Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
IdPanel | 41 | 147 | 63 | ||
IdPanel.ScrollThread | 414 | 18 | 10 |
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.appletgui; | |
22 | ||
23 | import jalview.datamodel.SequenceFeature; | |
24 | import jalview.datamodel.SequenceGroup; | |
25 | import jalview.datamodel.SequenceI; | |
26 | import jalview.urls.api.UrlProviderFactoryI; | |
27 | import jalview.urls.api.UrlProviderI; | |
28 | import jalview.urls.applet.AppletUrlProviderFactory; | |
29 | import jalview.viewmodel.AlignmentViewport; | |
30 | ||
31 | import java.awt.BorderLayout; | |
32 | import java.awt.Panel; | |
33 | import java.awt.event.InputEvent; | |
34 | import java.awt.event.MouseEvent; | |
35 | import java.awt.event.MouseListener; | |
36 | import java.awt.event.MouseMotionListener; | |
37 | import java.util.ArrayList; | |
38 | import java.util.HashMap; | |
39 | import java.util.List; | |
40 | ||
41 | public class IdPanel extends Panel | |
42 | implements MouseListener, MouseMotionListener | |
43 | { | |
44 | ||
45 | protected IdCanvas idCanvas; | |
46 | ||
47 | protected AlignmentViewport av; | |
48 | ||
49 | protected AlignmentPanel alignPanel; | |
50 | ||
51 | ScrollThread scrollThread = null; | |
52 | ||
53 | int lastid = -1; | |
54 | ||
55 | boolean mouseDragging = false; | |
56 | ||
57 | UrlProviderI urlProvider = null; | |
58 | ||
59 | 0 | public IdPanel(AlignViewport viewport, AlignmentPanel parent) |
60 | { | |
61 | 0 | this.av = viewport; |
62 | 0 | alignPanel = parent; |
63 | 0 | idCanvas = new IdCanvas(viewport); |
64 | 0 | setLayout(new BorderLayout()); |
65 | 0 | add(idCanvas, BorderLayout.CENTER); |
66 | 0 | idCanvas.addMouseListener(this); |
67 | 0 | idCanvas.addMouseMotionListener(this); |
68 | ||
69 | 0 | String label, url; |
70 | // TODO: add in group link parameter | |
71 | ||
72 | // make a list of label,url pairs | |
73 | 0 | HashMap<String, String> urlList = new HashMap<>(); |
74 | 0 | if (viewport.applet != null) |
75 | { | |
76 | 0 | for (int i = 1; i < 10; i++) |
77 | { | |
78 | 0 | label = viewport.applet.getParameter("linkLabel_" + i); |
79 | 0 | url = viewport.applet.getParameter("linkURL_" + i); |
80 | ||
81 | // only add non-null parameters | |
82 | 0 | if (label != null) |
83 | { | |
84 | 0 | urlList.put(label, url); |
85 | } | |
86 | } | |
87 | ||
88 | 0 | if (!urlList.isEmpty()) |
89 | { | |
90 | // set default as first entry in list | |
91 | 0 | String defaultUrl = viewport.applet.getParameter("linkLabel_1"); |
92 | 0 | UrlProviderFactoryI factory = new AppletUrlProviderFactory( |
93 | defaultUrl, urlList); | |
94 | 0 | urlProvider = factory.createUrlProvider(); |
95 | } | |
96 | } | |
97 | } | |
98 | ||
99 | Tooltip tooltip; | |
100 | ||
101 | 0 | @Override |
102 | public void mouseMoved(MouseEvent e) | |
103 | { | |
104 | 0 | int seq = alignPanel.seqPanel.findSeq(e); |
105 | ||
106 | 0 | SequenceI sequence = av.getAlignment().getSequenceAt(seq); |
107 | ||
108 | 0 | StringBuffer tooltiptext = new StringBuffer(); |
109 | 0 | if (sequence == null) |
110 | { | |
111 | 0 | return; |
112 | } | |
113 | 0 | if (sequence.getDescription() != null) |
114 | { | |
115 | 0 | tooltiptext.append(sequence.getDescription()); |
116 | 0 | tooltiptext.append("\n"); |
117 | } | |
118 | ||
119 | 0 | for (SequenceFeature sf : sequence.getFeatures() |
120 | .getNonPositionalFeatures()) | |
121 | { | |
122 | 0 | boolean nl = false; |
123 | 0 | if (sf.getFeatureGroup() != null) |
124 | { | |
125 | 0 | tooltiptext.append(sf.getFeatureGroup()); |
126 | 0 | nl = true; |
127 | } | |
128 | 0 | if (sf.getType() != null) |
129 | { | |
130 | 0 | tooltiptext.append(" "); |
131 | 0 | tooltiptext.append(sf.getType()); |
132 | 0 | nl = true; |
133 | } | |
134 | 0 | if (sf.getDescription() != null) |
135 | { | |
136 | 0 | tooltiptext.append(" "); |
137 | 0 | tooltiptext.append(sf.getDescription()); |
138 | 0 | nl = true; |
139 | } | |
140 | 0 | if (!Float.isNaN(sf.getScore()) && sf.getScore() != 0f) |
141 | { | |
142 | 0 | tooltiptext.append(" Score = "); |
143 | 0 | tooltiptext.append(sf.getScore()); |
144 | 0 | nl = true; |
145 | } | |
146 | 0 | if (sf.getStatus() != null && sf.getStatus().length() > 0) |
147 | { | |
148 | 0 | tooltiptext.append(" ("); |
149 | 0 | tooltiptext.append(sf.getStatus()); |
150 | 0 | tooltiptext.append(")"); |
151 | 0 | nl = true; |
152 | } | |
153 | 0 | if (nl) |
154 | { | |
155 | 0 | tooltiptext.append("\n"); |
156 | } | |
157 | } | |
158 | ||
159 | 0 | if (tooltiptext.length() == 0) |
160 | { | |
161 | // nothing to display - so clear tooltip if one is visible | |
162 | 0 | if (tooltip != null) |
163 | { | |
164 | 0 | tooltip.setVisible(false); |
165 | } | |
166 | 0 | tooltip = null; |
167 | 0 | tooltiptext = null; |
168 | 0 | return; |
169 | } | |
170 | 0 | if (tooltip == null) |
171 | { | |
172 | 0 | tooltip = new Tooltip( |
173 | sequence.getDisplayId(true) + "\n" + tooltiptext.toString(), | |
174 | idCanvas); | |
175 | } | |
176 | else | |
177 | { | |
178 | 0 | tooltip.setTip( |
179 | sequence.getDisplayId(true) + "\n" + tooltiptext.toString()); | |
180 | } | |
181 | 0 | tooltiptext = null; |
182 | } | |
183 | ||
184 | 0 | @Override |
185 | public void mouseDragged(MouseEvent e) | |
186 | { | |
187 | 0 | mouseDragging = true; |
188 | ||
189 | 0 | int seq = Math.max(0, alignPanel.seqPanel.findSeq(e)); |
190 | ||
191 | 0 | if (seq < lastid) |
192 | { | |
193 | 0 | selectSeqs(lastid - 1, seq); |
194 | } | |
195 | 0 | else if (seq > lastid) |
196 | { | |
197 | 0 | selectSeqs(lastid + 1, seq); |
198 | } | |
199 | ||
200 | 0 | lastid = seq; |
201 | 0 | alignPanel.paintAlignment(false, false); |
202 | } | |
203 | ||
204 | 0 | @Override |
205 | public void mouseClicked(MouseEvent e) | |
206 | { | |
207 | 0 | if (e.getClickCount() < 2) |
208 | { | |
209 | 0 | return; |
210 | } | |
211 | ||
212 | // get the sequence details | |
213 | 0 | int seq = alignPanel.seqPanel.findSeq(e); |
214 | 0 | SequenceI sq = av.getAlignment().getSequenceAt(seq); |
215 | 0 | if (sq == null) |
216 | { | |
217 | 0 | return; |
218 | } | |
219 | 0 | String id = sq.getName(); |
220 | ||
221 | // get the default url with the sequence details filled in | |
222 | 0 | if (urlProvider == null) |
223 | { | |
224 | 0 | return; |
225 | } | |
226 | 0 | String url = urlProvider.getPrimaryUrl(id); |
227 | 0 | String target = urlProvider.getPrimaryTarget(id); |
228 | 0 | try |
229 | { | |
230 | 0 | alignPanel.alignFrame.showURL(url, target); |
231 | } catch (Exception ex) | |
232 | { | |
233 | 0 | ex.printStackTrace(); |
234 | } | |
235 | } | |
236 | ||
237 | 0 | @Override |
238 | public void mouseEntered(MouseEvent e) | |
239 | { | |
240 | 0 | if (scrollThread != null) |
241 | { | |
242 | 0 | scrollThread.running = false; |
243 | } | |
244 | } | |
245 | ||
246 | 0 | @Override |
247 | public void mouseExited(MouseEvent e) | |
248 | { | |
249 | 0 | if (av.getWrapAlignment()) |
250 | { | |
251 | 0 | return; |
252 | } | |
253 | ||
254 | 0 | if (mouseDragging && e.getY() < 0 && av.getRanges().getStartSeq() > 0) |
255 | { | |
256 | 0 | scrollThread = new ScrollThread(true); |
257 | } | |
258 | ||
259 | 0 | if (mouseDragging && e.getY() >= getSize().height |
260 | && av.getAlignment().getHeight() > av.getRanges().getEndSeq()) | |
261 | { | |
262 | 0 | scrollThread = new ScrollThread(false); |
263 | } | |
264 | } | |
265 | ||
266 | 0 | @Override |
267 | public void mousePressed(MouseEvent e) | |
268 | { | |
269 | 0 | if (e.getClickCount() > 1) |
270 | { | |
271 | 0 | return; |
272 | } | |
273 | ||
274 | 0 | int y = e.getY(); |
275 | 0 | if (av.getWrapAlignment()) |
276 | { | |
277 | 0 | y -= 2 * av.getCharHeight(); |
278 | } | |
279 | ||
280 | 0 | int seq = alignPanel.seqPanel.findSeq(e); |
281 | ||
282 | 0 | if ((e.getModifiersEx() |
283 | & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK) | |
284 | { | |
285 | 0 | SequenceI sq = av.getAlignment().getSequenceAt(seq); |
286 | ||
287 | /* | |
288 | * build a new links menu based on the current links | |
289 | * and any non-positional features | |
290 | */ | |
291 | 0 | List<String> nlinks; |
292 | 0 | if (urlProvider != null) |
293 | { | |
294 | 0 | nlinks = urlProvider.getLinksForMenu(); |
295 | } | |
296 | else | |
297 | { | |
298 | 0 | nlinks = new ArrayList<>(); |
299 | } | |
300 | ||
301 | 0 | for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures()) |
302 | { | |
303 | 0 | if (sf.links != null) |
304 | { | |
305 | 0 | for (String link : sf.links) |
306 | { | |
307 | 0 | nlinks.add(link); |
308 | } | |
309 | } | |
310 | } | |
311 | ||
312 | 0 | APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks); |
313 | 0 | this.add(popup); |
314 | 0 | popup.show(this, e.getX(), e.getY()); |
315 | 0 | return; |
316 | } | |
317 | ||
318 | 0 | if ((av.getSelectionGroup() == null) |
319 | || ((!jalview.util.Platform.isControlDown(e) | |
320 | && !e.isShiftDown()) && av.getSelectionGroup() != null)) | |
321 | { | |
322 | 0 | av.setSelectionGroup(new SequenceGroup()); |
323 | 0 | av.getSelectionGroup().setStartRes(0); |
324 | 0 | av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1); |
325 | } | |
326 | ||
327 | 0 | if (e.isShiftDown() && lastid != -1) |
328 | { | |
329 | 0 | selectSeqs(lastid, seq); |
330 | } | |
331 | else | |
332 | { | |
333 | 0 | selectSeq(seq); |
334 | } | |
335 | ||
336 | 0 | alignPanel.paintAlignment(false, false); |
337 | } | |
338 | ||
339 | 0 | void selectSeq(int seq) |
340 | { | |
341 | 0 | lastid = seq; |
342 | 0 | SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); |
343 | 0 | av.getSelectionGroup().addOrRemove(pickedSeq, true); |
344 | } | |
345 | ||
346 | 0 | void selectSeqs(int start, int end) |
347 | { | |
348 | ||
349 | 0 | lastid = start; |
350 | ||
351 | 0 | if (end >= av.getAlignment().getHeight()) |
352 | { | |
353 | 0 | end = av.getAlignment().getHeight() - 1; |
354 | } | |
355 | ||
356 | 0 | if (end < start) |
357 | { | |
358 | 0 | int tmp = start; |
359 | 0 | start = end; |
360 | 0 | end = tmp; |
361 | 0 | lastid = end; |
362 | } | |
363 | 0 | if (av.getSelectionGroup() == null) |
364 | { | |
365 | 0 | av.setSelectionGroup(new SequenceGroup()); |
366 | } | |
367 | 0 | for (int i = start; i <= end; i++) |
368 | { | |
369 | 0 | av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), |
370 | i == end); | |
371 | } | |
372 | ||
373 | } | |
374 | ||
375 | 0 | @Override |
376 | public void mouseReleased(MouseEvent e) | |
377 | { | |
378 | 0 | if (scrollThread != null) |
379 | { | |
380 | 0 | scrollThread.running = false; |
381 | } | |
382 | ||
383 | 0 | if (av.getSelectionGroup() != null) |
384 | { | |
385 | 0 | av.getSelectionGroup().recalcConservation(); |
386 | } | |
387 | ||
388 | 0 | mouseDragging = false; |
389 | 0 | PaintRefresher.Refresh(this, av.getSequenceSetId()); |
390 | // always send selection message when mouse is released | |
391 | 0 | av.sendSelection(); |
392 | } | |
393 | ||
394 | 0 | public void highlightSearchResults(List<SequenceI> list) |
395 | { | |
396 | 0 | idCanvas.setHighlighted(list); |
397 | ||
398 | 0 | if (list == null || list.isEmpty()) |
399 | { | |
400 | 0 | return; |
401 | } | |
402 | ||
403 | 0 | int index = av.getAlignment().findIndex(list.get(0)); |
404 | ||
405 | // do we need to scroll the panel? | |
406 | 0 | if (av.getRanges().getStartSeq() > index |
407 | || av.getRanges().getEndSeq() < index) | |
408 | { | |
409 | 0 | av.getRanges().setStartSeq(index); |
410 | } | |
411 | } | |
412 | ||
413 | // this class allows scrolling off the bottom of the visible alignment | |
414 | class ScrollThread extends Thread | |
415 | { | |
416 | boolean running = false; | |
417 | ||
418 | boolean up = true; | |
419 | ||
420 | 0 | public ScrollThread(boolean isUp) |
421 | { | |
422 | 0 | this.up = isUp; |
423 | 0 | start(); |
424 | } | |
425 | ||
426 | 0 | public void stopScrolling() |
427 | { | |
428 | 0 | running = false; |
429 | } | |
430 | ||
431 | 0 | @Override |
432 | public void run() | |
433 | { | |
434 | 0 | running = true; |
435 | 0 | while (running) |
436 | { | |
437 | 0 | if (av.getRanges().scrollUp(up)) |
438 | { | |
439 | // scroll was ok, so add new sequence to selection | |
440 | 0 | int seq = av.getRanges().getStartSeq(); |
441 | 0 | if (!up) |
442 | { | |
443 | 0 | seq = av.getRanges().getEndSeq(); |
444 | } | |
445 | ||
446 | 0 | if (seq < lastid) |
447 | { | |
448 | 0 | selectSeqs(lastid - 1, seq); |
449 | } | |
450 | 0 | else if (seq > lastid && seq < av.getAlignment().getHeight()) |
451 | { | |
452 | 0 | selectSeqs(lastid + 1, seq); |
453 | } | |
454 | ||
455 | 0 | lastid = seq; |
456 | } | |
457 | else | |
458 | { | |
459 | 0 | running = false; |
460 | } | |
461 | ||
462 | 0 | alignPanel.paintAlignment(true, false); |
463 | 0 | try |
464 | { | |
465 | 0 | Thread.sleep(100); |
466 | } catch (Exception ex) | |
467 | { | |
468 | } | |
469 | } | |
470 | } | |
471 | } | |
472 | } |