 | if (ap == null) |
1265 | { | |
1266 | 0 | return null; |
1267 | } | |
1268 | 42 | return ap.getFeatureRenderer(); |
1269 | } | |
1270 | ||
1271 | 45 | protected void setStructureCommands(StructureCommandsI cmd) |
1272 | { | |
1273 | 45 | commandGenerator = cmd; |
1274 | } | |
1275 | ||
1276 | /** | |
1277 | * Records association of one chain id (formatted as "pdbid:chainCode") with | |
1278 | * the corresponding PDB file name | |
1279 | * | |
1280 | * @param chainId | |
1281 | * @param fileName | |
1282 | */ | |
1283 | 63 | public void addChainFile(String chainId, String fileName) |
1284 | { | |
1285 | 63 | chainFile.put(chainId, fileName); |
1286 | } | |
1287 | ||
1288 | /** | |
1289 | * Returns the PDB filename for the given chain id (formatted as | |
1290 | * "pdbid:chainCode"), or null if not found | |
1291 | * | |
1292 | * @param chainId | |
1293 | * @return | |
1294 | */ | |
1295 | 0 | protected String getFileForChain(String chainId) |
1296 | { | |
1297 | 0 | return chainFile.get(chainId); |
1298 | } | |
1299 | ||
1300 | 1191 | @Override |
1301 | public void updateColours(Object source) | |
1302 | { | |
1303 | 1191 | if (getViewer() == null) |
1304 | { | |
1305 | // can happen if a viewer was not instantiated or cleaned up and is still | |
1306 | // registered - mostly during tests | |
1307 | 44 | return; |
1308 | } | |
1309 | 1147 | AlignmentViewPanel ap = (AlignmentViewPanel) source; |
1310 | // ignore events from panels not used to colour this view | |
1311 | 1147 | if (!getViewer().isUsedForColourBy(ap)) |
1312 | { | |
1313 | 857 | return; |
1314 | } | |
1315 | 290 | if (!isLoadingFromArchive()) |
1316 | { | |
1317 | 290 | colourBySequence(ap); |
1318 | } | |
1319 | } | |
1320 | ||
1321 | 24 | public StructureCommandsI getCommandGenerator() |
1322 | { | |
1323 | 24 | return commandGenerator; |
1324 | } | |
1325 | ||
1326 | protected abstract ViewerType getViewerType(); | |
1327 | ||
1328 | /** | |
1329 | * Builds a data structure which records mapped structure residues for each | |
1330 | * colour. From this we can easily generate the viewer commands for colour by | |
1331 | * sequence. Constructs and returns a map of {@code Color} to | |
1332 | * {@code AtomSpecModel}, where the atomspec model holds | |
1333 | * | |
1334 | * <pre> | |
1335 | * Model ids | |
1336 | * Chains | |
1337 | * Residue positions | |
1338 | * </pre> | |
1339 | * | |
1340 | * Ordering is by order of addition (for colours), natural ordering (for | |
1341 | * models and chains) | |
1342 | * | |
1343 | * @param ssm | |
1344 | * @param sequence | |
1345 | * @param viewPanel | |
1346 | * @return | |
1347 | */ | |
1348 | 317 | protected Map<Object, AtomSpecModel> buildColoursMap( |
1349 | StructureSelectionManager ssm, SequenceI[][] sequence, | |
1350 | AlignmentViewPanel viewPanel) | |
1351 | { | |
1352 | 317 | String[] files = getStructureFiles(); |
1353 | 317 | SequenceRenderer sr = getSequenceRenderer(viewPanel); |
1354 | 317 | FeatureRenderer fr = viewPanel.getFeatureRenderer(); |
1355 | 317 | FeatureColourFinder finder = new FeatureColourFinder(fr); |
1356 | 317 | AlignViewportI viewport = viewPanel.getAlignViewport(); |
1357 | 317 | HiddenColumns cs = viewport.getAlignment().getHiddenColumns(); |
1358 | 308 | AlignmentI al = viewport.getAlignment(); |
1359 | 308 | Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<>(); |
1360 | 308 | Color lastColour = null; |
1361 | ||
1362 | 619 | for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) |
1363 | { | |
1364 | 311 | final String modelId = getModelIdForFile(files[pdbfnum]); |
1365 | 311 | StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); |
1366 | ||
1367 | 311 | if (mapping == null || mapping.length < 1) |
1368 | { | |
1369 | 30 | continue; |
1370 | } | |
1371 | ||
1372 | 281 | int startPos = -1, lastPos = -1; |
1373 | 281 | String lastChain = ""; |
1374 | 562 | for (int s = 0; s < sequence[pdbfnum].length; s++) |
1375 | { | |
1376 | 614 | for (int sp, m = 0; m < mapping.length; m++) |
1377 | { | |
1378 | 333 | final SequenceI seq = sequence[pdbfnum][s]; |
1379 | ? | if (mapping[m].getSequence() == seq |
1380 | && (sp = al.findIndex(seq)) > -1) | |
1381 | { | |
1382 | 276 | SequenceI asp = al.getSequenceAt(sp); |
1383 | 72330 | for (int r = 0; r < asp.getLength(); r++) |
1384 | { | |
1385 | // no mapping to gaps in sequence | |
1386 | 72056 | if (Comparison.isGap(asp.getCharAt(r))) |
1387 | { | |
1388 | 34264 | continue; |
1389 | } | |
1390 | 37792 | int pos = mapping[m].getPDBResNum(asp.findPosition(r)); |
1391 | ||
1392 | 37791 | if (pos < 1 || pos == lastPos) |
1393 | { | |
1394 | 16 | continue; |
1395 | } | |
1396 | ||
1397 | 37776 | Color colour = sr.getResidueColour(seq, r, finder); |
1398 | ||
1399 | /* | |
1400 | * darker colour for hidden regions | |
1401 | */ | |
1402 | 37776 | if (!cs.isVisible(r)) |
1403 | { | |
1404 | 6 | colour = Color.GRAY; |
1405 | } | |
1406 | ||
1407 | 37776 | final String chain = mapping[m].getChain(); |
1408 | ||
1409 | /* | |
1410 | * Just keep incrementing the end position for this colour range | |
1411 | * _unless_ colour, PDB model or chain has changed, or there is a | |
1412 | * gap in the mapped residue sequence | |
1413 | */ | |
1414 | 37774 | final boolean newColour = !colour.equals(lastColour); |
1415 | 37775 | final boolean nonContig = lastPos + 1 != pos; |
1416 | 37775 | final boolean newChain = !chain.equals(lastChain); |
1417 | 37775 | if (newColour || nonContig || newChain) |
1418 | { | |
1419 | 7686 | if (startPos != -1) |
1420 | { | |
1421 | 7410 | addAtomSpecRange(colourMap, lastColour, modelId, startPos, |
1422 | lastPos, lastChain); | |
1423 | } | |
1424 | 7686 | startPos = pos; |
1425 | } | |
1426 | 37775 | lastColour = colour; |
1427 | 37774 | lastPos = pos; |
1428 | 37776 | lastChain = chain; |
1429 | } | |
1430 | // final colour range | |
1431 | 276 | if (lastColour != null) |
1432 | { | |
1433 | 276 | addAtomSpecRange(colourMap, lastColour, modelId, startPos, |
1434 | lastPos, lastChain); | |
1435 | } | |
1436 | // break; | |
1437 | } | |
1438 | } | |
1439 | } | |
1440 | } | |
1441 | 308 | return colourMap; |
1442 | } | |
1443 | ||
1444 | /** | |
1445 | * todo better refactoring (map lookup or similar to get viewer structure id) | |
1446 | * | |
1447 | * @param pdbfnum | |
1448 | * @param file | |
1449 | * @return | |
1450 | */ | |
1451 | 0 | protected String getModelId(int pdbfnum, String file) |
1452 | { | |
1453 | 0 | return String.valueOf(pdbfnum); |
1454 | } | |
1455 | ||
1456 | /** | |
1457 | * Saves chains, formatted as "pdbId:chainCode", and lookups from this to the | |
1458 | * full PDB file path | |
1459 | * | |
1460 | * @param pdb | |
1461 | * @param file | |
1462 | */ | |
1463 | 44 | public void stashFoundChains(StructureFile pdb, String file) |
1464 | { | |
1465 | 107 | for (int i = 0; i < pdb.getChains().size(); i++) |
1466 | { | |
1467 | 63 | String chid = pdb.getId() + ":" + pdb.getChains().elementAt(i).id; |
1468 | 63 | addChainFile(chid, file); |
1469 | 63 | getChainNames().add(chid); |
1470 | } | |
1471 | } | |
1472 | ||
1473 | /** | |
1474 | * Helper method to add one contiguous range to the AtomSpec model for the | |
1475 | * given value (creating the model if necessary). As used by Jalview, | |
1476 | * {@code value} is | |
1477 | * <ul> | |
1478 | * <li>a colour, when building a 'colour structure by sequence' command</li> | |
1479 | * <li>a feature value, when building a 'set Chimera attributes from features' | |
1480 | * command</li> | |
1481 | * </ul> | |
1482 | * | |
1483 | * @param map | |
1484 | * @param value | |
1485 | * @param model | |
1486 | * @param startPos | |
1487 | * @param endPos | |
1488 | * @param chain | |
1489 | */ | |
1490 | 7686 | public static final void addAtomSpecRange(Map<Object, AtomSpecModel> map, |
1491 | Object value, String model, int startPos, int endPos, | |
1492 | String chain) | |
1493 | { | |
1494 | /* | |
1495 | * Get/initialize map of data for the colour | |
1496 | */ | |
1497 | 7686 | AtomSpecModel atomSpec = map.get(value); |
1498 | 7686 | if (atomSpec == null) |
1499 | { | |
1500 | 1649 | atomSpec = new AtomSpecModel(); |
1501 | 1649 | map.put(value, atomSpec); |
1502 | } | |
1503 | ||
1504 | 7686 | atomSpec.addRange(model, startPos, endPos, chain); |
1505 | } | |
1506 | ||
1507 | /** | |
1508 | * Returns the file extension (including '.' separator) to use for a saved | |
1509 | * viewer session file. Default is to return null (not supported), override as | |
1510 | * required. | |
1511 | * | |
1512 | * @return | |
1513 | */ | |
1514 | 0 | public String getSessionFileExtension() |
1515 | { | |
1516 | 0 | return null; |
1517 | } | |
1518 | ||
1519 | /** | |
1520 | * If supported, saves the state of the structure viewer to a temporary file | |
1521 | * and returns the file. Returns null and logs an error on any failure. | |
1522 | * | |
1523 | * @return | |
1524 | */ | |
1525 | 2 | public File saveSession() |
1526 | { | |
1527 | 2 | String prefix = getViewerType().toString(); |
1528 | 2 | String suffix = getSessionFileExtension(); |
1529 | 2 | File f = null; |
1530 | 2 | try |
1531 | { | |
1532 | 2 | f = File.createTempFile(prefix, suffix); |
1533 | 2 | saveSession(f); |
1534 | } catch (IOException e) | |
1535 | { | |
1536 | 0 | Console.error(String.format("Error saving %s session: %s", prefix, |
1537 | e.toString())); | |
1538 | } | |
1539 | ||
1540 | 2 | return f; |
1541 | } | |
1542 | ||
1543 | /** | |
1544 | * Use restoreSession when you want to restore a previously saved sesssion to | |
1545 | * the running viewer instance. | |
1546 | * | |
1547 | * @param absolutePath | |
1548 | */ | |
1549 | 0 | public void restoreSession(String absolutePath) |
1550 | { | |
1551 | 0 | String prefix = getViewerType().toString(); |
1552 | 0 | try |
1553 | { | |
1554 | ||
1555 | 0 | StructureCommandI cmd = commandGenerator.restoreSession(absolutePath); |
1556 | 0 | if (cmd != null) |
1557 | { | |
1558 | 0 | executeCommand(cmd, false); |
1559 | } | |
1560 | } catch (Throwable e) | |
1561 | { | |
1562 | 0 | Console.error(String.format("Error restoring %s session: %s", prefix, |
1563 | e.toString())); | |
1564 | } | |
1565 | ||
1566 | } | |
1567 | ||
1568 | /** | |
1569 | * Saves the structure viewer session to the given file | |
1570 | * | |
1571 | * @param f | |
1572 | */ | |
1573 | 2 | protected void saveSession(File f) |
1574 | { | |
1575 | 2 | StructureCommandI cmd = commandGenerator.saveSession(f.getPath()); |
1576 | 2 | if (cmd != null) |
1577 | { | |
1578 | 2 | executeCommand(cmd, false); |
1579 | } | |
1580 | } | |
1581 | ||
1582 | /** | |
1583 | * Returns true if the viewer is an external structure viewer for which the | |
1584 | * process is still alive, else false (for Jmol, or an external viewer which | |
1585 | * the user has independently closed) | |
1586 | * | |
1587 | * @return | |
1588 | */ | |
1589 | 23 | public boolean isViewerRunning() |
1590 | { | |
1591 | 23 | return false; |
1592 | } | |
1593 | ||
1594 | /** | |
1595 | * Closes Jalview's structure viewer panel and releases associated resources. | |
1596 | * If it is managing an external viewer program, and {@code forceClose} is | |
1597 | * true, also asks that program to close. | |
1598 | * | |
1599 | * @param forceClose | |
1600 | */ | |
1601 | 23 | public void closeViewer(boolean forceClose) |
1602 | { | |
1603 | 23 | getSsm().removeStructureViewerListener(this, this.getStructureFiles()); |
1604 | 23 | releaseUIResources(); |
1605 | ||
1606 | /* | |
1607 | * end the thread that closes this panel if the external viewer closes | |
1608 | */ | |
1609 | 23 | if (externalViewerMonitor != null) |
1610 | { | |
1611 | 0 | externalViewerMonitor.interrupt(); |
1612 | 0 | externalViewerMonitor = null; |
1613 | } | |
1614 | ||
1615 | 23 | stopListening(); |
1616 | ||
1617 | 23 | if (forceClose) |
1618 | { | |
1619 | 1 | StructureCommandI cmd = getCommandGenerator().closeViewer(); |
1620 | 1 | if (cmd != null) |
1621 | { | |
1622 | 0 | executeCommand(cmd, false); |
1623 | } | |
1624 | } | |
1625 | } | |
1626 | ||
1627 | /** | |
1628 | * Returns the URL of a help page for the structure viewer, or null if none is | |
1629 | * known | |
1630 | * | |
1631 | * @return | |
1632 | */ | |
1633 | 0 | public String getHelpURL() |
1634 | { | |
1635 | 0 | return null; |
1636 | } | |
1637 | ||
1638 | /** | |
1639 | * <pre> | |
1640 | * Helper method to build a map of | |
1641 | * { featureType, { feature value, AtomSpecModel } } | |
1642 | * </pre> | |
1643 | * | |
1644 | * @param viewPanel | |
1645 | * @return | |
1646 | */ | |
1647 | 0 | protected Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap( |
1648 | AlignmentViewPanel viewPanel) | |
1649 | { | |
1650 | 0 | Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<>(); |
1651 | 0 | String[] files = getStructureFiles(); |
1652 | 0 | if (files == null) |
1653 | { | |
1654 | 0 | return theMap; |
1655 | } | |
1656 | ||
1657 | 0 | FeatureRenderer fr = viewPanel.getFeatureRenderer(); |
1658 | 0 | if (fr == null) |
1659 | { | |
1660 | 0 | return theMap; |
1661 | } | |
1662 | ||
1663 | 0 | AlignViewportI viewport = viewPanel.getAlignViewport(); |
1664 | 0 | List<String> visibleFeatures = fr.getDisplayedFeatureTypes(); |
1665 | ||
1666 | /* | |
1667 | * if alignment is showing features from complement, we also transfer | |
1668 | * these features to the corresponding mapped structure residues | |
1669 | */ | |
1670 | 0 | boolean showLinkedFeatures = viewport.isShowComplementFeatures(); |
1671 | 0 | List<String> complementFeatures = new ArrayList<>(); |
1672 | 0 | FeatureRenderer complementRenderer = null; |
1673 | 0 | if (showLinkedFeatures) |
1674 | { | |
1675 | 0 | AlignViewportI comp = fr.getViewport().getCodingComplement(); |
1676 | 0 | if (comp != null) |
1677 | { | |
1678 | 0 | complementRenderer = Desktop.getAlignFrameFor(comp) |
1679 | .getFeatureRenderer(); | |
1680 | 0 | complementFeatures = complementRenderer.getDisplayedFeatureTypes(); |
1681 | } | |
1682 | } | |
1683 | 0 | if (visibleFeatures.isEmpty() && complementFeatures.isEmpty()) |
1684 | { | |
1685 | 0 | return theMap; |
1686 | } | |
1687 | ||
1688 | 0 | AlignmentI alignment = viewPanel.getAlignment(); |
1689 | 0 | SequenceI[][] seqs = getSequence(); |
1690 | ||
1691 | 0 | for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) |
1692 | { | |
1693 | 0 | String modelId = getModelIdForFile(files[pdbfnum]); |
1694 | 0 | StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); |
1695 | ||
1696 | 0 | if (mapping == null || mapping.length < 1) |
1697 | { | |
1698 | 0 | continue; |
1699 | } | |
1700 | ||
1701 | 0 | for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++) |
1702 | { | |
1703 | 0 | for (int m = 0; m < mapping.length; m++) |
1704 | { | |
1705 | 0 | final SequenceI seq = seqs[pdbfnum][seqNo]; |
1706 | 0 | int sp = alignment.findIndex(seq); |
1707 | 0 | StructureMapping structureMapping = mapping[m]; |
1708 | 0 | if (structureMapping.getSequence() == seq && sp > -1) |
1709 | { | |
1710 | /* | |
1711 | * found a sequence with a mapping to a structure; | |
1712 | * now scan its features | |
1713 | */ | |
1714 | 0 | if (!visibleFeatures.isEmpty()) |
1715 | { | |
1716 | 0 | scanSequenceFeatures(visibleFeatures, structureMapping, seq, |
1717 | theMap, modelId); | |
1718 | } | |
1719 | 0 | if (showLinkedFeatures) |
1720 | { | |
1721 | 0 | scanComplementFeatures(complementRenderer, structureMapping, |
1722 | seq, theMap, modelId); | |
1723 | } | |
1724 | } | |
1725 | } | |
1726 | } | |
1727 | } | |
1728 | 0 | return theMap; |
1729 | } | |
1730 | ||
1731 | /** | |
1732 | * Ask the structure viewer to open a session file. Returns true if | |
1733 | * successful, else false (or not supported). | |
1734 | * | |
1735 | * @param filepath | |
1736 | * @return | |
1737 | */ | |
1738 | 0 | public boolean openSession(String filepath) |
1739 | { | |
1740 | 0 | StructureCommandI cmd = getCommandGenerator().openSession(filepath); |
1741 | 0 | if (cmd == null) |
1742 | { | |
1743 | 0 | return false; |
1744 | } | |
1745 | 0 | executeCommand(cmd, true); |
1746 | // todo: test for failure - how? | |
1747 | 0 | return true; |
1748 | } | |
1749 | ||
1750 | /** | |
1751 | * Scans visible features in mapped positions of the CDS/peptide complement, | |
1752 | * and adds any found to the map of attribute values/structure positions | |
1753 | * | |
1754 | * @param complementRenderer | |
1755 | * @param structureMapping | |
1756 | * @param seq | |
1757 | * @param theMap | |
1758 | * @param modelNumber | |
1759 | */ | |
1760 | 0 | protected static void scanComplementFeatures( |
1761 | FeatureRenderer complementRenderer, | |
1762 | StructureMapping structureMapping, SequenceI seq, | |
1763 | Map<String, Map<Object, AtomSpecModel>> theMap, | |
1764 | String modelNumber) | |
1765 | { | |
1766 | /* | |
1767 | * for each sequence residue mapped to a structure position... | |
1768 | */ | |
1769 | 0 | for (int seqPos : structureMapping.getMapping().keySet()) |
1770 | { | |
1771 | /* | |
1772 | * find visible complementary features at mapped position(s) | |
1773 | */ | |
1774 | 0 | MappedFeatures mf = complementRenderer |
1775 | .findComplementFeaturesAtResidue(seq, seqPos); | |
1776 | 0 | if (mf != null) |
1777 | { | |
1778 | 0 | for (SequenceFeature sf : mf.features) |
1779 | { | |
1780 | 0 | String type = sf.getType(); |
1781 | ||
1782 | /* | |
1783 | * Don't copy features which originated from Chimera | |
1784 | */ | |
1785 | 0 | if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP |
1786 | .equals(sf.getFeatureGroup())) | |
1787 | { | |
1788 | 0 | continue; |
1789 | } | |
1790 | ||
1791 | /* | |
1792 | * record feature 'value' (score/description/type) as at the | |
1793 | * corresponding structure position | |
1794 | */ | |
1795 | 0 | List<int[]> mappedRanges = structureMapping |
1796 | .getPDBResNumRanges(seqPos, seqPos); | |
1797 | ||
1798 | 0 | if (!mappedRanges.isEmpty()) |
1799 | { | |
1800 | 0 | String value = sf.getDescription(); |
1801 | 0 | if (value == null || value.length() == 0) |
1802 | { | |
1803 | 0 | value = type; |
1804 | } | |
1805 | 0 | float score = sf.getScore(); |
1806 | 0 | if (score != 0f && !Float.isNaN(score)) |
1807 | { | |
1808 | 0 | value = Float.toString(score); |
1809 | } | |
1810 | 0 | Map<Object, AtomSpecModel> featureValues = theMap.get(type); |
1811 | 0 | if (featureValues == null) |
1812 | { | |
1813 | 0 | featureValues = new HashMap<>(); |
1814 | 0 | theMap.put(type, featureValues); |
1815 | } | |
1816 | 0 | for (int[] range : mappedRanges) |
1817 | { | |
1818 | 0 | addAtomSpecRange(featureValues, value, modelNumber, range[0], |
1819 | range[1], structureMapping.getChain()); | |
1820 | } | |
1821 | } | |
1822 | } | |
1823 | } | |
1824 | } | |
1825 | } | |
1826 | ||
1827 | /** | |
1828 | * Inspect features on the sequence; for each feature that is visible, | |
1829 | * determine its mapped ranges in the structure (if any) according to the | |
1830 | * given mapping, and add them to the map. | |
1831 | * | |
1832 | * @param visibleFeatures | |
1833 | * @param mapping | |
1834 | * @param seq | |
1835 | * @param theMap | |
1836 | * @param modelId | |
1837 | */ | |
1838 | 0 | protected static void scanSequenceFeatures(List<String> visibleFeatures, |
1839 | StructureMapping mapping, SequenceI seq, | |
1840 | Map<String, Map<Object, AtomSpecModel>> theMap, String modelId) | |
1841 | { | |
1842 | 0 | List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures( |
1843 | visibleFeatures.toArray(new String[visibleFeatures.size()])); | |
1844 | 0 | for (SequenceFeature sf : sfs) |
1845 | { | |
1846 | 0 | String type = sf.getType(); |
1847 | ||
1848 | /* | |
1849 | * Don't copy features which originated from Chimera | |
1850 | */ | |
1851 | 0 | if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP |
1852 | .equals(sf.getFeatureGroup())) | |
1853 | { | |
1854 | 0 | continue; |
1855 | } | |
1856 | ||
1857 | 0 | List<int[]> mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(), |
1858 | sf.getEnd()); | |
1859 | ||
1860 | 0 | if (!mappedRanges.isEmpty()) |
1861 | { | |
1862 | 0 | String value = sf.getDescription(); |
1863 | 0 | if (value == null || value.length() == 0) |
1864 | { | |
1865 | 0 | value = type; |
1866 | } | |
1867 | 0 | float score = sf.getScore(); |
1868 | 0 | if (score != 0f && !Float.isNaN(score)) |
1869 | { | |
1870 | 0 | value = Float.toString(score); |
1871 | } | |
1872 | 0 | Map<Object, AtomSpecModel> featureValues = theMap.get(type); |
1873 | 0 | if (featureValues == null) |
1874 | { | |
1875 | 0 | featureValues = new HashMap<>(); |
1876 | 0 | theMap.put(type, featureValues); |
1877 | } | |
1878 | 0 | for (int[] range : mappedRanges) |
1879 | { | |
1880 | 0 | addAtomSpecRange(featureValues, value, modelId, range[0], |
1881 | range[1], mapping.getChain()); | |
1882 | } | |
1883 | } | |
1884 | } | |
1885 | } | |
1886 | ||
1887 | /** | |
1888 | * Returns the number of structure files in the structure viewer and mapped to | |
1889 | * Jalview. This may be zero if the files are still in the process of loading | |
1890 | * in the viewer. | |
1891 | * | |
1892 | * @return | |
1893 | */ | |
1894 | 150 | public int getMappedStructureCount() |
1895 | { | |
1896 | 150 | String[] files = getStructureFiles(); |
1897 | 150 | return files == null ? 0 : files.length; |
1898 | } | |
1899 | ||
1900 | /** | |
1901 | * Starts a thread that waits for the external viewer program process to | |
1902 | * finish, so that we can then close the associated resources. This avoids | |
1903 | * leaving orphaned viewer panels in Jalview if the user closes the external | |
1904 | * viewer. | |
1905 | * | |
1906 | * @param p | |
1907 | */ | |
1908 | 0 | protected void startExternalViewerMonitor(Process p) |
1909 | { | |
1910 | 0 | externalViewerMonitor = new Thread(new Runnable() |
1911 | { | |
1912 | ||
1913 | 0 | @Override |
1914 | public void run() | |
1915 | { | |
1916 | 0 | try |
1917 | { | |
1918 | 0 | p.waitFor(); |
1919 | 0 | JalviewStructureDisplayI display = getViewer(); |
1920 | 0 | if (display != null) |
1921 | { | |
1922 | 0 | display.closeViewer(false); |
1923 | } | |
1924 | } catch (InterruptedException e) | |
1925 | { | |
1926 | // exit thread if Chimera Viewer is closed in Jalview | |
1927 | } | |
1928 | } | |
1929 | }); | |
1930 | 0 | externalViewerMonitor.start(); |
1931 | } | |
1932 | ||
1933 | /** | |
1934 | * If supported by the external structure viewer, sends it commands to notify | |
1935 | * model or selection changes to the specified URL (where Jalview has started | |
1936 | * a listener) | |
1937 | * | |
1938 | * @param uri | |
1939 | */ | |
1940 | 0 | protected void startListening(String uri) |
1941 | { | |
1942 | 0 | List<StructureCommandI> commands = getCommandGenerator() |
1943 | .startNotifications(uri); | |
1944 | 0 | if (commands != null) |
1945 | { | |
1946 | 0 | executeCommands(commands, false, null); |
1947 | } | |
1948 | } | |
1949 | ||
1950 | /** | |
1951 | * If supported by the external structure viewer, sends it commands to stop | |
1952 | * notifying model or selection changes | |
1953 | */ | |
1954 | 23 | protected void stopListening() |
1955 | { | |
1956 | 23 | List<StructureCommandI> commands = getCommandGenerator() |
1957 | .stopNotifications(); | |
1958 | 23 | if (commands != null) |
1959 | { | |
1960 | 0 | executeCommands(commands, false, null); |
1961 | } | |
1962 | } | |
1963 | ||
1964 | /** | |
1965 | * If supported by the structure viewer, queries it for all residue attributes | |
1966 | * with the given attribute name, and creates features on corresponding | |
1967 | * residues of the alignment. Returns the number of features added. | |
1968 | * | |
1969 | * @param attName | |
1970 | * @param alignmentPanel | |
1971 | * @return | |
1972 | */ | |
1973 | 0 | public int copyStructureAttributesToFeatures(String attName, |
1974 | AlignmentPanel alignmentPanel) | |
1975 | { | |
1976 | 0 | StructureCommandI cmd = getCommandGenerator() |
1977 | .getResidueAttributes(attName); | |
1978 | 0 | if (cmd == null) |
1979 | { | |
1980 | 0 | return 0; |
1981 | } | |
1982 | 0 | List<String> residueAttributes = executeCommand(cmd, true); |
1983 | ||
1984 | 0 | int featuresAdded = createFeaturesForAttributes(attName, |
1985 | residueAttributes); | |
1986 | 0 | if (featuresAdded > 0) |
1987 | { | |
1988 | 0 | alignmentPanel.getFeatureRenderer().featuresAdded(); |
1989 | } | |
1990 | 0 | return featuresAdded; |
1991 | } | |
1992 | ||
1993 | /** | |
1994 | * Parses {@code residueAttributes} and creates sequence features on any | |
1995 | * mapped alignment residues. Returns the number of features created. | |
1996 | * <p> | |
1997 | * {@code residueAttributes} is the reply from the structure viewer to a | |
1998 | * command to list any residue attributes for the given attribute name. Syntax | |
1999 | * and parsing of this is viewer-specific. | |
2000 | * | |
2001 | * @param attName | |
2002 | * @param residueAttributes | |
2003 | * @return | |
2004 | */ | |
2005 | 0 | protected int createFeaturesForAttributes(String attName, |
2006 | List<String> residueAttributes) | |
2007 | { | |
2008 | 0 | return 0; |
2009 | } | |
2010 | ||
2011 | /** | |
2012 | * list the ligands available for display/hiding in the current view | |
2013 | * | |
2014 | * @return HETATM CODE:Molecule name | |
2015 | */ | |
2016 | 0 | public Map<String, String> getHetatmNames() |
2017 | { | |
2018 | 0 | return Collections.EMPTY_MAP; |
2019 | } | |
2020 | ||
2021 | /** | |
2022 | * Generates and executes a command to show the given hetatm types as CPK | |
2023 | * | |
2024 | * @param toShow | |
2025 | * - one or more of strings from getHetatmNames | |
2026 | */ | |
2027 | 0 | public void showHetatms(List<String> toShow) |
2028 | { | |
2029 | 0 | executeCommands(commandGenerator.showHetatms(toShow), false, |
2030 | "Adjusting hetatm visibility"); | |
2031 | } | |
2032 | ||
2033 | } |