Class |
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Actions |
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JalviewLite | 87 | 612 | 293 | ||
JalviewLite.LoadJmolThread | 1791 | 16 | 9 | ||
JalviewLite.LoadingThread | 1840 | 231 | 81 |
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.bin; | |
22 | ||
23 | import java.applet.Applet; | |
24 | import java.awt.Button; | |
25 | import java.awt.Color; | |
26 | import java.awt.Component; | |
27 | import java.awt.EventQueue; | |
28 | import java.awt.Font; | |
29 | import java.awt.Frame; | |
30 | import java.awt.Graphics; | |
31 | import java.awt.event.ActionEvent; | |
32 | import java.awt.event.WindowAdapter; | |
33 | import java.awt.event.WindowEvent; | |
34 | import java.io.BufferedReader; | |
35 | import java.io.IOException; | |
36 | import java.io.InputStreamReader; | |
37 | import java.net.URL; | |
38 | import java.util.ArrayList; | |
39 | import java.util.Hashtable; | |
40 | import java.util.List; | |
41 | import java.util.Locale; | |
42 | import java.util.StringTokenizer; | |
43 | import java.util.Vector; | |
44 | ||
45 | import jalview.analysis.AlignmentUtils; | |
46 | import jalview.api.StructureSelectionManagerProvider; | |
47 | import jalview.appletgui.AlignFrame; | |
48 | import jalview.appletgui.AlignViewport; | |
49 | import jalview.appletgui.EmbmenuFrame; | |
50 | import jalview.appletgui.FeatureSettings; | |
51 | import jalview.appletgui.SplitFrame; | |
52 | import jalview.datamodel.Alignment; | |
53 | import jalview.datamodel.AlignmentI; | |
54 | import jalview.datamodel.AlignmentOrder; | |
55 | import jalview.datamodel.ColumnSelection; | |
56 | import jalview.datamodel.PDBEntry; | |
57 | import jalview.datamodel.Sequence; | |
58 | import jalview.datamodel.SequenceGroup; | |
59 | import jalview.datamodel.SequenceI; | |
60 | import jalview.io.AnnotationFile; | |
61 | import jalview.io.AppletFormatAdapter; | |
62 | import jalview.io.DataSourceType; | |
63 | import jalview.io.FileFormatI; | |
64 | import jalview.io.FileFormats; | |
65 | import jalview.io.FileParse; | |
66 | import jalview.io.IdentifyFile; | |
67 | import jalview.io.JPredFile; | |
68 | import jalview.io.JnetAnnotationMaker; | |
69 | import jalview.io.NewickFile; | |
70 | import jalview.javascript.JSFunctionExec; | |
71 | import jalview.javascript.JalviewLiteJsApi; | |
72 | import jalview.javascript.JsCallBack; | |
73 | import jalview.javascript.MouseOverStructureListener; | |
74 | import jalview.structure.SelectionListener; | |
75 | import jalview.structure.StructureSelectionManager; | |
76 | import jalview.util.ColorUtils; | |
77 | import jalview.util.HttpUtils; | |
78 | import jalview.util.MessageManager; | |
79 | import netscape.javascript.JSObject; | |
80 | ||
81 | /** | |
82 | * Jalview Applet. Runs in Java 1.18 runtime | |
83 | * | |
84 | * @author $author$ | |
85 | * @version $Revision: 1.92 $ | |
86 | */ | |
87 | public class JalviewLite extends Applet | |
88 | implements StructureSelectionManagerProvider, JalviewLiteJsApi | |
89 | { | |
90 | ||
91 | private static final String TRUE = "true"; | |
92 | ||
93 | private static final String FALSE = "false"; | |
94 | ||
95 | 0 | public StructureSelectionManager getStructureSelectionManager() |
96 | { | |
97 | 0 | return StructureSelectionManager.getStructureSelectionManager(this); |
98 | } | |
99 | ||
100 | // ///////////////////////////////////////// | |
101 | // The following public methods may be called | |
102 | // externally, eg via javascript in HTML page | |
103 | /* | |
104 | * (non-Javadoc) | |
105 | * | |
106 | * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences() | |
107 | */ | |
108 | 0 | @Override |
109 | public String getSelectedSequences() | |
110 | { | |
111 | 0 | return getSelectedSequencesFrom(getDefaultTargetFrame()); |
112 | } | |
113 | ||
114 | /* | |
115 | * (non-Javadoc) | |
116 | * | |
117 | * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String) | |
118 | */ | |
119 | 0 | @Override |
120 | public String getSelectedSequences(String sep) | |
121 | { | |
122 | 0 | return getSelectedSequencesFrom(getDefaultTargetFrame(), sep); |
123 | } | |
124 | ||
125 | /* | |
126 | * (non-Javadoc) | |
127 | * | |
128 | * @see | |
129 | * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui | |
130 | * .AlignFrame) | |
131 | */ | |
132 | 0 | @Override |
133 | public String getSelectedSequencesFrom(AlignFrame alf) | |
134 | { | |
135 | 0 | return getSelectedSequencesFrom(alf, separator); // ""+0x00AC); |
136 | } | |
137 | ||
138 | /* | |
139 | * (non-Javadoc) | |
140 | * | |
141 | * @see | |
142 | * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui | |
143 | * .AlignFrame, java.lang.String) | |
144 | */ | |
145 | 0 | @Override |
146 | public String getSelectedSequencesFrom(AlignFrame alf, String sep) | |
147 | { | |
148 | 0 | StringBuffer result = new StringBuffer(""); |
149 | 0 | if (sep == null || sep.length() == 0) |
150 | { | |
151 | 0 | sep = separator; // "+0x00AC; |
152 | } | |
153 | 0 | if (alf.viewport.getSelectionGroup() != null) |
154 | { | |
155 | 0 | SequenceI[] seqs = alf.viewport.getSelectionGroup() |
156 | .getSequencesInOrder(alf.viewport.getAlignment()); | |
157 | ||
158 | 0 | for (int i = 0; i < seqs.length; i++) |
159 | { | |
160 | 0 | result.append(seqs[i].getName()); |
161 | 0 | result.append(sep); |
162 | } | |
163 | } | |
164 | ||
165 | 0 | return result.toString(); |
166 | } | |
167 | ||
168 | /* | |
169 | * (non-Javadoc) | |
170 | * | |
171 | * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String, | |
172 | * java.lang.String, java.lang.String) | |
173 | */ | |
174 | 0 | @Override |
175 | public void highlight(String sequenceId, String position, | |
176 | String alignedPosition) | |
177 | { | |
178 | 0 | highlightIn(getDefaultTargetFrame(), sequenceId, position, |
179 | alignedPosition); | |
180 | } | |
181 | ||
182 | /* | |
183 | * (non-Javadoc) | |
184 | * | |
185 | * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame, | |
186 | * java.lang.String, java.lang.String, java.lang.String) | |
187 | */ | |
188 | 0 | @Override |
189 | public void highlightIn(final AlignFrame alf, final String sequenceId, | |
190 | final String position, final String alignedPosition) | |
191 | { | |
192 | // TODO: could try to highlight in all alignments if alf==null | |
193 | 0 | jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher( |
194 | alf.viewport.getAlignment().getSequencesArray()); | |
195 | 0 | final SequenceI sq = matcher.findIdMatch(sequenceId); |
196 | 0 | if (sq != null) |
197 | { | |
198 | 0 | int apos = -1; |
199 | 0 | try |
200 | { | |
201 | 0 | apos = Integer.valueOf(position).intValue(); |
202 | 0 | apos--; |
203 | } catch (NumberFormatException ex) | |
204 | { | |
205 | 0 | return; |
206 | } | |
207 | 0 | final StructureSelectionManagerProvider me = this; |
208 | 0 | final int pos = apos; |
209 | // use vamsas listener to broadcast to all listeners in scope | |
210 | 0 | if (alignedPosition != null |
211 | && (alignedPosition.trim().length() == 0 || alignedPosition | |
212 | .toLowerCase(Locale.ROOT).indexOf("false") > -1)) | |
213 | { | |
214 | 0 | java.awt.EventQueue.invokeLater(new Runnable() |
215 | { | |
216 | 0 | @Override |
217 | public void run() | |
218 | { | |
219 | 0 | StructureSelectionManager.getStructureSelectionManager(me) |
220 | .mouseOverVamsasSequence(sq, sq.findIndex(pos), null); | |
221 | } | |
222 | }); | |
223 | } | |
224 | else | |
225 | { | |
226 | 0 | java.awt.EventQueue.invokeLater(new Runnable() |
227 | { | |
228 | 0 | @Override |
229 | public void run() | |
230 | { | |
231 | 0 | StructureSelectionManager.getStructureSelectionManager(me) |
232 | .mouseOverVamsasSequence(sq, pos, null); | |
233 | } | |
234 | }); | |
235 | } | |
236 | } | |
237 | } | |
238 | ||
239 | /* | |
240 | * (non-Javadoc) | |
241 | * | |
242 | * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String, | |
243 | * java.lang.String) | |
244 | */ | |
245 | 0 | @Override |
246 | public void select(String sequenceIds, String columns) | |
247 | { | |
248 | 0 | selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator); |
249 | } | |
250 | ||
251 | /* | |
252 | * (non-Javadoc) | |
253 | * | |
254 | * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String, | |
255 | * java.lang.String, java.lang.String) | |
256 | */ | |
257 | 0 | @Override |
258 | public void select(String sequenceIds, String columns, String sep) | |
259 | { | |
260 | 0 | selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep); |
261 | } | |
262 | ||
263 | /* | |
264 | * (non-Javadoc) | |
265 | * | |
266 | * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame, | |
267 | * java.lang.String, java.lang.String) | |
268 | */ | |
269 | 0 | @Override |
270 | public void selectIn(AlignFrame alf, String sequenceIds, String columns) | |
271 | { | |
272 | 0 | selectIn(alf, sequenceIds, columns, separator); |
273 | } | |
274 | ||
275 | /* | |
276 | * (non-Javadoc) | |
277 | * | |
278 | * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame, | |
279 | * java.lang.String, java.lang.String, java.lang.String) | |
280 | */ | |
281 | 0 | @Override |
282 | public void selectIn(final AlignFrame alf, String sequenceIds, | |
283 | String columns, String sep) | |
284 | { | |
285 | 0 | if (sep == null || sep.length() == 0) |
286 | { | |
287 | 0 | sep = separator; |
288 | } | |
289 | else | |
290 | { | |
291 | 0 | if (debug) |
292 | { | |
293 | 0 | jalview.bin.Console |
294 | .errPrintln("Selecting region using separator string '" | |
295 | + separator + "'"); | |
296 | } | |
297 | } | |
298 | // deparse fields | |
299 | 0 | String[] ids = separatorListToArray(sequenceIds, sep); |
300 | 0 | String[] cols = separatorListToArray(columns, sep); |
301 | 0 | final SequenceGroup sel = new SequenceGroup(); |
302 | 0 | final ColumnSelection csel = new ColumnSelection(); |
303 | 0 | AlignmentI al = alf.viewport.getAlignment(); |
304 | 0 | jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher( |
305 | alf.viewport.getAlignment().getSequencesArray()); | |
306 | 0 | int start = 0, end = al.getWidth(), alw = al.getWidth(); |
307 | 0 | boolean seqsfound = true; |
308 | 0 | if (ids != null && ids.length > 0) |
309 | { | |
310 | 0 | seqsfound = false; |
311 | 0 | for (int i = 0; i < ids.length; i++) |
312 | { | |
313 | 0 | if (ids[i].trim().length() == 0) |
314 | { | |
315 | 0 | continue; |
316 | } | |
317 | 0 | SequenceI sq = matcher.findIdMatch(ids[i]); |
318 | 0 | if (sq != null) |
319 | { | |
320 | 0 | seqsfound = true; |
321 | 0 | sel.addSequence(sq, false); |
322 | } | |
323 | } | |
324 | } | |
325 | 0 | boolean inseqpos = false; |
326 | 0 | if (cols != null && cols.length > 0) |
327 | { | |
328 | 0 | boolean seset = false; |
329 | 0 | for (int i = 0; i < cols.length; i++) |
330 | { | |
331 | 0 | String cl = cols[i].trim(); |
332 | 0 | if (cl.length() == 0) |
333 | { | |
334 | 0 | continue; |
335 | } | |
336 | 0 | int p; |
337 | 0 | if ((p = cl.indexOf("-")) > -1) |
338 | { | |
339 | 0 | int from = -1, to = -1; |
340 | 0 | try |
341 | { | |
342 | 0 | from = Integer.valueOf(cl.substring(0, p)).intValue(); |
343 | 0 | from--; |
344 | } catch (NumberFormatException ex) | |
345 | { | |
346 | 0 | jalview.bin.Console.errPrintln( |
347 | "ERROR: Couldn't parse first integer in range element column selection string '" | |
348 | + cl + "' - format is 'from-to'"); | |
349 | 0 | return; |
350 | } | |
351 | 0 | try |
352 | { | |
353 | 0 | to = Integer.valueOf(cl.substring(p + 1)).intValue(); |
354 | 0 | to--; |
355 | } catch (NumberFormatException ex) | |
356 | { | |
357 | 0 | jalview.bin.Console.errPrintln( |
358 | "ERROR: Couldn't parse second integer in range element column selection string '" | |
359 | + cl + "' - format is 'from-to'"); | |
360 | 0 | return; |
361 | } | |
362 | 0 | if (from >= 0 && to >= 0) |
363 | { | |
364 | // valid range | |
365 | 0 | if (from < to) |
366 | { | |
367 | 0 | int t = to; |
368 | 0 | to = from; |
369 | 0 | to = t; |
370 | } | |
371 | 0 | if (!seset) |
372 | { | |
373 | 0 | start = from; |
374 | 0 | end = to; |
375 | 0 | seset = true; |
376 | } | |
377 | else | |
378 | { | |
379 | // comment to prevent range extension | |
380 | 0 | if (start > from) |
381 | { | |
382 | 0 | start = from; |
383 | } | |
384 | 0 | if (end < to) |
385 | { | |
386 | 0 | end = to; |
387 | } | |
388 | } | |
389 | 0 | for (int r = from; r <= to; r++) |
390 | { | |
391 | 0 | if (r >= 0 && r < alw) |
392 | { | |
393 | 0 | csel.addElement(r); |
394 | } | |
395 | } | |
396 | 0 | if (debug) |
397 | { | |
398 | 0 | jalview.bin.Console.errPrintln("Range '" + cl |
399 | + "' deparsed as [" + from + "," + to + "]"); | |
400 | } | |
401 | } | |
402 | else | |
403 | { | |
404 | 0 | jalview.bin.Console.errPrintln("ERROR: Invalid Range '" + cl |
405 | + "' deparsed as [" + from + "," + to + "]"); | |
406 | } | |
407 | } | |
408 | else | |
409 | { | |
410 | 0 | int r = -1; |
411 | 0 | try |
412 | { | |
413 | 0 | r = Integer.valueOf(cl).intValue(); |
414 | 0 | r--; |
415 | } catch (NumberFormatException ex) | |
416 | { | |
417 | 0 | if (cl.toLowerCase(Locale.ROOT).equals("sequence")) |
418 | { | |
419 | // we are in the dataset sequence's coordinate frame. | |
420 | 0 | inseqpos = true; |
421 | } | |
422 | else | |
423 | { | |
424 | 0 | jalview.bin.Console.errPrintln( |
425 | "ERROR: Couldn't parse integer from point selection element of column selection string '" | |
426 | + cl + "'"); | |
427 | 0 | return; |
428 | } | |
429 | } | |
430 | 0 | if (r >= 0 && r <= alw) |
431 | { | |
432 | 0 | if (!seset) |
433 | { | |
434 | 0 | start = r; |
435 | 0 | end = r; |
436 | 0 | seset = true; |
437 | } | |
438 | else | |
439 | { | |
440 | // comment to prevent range extension | |
441 | 0 | if (start > r) |
442 | { | |
443 | 0 | start = r; |
444 | } | |
445 | 0 | if (end < r) |
446 | { | |
447 | 0 | end = r; |
448 | } | |
449 | } | |
450 | 0 | csel.addElement(r); |
451 | 0 | if (debug) |
452 | { | |
453 | 0 | jalview.bin.Console.errPrintln("Point selection '" + cl |
454 | + "' deparsed as [" + r + "]"); | |
455 | } | |
456 | } | |
457 | else | |
458 | { | |
459 | 0 | jalview.bin.Console |
460 | .errPrintln("ERROR: Invalid Point selection '" + cl | |
461 | + "' deparsed as [" + r + "]"); | |
462 | } | |
463 | } | |
464 | } | |
465 | } | |
466 | 0 | if (seqsfound) |
467 | { | |
468 | // we only propagate the selection when it was the null selection, or the | |
469 | // given sequences were found in the alignment. | |
470 | 0 | if (inseqpos && sel.getSize() > 0) |
471 | { | |
472 | // assume first sequence provides reference frame ? | |
473 | 0 | SequenceI rs = sel.getSequenceAt(0); |
474 | 0 | start = rs.findIndex(start); |
475 | 0 | end = rs.findIndex(end); |
476 | 0 | List<Integer> cs = new ArrayList<>(csel.getSelected()); |
477 | 0 | csel.clear(); |
478 | 0 | for (Integer selectedCol : cs) |
479 | { | |
480 | 0 | csel.addElement(rs.findIndex(selectedCol)); |
481 | } | |
482 | } | |
483 | 0 | sel.setStartRes(start); |
484 | 0 | sel.setEndRes(end); |
485 | 0 | EventQueue.invokeLater(new Runnable() |
486 | { | |
487 | 0 | @Override |
488 | public void run() | |
489 | { | |
490 | 0 | alf.select(sel, csel, |
491 | alf.getAlignViewport().getAlignment().getHiddenColumns()); | |
492 | } | |
493 | }); | |
494 | } | |
495 | } | |
496 | ||
497 | /* | |
498 | * (non-Javadoc) | |
499 | * | |
500 | * @see | |
501 | * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang. | |
502 | * String, java.lang.String) | |
503 | */ | |
504 | 0 | @Override |
505 | public String getSelectedSequencesAsAlignment(String format, | |
506 | String suffix) | |
507 | { | |
508 | 0 | return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(), |
509 | format, suffix); | |
510 | } | |
511 | ||
512 | /* | |
513 | * (non-Javadoc) | |
514 | * | |
515 | * @see | |
516 | * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview | |
517 | * .appletgui.AlignFrame, java.lang.String, java.lang.String) | |
518 | */ | |
519 | 0 | @Override |
520 | public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, | |
521 | String format, String suffix) | |
522 | { | |
523 | 0 | try |
524 | { | |
525 | 0 | FileFormatI theFormat = FileFormats.getInstance().forName(format); |
526 | 0 | boolean seqlimits = suffix.equalsIgnoreCase(TRUE); |
527 | 0 | if (alf.viewport.getSelectionGroup() != null) |
528 | { | |
529 | // JBPNote: getSelectionAsNewSequence behaviour has changed - this | |
530 | // method now returns a full copy of sequence data | |
531 | // TODO consider using getSequenceSelection instead here | |
532 | 0 | String reply = new AppletFormatAdapter().formatSequences(theFormat, |
533 | new Alignment(alf.viewport.getSelectionAsNewSequence()), | |
534 | seqlimits); | |
535 | 0 | return reply; |
536 | } | |
537 | } catch (IllegalArgumentException ex) | |
538 | { | |
539 | 0 | ex.printStackTrace(); |
540 | 0 | return "Error retrieving alignment, possibly invalid format specifier: " |
541 | + format; | |
542 | } | |
543 | 0 | return ""; |
544 | } | |
545 | ||
546 | /* | |
547 | * (non-Javadoc) | |
548 | * | |
549 | * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder() | |
550 | */ | |
551 | 0 | @Override |
552 | public String getAlignmentOrder() | |
553 | { | |
554 | 0 | return getAlignmentOrderFrom(getDefaultTargetFrame()); |
555 | } | |
556 | ||
557 | /* | |
558 | * (non-Javadoc) | |
559 | * | |
560 | * @see | |
561 | * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame | |
562 | * ) | |
563 | */ | |
564 | 0 | @Override |
565 | public String getAlignmentOrderFrom(AlignFrame alf) | |
566 | { | |
567 | 0 | return getAlignmentOrderFrom(alf, separator); |
568 | } | |
569 | ||
570 | /* | |
571 | * (non-Javadoc) | |
572 | * | |
573 | * @see | |
574 | * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame | |
575 | * , java.lang.String) | |
576 | */ | |
577 | 0 | @Override |
578 | public String getAlignmentOrderFrom(AlignFrame alf, String sep) | |
579 | { | |
580 | 0 | AlignmentI alorder = alf.getAlignViewport().getAlignment(); |
581 | 0 | String[] order = new String[alorder.getHeight()]; |
582 | 0 | for (int i = 0; i < order.length; i++) |
583 | { | |
584 | 0 | order[i] = alorder.getSequenceAt(i).getName(); |
585 | } | |
586 | 0 | return arrayToSeparatorList(order); |
587 | } | |
588 | ||
589 | /* | |
590 | * (non-Javadoc) | |
591 | * | |
592 | * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String, | |
593 | * java.lang.String) | |
594 | */ | |
595 | 0 | @Override |
596 | public String orderBy(String order, String undoName) | |
597 | { | |
598 | 0 | return orderBy(order, undoName, separator); |
599 | } | |
600 | ||
601 | /* | |
602 | * (non-Javadoc) | |
603 | * | |
604 | * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String, | |
605 | * java.lang.String, java.lang.String) | |
606 | */ | |
607 | 0 | @Override |
608 | public String orderBy(String order, String undoName, String sep) | |
609 | { | |
610 | 0 | return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep); |
611 | } | |
612 | ||
613 | /* | |
614 | * (non-Javadoc) | |
615 | * | |
616 | * @see | |
617 | * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame, | |
618 | * java.lang.String, java.lang.String, java.lang.String) | |
619 | */ | |
620 | 0 | @Override |
621 | public String orderAlignmentBy(AlignFrame alf, String order, | |
622 | String undoName, String sep) | |
623 | { | |
624 | 0 | String[] ids = separatorListToArray(order, sep); |
625 | 0 | SequenceI[] sqs = null; |
626 | 0 | if (ids != null && ids.length > 0) |
627 | { | |
628 | 0 | jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher( |
629 | alf.viewport.getAlignment().getSequencesArray()); | |
630 | 0 | int s = 0; |
631 | 0 | sqs = new SequenceI[ids.length]; |
632 | 0 | for (int i = 0; i < ids.length; i++) |
633 | { | |
634 | 0 | if (ids[i].trim().length() == 0) |
635 | { | |
636 | 0 | continue; |
637 | } | |
638 | 0 | SequenceI sq = matcher.findIdMatch(ids[i]); |
639 | 0 | if (sq != null) |
640 | { | |
641 | 0 | sqs[s++] = sq; |
642 | } | |
643 | } | |
644 | 0 | if (s > 0) |
645 | { | |
646 | 0 | SequenceI[] sqq = new SequenceI[s]; |
647 | 0 | System.arraycopy(sqs, 0, sqq, 0, s); |
648 | 0 | sqs = sqq; |
649 | } | |
650 | else | |
651 | { | |
652 | 0 | sqs = null; |
653 | } | |
654 | } | |
655 | 0 | if (sqs == null) |
656 | { | |
657 | 0 | return ""; |
658 | } | |
659 | 0 | ; |
660 | 0 | final AlignmentOrder aorder = new AlignmentOrder(sqs); |
661 | ||
662 | 0 | if (undoName != null && undoName.trim().length() == 0) |
663 | { | |
664 | 0 | undoName = null; |
665 | } | |
666 | 0 | final String _undoName = undoName; |
667 | // TODO: deal with synchronization here: cannot raise any events until after | |
668 | // this has returned. | |
669 | 0 | return alf.sortBy(aorder, _undoName) ? TRUE : ""; |
670 | } | |
671 | ||
672 | /* | |
673 | * (non-Javadoc) | |
674 | * | |
675 | * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String) | |
676 | */ | |
677 | 0 | @Override |
678 | public String getAlignment(String format) | |
679 | { | |
680 | 0 | return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE); |
681 | } | |
682 | ||
683 | /* | |
684 | * (non-Javadoc) | |
685 | * | |
686 | * @see | |
687 | * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame, | |
688 | * java.lang.String) | |
689 | */ | |
690 | 0 | @Override |
691 | public String getAlignmentFrom(AlignFrame alf, String format) | |
692 | { | |
693 | 0 | return getAlignmentFrom(alf, format, TRUE); |
694 | } | |
695 | ||
696 | /* | |
697 | * (non-Javadoc) | |
698 | * | |
699 | * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String, | |
700 | * java.lang.String) | |
701 | */ | |
702 | 0 | @Override |
703 | public String getAlignment(String format, String suffix) | |
704 | { | |
705 | 0 | return getAlignmentFrom(getDefaultTargetFrame(), format, suffix); |
706 | } | |
707 | ||
708 | /* | |
709 | * (non-Javadoc) | |
710 | * | |
711 | * @see | |
712 | * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame, | |
713 | * java.lang.String, java.lang.String) | |
714 | */ | |
715 | 0 | @Override |
716 | public String getAlignmentFrom(AlignFrame alf, String format, | |
717 | String suffix) | |
718 | { | |
719 | 0 | try |
720 | { | |
721 | 0 | boolean seqlimits = suffix.equalsIgnoreCase(TRUE); |
722 | ||
723 | 0 | FileFormatI theFormat = FileFormats.getInstance().forName(format); |
724 | 0 | String reply = new AppletFormatAdapter().formatSequences(theFormat, |
725 | alf.viewport.getAlignment(), seqlimits); | |
726 | 0 | return reply; |
727 | } catch (IllegalArgumentException ex) | |
728 | { | |
729 | 0 | ex.printStackTrace(); |
730 | 0 | return "Error retrieving alignment, possibly invalid format specifier: " |
731 | + format; | |
732 | } | |
733 | } | |
734 | ||
735 | /* | |
736 | * (non-Javadoc) | |
737 | * | |
738 | * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String) | |
739 | */ | |
740 | 0 | @Override |
741 | public void loadAnnotation(String annotation) | |
742 | { | |
743 | 0 | loadAnnotationFrom(getDefaultTargetFrame(), annotation); |
744 | } | |
745 | ||
746 | /* | |
747 | * (non-Javadoc) | |
748 | * | |
749 | * @see | |
750 | * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame | |
751 | * , java.lang.String) | |
752 | */ | |
753 | 0 | @Override |
754 | public void loadAnnotationFrom(AlignFrame alf, String annotation) | |
755 | { | |
756 | 0 | if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(), |
757 | annotation, DataSourceType.PASTE)) | |
758 | { | |
759 | 0 | alf.alignPanel.fontChanged(); |
760 | 0 | alf.alignPanel.setScrollValues(0, 0); |
761 | } | |
762 | else | |
763 | { | |
764 | 0 | alf.parseFeaturesFile(annotation, DataSourceType.PASTE); |
765 | } | |
766 | } | |
767 | ||
768 | /* | |
769 | * (non-Javadoc) | |
770 | * | |
771 | * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String) | |
772 | */ | |
773 | 0 | @Override |
774 | public void loadFeatures(String features, boolean autoenabledisplay) | |
775 | { | |
776 | 0 | loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay); |
777 | } | |
778 | ||
779 | /* | |
780 | * (non-Javadoc) | |
781 | * | |
782 | * @see | |
783 | * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame | |
784 | * , java.lang.String) | |
785 | */ | |
786 | 0 | @Override |
787 | public boolean loadFeaturesFrom(AlignFrame alf, String features, | |
788 | boolean autoenabledisplay) | |
789 | { | |
790 | 0 | return alf.parseFeaturesFile(features, DataSourceType.PASTE, |
791 | autoenabledisplay); | |
792 | } | |
793 | ||
794 | /* | |
795 | * (non-Javadoc) | |
796 | * | |
797 | * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String) | |
798 | */ | |
799 | 0 | @Override |
800 | public String getFeatures(String format) | |
801 | { | |
802 | 0 | return getFeaturesFrom(getDefaultTargetFrame(), format); |
803 | } | |
804 | ||
805 | /* | |
806 | * (non-Javadoc) | |
807 | * | |
808 | * @see | |
809 | * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame, | |
810 | * java.lang.String) | |
811 | */ | |
812 | 0 | @Override |
813 | public String getFeaturesFrom(AlignFrame alf, String format) | |
814 | { | |
815 | 0 | return alf.outputFeatures(false, format); |
816 | } | |
817 | ||
818 | /* | |
819 | * (non-Javadoc) | |
820 | * | |
821 | * @see jalview.bin.JalviewLiteJsApi#getAnnotation() | |
822 | */ | |
823 | 0 | @Override |
824 | public String getAnnotation() | |
825 | { | |
826 | 0 | return getAnnotationFrom(getDefaultTargetFrame()); |
827 | } | |
828 | ||
829 | /* | |
830 | * (non-Javadoc) | |
831 | * | |
832 | * @see | |
833 | * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame | |
834 | * ) | |
835 | */ | |
836 | 0 | @Override |
837 | public String getAnnotationFrom(AlignFrame alf) | |
838 | { | |
839 | 0 | return alf.outputAnnotations(false); |
840 | } | |
841 | ||
842 | /* | |
843 | * (non-Javadoc) | |
844 | * | |
845 | * @see jalview.bin.JalviewLiteJsApi#newView() | |
846 | */ | |
847 | 0 | @Override |
848 | public AlignFrame newView() | |
849 | { | |
850 | 0 | return newViewFrom(getDefaultTargetFrame()); |
851 | } | |
852 | ||
853 | /* | |
854 | * (non-Javadoc) | |
855 | * | |
856 | * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String) | |
857 | */ | |
858 | 0 | @Override |
859 | public AlignFrame newView(String name) | |
860 | { | |
861 | 0 | return newViewFrom(getDefaultTargetFrame(), name); |
862 | } | |
863 | ||
864 | /* | |
865 | * (non-Javadoc) | |
866 | * | |
867 | * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame) | |
868 | */ | |
869 | 0 | @Override |
870 | public AlignFrame newViewFrom(AlignFrame alf) | |
871 | { | |
872 | 0 | return alf.newView(null); |
873 | } | |
874 | ||
875 | /* | |
876 | * (non-Javadoc) | |
877 | * | |
878 | * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame, | |
879 | * java.lang.String) | |
880 | */ | |
881 | 0 | @Override |
882 | public AlignFrame newViewFrom(AlignFrame alf, String name) | |
883 | { | |
884 | 0 | return alf.newView(name); |
885 | } | |
886 | ||
887 | /* | |
888 | * (non-Javadoc) | |
889 | * | |
890 | * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String, | |
891 | * java.lang.String) | |
892 | */ | |
893 | 0 | @Override |
894 | public AlignFrame loadAlignment(String text, String title) | |
895 | { | |
896 | 0 | AlignmentI al = null; |
897 | ||
898 | 0 | try |
899 | { | |
900 | 0 | FileFormatI format = new IdentifyFile().identify(text, |
901 | DataSourceType.PASTE); | |
902 | 0 | al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE, |
903 | format); | |
904 | 0 | if (al.getHeight() > 0) |
905 | { | |
906 | 0 | return new AlignFrame(al, this, title, false); |
907 | } | |
908 | } catch (IOException ex) | |
909 | { | |
910 | 0 | ex.printStackTrace(); |
911 | } | |
912 | 0 | return null; |
913 | } | |
914 | ||
915 | /* | |
916 | * (non-Javadoc) | |
917 | * | |
918 | * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String) | |
919 | */ | |
920 | 0 | @Override |
921 | public void setMouseoverListener(String listener) | |
922 | { | |
923 | 0 | setMouseoverListener(currentAlignFrame, listener); |
924 | } | |
925 | ||
926 | private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<>(); | |
927 | ||
928 | /* | |
929 | * (non-Javadoc) | |
930 | * | |
931 | * @see | |
932 | * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame | |
933 | * , java.lang.String) | |
934 | */ | |
935 | 0 | @Override |
936 | public void setMouseoverListener(AlignFrame af, String listener) | |
937 | { | |
938 | 0 | if (listener != null) |
939 | { | |
940 | 0 | listener = listener.trim(); |
941 | 0 | if (listener.length() == 0) |
942 | { | |
943 | 0 | jalview.bin.Console.errPrintln( |
944 | "jalview Javascript error: Ignoring empty function for mouseover listener."); | |
945 | 0 | return; |
946 | } | |
947 | } | |
948 | 0 | jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener( |
949 | this, af, listener); | |
950 | 0 | javascriptListeners.addElement(mol); |
951 | 0 | StructureSelectionManager.getStructureSelectionManager(this) |
952 | .addStructureViewerListener(mol); | |
953 | 0 | if (debug) |
954 | { | |
955 | 0 | jalview.bin.Console.errPrintln("Added a mouseover listener for " |
956 | 0 | + ((af == null) ? "All frames" |
957 | : "Just views for " | |
958 | + af.getAlignViewport().getSequenceSetId())); | |
959 | 0 | jalview.bin.Console.errPrintln("There are now " |
960 | + javascriptListeners.size() + " listeners in total."); | |
961 | } | |
962 | } | |
963 | ||
964 | /* | |
965 | * (non-Javadoc) | |
966 | * | |
967 | * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String) | |
968 | */ | |
969 | 0 | @Override |
970 | public void setSelectionListener(String listener) | |
971 | { | |
972 | 0 | setSelectionListener(null, listener); |
973 | } | |
974 | ||
975 | /* | |
976 | * (non-Javadoc) | |
977 | * | |
978 | * @see | |
979 | * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame | |
980 | * , java.lang.String) | |
981 | */ | |
982 | 0 | @Override |
983 | public void setSelectionListener(AlignFrame af, String listener) | |
984 | { | |
985 | 0 | if (listener != null) |
986 | { | |
987 | 0 | listener = listener.trim(); |
988 | 0 | if (listener.length() == 0) |
989 | { | |
990 | 0 | jalview.bin.Console.errPrintln( |
991 | "jalview Javascript error: Ignoring empty function for selection listener."); | |
992 | 0 | return; |
993 | } | |
994 | } | |
995 | 0 | jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender( |
996 | this, af, listener); | |
997 | 0 | javascriptListeners.addElement(mol); |
998 | 0 | StructureSelectionManager.getStructureSelectionManager(this) |
999 | .addSelectionListener(mol); | |
1000 | 0 | if (debug) |
1001 | { | |
1002 | 0 | jalview.bin.Console.errPrintln("Added a selection listener for " |
1003 | 0 | + ((af == null) ? "All frames" |
1004 | : "Just views for " | |
1005 | + af.getAlignViewport().getSequenceSetId())); | |
1006 | 0 | jalview.bin.Console.errPrintln("There are now " |
1007 | + javascriptListeners.size() + " listeners in total."); | |
1008 | } | |
1009 | } | |
1010 | ||
1011 | /** | |
1012 | * Callable from javascript to register a javascript function to pass events | |
1013 | * to a structure viewer. | |
1014 | * | |
1015 | * @param listener | |
1016 | * the name of a javascript function | |
1017 | * @param modelSet | |
1018 | * a token separated list of PDB file names listened for | |
1019 | * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String, | |
1020 | * java.lang.String) | |
1021 | */ | |
1022 | 0 | @Override |
1023 | public void setStructureListener(String listener, String modelSet) | |
1024 | { | |
1025 | 0 | if (listener != null) |
1026 | { | |
1027 | 0 | listener = listener.trim(); |
1028 | 0 | if (listener.length() == 0) |
1029 | { | |
1030 | 0 | jalview.bin.Console.errPrintln( |
1031 | "jalview Javascript error: Ignoring empty function for selection listener."); | |
1032 | 0 | return; |
1033 | } | |
1034 | } | |
1035 | 0 | MouseOverStructureListener mol = new MouseOverStructureListener(this, |
1036 | listener, separatorListToArray(modelSet)); | |
1037 | 0 | javascriptListeners.addElement(mol); |
1038 | 0 | StructureSelectionManager.getStructureSelectionManager(this) |
1039 | .addStructureViewerListener(mol); | |
1040 | 0 | if (debug) |
1041 | { | |
1042 | 0 | jalview.bin.Console |
1043 | .errPrintln("Added a javascript structure viewer listener '" | |
1044 | + listener + "'"); | |
1045 | 0 | jalview.bin.Console.errPrintln("There are now " |
1046 | + javascriptListeners.size() + " listeners in total."); | |
1047 | } | |
1048 | } | |
1049 | ||
1050 | /* | |
1051 | * (non-Javadoc) | |
1052 | * | |
1053 | * @see | |
1054 | * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui | |
1055 | * .AlignFrame, java.lang.String) | |
1056 | */ | |
1057 | 0 | @Override |
1058 | public void removeJavascriptListener(AlignFrame af, String listener) | |
1059 | { | |
1060 | 0 | if (listener != null) |
1061 | { | |
1062 | 0 | listener = listener.trim(); |
1063 | 0 | if (listener.length() == 0) |
1064 | { | |
1065 | 0 | listener = null; |
1066 | } | |
1067 | } | |
1068 | 0 | boolean rprt = false; |
1069 | 0 | for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;) |
1070 | { | |
1071 | 0 | Object lstn = javascriptListeners.elementAt(ms); |
1072 | 0 | JsCallBack lstner = (JsCallBack) lstn; |
1073 | 0 | if ((af == null || lstner.getAlignFrame() == af) && (listener == null |
1074 | || lstner.getListenerFunction().equals(listener))) | |
1075 | { | |
1076 | 0 | javascriptListeners.removeElement(lstner); |
1077 | 0 | msSize--; |
1078 | 0 | if (lstner instanceof SelectionListener) |
1079 | { | |
1080 | 0 | StructureSelectionManager.getStructureSelectionManager(this) |
1081 | .removeSelectionListener((SelectionListener) lstner); | |
1082 | } | |
1083 | else | |
1084 | { | |
1085 | 0 | StructureSelectionManager.getStructureSelectionManager(this) |
1086 | .removeStructureViewerListener(lstner, null); | |
1087 | } | |
1088 | 0 | rprt = debug; |
1089 | 0 | if (debug) |
1090 | { | |
1091 | 0 | jalview.bin.Console |
1092 | .errPrintln("Removed listener '" + listener + "'"); | |
1093 | } | |
1094 | } | |
1095 | else | |
1096 | { | |
1097 | 0 | ms++; |
1098 | } | |
1099 | } | |
1100 | 0 | if (rprt) |
1101 | { | |
1102 | 0 | jalview.bin.Console.errPrintln("There are now " |
1103 | + javascriptListeners.size() + " listeners in total."); | |
1104 | } | |
1105 | } | |
1106 | ||
1107 | 0 | @Override |
1108 | public void stop() | |
1109 | { | |
1110 | 0 | jalview.bin.Console.errPrintln("Applet " + getName() + " stop()."); |
1111 | 0 | tidyUp(); |
1112 | } | |
1113 | ||
1114 | 0 | @Override |
1115 | public void destroy() | |
1116 | { | |
1117 | 0 | jalview.bin.Console.errPrintln("Applet " + getName() + " destroy()."); |
1118 | 0 | tidyUp(); |
1119 | } | |
1120 | ||
1121 | 0 | private void tidyUp() |
1122 | { | |
1123 | 0 | removeAll(); |
1124 | 0 | if (currentAlignFrame != null && currentAlignFrame.viewport != null |
1125 | && currentAlignFrame.viewport.applet != null) | |
1126 | { | |
1127 | 0 | AlignViewport av = currentAlignFrame.viewport; |
1128 | 0 | currentAlignFrame.closeMenuItem_actionPerformed(); |
1129 | 0 | av.applet = null; |
1130 | 0 | currentAlignFrame = null; |
1131 | } | |
1132 | 0 | if (javascriptListeners != null) |
1133 | { | |
1134 | 0 | while (javascriptListeners.size() > 0) |
1135 | { | |
1136 | 0 | jalview.javascript.JSFunctionExec mol = javascriptListeners |
1137 | .elementAt(0); | |
1138 | 0 | javascriptListeners.removeElement(mol); |
1139 | 0 | if (mol instanceof SelectionListener) |
1140 | { | |
1141 | 0 | StructureSelectionManager.getStructureSelectionManager(this) |
1142 | .removeSelectionListener((SelectionListener) mol); | |
1143 | } | |
1144 | else | |
1145 | { | |
1146 | 0 | StructureSelectionManager.getStructureSelectionManager(this) |
1147 | .removeStructureViewerListener(mol, null); | |
1148 | } | |
1149 | 0 | mol.jvlite = null; |
1150 | } | |
1151 | } | |
1152 | 0 | if (jsFunctionExec != null) |
1153 | { | |
1154 | 0 | jsFunctionExec.stopQueue(); |
1155 | 0 | jsFunctionExec.jvlite = null; |
1156 | } | |
1157 | 0 | initialAlignFrame = null; |
1158 | 0 | jsFunctionExec = null; |
1159 | 0 | javascriptListeners = null; |
1160 | 0 | StructureSelectionManager.release(this); |
1161 | } | |
1162 | ||
1163 | private jalview.javascript.JSFunctionExec jsFunctionExec; | |
1164 | ||
1165 | /* | |
1166 | * (non-Javadoc) | |
1167 | * | |
1168 | * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String, | |
1169 | * java.lang.String, java.lang.String) | |
1170 | */ | |
1171 | 0 | @Override |
1172 | public void mouseOverStructure(final String pdbResNum, final String chain, | |
1173 | final String pdbfile) | |
1174 | { | |
1175 | 0 | final StructureSelectionManagerProvider me = this; |
1176 | 0 | java.awt.EventQueue.invokeLater(new Runnable() |
1177 | { | |
1178 | 0 | @Override |
1179 | public void run() | |
1180 | { | |
1181 | 0 | try |
1182 | { | |
1183 | 0 | StructureSelectionManager.getStructureSelectionManager(me) |
1184 | .mouseOverStructure(Integer.valueOf(pdbResNum).intValue(), | |
1185 | chain, pdbfile); | |
1186 | 0 | if (debug) |
1187 | { | |
1188 | 0 | System.err |
1189 | .println("mouseOver for '" + pdbResNum + "' in chain '" | |
1190 | + chain + "' in structure '" + pdbfile + "'"); | |
1191 | } | |
1192 | } catch (NumberFormatException e) | |
1193 | { | |
1194 | 0 | jalview.bin.Console |
1195 | .errPrintln("Ignoring invalid residue number string '" | |
1196 | + pdbResNum + "'"); | |
1197 | } | |
1198 | ||
1199 | } | |
1200 | }); | |
1201 | } | |
1202 | ||
1203 | /* | |
1204 | * (non-Javadoc) | |
1205 | * | |
1206 | * @see | |
1207 | * jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame, | |
1208 | * java.lang.String, java.lang.String) | |
1209 | */ | |
1210 | 0 | @Override |
1211 | public void scrollViewToIn(final AlignFrame alf, final String topRow, | |
1212 | final String leftHandColumn) | |
1213 | { | |
1214 | 0 | java.awt.EventQueue.invokeLater(new Runnable() |
1215 | { | |
1216 | 0 | @Override |
1217 | public void run() | |
1218 | { | |
1219 | 0 | try |
1220 | { | |
1221 | 0 | alf.scrollTo(Integer.valueOf(topRow).intValue(), |
1222 | Integer.valueOf(leftHandColumn).intValue()); | |
1223 | ||
1224 | } catch (Exception ex) | |
1225 | { | |
1226 | 0 | jalview.bin.Console |
1227 | .errPrintln("Couldn't parse integer arguments (topRow='" | |
1228 | + topRow + "' and leftHandColumn='" | |
1229 | + leftHandColumn + "')"); | |
1230 | 0 | ex.printStackTrace(); |
1231 | } | |
1232 | } | |
1233 | }); | |
1234 | } | |
1235 | ||
1236 | /* | |
1237 | * (non-Javadoc) | |
1238 | * | |
1239 | * @see | |
1240 | * jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui | |
1241 | * .AlignFrame, java.lang.String) | |
1242 | */ | |
1243 | 0 | @Override |
1244 | public void scrollViewToRowIn(final AlignFrame alf, final String topRow) | |
1245 | { | |
1246 | ||
1247 | 0 | java.awt.EventQueue.invokeLater(new Runnable() |
1248 | { | |
1249 | 0 | @Override |
1250 | public void run() | |
1251 | { | |
1252 | 0 | try |
1253 | { | |
1254 | 0 | alf.scrollToRow(Integer.valueOf(topRow).intValue()); |
1255 | ||
1256 | } catch (Exception ex) | |
1257 | { | |
1258 | 0 | jalview.bin.Console |
1259 | .errPrintln("Couldn't parse integer arguments (topRow='" | |
1260 | + topRow + "')"); | |
1261 | 0 | ex.printStackTrace(); |
1262 | } | |
1263 | ||
1264 | } | |
1265 | }); | |
1266 | } | |
1267 | ||
1268 | /* | |
1269 | * (non-Javadoc) | |
1270 | * | |
1271 | * @see | |
1272 | * jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui | |
1273 | * .AlignFrame, java.lang.String) | |
1274 | */ | |
1275 | 0 | @Override |
1276 | public void scrollViewToColumnIn(final AlignFrame alf, | |
1277 | final String leftHandColumn) | |
1278 | { | |
1279 | 0 | java.awt.EventQueue.invokeLater(new Runnable() |
1280 | { | |
1281 | ||
1282 | 0 | @Override |
1283 | public void run() | |
1284 | { | |
1285 | 0 | try |
1286 | { | |
1287 | 0 | alf.scrollToColumn(Integer.valueOf(leftHandColumn).intValue()); |
1288 | ||
1289 | } catch (Exception ex) | |
1290 | { | |
1291 | 0 | jalview.bin.Console.errPrintln( |
1292 | "Couldn't parse integer arguments (leftHandColumn='" | |
1293 | + leftHandColumn + "')"); | |
1294 | 0 | ex.printStackTrace(); |
1295 | } | |
1296 | } | |
1297 | }); | |
1298 | ||
1299 | } | |
1300 | ||
1301 | // ////////////////////////////////////////////// | |
1302 | // ////////////////////////////////////////////// | |
1303 | ||
1304 | public static int lastFrameX = 200; | |
1305 | ||
1306 | public static int lastFrameY = 200; | |
1307 | ||
1308 | boolean fileFound = true; | |
1309 | ||
1310 | String file = "No file"; | |
1311 | ||
1312 | String file2 = null; | |
1313 | ||
1314 | Button launcher = new Button( | |
1315 | MessageManager.getString("label.start_jalview")); | |
1316 | ||
1317 | /** | |
1318 | * The currentAlignFrame is static, it will change if and when the user | |
1319 | * selects a new window. Note that it will *never* point back to the embedded | |
1320 | * AlignFrame if the applet is started as embedded on the page and then | |
1321 | * afterwards a new view is created. | |
1322 | */ | |
1323 | public AlignFrame currentAlignFrame = null; | |
1324 | ||
1325 | /** | |
1326 | * This is the first frame to be displayed, and does not change. API calls | |
1327 | * will default to this instance if currentAlignFrame is null. | |
1328 | */ | |
1329 | AlignFrame initialAlignFrame = null; | |
1330 | ||
1331 | boolean embedded = false; | |
1332 | ||
1333 | private boolean checkForJmol = true; | |
1334 | ||
1335 | private boolean checkedForJmol = false; // ensure we don't check for jmol | |
1336 | ||
1337 | // every time the app is re-inited | |
1338 | ||
1339 | public boolean jmolAvailable = false; | |
1340 | ||
1341 | private boolean alignPdbStructures = false; | |
1342 | ||
1343 | /** | |
1344 | * use an external structure viewer exclusively (no jmols or mc_views will be | |
1345 | * opened by JalviewLite itself) | |
1346 | */ | |
1347 | public boolean useXtrnalSviewer = false; | |
1348 | ||
1349 | public static boolean debug = false; | |
1350 | ||
1351 | static String builddate = null, version = null, installation = null; | |
1352 | ||
1353 | 0 | private static void initBuildDetails() |
1354 | { | |
1355 | 0 | if (builddate == null) |
1356 | { | |
1357 | 0 | builddate = "unknown"; |
1358 | 0 | version = "test"; |
1359 | 0 | installation = "applet"; |
1360 | 0 | java.net.URL url = JalviewLite.class |
1361 | .getResource("/.build_properties"); | |
1362 | 0 | if (url != null) |
1363 | { | |
1364 | 0 | try |
1365 | { | |
1366 | 0 | BufferedReader reader = new BufferedReader( |
1367 | new InputStreamReader(HttpUtils.openStream(url))); | |
1368 | 0 | String line; |
1369 | 0 | while ((line = reader.readLine()) != null) |
1370 | { | |
1371 | 0 | if (line.indexOf("VERSION") > -1) |
1372 | { | |
1373 | 0 | version = line.substring(line.indexOf("=") + 1); |
1374 | } | |
1375 | 0 | if (line.indexOf("BUILD_DATE") > -1) |
1376 | { | |
1377 | 0 | builddate = line.substring(line.indexOf("=") + 1); |
1378 | } | |
1379 | 0 | if (line.indexOf("INSTALLATION") > -1) |
1380 | { | |
1381 | 0 | installation = line.substring(line.indexOf("=") + 1); |
1382 | } | |
1383 | } | |
1384 | } catch (Exception ex) | |
1385 | { | |
1386 | 0 | ex.printStackTrace(); |
1387 | } | |
1388 | } | |
1389 | } | |
1390 | } | |
1391 | ||
1392 | 0 | public static String getBuildDate() |
1393 | { | |
1394 | 0 | initBuildDetails(); |
1395 | 0 | return builddate; |
1396 | } | |
1397 | ||
1398 | 0 | public static String getInstallation() |
1399 | { | |
1400 | 0 | initBuildDetails(); |
1401 | 0 | return installation; |
1402 | } | |
1403 | ||
1404 | 0 | public static String getVersion() |
1405 | { | |
1406 | 0 | initBuildDetails(); |
1407 | 0 | return version; |
1408 | } | |
1409 | ||
1410 | // public JSObject scriptObject = null; | |
1411 | ||
1412 | /** | |
1413 | * init method for Jalview Applet | |
1414 | */ | |
1415 | 0 | @Override |
1416 | public void init() | |
1417 | { | |
1418 | 0 | debug = TRUE.equalsIgnoreCase(getParameter("debug")); |
1419 | 0 | try |
1420 | { | |
1421 | 0 | if (debug) |
1422 | { | |
1423 | 0 | jalview.bin.Console.errPrintln("Applet context is '" |
1424 | + getAppletContext().getClass().toString() + "'"); | |
1425 | } | |
1426 | 0 | JSObject scriptObject = JSObject.getWindow(this); |
1427 | 0 | if (debug && scriptObject != null) |
1428 | { | |
1429 | 0 | jalview.bin.Console |
1430 | .errPrintln("Applet has Javascript callback support."); | |
1431 | } | |
1432 | ||
1433 | } catch (Exception ex) | |
1434 | { | |
1435 | 0 | jalview.bin.Console.errPrintln( |
1436 | "Warning: No JalviewLite javascript callbacks available."); | |
1437 | 0 | if (debug) |
1438 | { | |
1439 | 0 | ex.printStackTrace(); |
1440 | } | |
1441 | } | |
1442 | ||
1443 | 0 | if (debug) |
1444 | { | |
1445 | 0 | jalview.bin.Console.errPrintln("JalviewLite Version " + getVersion()); |
1446 | 0 | jalview.bin.Console.errPrintln("Build Date : " + getBuildDate()); |
1447 | 0 | jalview.bin.Console.errPrintln("Installation : " + getInstallation()); |
1448 | } | |
1449 | 0 | String externalsviewer = getParameter("externalstructureviewer"); |
1450 | 0 | if (externalsviewer != null) |
1451 | { | |
1452 | 0 | useXtrnalSviewer = externalsviewer.trim().toLowerCase(Locale.ROOT) |
1453 | .equals(TRUE); | |
1454 | } | |
1455 | /** | |
1456 | * if true disable the check for jmol | |
1457 | */ | |
1458 | 0 | String chkforJmol = getParameter("nojmol"); |
1459 | 0 | if (chkforJmol != null) |
1460 | { | |
1461 | 0 | checkForJmol = !chkforJmol.equals(TRUE); |
1462 | } | |
1463 | /** | |
1464 | * get the separator parameter if present | |
1465 | */ | |
1466 | 0 | String sep = getParameter("separator"); |
1467 | 0 | if (sep != null) |
1468 | { | |
1469 | 0 | if (sep.length() > 0) |
1470 | { | |
1471 | 0 | separator = sep; |
1472 | 0 | if (debug) |
1473 | { | |
1474 | 0 | jalview.bin.Console |
1475 | .errPrintln("Separator set to '" + separator + "'"); | |
1476 | } | |
1477 | } | |
1478 | else | |
1479 | { | |
1480 | 0 | throw new Error(MessageManager |
1481 | .getString("error.invalid_separator_parameter")); | |
1482 | } | |
1483 | } | |
1484 | 0 | int r = 255; |
1485 | 0 | int g = 255; |
1486 | 0 | int b = 255; |
1487 | 0 | String param = getParameter("RGB"); |
1488 | ||
1489 | 0 | if (param != null) |
1490 | { | |
1491 | 0 | try |
1492 | { | |
1493 | 0 | r = Integer.parseInt(param.substring(0, 2), 16); |
1494 | 0 | g = Integer.parseInt(param.substring(2, 4), 16); |
1495 | 0 | b = Integer.parseInt(param.substring(4, 6), 16); |
1496 | } catch (Exception ex) | |
1497 | { | |
1498 | 0 | r = 255; |
1499 | 0 | g = 255; |
1500 | 0 | b = 255; |
1501 | } | |
1502 | } | |
1503 | 0 | param = getParameter("label"); |
1504 | 0 | if (param != null) |
1505 | { | |
1506 | 0 | launcher.setLabel(param); |
1507 | } | |
1508 | ||
1509 | 0 | setBackground(new Color(r, g, b)); |
1510 | ||
1511 | 0 | file = getParameter("file"); |
1512 | ||
1513 | 0 | if (file == null) |
1514 | { | |
1515 | // Maybe the sequences are added as parameters | |
1516 | 0 | StringBuffer data = new StringBuffer("PASTE"); |
1517 | 0 | int i = 1; |
1518 | 0 | while ((file = getParameter("sequence" + i)) != null) |
1519 | { | |
1520 | 0 | data.append(file.toString() + "\n"); |
1521 | 0 | i++; |
1522 | } | |
1523 | 0 | if (data.length() > 5) |
1524 | { | |
1525 | 0 | file = data.toString(); |
1526 | } | |
1527 | } | |
1528 | 0 | if (getDefaultParameter("enableSplitFrame", true)) |
1529 | { | |
1530 | 0 | file2 = getParameter("file2"); |
1531 | } | |
1532 | ||
1533 | 0 | embedded = TRUE.equalsIgnoreCase(getParameter("embedded")); |
1534 | 0 | if (embedded) |
1535 | { | |
1536 | 0 | LoadingThread loader = new LoadingThread(file, file2, this); |
1537 | 0 | loader.start(); |
1538 | } | |
1539 | 0 | else if (file != null) |
1540 | { | |
1541 | /* | |
1542 | * Start the applet immediately or show a button to start it | |
1543 | */ | |
1544 | 0 | if (FALSE.equalsIgnoreCase(getParameter("showbutton"))) |
1545 | { | |
1546 | 0 | LoadingThread loader = new LoadingThread(file, file2, this); |
1547 | 0 | loader.start(); |
1548 | } | |
1549 | else | |
1550 | { | |
1551 | 0 | add(launcher); |
1552 | 0 | launcher.addActionListener(new java.awt.event.ActionListener() |
1553 | { | |
1554 | 0 | @Override |
1555 | public void actionPerformed(ActionEvent e) | |
1556 | { | |
1557 | 0 | LoadingThread loader = new LoadingThread(file, file2, |
1558 | JalviewLite.this); | |
1559 | 0 | loader.start(); |
1560 | } | |
1561 | }); | |
1562 | } | |
1563 | } | |
1564 | else | |
1565 | { | |
1566 | // jalview initialisation with no alignment. loadAlignment() method can | |
1567 | // still be called to open new alignments. | |
1568 | 0 | file = "NO FILE"; |
1569 | 0 | fileFound = false; |
1570 | 0 | callInitCallback(); |
1571 | } | |
1572 | } | |
1573 | ||
1574 | 0 | private void initLiveConnect() |
1575 | { | |
1576 | // try really hard to get the liveConnect thing working | |
1577 | 0 | boolean notFailed = false; |
1578 | 0 | int tries = 0; |
1579 | 0 | while (!notFailed && tries < 10) |
1580 | { | |
1581 | 0 | if (tries > 0) |
1582 | { | |
1583 | 0 | jalview.bin.Console |
1584 | .errPrintln("LiveConnect request thread going to sleep."); | |
1585 | } | |
1586 | 0 | try |
1587 | { | |
1588 | 0 | Thread.sleep(700 * (1 + tries)); |
1589 | } catch (InterruptedException q) | |
1590 | { | |
1591 | } | |
1592 | 0 | ; |
1593 | 0 | if (tries++ > 0) |
1594 | { | |
1595 | 0 | jalview.bin.Console |
1596 | .errPrintln("LiveConnect request thread woken up."); | |
1597 | } | |
1598 | 0 | try |
1599 | { | |
1600 | 0 | JSObject scriptObject = JSObject.getWindow(this); |
1601 | 0 | if (scriptObject.eval("navigator") != null) |
1602 | { | |
1603 | 0 | notFailed = true; |
1604 | } | |
1605 | } catch (Exception jsex) | |
1606 | { | |
1607 | 0 | jalview.bin.Console.errPrintln("Attempt " + tries |
1608 | + " to access LiveConnect javascript failed."); | |
1609 | } | |
1610 | } | |
1611 | } | |
1612 | ||
1613 | 0 | private void callInitCallback() |
1614 | { | |
1615 | 0 | String initjscallback = getParameter("oninit"); |
1616 | 0 | if (initjscallback == null) |
1617 | { | |
1618 | 0 | return; |
1619 | } | |
1620 | 0 | initjscallback = initjscallback.trim(); |
1621 | 0 | if (initjscallback.length() > 0) |
1622 | { | |
1623 | 0 | JSObject scriptObject = null; |
1624 | 0 | try |
1625 | { | |
1626 | 0 | scriptObject = JSObject.getWindow(this); |
1627 | } catch (Exception ex) | |
1628 | { | |
1629 | } | |
1630 | 0 | ; |
1631 | // try really hard to let the browser plugin know we want liveconnect | |
1632 | 0 | initLiveConnect(); |
1633 | ||
1634 | 0 | if (scriptObject != null) |
1635 | { | |
1636 | 0 | try |
1637 | { | |
1638 | // do onInit with the JS executor thread | |
1639 | 0 | new JSFunctionExec(this).executeJavascriptFunction(true, |
1640 | initjscallback, null, | |
1641 | "Calling oninit callback '" + initjscallback + "'."); | |
1642 | } catch (Exception e) | |
1643 | { | |
1644 | 0 | jalview.bin.Console |
1645 | .errPrintln("Exception when executing _oninit callback '" | |
1646 | + initjscallback + "'."); | |
1647 | 0 | e.printStackTrace(); |
1648 | } | |
1649 | } | |
1650 | else | |
1651 | { | |
1652 | 0 | jalview.bin.Console.errPrintln("Not executing _oninit callback '" |
1653 | + initjscallback + "' - no scripting allowed."); | |
1654 | } | |
1655 | } | |
1656 | } | |
1657 | ||
1658 | /** | |
1659 | * Initialises and displays a new java.awt.Frame | |
1660 | * | |
1661 | * @param frame | |
1662 | * java.awt.Frame to be displayed | |
1663 | * @param title | |
1664 | * title of new frame | |
1665 | * @param width | |
1666 | * width if new frame | |
1667 | * @param height | |
1668 | * height of new frame | |
1669 | */ | |
1670 | 0 | public static void addFrame(final Frame frame, String title, int width, |
1671 | int height) | |
1672 | { | |
1673 | 0 | frame.setLocation(lastFrameX, lastFrameY); |
1674 | 0 | lastFrameX += 40; |
1675 | 0 | lastFrameY += 40; |
1676 | 0 | frame.setSize(width, height); |
1677 | 0 | frame.setTitle(title); |
1678 | 0 | frame.addWindowListener(new WindowAdapter() |
1679 | { | |
1680 | 0 | @Override |
1681 | public void windowClosing(WindowEvent e) | |
1682 | { | |
1683 | 0 | if (frame instanceof AlignFrame) |
1684 | { | |
1685 | 0 | AlignViewport vp = ((AlignFrame) frame).viewport; |
1686 | 0 | ((AlignFrame) frame).closeMenuItem_actionPerformed(); |
1687 | 0 | if (vp.applet.currentAlignFrame == frame) |
1688 | { | |
1689 | 0 | vp.applet.currentAlignFrame = null; |
1690 | } | |
1691 | 0 | vp.applet = null; |
1692 | 0 | vp = null; |
1693 | ||
1694 | } | |
1695 | 0 | lastFrameX -= 40; |
1696 | 0 | lastFrameY -= 40; |
1697 | 0 | if (frame instanceof EmbmenuFrame) |
1698 | { | |
1699 | 0 | ((EmbmenuFrame) frame).destroyMenus(); |
1700 | } | |
1701 | 0 | frame.setMenuBar(null); |
1702 | 0 | frame.dispose(); |
1703 | } | |
1704 | ||
1705 | 0 | @Override |
1706 | public void windowActivated(WindowEvent e) | |
1707 | { | |
1708 | 0 | if (frame instanceof AlignFrame) |
1709 | { | |
1710 | 0 | ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame; |
1711 | 0 | if (debug) |
1712 | { | |
1713 | 0 | jalview.bin.Console.errPrintln("Activated window " + frame); |
1714 | } | |
1715 | } | |
1716 | // be good. | |
1717 | 0 | super.windowActivated(e); |
1718 | } | |
1719 | /* | |
1720 | * Probably not necessary to do this - see TODO above. (non-Javadoc) | |
1721 | * | |
1722 | * @see | |
1723 | * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent | |
1724 | * ) | |
1725 | * | |
1726 | * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame == | |
1727 | * frame) { currentAlignFrame = null; if (debug) { | |
1728 | * jalview.bin.Console.errPrintln("Deactivated window "+frame); } } | |
1729 | * super.windowDeactivated(e); } | |
1730 | */ | |
1731 | }); | |
1732 | 0 | frame.setVisible(true); |
1733 | } | |
1734 | ||
1735 | /** | |
1736 | * This paints the background surrounding the "Launch Jalview button" <br> | |
1737 | * <br> | |
1738 | * If file given in parameter not found, displays error message | |
1739 | * | |
1740 | * @param g | |
1741 | * graphics context | |
1742 | */ | |
1743 | 0 | @Override |
1744 | public void paint(Graphics g) | |
1745 | { | |
1746 | 0 | if (!fileFound) |
1747 | { | |
1748 | 0 | g.setColor(new Color(200, 200, 200)); |
1749 | 0 | g.setColor(Color.cyan); |
1750 | 0 | g.fillRect(0, 0, getSize().width, getSize().height); |
1751 | 0 | g.setColor(Color.red); |
1752 | 0 | g.drawString( |
1753 | MessageManager.getString("label.jalview_cannot_open_file"), 5, | |
1754 | 15); | |
1755 | 0 | g.drawString("\"" + file + "\"", 5, 30); |
1756 | } | |
1757 | 0 | else if (embedded) |
1758 | { | |
1759 | 0 | g.setColor(Color.black); |
1760 | 0 | g.setFont(new Font("Arial", Font.BOLD, 24)); |
1761 | 0 | g.drawString(MessageManager.getString("label.jalview_applet"), 50, |
1762 | getSize().height / 2 - 30); | |
1763 | 0 | g.drawString(MessageManager.getString("label.loading_data") + "...", |
1764 | 50, getSize().height / 2); | |
1765 | } | |
1766 | } | |
1767 | ||
1768 | /** | |
1769 | * get all components associated with the applet of the given type | |
1770 | * | |
1771 | * @param class1 | |
1772 | * @return | |
1773 | */ | |
1774 | 0 | public Vector getAppletWindow(Class class1) |
1775 | { | |
1776 | 0 | Vector wnds = new Vector(); |
1777 | 0 | Component[] cmp = getComponents(); |
1778 | 0 | if (cmp != null) |
1779 | { | |
1780 | 0 | for (int i = 0; i < cmp.length; i++) |
1781 | { | |
1782 | 0 | if (class1.isAssignableFrom(cmp[i].getClass())) |
1783 | { | |
1784 | 0 | wnds.addElement(cmp); |
1785 | } | |
1786 | } | |
1787 | } | |
1788 | 0 | return wnds; |
1789 | } | |
1790 | ||
1791 | class LoadJmolThread extends Thread | |
1792 | { | |
1793 | private boolean running = false; | |
1794 | ||
1795 | 0 | @Override |
1796 | public void run() | |
1797 | { | |
1798 | 0 | if (running || checkedForJmol) |
1799 | { | |
1800 | 0 | return; |
1801 | } | |
1802 | 0 | running = true; |
1803 | 0 | if (checkForJmol) |
1804 | { | |
1805 | 0 | try |
1806 | { | |
1807 | 0 | if (!System.getProperty("java.version").startsWith("1.1")) |
1808 | { | |
1809 | 0 | Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter"); |
1810 | 0 | jmolAvailable = true; |
1811 | } | |
1812 | 0 | if (!jmolAvailable) |
1813 | { | |
1814 | 0 | jalview.bin.Console.outPrintln( |
1815 | "Jmol not available - Using mc_view for structures"); | |
1816 | } | |
1817 | } catch (java.lang.ClassNotFoundException ex) | |
1818 | { | |
1819 | } | |
1820 | } | |
1821 | else | |
1822 | { | |
1823 | 0 | jmolAvailable = false; |
1824 | 0 | if (debug) |
1825 | { | |
1826 | 0 | jalview.bin.Console.errPrintln( |
1827 | "Skipping Jmol check. Will use mc_view (probably)"); | |
1828 | } | |
1829 | } | |
1830 | 0 | checkedForJmol = true; |
1831 | 0 | running = false; |
1832 | } | |
1833 | ||
1834 | 0 | public boolean notFinished() |
1835 | { | |
1836 | 0 | return running || !checkedForJmol; |
1837 | } | |
1838 | } | |
1839 | ||
1840 | class LoadingThread extends Thread | |
1841 | { | |
1842 | /** | |
1843 | * State variable: protocol for access to file source | |
1844 | */ | |
1845 | DataSourceType protocol; | |
1846 | ||
1847 | String _file; // alignment file or URL spec | |
1848 | ||
1849 | String _file2; // second alignment file or URL spec | |
1850 | ||
1851 | JalviewLite applet; | |
1852 | ||
1853 | 0 | private void dbgMsg(String msg) |
1854 | { | |
1855 | 0 | if (JalviewLite.debug) |
1856 | { | |
1857 | 0 | jalview.bin.Console.errPrintln(msg); |
1858 | } | |
1859 | } | |
1860 | ||
1861 | /** | |
1862 | * update the protocol state variable for accessing the datasource located | |
1863 | * by file. | |
1864 | * | |
1865 | * @param path | |
1866 | * @return possibly updated datasource string | |
1867 | */ | |
1868 | 0 | public String resolveFileProtocol(String path) |
1869 | { | |
1870 | /* | |
1871 | * is it paste data? | |
1872 | */ | |
1873 | 0 | if (path.startsWith("PASTE")) |
1874 | { | |
1875 | 0 | protocol = DataSourceType.PASTE; |
1876 | 0 | return path.substring(5); |
1877 | } | |
1878 | ||
1879 | /* | |
1880 | * is it a URL? | |
1881 | */ | |
1882 | 0 | if (path.indexOf("://") != -1) |
1883 | { | |
1884 | 0 | protocol = DataSourceType.URL; |
1885 | 0 | return path; |
1886 | } | |
1887 | ||
1888 | /* | |
1889 | * try relative to document root | |
1890 | */ | |
1891 | 0 | URL documentBase = getDocumentBase(); |
1892 | 0 | String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase); |
1893 | 0 | if (HttpUtils.isValidUrl(withDocBase)) |
1894 | { | |
1895 | 0 | if (debug) |
1896 | { | |
1897 | 0 | jalview.bin.Console.errPrintln("Prepended document base '" |
1898 | + documentBase + "' to make: '" + withDocBase + "'"); | |
1899 | } | |
1900 | 0 | protocol = DataSourceType.URL; |
1901 | 0 | return withDocBase; |
1902 | } | |
1903 | ||
1904 | /* | |
1905 | * try relative to codebase (if different to document base) | |
1906 | */ | |
1907 | 0 | URL codeBase = getCodeBase(); |
1908 | 0 | String withCodeBase = applet.resolveUrlForLocalOrAbsolute(path, |
1909 | codeBase); | |
1910 | 0 | if (!withCodeBase.equals(withDocBase) |
1911 | && HttpUtils.isValidUrl(withCodeBase)) | |
1912 | { | |
1913 | 0 | protocol = DataSourceType.URL; |
1914 | 0 | if (debug) |
1915 | { | |
1916 | 0 | jalview.bin.Console.errPrintln("Prepended codebase '" + codeBase |
1917 | + "' to make: '" + withCodeBase + "'"); | |
1918 | } | |
1919 | 0 | return withCodeBase; |
1920 | } | |
1921 | ||
1922 | /* | |
1923 | * try locating by classloader; try this last so files in the directory | |
1924 | * are resolved using document base | |
1925 | */ | |
1926 | 0 | if (inArchive(path)) |
1927 | { | |
1928 | 0 | protocol = DataSourceType.CLASSLOADER; |
1929 | } | |
1930 | 0 | return path; |
1931 | } | |
1932 | ||
1933 | 0 | public LoadingThread(String file, String file2, JalviewLite _applet) |
1934 | { | |
1935 | 0 | this._file = file; |
1936 | 0 | this._file2 = file2; |
1937 | 0 | applet = _applet; |
1938 | } | |
1939 | ||
1940 | 0 | @Override |
1941 | public void run() | |
1942 | { | |
1943 | 0 | LoadJmolThread jmolchecker = new LoadJmolThread(); |
1944 | 0 | jmolchecker.start(); |
1945 | 0 | while (jmolchecker.notFinished()) |
1946 | { | |
1947 | // wait around until the Jmol check is complete. | |
1948 | 0 | try |
1949 | { | |
1950 | 0 | Thread.sleep(2); |
1951 | } catch (Exception e) | |
1952 | { | |
1953 | } | |
1954 | } | |
1955 | 0 | startLoading(); |
1956 | // applet.callInitCallback(); | |
1957 | } | |
1958 | ||
1959 | /** | |
1960 | * Load the alignment and any related files as specified by applet | |
1961 | * parameters | |
1962 | */ | |
1963 | 0 | private void startLoading() |
1964 | { | |
1965 | 0 | dbgMsg("Loading thread started with:\n>>file\n" + _file |
1966 | + ">>endfile"); | |
1967 | ||
1968 | 0 | dbgMsg("Loading started."); |
1969 | ||
1970 | 0 | AlignFrame newAlignFrame = readAlignment(_file); |
1971 | 0 | AlignFrame newAlignFrame2 = readAlignment(_file2); |
1972 | 0 | if (newAlignFrame != null) |
1973 | { | |
1974 | 0 | addToDisplay(newAlignFrame, newAlignFrame2); |
1975 | 0 | loadTree(newAlignFrame); |
1976 | ||
1977 | 0 | loadScoreFile(newAlignFrame); |
1978 | ||
1979 | 0 | loadFeatures(newAlignFrame); |
1980 | ||
1981 | 0 | loadAnnotations(newAlignFrame); |
1982 | ||
1983 | 0 | loadJnetFile(newAlignFrame); |
1984 | ||
1985 | 0 | loadPdbFiles(newAlignFrame); |
1986 | } | |
1987 | else | |
1988 | { | |
1989 | 0 | fileFound = false; |
1990 | 0 | applet.remove(launcher); |
1991 | 0 | applet.repaint(); |
1992 | } | |
1993 | 0 | callInitCallback(); |
1994 | } | |
1995 | ||
1996 | /** | |
1997 | * Add an AlignFrame to the display; or if two are provided, a SplitFrame. | |
1998 | * | |
1999 | * @param af | |
2000 | * @param af2 | |
2001 | */ | |
2002 | 0 | public void addToDisplay(AlignFrame af, AlignFrame af2) |
2003 | { | |
2004 | 0 | if (af2 != null) |
2005 | { | |
2006 | 0 | AlignmentI al1 = af.viewport.getAlignment(); |
2007 | 0 | AlignmentI al2 = af2.viewport.getAlignment(); |
2008 | 0 | AlignmentI cdna = al1.isNucleotide() ? al1 : al2; |
2009 | 0 | AlignmentI prot = al1.isNucleotide() ? al2 : al1; |
2010 | 0 | if (AlignmentUtils.mapProteinAlignmentToCdna(prot, cdna)) |
2011 | { | |
2012 | 0 | al2.alignAs(al1); |
2013 | 0 | SplitFrame sf = new SplitFrame(af, af2); |
2014 | 0 | sf.addToDisplay(embedded, JalviewLite.this); |
2015 | 0 | return; |
2016 | } | |
2017 | else | |
2018 | { | |
2019 | 0 | String msg = "Could not map any sequence in " + af2.getTitle() |
2020 | + " as " | |
2021 | 0 | + (al1.isNucleotide() ? "protein product" : "cDNA") |
2022 | + " for " + af.getTitle(); | |
2023 | 0 | jalview.bin.Console.errPrintln(msg); |
2024 | } | |
2025 | } | |
2026 | ||
2027 | 0 | af.addToDisplay(embedded); |
2028 | } | |
2029 | ||
2030 | /** | |
2031 | * Read the alignment file (from URL, text 'paste', or archive by | |
2032 | * classloader). | |
2033 | * | |
2034 | * @return | |
2035 | */ | |
2036 | 0 | protected AlignFrame readAlignment(String fileParam) |
2037 | { | |
2038 | 0 | if (fileParam == null) |
2039 | { | |
2040 | 0 | return null; |
2041 | } | |
2042 | 0 | String resolvedFile = resolveFileProtocol(fileParam); |
2043 | 0 | AlignmentI al = null; |
2044 | 0 | try |
2045 | { | |
2046 | 0 | FileFormatI format = new IdentifyFile().identify(resolvedFile, |
2047 | protocol); | |
2048 | 0 | dbgMsg("File identified as '" + format + "'"); |
2049 | 0 | al = new AppletFormatAdapter().readFile(resolvedFile, protocol, |
2050 | format); | |
2051 | 0 | if ((al != null) && (al.getHeight() > 0)) |
2052 | { | |
2053 | 0 | dbgMsg("Successfully loaded file."); |
2054 | 0 | al.setDataset(null); |
2055 | 0 | AlignFrame newAlignFrame = new AlignFrame(al, applet, |
2056 | resolvedFile, embedded, false); | |
2057 | 0 | newAlignFrame.setTitle(resolvedFile); |
2058 | 0 | if (initialAlignFrame == null) |
2059 | { | |
2060 | 0 | initialAlignFrame = newAlignFrame; |
2061 | } | |
2062 | // update the focus. | |
2063 | 0 | currentAlignFrame = newAlignFrame; |
2064 | ||
2065 | 0 | if (protocol == DataSourceType.PASTE) |
2066 | { | |
2067 | 0 | newAlignFrame.setTitle(MessageManager |
2068 | .formatMessage("label.sequences_from", new Object[] | |
2069 | { applet.getDocumentBase().toString() })); | |
2070 | } | |
2071 | ||
2072 | 0 | newAlignFrame.statusBar.setText(MessageManager.formatMessage( |
2073 | "label.successfully_loaded_file", new Object[] | |
2074 | { resolvedFile })); | |
2075 | ||
2076 | 0 | return newAlignFrame; |
2077 | } | |
2078 | } catch (java.io.IOException ex) | |
2079 | { | |
2080 | 0 | dbgMsg("File load exception."); |
2081 | 0 | ex.printStackTrace(); |
2082 | 0 | if (debug) |
2083 | { | |
2084 | 0 | try |
2085 | { | |
2086 | 0 | FileParse fp = new FileParse(resolvedFile, protocol); |
2087 | 0 | String ln = null; |
2088 | 0 | dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "(" |
2089 | + protocol + ")"); | |
2090 | 0 | while ((ln = fp.nextLine()) != null) |
2091 | { | |
2092 | 0 | dbgMsg(ln); |
2093 | } | |
2094 | 0 | dbgMsg(">>>Dump finished."); |
2095 | } catch (Exception e) | |
2096 | { | |
2097 | 0 | jalview.bin.Console.errPrintln( |
2098 | "Exception when trying to dump the content of the file parameter."); | |
2099 | 0 | e.printStackTrace(); |
2100 | } | |
2101 | } | |
2102 | } | |
2103 | 0 | return null; |
2104 | } | |
2105 | ||
2106 | /** | |
2107 | * Load PDBFiles if any specified by parameter(s). Returns true if loaded, | |
2108 | * else false. | |
2109 | * | |
2110 | * @param alignFrame | |
2111 | * @return | |
2112 | */ | |
2113 | 0 | protected boolean loadPdbFiles(AlignFrame alignFrame) |
2114 | { | |
2115 | 0 | boolean result = false; |
2116 | /* | |
2117 | * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 - | |
2118 | * related to JAL-434 | |
2119 | */ | |
2120 | ||
2121 | 0 | applet.setAlignPdbStructures( |
2122 | getDefaultParameter("alignpdbfiles", false)); | |
2123 | /* | |
2124 | * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B | |
2125 | * PDB|1GAQ|1GAQ|C"> | |
2126 | * | |
2127 | * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB"> | |
2128 | * | |
2129 | * <param name="PDBfile3" value="1q0o Q45135_9MICO"> | |
2130 | */ | |
2131 | ||
2132 | 0 | int pdbFileCount = 0; |
2133 | // Accumulate pdbs here if they are heading for the same view (if | |
2134 | // alignPdbStructures is true) | |
2135 | 0 | Vector pdbs = new Vector(); |
2136 | // create a lazy matcher if we're asked to | |
2137 | 0 | jalview.analysis.SequenceIdMatcher matcher = (applet |
2138 | .getDefaultParameter("relaxedidmatch", false)) | |
2139 | ? new jalview.analysis.SequenceIdMatcher( | |
2140 | alignFrame.getAlignViewport().getAlignment() | |
2141 | .getSequencesArray()) | |
2142 | : null; | |
2143 | ||
2144 | 0 | String param; |
2145 | 0 | do |
2146 | { | |
2147 | 0 | if (pdbFileCount > 0) |
2148 | { | |
2149 | 0 | param = applet.getParameter("PDBFILE" + pdbFileCount); |
2150 | } | |
2151 | else | |
2152 | { | |
2153 | 0 | param = applet.getParameter("PDBFILE"); |
2154 | } | |
2155 | ||
2156 | 0 | if (param != null) |
2157 | { | |
2158 | 0 | PDBEntry pdb = new PDBEntry(); |
2159 | ||
2160 | 0 | String seqstring; |
2161 | 0 | SequenceI[] seqs = null; |
2162 | 0 | String[] chains = null; |
2163 | ||
2164 | 0 | StringTokenizer st = new StringTokenizer(param, " "); |
2165 | ||
2166 | 0 | if (st.countTokens() < 2) |
2167 | { | |
2168 | 0 | String sequence = applet.getParameter("PDBSEQ"); |
2169 | 0 | if (sequence != null) |
2170 | { | |
2171 | 0 | seqs = new SequenceI[] { matcher == null |
2172 | ? (Sequence) alignFrame.getAlignViewport() | |
2173 | .getAlignment().findName(sequence) | |
2174 | : matcher.findIdMatch(sequence) }; | |
2175 | } | |
2176 | ||
2177 | } | |
2178 | else | |
2179 | { | |
2180 | 0 | param = st.nextToken(); |
2181 | 0 | List<SequenceI> tmp = new ArrayList<>(); |
2182 | 0 | List<String> tmp2 = new ArrayList<>(); |
2183 | ||
2184 | 0 | while (st.hasMoreTokens()) |
2185 | { | |
2186 | 0 | seqstring = st.nextToken(); |
2187 | 0 | StringTokenizer st2 = new StringTokenizer(seqstring, "="); |
2188 | 0 | if (st2.countTokens() > 1) |
2189 | { | |
2190 | // This is the chain | |
2191 | 0 | tmp2.add(st2.nextToken()); |
2192 | 0 | seqstring = st2.nextToken(); |
2193 | } | |
2194 | 0 | tmp.add(matcher == null |
2195 | ? (Sequence) alignFrame.getAlignViewport() | |
2196 | .getAlignment().findName(seqstring) | |
2197 | : matcher.findIdMatch(seqstring)); | |
2198 | } | |
2199 | ||
2200 | 0 | seqs = tmp.toArray(new SequenceI[tmp.size()]); |
2201 | 0 | if (tmp2.size() == tmp.size()) |
2202 | { | |
2203 | 0 | chains = tmp2.toArray(new String[tmp2.size()]); |
2204 | } | |
2205 | } | |
2206 | 0 | param = resolveFileProtocol(param); |
2207 | // TODO check JAL-357 for files in a jar (CLASSLOADER) | |
2208 | 0 | pdb.setFile(param); |
2209 | ||
2210 | 0 | if (seqs != null) |
2211 | { | |
2212 | 0 | for (int i = 0; i < seqs.length; i++) |
2213 | { | |
2214 | 0 | if (seqs[i] != null) |
2215 | { | |
2216 | 0 | ((Sequence) seqs[i]).addPDBId(pdb); |
2217 | 0 | StructureSelectionManager |
2218 | .getStructureSelectionManager(applet) | |
2219 | .registerPDBEntry(pdb); | |
2220 | } | |
2221 | else | |
2222 | { | |
2223 | 0 | if (JalviewLite.debug) |
2224 | { | |
2225 | // this may not really be a problem but we give a warning | |
2226 | // anyway | |
2227 | 0 | jalview.bin.Console.errPrintln( |
2228 | "Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence " | |
2229 | + i + ")"); | |
2230 | } | |
2231 | } | |
2232 | } | |
2233 | ||
2234 | 0 | if (!alignPdbStructures) |
2235 | { | |
2236 | 0 | alignFrame.newStructureView(applet, pdb, seqs, chains, |
2237 | protocol); | |
2238 | } | |
2239 | else | |
2240 | { | |
2241 | 0 | pdbs.addElement(new Object[] { pdb, seqs, chains, protocol }); |
2242 | } | |
2243 | } | |
2244 | } | |
2245 | ||
2246 | 0 | pdbFileCount++; |
2247 | 0 | } while (param != null || pdbFileCount < 10); |
2248 | 0 | if (pdbs.size() > 0) |
2249 | { | |
2250 | 0 | SequenceI[][] seqs = new SequenceI[pdbs.size()][]; |
2251 | 0 | PDBEntry[] pdb = new PDBEntry[pdbs.size()]; |
2252 | 0 | String[][] chains = new String[pdbs.size()][]; |
2253 | 0 | String[] protocols = new String[pdbs.size()]; |
2254 | 0 | for (int pdbsi = 0, pdbsiSize = pdbs |
2255 | 0 | .size(); pdbsi < pdbsiSize; pdbsi++) |
2256 | { | |
2257 | 0 | Object[] o = (Object[]) pdbs.elementAt(pdbsi); |
2258 | 0 | pdb[pdbsi] = (PDBEntry) o[0]; |
2259 | 0 | seqs[pdbsi] = (SequenceI[]) o[1]; |
2260 | 0 | chains[pdbsi] = (String[]) o[2]; |
2261 | 0 | protocols[pdbsi] = (String) o[3]; |
2262 | } | |
2263 | 0 | alignFrame.alignedStructureView(applet, pdb, seqs, chains, |
2264 | protocols); | |
2265 | 0 | result = true; |
2266 | } | |
2267 | 0 | return result; |
2268 | } | |
2269 | ||
2270 | /** | |
2271 | * Load in a Jnetfile if specified by parameter. Returns true if loaded, | |
2272 | * else false. | |
2273 | * | |
2274 | * @param alignFrame | |
2275 | * @return | |
2276 | */ | |
2277 | 0 | protected boolean loadJnetFile(AlignFrame alignFrame) |
2278 | { | |
2279 | 0 | boolean result = false; |
2280 | 0 | String param = applet.getParameter("jnetfile"); |
2281 | 0 | if (param == null) |
2282 | { | |
2283 | // jnet became jpred around 2016 | |
2284 | 0 | param = applet.getParameter("jpredfile"); |
2285 | } | |
2286 | 0 | if (param != null) |
2287 | { | |
2288 | 0 | try |
2289 | { | |
2290 | 0 | param = resolveFileProtocol(param); |
2291 | 0 | JPredFile predictions = new JPredFile(param, protocol); |
2292 | 0 | JnetAnnotationMaker.add_annotation(predictions, |
2293 | alignFrame.viewport.getAlignment(), 0, false); | |
2294 | // false == do not add sequence profile from concise output | |
2295 | ||
2296 | 0 | alignFrame.viewport.getAlignment().setupJPredAlignment(); |
2297 | ||
2298 | 0 | alignFrame.alignPanel.fontChanged(); |
2299 | 0 | alignFrame.alignPanel.setScrollValues(0, 0); |
2300 | 0 | result = true; |
2301 | } catch (Exception ex) | |
2302 | { | |
2303 | 0 | ex.printStackTrace(); |
2304 | } | |
2305 | } | |
2306 | 0 | return result; |
2307 | } | |
2308 | ||
2309 | /** | |
2310 | * Load annotations if specified by parameter. Returns true if loaded, else | |
2311 | * false. | |
2312 | * | |
2313 | * @param alignFrame | |
2314 | * @return | |
2315 | */ | |
2316 | 0 | protected boolean loadAnnotations(AlignFrame alignFrame) |
2317 | { | |
2318 | 0 | boolean result = false; |
2319 | 0 | String param = applet.getParameter("annotations"); |
2320 | 0 | if (param != null) |
2321 | { | |
2322 | 0 | param = resolveFileProtocol(param); |
2323 | ||
2324 | 0 | if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport, |
2325 | param, protocol)) | |
2326 | { | |
2327 | 0 | alignFrame.alignPanel.fontChanged(); |
2328 | 0 | alignFrame.alignPanel.setScrollValues(0, 0); |
2329 | 0 | result = true; |
2330 | } | |
2331 | else | |
2332 | { | |
2333 | 0 | jalview.bin.Console.errPrintln( |
2334 | "Annotations were not added from annotation file '" | |
2335 | + param + "'"); | |
2336 | } | |
2337 | } | |
2338 | 0 | return result; |
2339 | } | |
2340 | ||
2341 | /** | |
2342 | * Load features file and view settings as specified by parameters. Returns | |
2343 | * true if features were loaded, else false. | |
2344 | * | |
2345 | * @param alignFrame | |
2346 | * @return | |
2347 | */ | |
2348 | 0 | protected boolean loadFeatures(AlignFrame alignFrame) |
2349 | { | |
2350 | 0 | boolean result = false; |
2351 | // /////////////////////////// | |
2352 | // modify display of features | |
2353 | // we do this before any features have been loaded, ensuring any hidden | |
2354 | // groups are hidden when features first displayed | |
2355 | // | |
2356 | // hide specific groups | |
2357 | // | |
2358 | 0 | String param = applet.getParameter("hidefeaturegroups"); |
2359 | 0 | if (param != null) |
2360 | { | |
2361 | 0 | alignFrame.setFeatureGroupState(separatorListToArray(param), false); |
2362 | // applet.setFeatureGroupStateOn(newAlignFrame, param, false); | |
2363 | } | |
2364 | // show specific groups | |
2365 | 0 | param = applet.getParameter("showfeaturegroups"); |
2366 | 0 | if (param != null) |
2367 | { | |
2368 | 0 | alignFrame.setFeatureGroupState(separatorListToArray(param), true); |
2369 | // applet.setFeatureGroupStateOn(newAlignFrame, param, true); | |
2370 | } | |
2371 | // and now load features | |
2372 | 0 | param = applet.getParameter("features"); |
2373 | 0 | if (param != null) |
2374 | { | |
2375 | 0 | param = resolveFileProtocol(param); |
2376 | ||
2377 | 0 | result = alignFrame.parseFeaturesFile(param, protocol); |
2378 | } | |
2379 | ||
2380 | 0 | param = applet.getParameter("showFeatureSettings"); |
2381 | 0 | if (param != null && param.equalsIgnoreCase(TRUE)) |
2382 | { | |
2383 | 0 | alignFrame.viewport.setShowSequenceFeatures(true); |
2384 | 0 | new FeatureSettings(alignFrame.alignPanel); |
2385 | } | |
2386 | 0 | return result; |
2387 | } | |
2388 | ||
2389 | /** | |
2390 | * Load a score file if specified by parameter. Returns true if file was | |
2391 | * loaded, else false. | |
2392 | * | |
2393 | * @param alignFrame | |
2394 | */ | |
2395 | 0 | protected boolean loadScoreFile(AlignFrame alignFrame) |
2396 | { | |
2397 | 0 | boolean result = false; |
2398 | 0 | String sScoreFile = applet.getParameter("scoreFile"); |
2399 | 0 | if (sScoreFile != null && !"".equals(sScoreFile)) |
2400 | { | |
2401 | 0 | try |
2402 | { | |
2403 | 0 | if (debug) |
2404 | { | |
2405 | 0 | jalview.bin.Console.errPrintln( |
2406 | "Attempting to load T-COFFEE score file from the scoreFile parameter"); | |
2407 | } | |
2408 | 0 | result = alignFrame.loadScoreFile(sScoreFile); |
2409 | 0 | if (!result) |
2410 | { | |
2411 | 0 | jalview.bin.Console.errPrintln( |
2412 | "Failed to parse T-COFFEE parameter as a valid score file ('" | |
2413 | + sScoreFile + "')"); | |
2414 | } | |
2415 | } catch (Exception e) | |
2416 | { | |
2417 | 0 | System.err.printf("Cannot read score file: '%s'. Cause: %s \n", |
2418 | sScoreFile, e.getMessage()); | |
2419 | } | |
2420 | } | |
2421 | 0 | return result; |
2422 | } | |
2423 | ||
2424 | /** | |
2425 | * Load a tree for the alignment if specified by parameter. Returns true if | |
2426 | * a tree was loaded, else false. | |
2427 | * | |
2428 | * @param alignFrame | |
2429 | * @return | |
2430 | */ | |
2431 | 0 | protected boolean loadTree(AlignFrame alignFrame) |
2432 | { | |
2433 | 0 | boolean result = false; |
2434 | 0 | String treeFile = applet.getParameter("tree"); |
2435 | 0 | if (treeFile == null) |
2436 | { | |
2437 | 0 | treeFile = applet.getParameter("treeFile"); |
2438 | } | |
2439 | ||
2440 | 0 | if (treeFile != null) |
2441 | { | |
2442 | 0 | try |
2443 | { | |
2444 | 0 | treeFile = resolveFileProtocol(treeFile); |
2445 | 0 | NewickFile fin = new NewickFile(treeFile, protocol); |
2446 | 0 | fin.parse(); |
2447 | ||
2448 | 0 | if (fin.getTree() != null) |
2449 | { | |
2450 | 0 | alignFrame.loadTree(fin, treeFile); |
2451 | 0 | result = true; |
2452 | 0 | dbgMsg("Successfully imported tree."); |
2453 | } | |
2454 | else | |
2455 | { | |
2456 | 0 | dbgMsg("Tree parameter did not resolve to a valid tree."); |
2457 | } | |
2458 | } catch (Exception ex) | |
2459 | { | |
2460 | 0 | ex.printStackTrace(); |
2461 | } | |
2462 | } | |
2463 | 0 | return result; |
2464 | } | |
2465 | ||
2466 | /** | |
2467 | * Discovers whether the given file is in the Applet Archive | |
2468 | * | |
2469 | * @param f | |
2470 | * String | |
2471 | * @return boolean | |
2472 | */ | |
2473 | 0 | boolean inArchive(String f) |
2474 | { | |
2475 | // This might throw a security exception in certain browsers | |
2476 | // Netscape Communicator for instance. | |
2477 | 0 | try |
2478 | { | |
2479 | 0 | boolean rtn = (getClass().getResourceAsStream("/" + f) != null); |
2480 | 0 | if (debug) |
2481 | { | |
2482 | 0 | jalview.bin.Console.errPrintln("Resource '" + f + "' was " |
2483 | 0 | + (rtn ? "" : "not ") + "located by classloader."); |
2484 | } | |
2485 | 0 | return rtn; |
2486 | } catch (Exception ex) | |
2487 | { | |
2488 | 0 | jalview.bin.Console.outPrintln( |
2489 | "Exception checking resources: " + f + " " + ex); | |
2490 | 0 | return false; |
2491 | } | |
2492 | } | |
2493 | } | |
2494 | ||
2495 | /** | |
2496 | * @return the default alignFrame acted on by the public applet methods. May | |
2497 | * return null with an error message on System.err indicating the | |
2498 | * fact. | |
2499 | */ | |
2500 | 0 | public AlignFrame getDefaultTargetFrame() |
2501 | { | |
2502 | 0 | if (currentAlignFrame != null) |
2503 | { | |
2504 | 0 | return currentAlignFrame; |
2505 | } | |
2506 | 0 | if (initialAlignFrame != null) |
2507 | { | |
2508 | 0 | return initialAlignFrame; |
2509 | } | |
2510 | 0 | jalview.bin.Console.errPrintln( |
2511 | "Implementation error: Jalview Applet API cannot work out which AlignFrame to use."); | |
2512 | 0 | return null; |
2513 | } | |
2514 | ||
2515 | /** | |
2516 | * separator used for separatorList | |
2517 | */ | |
2518 | protected String separator = "" + ((char) 0x00AC); // the default used to be | |
2519 | // '|' but many sequence | |
2520 | // IDS include pipes. | |
2521 | ||
2522 | /** | |
2523 | * set to enable the URL based javascript execution mechanism | |
2524 | */ | |
2525 | public boolean jsfallbackEnabled = false; | |
2526 | ||
2527 | /** | |
2528 | * parse the string into a list | |
2529 | * | |
2530 | * @param list | |
2531 | * @return elements separated by separator | |
2532 | */ | |
2533 | 0 | public String[] separatorListToArray(String list) |
2534 | { | |
2535 | 0 | return separatorListToArray(list, separator); |
2536 | } | |
2537 | ||
2538 | /** | |
2539 | * parse the string into a list | |
2540 | * | |
2541 | * @param list | |
2542 | * @param separator | |
2543 | * @return elements separated by separator | |
2544 | */ | |
2545 | 7 | public static String[] separatorListToArray(String list, String separator) |
2546 | { | |
2547 | // TODO use StringUtils version (slightly different...) | |
2548 | 7 | int seplen = separator.length(); |
2549 | 7 | if (list == null || list.equals("") || list.equals(separator)) |
2550 | { | |
2551 | 4 | return null; |
2552 | } | |
2553 | 3 | java.util.Vector jv = new Vector(); |
2554 | 3 | int cp = 0, pos; |
2555 | ? | while ((pos = list.indexOf(separator, cp)) > cp) |
2556 | { | |
2557 | 5 | jv.addElement(list.substring(cp, pos)); |
2558 | 5 | cp = pos + seplen; |
2559 | } | |
2560 | 3 | if (cp < list.length()) |
2561 | { | |
2562 | 0 | String c = list.substring(cp); |
2563 | 0 | if (!c.equals(separator)) |
2564 | { | |
2565 | 0 | jv.addElement(c); |
2566 | } | |
2567 | } | |
2568 | 3 | if (jv.size() > 0) |
2569 | { | |
2570 | 3 | String[] v = new String[jv.size()]; |
2571 | 8 | for (int i = 0; i < v.length; i++) |
2572 | { | |
2573 | 5 | v[i] = (String) jv.elementAt(i); |
2574 | } | |
2575 | 3 | jv.removeAllElements(); |
2576 | 3 | if (debug) |
2577 | { | |
2578 | 0 | jalview.bin.Console.errPrintln("Array from '" + separator |
2579 | + "' separated List:\n" + v.length); | |
2580 | 0 | for (int i = 0; i < v.length; i++) |
2581 | { | |
2582 | 0 | jalview.bin.Console.errPrintln("item " + i + " '" + v[i] + "'"); |
2583 | } | |
2584 | } | |
2585 | 3 | return v; |
2586 | } | |
2587 | 0 | if (debug) |
2588 | { | |
2589 | 0 | jalview.bin.Console.errPrintln( |
2590 | "Empty Array from '" + separator + "' separated List"); | |
2591 | } | |
2592 | 0 | return null; |
2593 | } | |
2594 | ||
2595 | /** | |
2596 | * concatenate the list with separator | |
2597 | * | |
2598 | * @param list | |
2599 | * @return concatenated string | |
2600 | */ | |
2601 | 0 | public String arrayToSeparatorList(String[] list) |
2602 | { | |
2603 | 0 | return arrayToSeparatorList(list, separator); |
2604 | } | |
2605 | ||
2606 | /** | |
2607 | * concatenate the list with separator | |
2608 | * | |
2609 | * @param list | |
2610 | * @param separator | |
2611 | * @return concatenated string | |
2612 | */ | |
2613 | 0 | public static String arrayToSeparatorList(String[] list, String separator) |
2614 | { | |
2615 | // TODO use StringUtils version | |
2616 | 0 | StringBuffer v = new StringBuffer(); |
2617 | 0 | if (list != null && list.length > 0) |
2618 | { | |
2619 | 0 | for (int i = 0, iSize = list.length; i < iSize; i++) |
2620 | { | |
2621 | 0 | if (list[i] != null) |
2622 | { | |
2623 | 0 | if (i > 0) |
2624 | { | |
2625 | 0 | v.append(separator); |
2626 | } | |
2627 | 0 | v.append(list[i]); |
2628 | } | |
2629 | } | |
2630 | 0 | if (debug) |
2631 | { | |
2632 | 0 | System.err |
2633 | .println("Returning '" + separator + "' separated List:\n"); | |
2634 | 0 | jalview.bin.Console.errPrintln(v); |
2635 | } | |
2636 | 0 | return v.toString(); |
2637 | } | |
2638 | 0 | if (debug) |
2639 | { | |
2640 | 0 | jalview.bin.Console.errPrintln( |
2641 | "Returning empty '" + separator + "' separated List\n"); | |
2642 | } | |
2643 | 0 | return "" + separator; |
2644 | } | |
2645 | ||
2646 | /* | |
2647 | * (non-Javadoc) | |
2648 | * | |
2649 | * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups() | |
2650 | */ | |
2651 | 0 | @Override |
2652 | public String getFeatureGroups() | |
2653 | { | |
2654 | 0 | String lst = arrayToSeparatorList( |
2655 | getDefaultTargetFrame().getFeatureGroups()); | |
2656 | 0 | return lst; |
2657 | } | |
2658 | ||
2659 | /* | |
2660 | * (non-Javadoc) | |
2661 | * | |
2662 | * @see | |
2663 | * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame | |
2664 | * ) | |
2665 | */ | |
2666 | 0 | @Override |
2667 | public String getFeatureGroupsOn(AlignFrame alf) | |
2668 | { | |
2669 | 0 | String lst = arrayToSeparatorList(alf.getFeatureGroups()); |
2670 | 0 | return lst; |
2671 | } | |
2672 | ||
2673 | /* | |
2674 | * (non-Javadoc) | |
2675 | * | |
2676 | * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean) | |
2677 | */ | |
2678 | 0 | @Override |
2679 | public String getFeatureGroupsOfState(boolean visible) | |
2680 | { | |
2681 | 0 | return arrayToSeparatorList( |
2682 | getDefaultTargetFrame().getFeatureGroupsOfState(visible)); | |
2683 | } | |
2684 | ||
2685 | /* | |
2686 | * (non-Javadoc) | |
2687 | * | |
2688 | * @see | |
2689 | * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui | |
2690 | * .AlignFrame, boolean) | |
2691 | */ | |
2692 | 0 | @Override |
2693 | public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible) | |
2694 | { | |
2695 | 0 | return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible)); |
2696 | } | |
2697 | ||
2698 | /* | |
2699 | * (non-Javadoc) | |
2700 | * | |
2701 | * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui. | |
2702 | * AlignFrame, java.lang.String, boolean) | |
2703 | */ | |
2704 | 0 | @Override |
2705 | public void setFeatureGroupStateOn(final AlignFrame alf, | |
2706 | final String groups, boolean state) | |
2707 | { | |
2708 | 0 | final boolean st = state;// !(state==null || state.equals("") || |
2709 | // state.toLowerCase(Locale.ROOT).equals("false")); | |
2710 | 0 | java.awt.EventQueue.invokeLater(new Runnable() |
2711 | { | |
2712 | 0 | @Override |
2713 | public void run() | |
2714 | { | |
2715 | 0 | alf.setFeatureGroupState(separatorListToArray(groups), st); |
2716 | } | |
2717 | }); | |
2718 | } | |
2719 | ||
2720 | /* | |
2721 | * (non-Javadoc) | |
2722 | * | |
2723 | * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String, | |
2724 | * boolean) | |
2725 | */ | |
2726 | 0 | @Override |
2727 | public void setFeatureGroupState(String groups, boolean state) | |
2728 | { | |
2729 | 0 | setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state); |
2730 | } | |
2731 | ||
2732 | /* | |
2733 | * (non-Javadoc) | |
2734 | * | |
2735 | * @see jalview.bin.JalviewLiteJsApi#getSeparator() | |
2736 | */ | |
2737 | 0 | @Override |
2738 | public String getSeparator() | |
2739 | { | |
2740 | 0 | return separator; |
2741 | } | |
2742 | ||
2743 | /* | |
2744 | * (non-Javadoc) | |
2745 | * | |
2746 | * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String) | |
2747 | */ | |
2748 | 0 | @Override |
2749 | public void setSeparator(String separator) | |
2750 | { | |
2751 | 0 | if (separator == null || separator.length() < 1) |
2752 | { | |
2753 | // reset to default | |
2754 | 0 | separator = "" + ((char) 0x00AC); |
2755 | } | |
2756 | 0 | this.separator = separator; |
2757 | 0 | if (debug) |
2758 | { | |
2759 | 0 | jalview.bin.Console |
2760 | .errPrintln("Default Separator now: '" + separator + "'"); | |
2761 | } | |
2762 | } | |
2763 | ||
2764 | /** | |
2765 | * get boolean value of applet parameter 'name' and return default if | |
2766 | * parameter is not set | |
2767 | * | |
2768 | * @param name | |
2769 | * name of paremeter | |
2770 | * @param def | |
2771 | * the value to return otherwise | |
2772 | * @return true or false | |
2773 | */ | |
2774 | 0 | public boolean getDefaultParameter(String name, boolean def) |
2775 | { | |
2776 | 0 | String stn; |
2777 | 0 | if ((stn = getParameter(name)) == null) |
2778 | { | |
2779 | 0 | return def; |
2780 | } | |
2781 | 0 | if (TRUE.equalsIgnoreCase(stn)) |
2782 | { | |
2783 | 0 | return true; |
2784 | } | |
2785 | 0 | return false; |
2786 | } | |
2787 | ||
2788 | /* | |
2789 | * (non-Javadoc) | |
2790 | * | |
2791 | * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame, | |
2792 | * java.lang.String, java.lang.String, java.lang.String) | |
2793 | */ | |
2794 | 0 | @Override |
2795 | public boolean addPdbFile(AlignFrame alFrame, String sequenceId, | |
2796 | String pdbEntryString, String pdbFile) | |
2797 | { | |
2798 | 0 | return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile); |
2799 | } | |
2800 | ||
2801 | 0 | protected void setAlignPdbStructures(boolean alignPdbStructures) |
2802 | { | |
2803 | 0 | this.alignPdbStructures = alignPdbStructures; |
2804 | } | |
2805 | ||
2806 | 0 | public boolean isAlignPdbStructures() |
2807 | { | |
2808 | 0 | return alignPdbStructures; |
2809 | } | |
2810 | ||
2811 | 0 | @Override |
2812 | public void start() | |
2813 | { | |
2814 | // callInitCallback(); | |
2815 | } | |
2816 | ||
2817 | private Hashtable<String, long[]> jshashes = new Hashtable<>(); | |
2818 | ||
2819 | private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<>(); | |
2820 | ||
2821 | 0 | public void setJsMessageSet(String messageclass, String viewId, |
2822 | String[] colcommands) | |
2823 | { | |
2824 | 0 | Hashtable<String, String[]> msgset = jsmessages.get(messageclass); |
2825 | 0 | if (msgset == null) |
2826 | { | |
2827 | 0 | msgset = new Hashtable<>(); |
2828 | 0 | jsmessages.put(messageclass, msgset); |
2829 | } | |
2830 | 0 | msgset.put(viewId, colcommands); |
2831 | 0 | long[] l = new long[colcommands.length]; |
2832 | 0 | for (int i = 0; i < colcommands.length; i++) |
2833 | { | |
2834 | 0 | l[i] = colcommands[i].hashCode(); |
2835 | } | |
2836 | 0 | jshashes.put(messageclass + "|" + viewId, l); |
2837 | } | |
2838 | ||
2839 | /* | |
2840 | * (non-Javadoc) | |
2841 | * | |
2842 | * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String, | |
2843 | * java.lang.String) | |
2844 | */ | |
2845 | 0 | @Override |
2846 | public String getJsMessage(String messageclass, String viewId) | |
2847 | { | |
2848 | 0 | Hashtable<String, String[]> msgset = jsmessages.get(messageclass); |
2849 | 0 | if (msgset != null) |
2850 | { | |
2851 | 0 | String[] msgs = msgset.get(viewId); |
2852 | 0 | if (msgs != null) |
2853 | { | |
2854 | 0 | for (int i = 0; i < msgs.length; i++) |
2855 | { | |
2856 | 0 | if (msgs[i] != null) |
2857 | { | |
2858 | 0 | String m = msgs[i]; |
2859 | 0 | msgs[i] = null; |
2860 | 0 | return m; |
2861 | } | |
2862 | } | |
2863 | } | |
2864 | } | |
2865 | 0 | return ""; |
2866 | } | |
2867 | ||
2868 | 0 | public boolean isJsMessageSetChanged(String string, String string2, |
2869 | String[] colcommands) | |
2870 | { | |
2871 | 0 | long[] l = jshashes.get(string + "|" + string2); |
2872 | 0 | if (l == null && colcommands != null) |
2873 | { | |
2874 | 0 | return true; |
2875 | } | |
2876 | 0 | for (int i = 0; i < colcommands.length; i++) |
2877 | { | |
2878 | 0 | if (l[i] != colcommands[i].hashCode()) |
2879 | { | |
2880 | 0 | return true; |
2881 | } | |
2882 | } | |
2883 | 0 | return false; |
2884 | } | |
2885 | ||
2886 | private Vector jsExecQueue = new Vector(); | |
2887 | ||
2888 | 0 | public Vector getJsExecQueue() |
2889 | { | |
2890 | 0 | return jsExecQueue; |
2891 | } | |
2892 | ||
2893 | 0 | public void setExecutor(JSFunctionExec jsFunctionExec2) |
2894 | { | |
2895 | 0 | jsFunctionExec = jsFunctionExec2; |
2896 | } | |
2897 | ||
2898 | /** | |
2899 | * return the given colour value parameter or the given default if parameter | |
2900 | * not given | |
2901 | * | |
2902 | * @param colparam | |
2903 | * @param defcolour | |
2904 | * @return | |
2905 | */ | |
2906 | 0 | public Color getDefaultColourParameter(String colparam, Color defcolour) |
2907 | { | |
2908 | 0 | String colprop = getParameter(colparam); |
2909 | 0 | if (colprop == null || colprop.trim().length() == 0) |
2910 | { | |
2911 | 0 | return defcolour; |
2912 | } | |
2913 | 0 | Color col = ColorUtils.parseColourString(colprop); |
2914 | 0 | if (col == null) |
2915 | { | |
2916 | 0 | jalview.bin.Console.errPrintln("Couldn't parse '" + colprop |
2917 | + "' as a colour for " + colparam); | |
2918 | } | |
2919 | 0 | return (col == null) ? defcolour : col; |
2920 | } | |
2921 | ||
2922 | 0 | public void openJalviewHelpUrl() |
2923 | { | |
2924 | 0 | String helpUrl = getParameter("jalviewhelpurl"); |
2925 | 0 | if (helpUrl == null || helpUrl.trim().length() < 5) |
2926 | { | |
2927 | 0 | helpUrl = "http://www.jalview.org/help.html"; |
2928 | } | |
2929 | 0 | showURL(helpUrl, "HELP"); |
2930 | } | |
2931 | ||
2932 | /** | |
2933 | * form a complete URL given a path to a resource and a reference location on | |
2934 | * the same server | |
2935 | * | |
2936 | * @param targetPath | |
2937 | * - an absolute path on the same server as localref or a document | |
2938 | * located relative to localref | |
2939 | * @param localref | |
2940 | * - a URL on the same server as url | |
2941 | * @return a complete URL for the resource located by url | |
2942 | */ | |
2943 | 0 | private String resolveUrlForLocalOrAbsolute(String targetPath, |
2944 | URL localref) | |
2945 | { | |
2946 | 0 | String resolvedPath = ""; |
2947 | 0 | if (targetPath.startsWith("/")) |
2948 | { | |
2949 | 0 | String codebase = localref.toString(); |
2950 | 0 | String localfile = localref.getFile(); |
2951 | 0 | resolvedPath = codebase.substring(0, |
2952 | codebase.length() - localfile.length()) + targetPath; | |
2953 | 0 | return resolvedPath; |
2954 | } | |
2955 | ||
2956 | /* | |
2957 | * get URL path and strip off any trailing file e.g. | |
2958 | * www.jalview.org/examples/index.html#applets?a=b is trimmed to | |
2959 | * www.jalview.org/examples/ | |
2960 | */ | |
2961 | 0 | String urlPath = localref.toString(); |
2962 | 0 | String directoryPath = urlPath; |
2963 | 0 | int lastSeparator = directoryPath.lastIndexOf("/"); |
2964 | 0 | if (lastSeparator > 0) |
2965 | { | |
2966 | 0 | directoryPath = directoryPath.substring(0, lastSeparator + 1); |
2967 | } | |
2968 | ||
2969 | 0 | if (targetPath.startsWith("/")) |
2970 | { | |
2971 | /* | |
2972 | * construct absolute URL to a file on the server - this is not allowed? | |
2973 | */ | |
2974 | // String localfile = localref.getFile(); | |
2975 | // resolvedPath = urlPath.substring(0, | |
2976 | // urlPath.length() - localfile.length()) | |
2977 | // + targetPath; | |
2978 | 0 | resolvedPath = directoryPath + targetPath.substring(1); |
2979 | } | |
2980 | else | |
2981 | { | |
2982 | 0 | resolvedPath = directoryPath + targetPath; |
2983 | } | |
2984 | 0 | if (debug) |
2985 | { | |
2986 | 0 | jalview.bin.Console.errPrintln( |
2987 | "resolveUrlForLocalOrAbsolute returning " + resolvedPath); | |
2988 | } | |
2989 | 0 | return resolvedPath; |
2990 | } | |
2991 | ||
2992 | /** | |
2993 | * open a URL in the browser - resolving it according to relative refs and | |
2994 | * coping with javascript: protocol if necessary. | |
2995 | * | |
2996 | * @param url | |
2997 | * @param target | |
2998 | */ | |
2999 | 0 | public void showURL(String url, String target) |
3000 | { | |
3001 | 0 | try |
3002 | { | |
3003 | 0 | if (url.indexOf(":") == -1) |
3004 | { | |
3005 | // TODO: verify (Bas Vroling bug) prepend codebase or server URL to | |
3006 | // form valid URL | |
3007 | // Should really use docbase, not codebase. | |
3008 | 0 | URL prepend; |
3009 | 0 | url = resolveUrlForLocalOrAbsolute(url, |
3010 | 0 | prepend = getDefaultParameter("resolvetocodebase", false) |
3011 | ? getCodeBase() | |
3012 | : getDocumentBase()); | |
3013 | 0 | if (debug) |
3014 | { | |
3015 | 0 | jalview.bin.Console.errPrintln("Show url (prepended " + prepend |
3016 | + " - toggle resolvetocodebase if code/docbase resolution is wrong): " | |
3017 | + url); | |
3018 | } | |
3019 | } | |
3020 | else | |
3021 | { | |
3022 | 0 | if (debug) |
3023 | { | |
3024 | 0 | jalview.bin.Console.errPrintln("Show url: " + url); |
3025 | } | |
3026 | } | |
3027 | 0 | if (url.indexOf("javascript:") == 0) |
3028 | { | |
3029 | // no target for the javascript context | |
3030 | 0 | getAppletContext().showDocument(new java.net.URL(url)); |
3031 | } | |
3032 | else | |
3033 | { | |
3034 | 0 | getAppletContext().showDocument(new java.net.URL(url), target); |
3035 | } | |
3036 | } catch (Exception ex) | |
3037 | { | |
3038 | 0 | ex.printStackTrace(); |
3039 | } | |
3040 | } | |
3041 | ||
3042 | /** | |
3043 | * bind structures in a viewer to any matching sequences in an alignFrame (use | |
3044 | * sequenceIds to limit scope of search to specific sequences) | |
3045 | * | |
3046 | * @param alFrame | |
3047 | * @param viewer | |
3048 | * @param sequenceIds | |
3049 | * @return TODO: consider making an exception structure for indicating when | |
3050 | * binding fails public SequenceStructureBinding | |
3051 | * addStructureViewInstance( AlignFrame alFrame, Object viewer, String | |
3052 | * sequenceIds) { | |
3053 | * | |
3054 | * if (sequenceIds != null && sequenceIds.length() > 0) { return | |
3055 | * alFrame.addStructureViewInstance(viewer, | |
3056 | * separatorListToArray(sequenceIds)); } else { return | |
3057 | * alFrame.addStructureViewInstance(viewer, null); } // return null; } | |
3058 | */ | |
3059 | } |