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SeqPanel | 61 | 664 | 325 | ||
SeqPanel.ScrollThread | 1709 | 16 | 18 |
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.api.AlignViewportI; | |
24 | import jalview.commands.EditCommand; | |
25 | import jalview.commands.EditCommand.Action; | |
26 | import jalview.datamodel.AlignmentI; | |
27 | import jalview.datamodel.ColumnSelection; | |
28 | import jalview.datamodel.HiddenColumns; | |
29 | import jalview.datamodel.SearchResultMatchI; | |
30 | import jalview.datamodel.SearchResults; | |
31 | import jalview.datamodel.SearchResultsI; | |
32 | import jalview.datamodel.Sequence; | |
33 | import jalview.datamodel.SequenceFeature; | |
34 | import jalview.datamodel.SequenceGroup; | |
35 | import jalview.datamodel.SequenceI; | |
36 | import jalview.schemes.ResidueProperties; | |
37 | import jalview.structure.SelectionListener; | |
38 | import jalview.structure.SelectionSource; | |
39 | import jalview.structure.SequenceListener; | |
40 | import jalview.structure.StructureSelectionManager; | |
41 | import jalview.structure.VamsasSource; | |
42 | import jalview.util.Comparison; | |
43 | import jalview.util.MappingUtils; | |
44 | import jalview.util.MessageManager; | |
45 | import jalview.util.Platform; | |
46 | import jalview.viewmodel.AlignmentViewport; | |
47 | ||
48 | import java.awt.BorderLayout; | |
49 | import java.awt.Font; | |
50 | import java.awt.FontMetrics; | |
51 | import java.awt.Panel; | |
52 | import java.awt.Point; | |
53 | import java.awt.event.InputEvent; | |
54 | import java.awt.event.MouseEvent; | |
55 | import java.awt.event.MouseListener; | |
56 | import java.awt.event.MouseMotionListener; | |
57 | import java.util.Collections; | |
58 | import java.util.List; | |
59 | import java.util.Vector; | |
60 | ||
61 | public class SeqPanel extends Panel implements MouseMotionListener, | |
62 | MouseListener, SequenceListener, SelectionListener | |
63 | { | |
64 | ||
65 | public SeqCanvas seqCanvas; | |
66 | ||
67 | public AlignmentPanel ap; | |
68 | ||
69 | protected int lastres; | |
70 | ||
71 | protected int startseq; | |
72 | ||
73 | protected AlignViewport av; | |
74 | ||
75 | // if character is inserted or deleted, we will need to recalculate the | |
76 | // conservation | |
77 | boolean seqEditOccurred = false; | |
78 | ||
79 | ScrollThread scrollThread = null; | |
80 | ||
81 | boolean mouseDragging = false; | |
82 | ||
83 | boolean editingSeqs = false; | |
84 | ||
85 | boolean groupEditing = false; | |
86 | ||
87 | int oldSeq = -1; | |
88 | ||
89 | boolean changeEndSeq = false; | |
90 | ||
91 | boolean changeStartSeq = false; | |
92 | ||
93 | boolean changeEndRes = false; | |
94 | ||
95 | boolean changeStartRes = false; | |
96 | ||
97 | SequenceGroup stretchGroup = null; | |
98 | ||
99 | StringBuffer keyboardNo1; | |
100 | ||
101 | StringBuffer keyboardNo2; | |
102 | ||
103 | boolean mouseWheelPressed = false; | |
104 | ||
105 | Point lastMousePress; | |
106 | ||
107 | EditCommand editCommand; | |
108 | ||
109 | StructureSelectionManager ssm; | |
110 | ||
111 | 0 | public SeqPanel(AlignViewport avp, AlignmentPanel p) |
112 | { | |
113 | 0 | this.av = avp; |
114 | ||
115 | 0 | seqCanvas = new SeqCanvas(avp); |
116 | 0 | setLayout(new BorderLayout()); |
117 | 0 | add(seqCanvas); |
118 | ||
119 | 0 | ap = p; |
120 | ||
121 | 0 | seqCanvas.addMouseMotionListener(this); |
122 | 0 | seqCanvas.addMouseListener(this); |
123 | 0 | ssm = StructureSelectionManager.getStructureSelectionManager(av.applet); |
124 | 0 | ssm.addStructureViewerListener(this); |
125 | 0 | ssm.addSelectionListener(this); |
126 | ||
127 | 0 | seqCanvas.repaint(); |
128 | } | |
129 | ||
130 | 0 | void endEditing() |
131 | { | |
132 | 0 | if (editCommand != null && editCommand.getSize() > 0) |
133 | { | |
134 | 0 | ap.alignFrame.addHistoryItem(editCommand); |
135 | 0 | av.firePropertyChange("alignment", null, |
136 | av.getAlignment().getSequences()); | |
137 | } | |
138 | ||
139 | 0 | startseq = -1; |
140 | 0 | lastres = -1; |
141 | 0 | editingSeqs = false; |
142 | 0 | groupEditing = false; |
143 | 0 | keyboardNo1 = null; |
144 | 0 | keyboardNo2 = null; |
145 | 0 | editCommand = null; |
146 | } | |
147 | ||
148 | 0 | void setCursorRow() |
149 | { | |
150 | 0 | seqCanvas.cursorY = getKeyboardNo1() - 1; |
151 | 0 | scrollToVisible(true); |
152 | } | |
153 | ||
154 | 0 | void setCursorColumn() |
155 | { | |
156 | 0 | seqCanvas.cursorX = getKeyboardNo1() - 1; |
157 | 0 | scrollToVisible(true); |
158 | } | |
159 | ||
160 | 0 | void setCursorRowAndColumn() |
161 | { | |
162 | 0 | if (keyboardNo2 == null) |
163 | { | |
164 | 0 | keyboardNo2 = new StringBuffer(); |
165 | } | |
166 | else | |
167 | { | |
168 | 0 | seqCanvas.cursorX = getKeyboardNo1() - 1; |
169 | 0 | seqCanvas.cursorY = getKeyboardNo2() - 1; |
170 | 0 | scrollToVisible(true); |
171 | } | |
172 | } | |
173 | ||
174 | 0 | void setCursorPosition() |
175 | { | |
176 | 0 | SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); |
177 | ||
178 | 0 | seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1; |
179 | 0 | scrollToVisible(true); |
180 | } | |
181 | ||
182 | 0 | void moveCursor(int dx, int dy) |
183 | { | |
184 | 0 | seqCanvas.cursorX += dx; |
185 | 0 | seqCanvas.cursorY += dy; |
186 | 0 | if (av.hasHiddenColumns() && !av.getAlignment().getHiddenColumns() |
187 | .isVisible(seqCanvas.cursorX)) | |
188 | { | |
189 | 0 | int original = seqCanvas.cursorX - dx; |
190 | 0 | int maxWidth = av.getAlignment().getWidth(); |
191 | ||
192 | 0 | while (!av.getAlignment().getHiddenColumns() |
193 | .isVisible(seqCanvas.cursorX) && seqCanvas.cursorX < maxWidth | |
194 | && seqCanvas.cursorX > 0) | |
195 | { | |
196 | 0 | seqCanvas.cursorX += dx; |
197 | } | |
198 | ||
199 | 0 | if (seqCanvas.cursorX >= maxWidth || !av.getAlignment() |
200 | .getHiddenColumns().isVisible(seqCanvas.cursorX)) | |
201 | { | |
202 | 0 | seqCanvas.cursorX = original; |
203 | } | |
204 | } | |
205 | 0 | scrollToVisible(false); |
206 | } | |
207 | ||
208 | /** | |
209 | * Scroll to make the cursor visible in the viewport. | |
210 | * | |
211 | * @param jump | |
212 | * just jump to the location rather than scrolling | |
213 | */ | |
214 | 0 | void scrollToVisible(boolean jump) |
215 | { | |
216 | 0 | if (seqCanvas.cursorX < 0) |
217 | { | |
218 | 0 | seqCanvas.cursorX = 0; |
219 | } | |
220 | 0 | else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1) |
221 | { | |
222 | 0 | seqCanvas.cursorX = av.getAlignment().getWidth() - 1; |
223 | } | |
224 | ||
225 | 0 | if (seqCanvas.cursorY < 0) |
226 | { | |
227 | 0 | seqCanvas.cursorY = 0; |
228 | } | |
229 | 0 | else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1) |
230 | { | |
231 | 0 | seqCanvas.cursorY = av.getAlignment().getHeight() - 1; |
232 | } | |
233 | ||
234 | 0 | endEditing(); |
235 | ||
236 | 0 | boolean repaintNeeded = true; |
237 | 0 | if (jump) |
238 | { | |
239 | // only need to repaint if the viewport did not move, as otherwise it will | |
240 | // get a repaint | |
241 | 0 | repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX, |
242 | seqCanvas.cursorY); | |
243 | } | |
244 | else | |
245 | { | |
246 | 0 | if (av.getWrapAlignment()) |
247 | { | |
248 | 0 | av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX); |
249 | } | |
250 | else | |
251 | { | |
252 | 0 | av.getRanges().scrollToVisible(seqCanvas.cursorX, |
253 | seqCanvas.cursorY); | |
254 | } | |
255 | } | |
256 | 0 | setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), |
257 | seqCanvas.cursorX, seqCanvas.cursorY); | |
258 | ||
259 | 0 | if (repaintNeeded) |
260 | { | |
261 | 0 | seqCanvas.repaint(); |
262 | } | |
263 | } | |
264 | ||
265 | 0 | void setSelectionAreaAtCursor(boolean topLeft) |
266 | { | |
267 | 0 | SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); |
268 | ||
269 | 0 | if (av.getSelectionGroup() != null) |
270 | { | |
271 | 0 | SequenceGroup sg = av.getSelectionGroup(); |
272 | // Find the top and bottom of this group | |
273 | 0 | int min = av.getAlignment().getHeight(), max = 0; |
274 | 0 | for (int i = 0; i < sg.getSize(); i++) |
275 | { | |
276 | 0 | int index = av.getAlignment().findIndex(sg.getSequenceAt(i)); |
277 | 0 | if (index > max) |
278 | { | |
279 | 0 | max = index; |
280 | } | |
281 | 0 | if (index < min) |
282 | { | |
283 | 0 | min = index; |
284 | } | |
285 | } | |
286 | ||
287 | 0 | max++; |
288 | ||
289 | 0 | if (topLeft) |
290 | { | |
291 | 0 | sg.setStartRes(seqCanvas.cursorX); |
292 | 0 | if (sg.getEndRes() < seqCanvas.cursorX) |
293 | { | |
294 | 0 | sg.setEndRes(seqCanvas.cursorX); |
295 | } | |
296 | ||
297 | 0 | min = seqCanvas.cursorY; |
298 | } | |
299 | else | |
300 | { | |
301 | 0 | sg.setEndRes(seqCanvas.cursorX); |
302 | 0 | if (sg.getStartRes() > seqCanvas.cursorX) |
303 | { | |
304 | 0 | sg.setStartRes(seqCanvas.cursorX); |
305 | } | |
306 | ||
307 | 0 | max = seqCanvas.cursorY + 1; |
308 | } | |
309 | ||
310 | 0 | if (min > max) |
311 | { | |
312 | // Only the user can do this | |
313 | 0 | av.setSelectionGroup(null); |
314 | } | |
315 | else | |
316 | { | |
317 | // Now add any sequences between min and max | |
318 | 0 | sg.clear(); |
319 | 0 | for (int i = min; i < max; i++) |
320 | { | |
321 | 0 | sg.addSequence(av.getAlignment().getSequenceAt(i), false); |
322 | } | |
323 | } | |
324 | } | |
325 | ||
326 | 0 | if (av.getSelectionGroup() == null) |
327 | { | |
328 | 0 | SequenceGroup sg = new SequenceGroup(); |
329 | 0 | sg.setStartRes(seqCanvas.cursorX); |
330 | 0 | sg.setEndRes(seqCanvas.cursorX); |
331 | 0 | sg.addSequence(sequence, false); |
332 | 0 | av.setSelectionGroup(sg); |
333 | } | |
334 | 0 | ap.paintAlignment(false, false); |
335 | 0 | av.sendSelection(); |
336 | } | |
337 | ||
338 | 0 | void insertGapAtCursor(boolean group) |
339 | { | |
340 | 0 | groupEditing = group; |
341 | 0 | startseq = seqCanvas.cursorY; |
342 | 0 | lastres = seqCanvas.cursorX; |
343 | 0 | editSequence(true, seqCanvas.cursorX + getKeyboardNo1()); |
344 | 0 | endEditing(); |
345 | } | |
346 | ||
347 | 0 | void deleteGapAtCursor(boolean group) |
348 | { | |
349 | 0 | groupEditing = group; |
350 | 0 | startseq = seqCanvas.cursorY; |
351 | 0 | lastres = seqCanvas.cursorX + getKeyboardNo1(); |
352 | 0 | editSequence(false, seqCanvas.cursorX); |
353 | 0 | endEditing(); |
354 | } | |
355 | ||
356 | 0 | void numberPressed(char value) |
357 | { | |
358 | 0 | if (keyboardNo1 == null) |
359 | { | |
360 | 0 | keyboardNo1 = new StringBuffer(); |
361 | } | |
362 | ||
363 | 0 | if (keyboardNo2 != null) |
364 | { | |
365 | 0 | keyboardNo2.append(value); |
366 | } | |
367 | else | |
368 | { | |
369 | 0 | keyboardNo1.append(value); |
370 | } | |
371 | } | |
372 | ||
373 | 0 | int getKeyboardNo1() |
374 | { | |
375 | 0 | try |
376 | { | |
377 | 0 | if (keyboardNo1 != null) |
378 | { | |
379 | 0 | int value = Integer.parseInt(keyboardNo1.toString()); |
380 | 0 | keyboardNo1 = null; |
381 | 0 | return value; |
382 | } | |
383 | } catch (Exception x) | |
384 | { | |
385 | } | |
386 | 0 | keyboardNo1 = null; |
387 | 0 | return 1; |
388 | } | |
389 | ||
390 | 0 | int getKeyboardNo2() |
391 | { | |
392 | 0 | try |
393 | { | |
394 | 0 | if (keyboardNo2 != null) |
395 | { | |
396 | 0 | int value = Integer.parseInt(keyboardNo2.toString()); |
397 | 0 | keyboardNo2 = null; |
398 | 0 | return value; |
399 | } | |
400 | } catch (Exception x) | |
401 | { | |
402 | } | |
403 | 0 | keyboardNo2 = null; |
404 | 0 | return 1; |
405 | } | |
406 | ||
407 | /** | |
408 | * Set status message in alignment panel | |
409 | * | |
410 | * @param sequence | |
411 | * aligned sequence object | |
412 | * @param column | |
413 | * alignment column | |
414 | * @param seq | |
415 | * index of sequence in alignment | |
416 | */ | |
417 | 0 | void setStatusMessage(SequenceI sequence, int column, int seq) |
418 | { | |
419 | // TODO remove duplication of identical gui method | |
420 | 0 | StringBuilder text = new StringBuilder(32); |
421 | 0 | String seqno = seq == -1 ? "" : " " + (seq + 1); |
422 | 0 | text.append("Sequence" + seqno + " ID: " + sequence.getName()); |
423 | ||
424 | 0 | String residue = null; |
425 | /* | |
426 | * Try to translate the display character to residue name (null for gap). | |
427 | */ | |
428 | 0 | final String displayChar = String.valueOf(sequence.getCharAt(column)); |
429 | 0 | if (av.getAlignment().isNucleotide()) |
430 | { | |
431 | 0 | residue = ResidueProperties.nucleotideName.get(displayChar); |
432 | 0 | if (residue != null) |
433 | { | |
434 | 0 | text.append(" Nucleotide: ").append(residue); |
435 | } | |
436 | } | |
437 | else | |
438 | { | |
439 | 0 | residue = "X".equalsIgnoreCase(displayChar) ? "X" |
440 | 0 | : ("*".equals(displayChar) ? "STOP" |
441 | : ResidueProperties.aa2Triplet.get(displayChar)); | |
442 | 0 | if (residue != null) |
443 | { | |
444 | 0 | text.append(" Residue: ").append(residue); |
445 | } | |
446 | } | |
447 | ||
448 | 0 | int pos = -1; |
449 | 0 | if (residue != null) |
450 | { | |
451 | 0 | pos = sequence.findPosition(column); |
452 | 0 | text.append(" (").append(Integer.toString(pos)).append(")"); |
453 | } | |
454 | ||
455 | 0 | ap.alignFrame.statusBar.setText(text.toString()); |
456 | } | |
457 | ||
458 | /** | |
459 | * Set the status bar message to highlight the first matched position in | |
460 | * search results. | |
461 | * | |
462 | * @param results | |
463 | * @return true if results were matched, false if not | |
464 | */ | |
465 | 0 | private boolean setStatusMessage(SearchResultsI results) |
466 | { | |
467 | 0 | AlignmentI al = this.av.getAlignment(); |
468 | 0 | int sequenceIndex = al.findIndex(results); |
469 | 0 | if (sequenceIndex == -1) |
470 | { | |
471 | 0 | return false; |
472 | } | |
473 | 0 | SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence(); |
474 | 0 | for (SearchResultMatchI m : results.getResults()) |
475 | { | |
476 | 0 | SequenceI seq = m.getSequence(); |
477 | 0 | if (seq.getDatasetSequence() != null) |
478 | { | |
479 | 0 | seq = seq.getDatasetSequence(); |
480 | } | |
481 | ||
482 | 0 | if (seq == ds) |
483 | { | |
484 | /* | |
485 | * Convert position in sequence (base 1) to sequence character array | |
486 | * index (base 0) | |
487 | */ | |
488 | 0 | int start = m.getStart() - m.getSequence().getStart(); |
489 | 0 | setStatusMessage(seq, start, sequenceIndex); |
490 | 0 | return true; |
491 | } | |
492 | } | |
493 | 0 | return false; |
494 | } | |
495 | ||
496 | 0 | @Override |
497 | public void mousePressed(MouseEvent evt) | |
498 | { | |
499 | 0 | lastMousePress = evt.getPoint(); |
500 | ||
501 | // For now, ignore the mouseWheel font resizing on Macs | |
502 | // As the Button2_mask always seems to be true | |
503 | 0 | if (Platform.isWinMiddleButton(evt)) |
504 | { | |
505 | 0 | mouseWheelPressed = true; |
506 | 0 | return; |
507 | } | |
508 | ||
509 | 0 | if (evt.isShiftDown() || evt.isControlDown() || evt.isAltDown()) |
510 | { | |
511 | 0 | if (evt.isControlDown() || evt.isAltDown()) |
512 | { | |
513 | 0 | groupEditing = true; |
514 | } | |
515 | 0 | editingSeqs = true; |
516 | } | |
517 | else | |
518 | { | |
519 | 0 | doMousePressedDefineMode(evt); |
520 | 0 | return; |
521 | } | |
522 | ||
523 | 0 | int seq = findSeq(evt); |
524 | 0 | int res = findColumn(evt); |
525 | ||
526 | 0 | if (seq < 0 || res < 0) |
527 | { | |
528 | 0 | return; |
529 | } | |
530 | ||
531 | 0 | if ((seq < av.getAlignment().getHeight()) |
532 | && (res < av.getAlignment().getSequenceAt(seq).getLength())) | |
533 | { | |
534 | 0 | startseq = seq; |
535 | 0 | lastres = res; |
536 | } | |
537 | else | |
538 | { | |
539 | 0 | startseq = -1; |
540 | 0 | lastres = -1; |
541 | } | |
542 | ||
543 | 0 | return; |
544 | } | |
545 | ||
546 | 0 | @Override |
547 | public void mouseClicked(MouseEvent evt) | |
548 | { | |
549 | 0 | SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt)); |
550 | 0 | if (evt.getClickCount() > 1) |
551 | { | |
552 | 0 | if (av.getSelectionGroup() != null |
553 | && av.getSelectionGroup().getSize() == 1 | |
554 | && av.getSelectionGroup().getEndRes() | |
555 | - av.getSelectionGroup().getStartRes() < 2) | |
556 | { | |
557 | 0 | av.setSelectionGroup(null); |
558 | } | |
559 | ||
560 | 0 | int column = findColumn(evt); |
561 | 0 | List<SequenceFeature> features = findFeaturesAtColumn(sequence, |
562 | column + 1); | |
563 | ||
564 | 0 | if (!features.isEmpty()) |
565 | { | |
566 | 0 | SearchResultsI highlight = new SearchResults(); |
567 | 0 | highlight.addResult(sequence, features.get(0).getBegin(), |
568 | features.get(0).getEnd()); | |
569 | 0 | seqCanvas.highlightSearchResults(highlight); |
570 | 0 | seqCanvas.getFeatureRenderer().amendFeatures( |
571 | Collections.singletonList(sequence), features, false, ap); | |
572 | 0 | av.setSearchResults(null); // clear highlighting |
573 | 0 | seqCanvas.repaint(); // draw new/amended features |
574 | } | |
575 | } | |
576 | } | |
577 | ||
578 | 0 | @Override |
579 | public void mouseReleased(MouseEvent evt) | |
580 | { | |
581 | 0 | boolean didDrag = mouseDragging; // did we come here after a drag |
582 | 0 | mouseDragging = false; |
583 | 0 | mouseWheelPressed = false; |
584 | ||
585 | 0 | if (!editingSeqs) |
586 | { | |
587 | 0 | doMouseReleasedDefineMode(evt, didDrag); |
588 | 0 | return; |
589 | } | |
590 | ||
591 | 0 | endEditing(); |
592 | ||
593 | } | |
594 | ||
595 | int startWrapBlock = -1; | |
596 | ||
597 | int wrappedBlock = -1; | |
598 | ||
599 | /** | |
600 | * Returns the aligned sequence position (base 0) at the mouse position, or | |
601 | * the closest visible one | |
602 | * | |
603 | * @param evt | |
604 | * @return | |
605 | */ | |
606 | 0 | int findColumn(MouseEvent evt) |
607 | { | |
608 | 0 | int res = 0; |
609 | 0 | int x = evt.getX(); |
610 | ||
611 | 0 | int startRes = av.getRanges().getStartRes(); |
612 | 0 | if (av.getWrapAlignment()) |
613 | { | |
614 | ||
615 | 0 | int hgap = av.getCharHeight(); |
616 | 0 | if (av.getScaleAboveWrapped()) |
617 | { | |
618 | 0 | hgap += av.getCharHeight(); |
619 | } | |
620 | ||
621 | 0 | int cHeight = av.getAlignment().getHeight() * av.getCharHeight() |
622 | + hgap + seqCanvas.getAnnotationHeight(); | |
623 | ||
624 | 0 | int y = evt.getY(); |
625 | 0 | y -= hgap; |
626 | 0 | x = Math.max(0, x - seqCanvas.LABEL_WEST); |
627 | ||
628 | 0 | int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width); |
629 | 0 | if (cwidth < 1) |
630 | { | |
631 | 0 | return 0; |
632 | } | |
633 | ||
634 | 0 | wrappedBlock = y / cHeight; |
635 | 0 | wrappedBlock += startRes / cwidth; |
636 | 0 | int startOffset = startRes % cwidth; // in case start is scrolled right |
637 | // from 0 | |
638 | 0 | res = wrappedBlock * cwidth + startOffset |
639 | + +Math.min(cwidth - 1, x / av.getCharWidth()); | |
640 | } | |
641 | else | |
642 | { | |
643 | 0 | res = (x / av.getCharWidth()) + startRes; |
644 | } | |
645 | ||
646 | 0 | if (av.hasHiddenColumns()) |
647 | { | |
648 | 0 | res = av.getAlignment().getHiddenColumns() |
649 | .visibleToAbsoluteColumn(res); | |
650 | } | |
651 | ||
652 | 0 | return res; |
653 | ||
654 | } | |
655 | ||
656 | 0 | int findSeq(MouseEvent evt) |
657 | { | |
658 | 0 | final int sqnum = findAlRow(evt); |
659 | 0 | return (sqnum < 0) ? 0 : sqnum; |
660 | } | |
661 | ||
662 | /** | |
663 | * | |
664 | * @param evt | |
665 | * @return row in alignment that was selected (or -1 for column selection) | |
666 | */ | |
667 | 0 | private int findAlRow(MouseEvent evt) |
668 | { | |
669 | 0 | int seq = 0; |
670 | 0 | int y = evt.getY(); |
671 | ||
672 | 0 | if (av.getWrapAlignment()) |
673 | { | |
674 | 0 | int hgap = av.getCharHeight(); |
675 | 0 | if (av.getScaleAboveWrapped()) |
676 | { | |
677 | 0 | hgap += av.getCharHeight(); |
678 | } | |
679 | ||
680 | 0 | int cHeight = av.getAlignment().getHeight() * av.getCharHeight() |
681 | + hgap + seqCanvas.getAnnotationHeight(); | |
682 | ||
683 | 0 | y -= hgap; |
684 | ||
685 | 0 | seq = Math.min((y % cHeight) / av.getCharHeight(), |
686 | av.getAlignment().getHeight() - 1); | |
687 | 0 | if (seq < 0) |
688 | { | |
689 | 0 | seq = -1; |
690 | } | |
691 | } | |
692 | else | |
693 | { | |
694 | 0 | seq = Math.min( |
695 | (y / av.getCharHeight()) + av.getRanges().getStartSeq(), | |
696 | av.getAlignment().getHeight() - 1); | |
697 | 0 | if (seq < 0) |
698 | { | |
699 | 0 | seq = -1; |
700 | } | |
701 | } | |
702 | ||
703 | 0 | return seq; |
704 | } | |
705 | ||
706 | 0 | public void doMousePressed(MouseEvent evt) |
707 | { | |
708 | ||
709 | 0 | int seq = findSeq(evt); |
710 | 0 | int res = findColumn(evt); |
711 | ||
712 | 0 | if (seq < av.getAlignment().getHeight() |
713 | && res < av.getAlignment().getSequenceAt(seq).getLength()) | |
714 | { | |
715 | // char resstr = align.getSequenceAt(seq).getSequence().charAt(res); | |
716 | // Find the residue's position in the sequence (res is the position | |
717 | // in the alignment | |
718 | ||
719 | 0 | startseq = seq; |
720 | 0 | lastres = res; |
721 | } | |
722 | else | |
723 | { | |
724 | 0 | startseq = -1; |
725 | 0 | lastres = -1; |
726 | } | |
727 | ||
728 | 0 | return; |
729 | } | |
730 | ||
731 | String lastMessage; | |
732 | ||
733 | 0 | @Override |
734 | public void mouseOverSequence(SequenceI sequence, int index, int pos) | |
735 | { | |
736 | 0 | String tmp = sequence.hashCode() + index + ""; |
737 | 0 | if (lastMessage == null || !lastMessage.equals(tmp)) |
738 | { | |
739 | 0 | ssm.mouseOverSequence(sequence, index, pos, av); |
740 | } | |
741 | ||
742 | 0 | lastMessage = tmp; |
743 | } | |
744 | ||
745 | 0 | @Override |
746 | public String highlightSequence(SearchResultsI results) | |
747 | { | |
748 | 0 | if (av.isFollowHighlight()) |
749 | { | |
750 | // don't allow highlight of protein/cDNA to also scroll a complementary | |
751 | // panel,as this sets up a feedback loop (scrolling panel 1 causes moused | |
752 | // over residue to change abruptly, causing highlighted residue in panel 2 | |
753 | // to change, causing a scroll in panel 1 etc) | |
754 | 0 | ap.setToScrollComplementPanel(false); |
755 | 0 | if (ap.scrollToPosition(results, true)) |
756 | { | |
757 | 0 | ap.alignFrame.repaint(); |
758 | } | |
759 | 0 | ap.setToScrollComplementPanel(true); |
760 | } | |
761 | 0 | setStatusMessage(results); |
762 | 0 | seqCanvas.highlightSearchResults(results); |
763 | 0 | return null; |
764 | } | |
765 | ||
766 | 0 | @Override |
767 | public VamsasSource getVamsasSource() | |
768 | { | |
769 | 0 | return this.ap == null ? null : this.ap.av; |
770 | } | |
771 | ||
772 | 0 | @Override |
773 | public void updateColours(SequenceI seq, int index) | |
774 | { | |
775 | 0 | jalview.bin.Console.outPrintln("update the seqPanel colours"); |
776 | // repaint(); | |
777 | } | |
778 | ||
779 | 0 | @Override |
780 | public void mouseMoved(MouseEvent evt) | |
781 | { | |
782 | 0 | final int column = findColumn(evt); |
783 | 0 | int seq = findSeq(evt); |
784 | ||
785 | 0 | if (seq >= av.getAlignment().getHeight() || seq < 0 || column < 0) |
786 | { | |
787 | 0 | if (tooltip != null) |
788 | { | |
789 | 0 | tooltip.setTip(""); |
790 | } | |
791 | 0 | return; |
792 | } | |
793 | ||
794 | 0 | SequenceI sequence = av.getAlignment().getSequenceAt(seq); |
795 | 0 | if (column > sequence.getLength()) |
796 | { | |
797 | 0 | if (tooltip != null) |
798 | { | |
799 | 0 | tooltip.setTip(""); |
800 | } | |
801 | 0 | return; |
802 | } | |
803 | ||
804 | 0 | final char ch = sequence.getCharAt(column); |
805 | 0 | boolean isGapped = Comparison.isGap(ch); |
806 | // find residue at column (or nearest if at a gap) | |
807 | 0 | int respos = sequence.findPosition(column); |
808 | ||
809 | 0 | if (ssm != null && !isGapped) |
810 | { | |
811 | 0 | mouseOverSequence(sequence, column, respos); |
812 | } | |
813 | ||
814 | 0 | StringBuilder text = new StringBuilder(); |
815 | 0 | text.append("Sequence ").append(Integer.toString(seq + 1)) |
816 | .append(" ID: ").append(sequence.getName()); | |
817 | ||
818 | 0 | if (!isGapped) |
819 | { | |
820 | 0 | if (av.getAlignment().isNucleotide()) |
821 | { | |
822 | 0 | String base = ResidueProperties.nucleotideName.get(ch); |
823 | 0 | text.append(" Nucleotide: ").append(base == null ? ch : base); |
824 | } | |
825 | else | |
826 | { | |
827 | 0 | String residue = (ch == 'x' || ch == 'X') ? "X" |
828 | : ResidueProperties.aa2Triplet.get(String.valueOf(ch)); | |
829 | 0 | text.append(" Residue: ").append(residue == null ? ch : residue); |
830 | } | |
831 | 0 | text.append(" (").append(Integer.toString(respos)).append(")"); |
832 | } | |
833 | ||
834 | 0 | ap.alignFrame.statusBar.setText(text.toString()); |
835 | ||
836 | 0 | StringBuilder tooltipText = new StringBuilder(); |
837 | 0 | SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence); |
838 | 0 | if (groups != null) |
839 | { | |
840 | 0 | for (int g = 0; g < groups.length; g++) |
841 | { | |
842 | 0 | if (groups[g].getStartRes() <= column |
843 | && groups[g].getEndRes() >= column) | |
844 | { | |
845 | 0 | if (!groups[g].getName().startsWith("JTreeGroup") |
846 | && !groups[g].getName().startsWith("JGroup")) | |
847 | { | |
848 | 0 | tooltipText.append(groups[g].getName()).append(" "); |
849 | } | |
850 | 0 | if (groups[g].getDescription() != null) |
851 | { | |
852 | 0 | tooltipText.append(groups[g].getDescription()); |
853 | } | |
854 | 0 | tooltipText.append("\n"); |
855 | } | |
856 | } | |
857 | } | |
858 | ||
859 | /* | |
860 | * add feature details to tooltip, including any that straddle | |
861 | * a gapped position | |
862 | */ | |
863 | 0 | if (av.isShowSequenceFeatures()) |
864 | { | |
865 | 0 | List<SequenceFeature> allFeatures = findFeaturesAtColumn(sequence, |
866 | column + 1); | |
867 | 0 | for (SequenceFeature sf : allFeatures) |
868 | { | |
869 | 0 | tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end); |
870 | ||
871 | 0 | if (sf.getDescription() != null) |
872 | { | |
873 | 0 | tooltipText.append(" " + sf.getDescription()); |
874 | } | |
875 | ||
876 | 0 | if (sf.getValue("status") != null) |
877 | { | |
878 | 0 | String status = sf.getValue("status").toString(); |
879 | 0 | if (status.length() > 0) |
880 | { | |
881 | 0 | tooltipText.append(" (" + sf.getValue("status") + ")"); |
882 | } | |
883 | } | |
884 | 0 | tooltipText.append("\n"); |
885 | } | |
886 | } | |
887 | ||
888 | 0 | if (tooltip == null) |
889 | { | |
890 | 0 | tooltip = new Tooltip(tooltipText.toString(), seqCanvas); |
891 | } | |
892 | else | |
893 | { | |
894 | 0 | tooltip.setTip(tooltipText.toString()); |
895 | } | |
896 | } | |
897 | ||
898 | /** | |
899 | * Returns features at the specified aligned column on the given sequence. | |
900 | * Non-positional features are not included. If the column has a gap, then | |
901 | * enclosing features are included (but not contact features). | |
902 | * | |
903 | * @param sequence | |
904 | * @param column | |
905 | * (1..) | |
906 | * @return | |
907 | */ | |
908 | 0 | List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column) |
909 | { | |
910 | 0 | return seqCanvas.getFeatureRenderer().findFeaturesAtColumn(sequence, |
911 | column); | |
912 | } | |
913 | ||
914 | Tooltip tooltip; | |
915 | ||
916 | /** | |
917 | * set when the current UI interaction has resulted in a change that requires | |
918 | * overview shading to be recalculated. this could be changed to something | |
919 | * more expressive that indicates what actually has changed, so selective | |
920 | * redraws can be applied | |
921 | */ | |
922 | private boolean needOverviewUpdate; // TODO: refactor to avcontroller | |
923 | ||
924 | 0 | @Override |
925 | public void mouseDragged(MouseEvent evt) | |
926 | { | |
927 | 0 | if (mouseWheelPressed) |
928 | { | |
929 | 0 | int oldWidth = av.getCharWidth(); |
930 | ||
931 | // Which is bigger, left-right or up-down? | |
932 | 0 | if (Math.abs(evt.getY() - lastMousePress.y) > Math |
933 | .abs(evt.getX() - lastMousePress.x)) | |
934 | { | |
935 | 0 | int fontSize = av.font.getSize(); |
936 | ||
937 | 0 | if (evt.getY() < lastMousePress.y && av.getCharHeight() > 1) |
938 | { | |
939 | 0 | fontSize--; |
940 | } | |
941 | 0 | else if (evt.getY() > lastMousePress.y) |
942 | { | |
943 | 0 | fontSize++; |
944 | } | |
945 | ||
946 | 0 | if (fontSize < 1) |
947 | { | |
948 | 0 | fontSize = 1; |
949 | } | |
950 | ||
951 | 0 | av.setFont( |
952 | new Font(av.font.getName(), av.font.getStyle(), fontSize), | |
953 | true); | |
954 | 0 | av.setCharWidth(oldWidth); |
955 | } | |
956 | else | |
957 | { | |
958 | 0 | if (evt.getX() < lastMousePress.x && av.getCharWidth() > 1) |
959 | { | |
960 | 0 | av.setCharWidth(av.getCharWidth() - 1); |
961 | } | |
962 | 0 | else if (evt.getX() > lastMousePress.x) |
963 | { | |
964 | 0 | av.setCharWidth(av.getCharWidth() + 1); |
965 | } | |
966 | ||
967 | 0 | if (av.getCharWidth() < 1) |
968 | { | |
969 | 0 | av.setCharWidth(1); |
970 | } | |
971 | } | |
972 | ||
973 | 0 | ap.fontChanged(); |
974 | ||
975 | 0 | FontMetrics fm = getFontMetrics(av.getFont()); |
976 | 0 | av.validCharWidth = fm.charWidth('M') <= av.getCharWidth(); |
977 | ||
978 | 0 | lastMousePress = evt.getPoint(); |
979 | ||
980 | 0 | ap.paintAlignment(false, false); |
981 | 0 | ap.annotationPanel.image = null; |
982 | 0 | return; |
983 | } | |
984 | ||
985 | 0 | if (!editingSeqs) |
986 | { | |
987 | 0 | doMouseDraggedDefineMode(evt); |
988 | 0 | return; |
989 | } | |
990 | ||
991 | 0 | int res = findColumn(evt); |
992 | ||
993 | 0 | if (res < 0) |
994 | { | |
995 | 0 | res = 0; |
996 | } | |
997 | ||
998 | 0 | if ((lastres == -1) || (lastres == res)) |
999 | { | |
1000 | 0 | return; |
1001 | } | |
1002 | ||
1003 | 0 | if ((res < av.getAlignment().getWidth()) && (res < lastres)) |
1004 | { | |
1005 | // dragLeft, delete gap | |
1006 | 0 | editSequence(false, res); |
1007 | } | |
1008 | else | |
1009 | { | |
1010 | 0 | editSequence(true, res); |
1011 | } | |
1012 | ||
1013 | 0 | mouseDragging = true; |
1014 | 0 | if (scrollThread != null) |
1015 | { | |
1016 | 0 | scrollThread.setEvent(evt); |
1017 | } | |
1018 | ||
1019 | } | |
1020 | ||
1021 | 0 | synchronized void editSequence(boolean insertGap, int startres) |
1022 | { | |
1023 | 0 | int fixedLeft = -1; |
1024 | 0 | int fixedRight = -1; |
1025 | 0 | boolean fixedColumns = false; |
1026 | 0 | SequenceGroup sg = av.getSelectionGroup(); |
1027 | ||
1028 | 0 | SequenceI seq = av.getAlignment().getSequenceAt(startseq); |
1029 | ||
1030 | 0 | if (!groupEditing && av.hasHiddenRows()) |
1031 | { | |
1032 | 0 | if (av.isHiddenRepSequence(seq)) |
1033 | { | |
1034 | 0 | sg = av.getRepresentedSequences(seq); |
1035 | 0 | groupEditing = true; |
1036 | } | |
1037 | } | |
1038 | ||
1039 | 0 | StringBuffer message = new StringBuffer(); |
1040 | 0 | if (groupEditing) |
1041 | { | |
1042 | 0 | message.append(MessageManager.getString("action.edit_group")) |
1043 | .append(":"); | |
1044 | 0 | if (editCommand == null) |
1045 | { | |
1046 | 0 | editCommand = new EditCommand( |
1047 | MessageManager.getString("action.edit_group")); | |
1048 | } | |
1049 | } | |
1050 | else | |
1051 | { | |
1052 | 0 | message.append(MessageManager.getString("label.edit_sequence")) |
1053 | .append(" " + seq.getName()); | |
1054 | 0 | String label = seq.getName(); |
1055 | 0 | if (label.length() > 10) |
1056 | { | |
1057 | 0 | label = label.substring(0, 10); |
1058 | } | |
1059 | 0 | if (editCommand == null) |
1060 | { | |
1061 | 0 | editCommand = new EditCommand(MessageManager |
1062 | .formatMessage("label.edit_params", new String[] | |
1063 | { label })); | |
1064 | } | |
1065 | } | |
1066 | ||
1067 | 0 | if (insertGap) |
1068 | { | |
1069 | 0 | message.append(" insert "); |
1070 | } | |
1071 | else | |
1072 | { | |
1073 | 0 | message.append(" delete "); |
1074 | } | |
1075 | ||
1076 | 0 | message.append(Math.abs(startres - lastres) + " gaps."); |
1077 | 0 | ap.alignFrame.statusBar.setText(message.toString()); |
1078 | ||
1079 | // Are we editing within a selection group? | |
1080 | 0 | if (groupEditing || (sg != null |
1081 | && sg.getSequences(av.getHiddenRepSequences()).contains(seq))) | |
1082 | { | |
1083 | 0 | fixedColumns = true; |
1084 | ||
1085 | // sg might be null as the user may only see 1 sequence, | |
1086 | // but the sequence represents a group | |
1087 | 0 | if (sg == null) |
1088 | { | |
1089 | 0 | if (!av.isHiddenRepSequence(seq)) |
1090 | { | |
1091 | 0 | endEditing(); |
1092 | 0 | return; |
1093 | } | |
1094 | ||
1095 | 0 | sg = av.getRepresentedSequences(seq); |
1096 | } | |
1097 | ||
1098 | 0 | fixedLeft = sg.getStartRes(); |
1099 | 0 | fixedRight = sg.getEndRes(); |
1100 | ||
1101 | 0 | if ((startres < fixedLeft && lastres >= fixedLeft) |
1102 | || (startres >= fixedLeft && lastres < fixedLeft) | |
1103 | || (startres > fixedRight && lastres <= fixedRight) | |
1104 | || (startres <= fixedRight && lastres > fixedRight)) | |
1105 | { | |
1106 | 0 | endEditing(); |
1107 | 0 | return; |
1108 | } | |
1109 | ||
1110 | 0 | if (fixedLeft > startres) |
1111 | { | |
1112 | 0 | fixedRight = fixedLeft - 1; |
1113 | 0 | fixedLeft = 0; |
1114 | } | |
1115 | 0 | else if (fixedRight < startres) |
1116 | { | |
1117 | 0 | fixedLeft = fixedRight; |
1118 | 0 | fixedRight = -1; |
1119 | } | |
1120 | } | |
1121 | ||
1122 | 0 | if (av.hasHiddenColumns()) |
1123 | { | |
1124 | 0 | fixedColumns = true; |
1125 | 0 | int y1 = av.getAlignment().getHiddenColumns() |
1126 | .getNextHiddenBoundary(true, startres); | |
1127 | 0 | int y2 = av.getAlignment().getHiddenColumns() |
1128 | .getNextHiddenBoundary(false, startres); | |
1129 | ||
1130 | 0 | if ((insertGap && startres > y1 && lastres < y1) |
1131 | || (!insertGap && startres < y2 && lastres > y2)) | |
1132 | { | |
1133 | 0 | endEditing(); |
1134 | 0 | return; |
1135 | } | |
1136 | ||
1137 | // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~"); | |
1138 | // Selection spans a hidden region | |
1139 | 0 | if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1)) |
1140 | { | |
1141 | 0 | if (startres >= y2) |
1142 | { | |
1143 | 0 | fixedLeft = y2; |
1144 | } | |
1145 | else | |
1146 | { | |
1147 | 0 | fixedRight = y2 - 1; |
1148 | } | |
1149 | } | |
1150 | } | |
1151 | ||
1152 | 0 | if (groupEditing) |
1153 | { | |
1154 | 0 | SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences()) |
1155 | .toArray(new SequenceI[0]); | |
1156 | ||
1157 | // drag to right | |
1158 | 0 | if (insertGap) |
1159 | { | |
1160 | // If the user has selected the whole sequence, and is dragging to | |
1161 | // the right, we can still extend the alignment and selectionGroup | |
1162 | 0 | if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight |
1163 | && sg.getEndRes() == av.getAlignment().getWidth() - 1) | |
1164 | { | |
1165 | 0 | sg.setEndRes(av.getAlignment().getWidth() + startres - lastres); |
1166 | 0 | fixedRight = sg.getEndRes(); |
1167 | } | |
1168 | ||
1169 | // Is it valid with fixed columns?? | |
1170 | // Find the next gap before the end | |
1171 | // of the visible region boundary | |
1172 | 0 | boolean blank = false; |
1173 | 0 | for (; fixedRight > lastres; fixedRight--) |
1174 | { | |
1175 | 0 | blank = true; |
1176 | ||
1177 | 0 | for (SequenceI gs : groupSeqs) |
1178 | { | |
1179 | 0 | for (int j = 0; j < startres - lastres; j++) |
1180 | { | |
1181 | 0 | if (!jalview.util.Comparison |
1182 | .isGap(gs.getCharAt(fixedRight - j))) | |
1183 | { | |
1184 | 0 | blank = false; |
1185 | 0 | break; |
1186 | } | |
1187 | } | |
1188 | } | |
1189 | 0 | if (blank) |
1190 | { | |
1191 | 0 | break; |
1192 | } | |
1193 | } | |
1194 | ||
1195 | 0 | if (!blank) |
1196 | { | |
1197 | 0 | if (sg.getSize() == av.getAlignment().getHeight()) |
1198 | { | |
1199 | 0 | if ((av.hasHiddenColumns() |
1200 | && startres < av.getAlignment().getHiddenColumns() | |
1201 | .getNextHiddenBoundary(false, startres))) | |
1202 | { | |
1203 | 0 | endEditing(); |
1204 | 0 | return; |
1205 | } | |
1206 | ||
1207 | 0 | int alWidth = av.getAlignment().getWidth(); |
1208 | 0 | if (av.hasHiddenRows()) |
1209 | { | |
1210 | 0 | int hwidth = av.getAlignment().getHiddenSequences() |
1211 | .getWidth(); | |
1212 | 0 | if (hwidth > alWidth) |
1213 | { | |
1214 | 0 | alWidth = hwidth; |
1215 | } | |
1216 | } | |
1217 | // We can still insert gaps if the selectionGroup | |
1218 | // contains all the sequences | |
1219 | 0 | sg.setEndRes(sg.getEndRes() + startres - lastres); |
1220 | 0 | fixedRight = alWidth + startres - lastres; |
1221 | } | |
1222 | else | |
1223 | { | |
1224 | 0 | endEditing(); |
1225 | 0 | return; |
1226 | } | |
1227 | } | |
1228 | } | |
1229 | ||
1230 | // drag to left | |
1231 | 0 | else if (!insertGap) |
1232 | { | |
1233 | // / Are we able to delete? | |
1234 | // ie are all columns blank? | |
1235 | ||
1236 | 0 | for (SequenceI gs : groupSeqs) |
1237 | { | |
1238 | 0 | for (int j = startres; j < lastres; j++) |
1239 | { | |
1240 | 0 | if (gs.getLength() <= j) |
1241 | { | |
1242 | 0 | continue; |
1243 | } | |
1244 | ||
1245 | 0 | if (!jalview.util.Comparison.isGap(gs.getCharAt(j))) |
1246 | { | |
1247 | // Not a gap, block edit not valid | |
1248 | 0 | endEditing(); |
1249 | 0 | return; |
1250 | } | |
1251 | } | |
1252 | } | |
1253 | } | |
1254 | ||
1255 | 0 | if (insertGap) |
1256 | { | |
1257 | // dragging to the right | |
1258 | 0 | if (fixedColumns && fixedRight != -1) |
1259 | { | |
1260 | 0 | for (int j = lastres; j < startres; j++) |
1261 | { | |
1262 | 0 | insertChar(j, groupSeqs, fixedRight); |
1263 | } | |
1264 | } | |
1265 | else | |
1266 | { | |
1267 | 0 | editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, startres, |
1268 | startres - lastres, av.getAlignment(), true); | |
1269 | } | |
1270 | } | |
1271 | else | |
1272 | { | |
1273 | // dragging to the left | |
1274 | 0 | if (fixedColumns && fixedRight != -1) |
1275 | { | |
1276 | 0 | for (int j = lastres; j > startres; j--) |
1277 | { | |
1278 | 0 | deleteChar(startres, groupSeqs, fixedRight); |
1279 | } | |
1280 | } | |
1281 | else | |
1282 | { | |
1283 | 0 | editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, startres, |
1284 | lastres - startres, av.getAlignment(), true); | |
1285 | } | |
1286 | ||
1287 | } | |
1288 | } | |
1289 | else | |
1290 | // ///Editing a single sequence/////////// | |
1291 | { | |
1292 | 0 | if (insertGap) |
1293 | { | |
1294 | // dragging to the right | |
1295 | 0 | if (fixedColumns && fixedRight != -1) |
1296 | { | |
1297 | 0 | for (int j = lastres; j < startres; j++) |
1298 | { | |
1299 | 0 | insertChar(j, new SequenceI[] { seq }, fixedRight); |
1300 | } | |
1301 | } | |
1302 | else | |
1303 | { | |
1304 | 0 | editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, |
1305 | lastres, startres - lastres, av.getAlignment(), true); | |
1306 | } | |
1307 | } | |
1308 | else | |
1309 | { | |
1310 | // dragging to the left | |
1311 | 0 | if (fixedColumns && fixedRight != -1) |
1312 | { | |
1313 | 0 | for (int j = lastres; j > startres; j--) |
1314 | { | |
1315 | 0 | if (!jalview.util.Comparison.isGap(seq.getCharAt(startres))) |
1316 | { | |
1317 | 0 | endEditing(); |
1318 | 0 | break; |
1319 | } | |
1320 | 0 | deleteChar(startres, new SequenceI[] { seq }, fixedRight); |
1321 | } | |
1322 | } | |
1323 | else | |
1324 | { | |
1325 | // could be a keyboard edit trying to delete none gaps | |
1326 | 0 | int max = 0; |
1327 | 0 | for (int m = startres; m < lastres; m++) |
1328 | { | |
1329 | 0 | if (!jalview.util.Comparison.isGap(seq.getCharAt(m))) |
1330 | { | |
1331 | 0 | break; |
1332 | } | |
1333 | 0 | max++; |
1334 | } | |
1335 | ||
1336 | 0 | if (max > 0) |
1337 | { | |
1338 | 0 | editCommand.appendEdit(Action.DELETE_GAP, |
1339 | new SequenceI[] | |
1340 | { seq }, startres, max, av.getAlignment(), true); | |
1341 | } | |
1342 | } | |
1343 | } | |
1344 | } | |
1345 | ||
1346 | 0 | lastres = startres; |
1347 | 0 | seqCanvas.repaint(); |
1348 | } | |
1349 | ||
1350 | 0 | void insertChar(int j, SequenceI[] seq, int fixedColumn) |
1351 | { | |
1352 | 0 | int blankColumn = fixedColumn; |
1353 | 0 | for (int s = 0; s < seq.length; s++) |
1354 | { | |
1355 | // Find the next gap before the end of the visible region boundary | |
1356 | // If lastCol > j, theres a boundary after the gap insertion | |
1357 | ||
1358 | 0 | for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) |
1359 | { | |
1360 | 0 | if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn))) |
1361 | { | |
1362 | // Theres a space, so break and insert the gap | |
1363 | 0 | break; |
1364 | } | |
1365 | } | |
1366 | ||
1367 | 0 | if (blankColumn <= j) |
1368 | { | |
1369 | 0 | blankColumn = fixedColumn; |
1370 | 0 | endEditing(); |
1371 | 0 | return; |
1372 | } | |
1373 | } | |
1374 | ||
1375 | 0 | editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1, |
1376 | av.getAlignment(), true); | |
1377 | ||
1378 | 0 | editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(), |
1379 | true); | |
1380 | ||
1381 | } | |
1382 | ||
1383 | 0 | void deleteChar(int j, SequenceI[] seq, int fixedColumn) |
1384 | { | |
1385 | ||
1386 | 0 | editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, av.getAlignment(), |
1387 | true); | |
1388 | ||
1389 | 0 | editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1, |
1390 | av.getAlignment(), true); | |
1391 | } | |
1392 | ||
1393 | // //////////////////////////////////////// | |
1394 | // ///Everything below this is for defining the boundary of the rubberband | |
1395 | // //////////////////////////////////////// | |
1396 | 0 | public void doMousePressedDefineMode(MouseEvent evt) |
1397 | { | |
1398 | 0 | if (scrollThread != null) |
1399 | { | |
1400 | 0 | scrollThread.threadRunning = false; |
1401 | 0 | scrollThread = null; |
1402 | } | |
1403 | ||
1404 | 0 | int column = findColumn(evt); |
1405 | 0 | int seq = findSeq(evt); |
1406 | 0 | oldSeq = seq; |
1407 | 0 | startWrapBlock = wrappedBlock; |
1408 | ||
1409 | 0 | if (seq == -1) |
1410 | { | |
1411 | 0 | return; |
1412 | } | |
1413 | ||
1414 | 0 | SequenceI sequence = av.getAlignment().getSequenceAt(seq); |
1415 | ||
1416 | 0 | if (sequence == null || column > sequence.getLength()) |
1417 | { | |
1418 | 0 | return; |
1419 | } | |
1420 | ||
1421 | 0 | stretchGroup = av.getSelectionGroup(); |
1422 | ||
1423 | 0 | if (stretchGroup == null || !stretchGroup.contains(sequence, column)) |
1424 | { | |
1425 | 0 | stretchGroup = av.getAlignment().findGroup(sequence, column); |
1426 | 0 | if (stretchGroup != null) |
1427 | { | |
1428 | // only update the current selection if the popup menu has a group to | |
1429 | // focus on | |
1430 | 0 | av.setSelectionGroup(stretchGroup); |
1431 | } | |
1432 | } | |
1433 | ||
1434 | // DETECT RIGHT MOUSE BUTTON IN AWT | |
1435 | 0 | if ((evt.getModifiersEx() |
1436 | & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK) | |
1437 | { | |
1438 | 0 | List<SequenceFeature> allFeatures = findFeaturesAtColumn(sequence, |
1439 | sequence.findPosition(column + 1)); | |
1440 | ||
1441 | 0 | Vector<String> links = null; |
1442 | 0 | for (SequenceFeature sf : allFeatures) |
1443 | { | |
1444 | 0 | if (sf.links != null) |
1445 | { | |
1446 | 0 | if (links == null) |
1447 | { | |
1448 | 0 | links = new Vector<>(); |
1449 | } | |
1450 | 0 | links.addAll(sf.links); |
1451 | } | |
1452 | } | |
1453 | 0 | APopupMenu popup = new APopupMenu(ap, null, links); |
1454 | 0 | this.add(popup); |
1455 | 0 | popup.show(this, evt.getX(), evt.getY()); |
1456 | 0 | return; |
1457 | } | |
1458 | ||
1459 | 0 | if (av.cursorMode) |
1460 | { | |
1461 | 0 | seqCanvas.cursorX = findColumn(evt); |
1462 | 0 | seqCanvas.cursorY = findSeq(evt); |
1463 | 0 | seqCanvas.repaint(); |
1464 | 0 | return; |
1465 | } | |
1466 | ||
1467 | // Only if left mouse button do we want to change group sizes | |
1468 | ||
1469 | 0 | if (stretchGroup == null) |
1470 | { | |
1471 | // define a new group here | |
1472 | 0 | SequenceGroup sg = new SequenceGroup(); |
1473 | 0 | sg.setStartRes(column); |
1474 | 0 | sg.setEndRes(column); |
1475 | 0 | sg.addSequence(sequence, false); |
1476 | 0 | av.setSelectionGroup(sg); |
1477 | 0 | stretchGroup = sg; |
1478 | ||
1479 | 0 | if (av.getConservationSelected()) |
1480 | { | |
1481 | 0 | SliderPanel.setConservationSlider(ap, av.getResidueShading(), |
1482 | ap.getViewName()); | |
1483 | } | |
1484 | 0 | if (av.getAbovePIDThreshold()) |
1485 | { | |
1486 | 0 | SliderPanel.setPIDSliderSource(ap, av.getResidueShading(), |
1487 | ap.getViewName()); | |
1488 | } | |
1489 | ||
1490 | } | |
1491 | } | |
1492 | ||
1493 | 0 | public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag) |
1494 | { | |
1495 | 0 | if (stretchGroup == null) |
1496 | { | |
1497 | 0 | return; |
1498 | } | |
1499 | // always do this - annotation has own state | |
1500 | // but defer colourscheme update until hidden sequences are passed in | |
1501 | 0 | boolean vischange = stretchGroup.recalcConservation(true); |
1502 | // here we rely on stretchGroup == av.getSelection() | |
1503 | 0 | needOverviewUpdate |= vischange && av.isSelectionDefinedGroup() |
1504 | && afterDrag; | |
1505 | 0 | if (stretchGroup.cs != null) |
1506 | { | |
1507 | 0 | stretchGroup.cs.alignmentChanged(stretchGroup, |
1508 | av.getHiddenRepSequences()); | |
1509 | ||
1510 | 0 | if (stretchGroup.cs.conservationApplied()) |
1511 | { | |
1512 | 0 | SliderPanel.setConservationSlider(ap, stretchGroup.cs, |
1513 | stretchGroup.getName()); | |
1514 | } | |
1515 | 0 | if (stretchGroup.cs.getThreshold() > 0) |
1516 | { | |
1517 | 0 | SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, |
1518 | stretchGroup.getName()); | |
1519 | } | |
1520 | } | |
1521 | 0 | PaintRefresher.Refresh(ap, av.getSequenceSetId()); |
1522 | 0 | ap.paintAlignment(needOverviewUpdate, needOverviewUpdate); |
1523 | 0 | needOverviewUpdate = false; |
1524 | 0 | changeEndRes = false; |
1525 | 0 | changeStartRes = false; |
1526 | 0 | stretchGroup = null; |
1527 | 0 | av.sendSelection(); |
1528 | } | |
1529 | ||
1530 | 0 | public void doMouseDraggedDefineMode(MouseEvent evt) |
1531 | { | |
1532 | 0 | int res = findColumn(evt); |
1533 | 0 | int y = findSeq(evt); |
1534 | ||
1535 | 0 | if (wrappedBlock != startWrapBlock) |
1536 | { | |
1537 | 0 | return; |
1538 | } | |
1539 | ||
1540 | 0 | if (stretchGroup == null) |
1541 | { | |
1542 | 0 | return; |
1543 | } | |
1544 | ||
1545 | 0 | mouseDragging = true; |
1546 | ||
1547 | 0 | if (y > av.getAlignment().getHeight()) |
1548 | { | |
1549 | 0 | y = av.getAlignment().getHeight() - 1; |
1550 | } | |
1551 | ||
1552 | 0 | if (res >= av.getAlignment().getWidth()) |
1553 | { | |
1554 | 0 | res = av.getAlignment().getWidth() - 1; |
1555 | } | |
1556 | ||
1557 | 0 | if (stretchGroup.getEndRes() == res) |
1558 | { | |
1559 | // Edit end res position of selected group | |
1560 | 0 | changeEndRes = true; |
1561 | } | |
1562 | 0 | else if (stretchGroup.getStartRes() == res) |
1563 | { | |
1564 | // Edit start res position of selected group | |
1565 | 0 | changeStartRes = true; |
1566 | } | |
1567 | ||
1568 | 0 | if (res < 0) |
1569 | { | |
1570 | 0 | res = 0; |
1571 | } | |
1572 | ||
1573 | 0 | if (changeEndRes) |
1574 | { | |
1575 | 0 | if (res > (stretchGroup.getStartRes() - 1)) |
1576 | { | |
1577 | 0 | stretchGroup.setEndRes(res); |
1578 | 0 | needOverviewUpdate |= av.isSelectionDefinedGroup(); |
1579 | } | |
1580 | } | |
1581 | 0 | else if (changeStartRes) |
1582 | { | |
1583 | 0 | if (res < (stretchGroup.getEndRes() + 1)) |
1584 | { | |
1585 | 0 | stretchGroup.setStartRes(res); |
1586 | 0 | needOverviewUpdate |= av.isSelectionDefinedGroup(); |
1587 | } | |
1588 | } | |
1589 | ||
1590 | 0 | int dragDirection = 0; |
1591 | ||
1592 | 0 | if (y > oldSeq) |
1593 | { | |
1594 | 0 | dragDirection = 1; |
1595 | } | |
1596 | 0 | else if (y < oldSeq) |
1597 | { | |
1598 | 0 | dragDirection = -1; |
1599 | } | |
1600 | ||
1601 | 0 | while ((y != oldSeq) && (oldSeq > -1) |
1602 | && (y < av.getAlignment().getHeight())) | |
1603 | { | |
1604 | // This routine ensures we don't skip any sequences, as the | |
1605 | // selection is quite slow. | |
1606 | 0 | Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); |
1607 | ||
1608 | 0 | oldSeq += dragDirection; |
1609 | ||
1610 | 0 | if (oldSeq < 0) |
1611 | { | |
1612 | 0 | break; |
1613 | } | |
1614 | ||
1615 | 0 | Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); |
1616 | ||
1617 | 0 | if (stretchGroup.getSequences(null).contains(nextSeq)) |
1618 | { | |
1619 | 0 | stretchGroup.deleteSequence(seq, false); |
1620 | 0 | needOverviewUpdate |= av.isSelectionDefinedGroup(); |
1621 | } | |
1622 | else | |
1623 | { | |
1624 | 0 | if (seq != null) |
1625 | { | |
1626 | 0 | stretchGroup.addSequence(seq, false); |
1627 | } | |
1628 | ||
1629 | 0 | stretchGroup.addSequence(nextSeq, false); |
1630 | 0 | needOverviewUpdate |= av.isSelectionDefinedGroup(); |
1631 | } | |
1632 | } | |
1633 | ||
1634 | 0 | if (oldSeq < 0) |
1635 | { | |
1636 | 0 | oldSeq = -1; |
1637 | } | |
1638 | ||
1639 | 0 | if (res > av.getRanges().getEndRes() |
1640 | || res < av.getRanges().getStartRes() | |
1641 | || y < av.getRanges().getStartSeq() | |
1642 | || y > av.getRanges().getEndSeq()) | |
1643 | { | |
1644 | 0 | mouseExited(evt); |
1645 | } | |
1646 | ||
1647 | 0 | if ((scrollThread != null) && (scrollThread.isRunning())) |
1648 | { | |
1649 | 0 | scrollThread.setEvent(evt); |
1650 | } | |
1651 | ||
1652 | 0 | seqCanvas.repaint(); |
1653 | } | |
1654 | ||
1655 | 0 | @Override |
1656 | public void mouseEntered(MouseEvent e) | |
1657 | { | |
1658 | 0 | if (oldSeq < 0) |
1659 | { | |
1660 | 0 | oldSeq = 0; |
1661 | } | |
1662 | ||
1663 | 0 | if ((scrollThread != null) && (scrollThread.isRunning())) |
1664 | { | |
1665 | 0 | scrollThread.stopScrolling(); |
1666 | 0 | scrollThread = null; |
1667 | } | |
1668 | } | |
1669 | ||
1670 | 0 | @Override |
1671 | public void mouseExited(MouseEvent e) | |
1672 | { | |
1673 | 0 | if (av.getWrapAlignment()) |
1674 | { | |
1675 | 0 | return; |
1676 | } | |
1677 | ||
1678 | 0 | if (mouseDragging && scrollThread == null) |
1679 | { | |
1680 | 0 | scrollThread = new ScrollThread(); |
1681 | } | |
1682 | } | |
1683 | ||
1684 | 0 | void scrollCanvas(MouseEvent evt) |
1685 | { | |
1686 | 0 | if (evt == null) |
1687 | { | |
1688 | 0 | if ((scrollThread != null) && (scrollThread.isRunning())) |
1689 | { | |
1690 | 0 | scrollThread.stopScrolling(); |
1691 | 0 | scrollThread = null; |
1692 | } | |
1693 | 0 | mouseDragging = false; |
1694 | } | |
1695 | else | |
1696 | { | |
1697 | 0 | if (scrollThread == null) |
1698 | { | |
1699 | 0 | scrollThread = new ScrollThread(); |
1700 | } | |
1701 | ||
1702 | 0 | mouseDragging = true; |
1703 | 0 | scrollThread.setEvent(evt); |
1704 | } | |
1705 | ||
1706 | } | |
1707 | ||
1708 | // this class allows scrolling off the bottom of the visible alignment | |
1709 | class ScrollThread extends Thread | |
1710 | { | |
1711 | MouseEvent evt; | |
1712 | ||
1713 | private volatile boolean threadRunning = true; | |
1714 | ||
1715 | 0 | public ScrollThread() |
1716 | { | |
1717 | 0 | start(); |
1718 | } | |
1719 | ||
1720 | 0 | public void setEvent(MouseEvent e) |
1721 | { | |
1722 | 0 | evt = e; |
1723 | } | |
1724 | ||
1725 | 0 | public void stopScrolling() |
1726 | { | |
1727 | 0 | threadRunning = false; |
1728 | } | |
1729 | ||
1730 | 0 | public boolean isRunning() |
1731 | { | |
1732 | 0 | return threadRunning; |
1733 | } | |
1734 | ||
1735 | 0 | @Override |
1736 | public void run() | |
1737 | { | |
1738 | 0 | while (threadRunning) |
1739 | { | |
1740 | ||
1741 | 0 | if (evt != null) |
1742 | { | |
1743 | ||
1744 | 0 | if (mouseDragging && evt.getY() < 0 |
1745 | && av.getRanges().getStartSeq() > 0) | |
1746 | { | |
1747 | 0 | av.getRanges().scrollUp(true); |
1748 | } | |
1749 | ||
1750 | 0 | if (mouseDragging && evt.getY() >= getSize().height && av |
1751 | .getAlignment().getHeight() > av.getRanges().getEndSeq()) | |
1752 | { | |
1753 | 0 | av.getRanges().scrollUp(false); |
1754 | } | |
1755 | ||
1756 | 0 | if (mouseDragging && evt.getX() < 0) |
1757 | { | |
1758 | 0 | av.getRanges().scrollRight(false); |
1759 | } | |
1760 | ||
1761 | 0 | else if (mouseDragging && evt.getX() >= getSize().width) |
1762 | { | |
1763 | 0 | av.getRanges().scrollRight(true); |
1764 | } | |
1765 | } | |
1766 | ||
1767 | 0 | try |
1768 | { | |
1769 | 0 | Thread.sleep(75); |
1770 | } catch (Exception ex) | |
1771 | { | |
1772 | } | |
1773 | } | |
1774 | } | |
1775 | } | |
1776 | ||
1777 | /** | |
1778 | * modify current selection according to a received message. | |
1779 | */ | |
1780 | 0 | @Override |
1781 | public void selection(SequenceGroup seqsel, ColumnSelection colsel, | |
1782 | HiddenColumns hidden, SelectionSource source) | |
1783 | { | |
1784 | // TODO: fix this hack - source of messages is align viewport, but SeqPanel | |
1785 | // handles selection messages... | |
1786 | // TODO: extend config options to allow user to control if selections may be | |
1787 | // shared between viewports. | |
1788 | 0 | if (av != null && (av == source || !av.followSelection |
1789 | || (source instanceof AlignViewport | |
1790 | && ((AlignmentViewport) source).getSequenceSetId() | |
1791 | .equals(av.getSequenceSetId())))) | |
1792 | { | |
1793 | 0 | return; |
1794 | } | |
1795 | ||
1796 | /* | |
1797 | * Check for selection in a view of which this one is a dna/protein | |
1798 | * complement. | |
1799 | */ | |
1800 | 0 | if (selectionFromTranslation(seqsel, colsel, hidden, source)) |
1801 | { | |
1802 | 0 | return; |
1803 | } | |
1804 | ||
1805 | // do we want to thread this ? (contention with seqsel and colsel locks, I | |
1806 | // suspect) | |
1807 | /* | |
1808 | * only copy colsel if there is a real intersection between | |
1809 | * sequence selection and this panel's alignment | |
1810 | */ | |
1811 | 0 | boolean repaint = false; |
1812 | 0 | boolean copycolsel = false; |
1813 | 0 | if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true)) |
1814 | { | |
1815 | 0 | SequenceGroup sgroup = null; |
1816 | 0 | if (seqsel != null && seqsel.getSize() > 0) |
1817 | { | |
1818 | 0 | if (av.getAlignment() == null) |
1819 | { | |
1820 | 0 | jalview.bin.Console.outPrintln( |
1821 | "Selection message: alignviewport av SeqSetId=" | |
1822 | + av.getSequenceSetId() + " ViewId=" | |
1823 | + av.getViewId() | |
1824 | + " 's alignment is NULL! returning immediatly."); | |
1825 | 0 | return; |
1826 | } | |
1827 | 0 | sgroup = seqsel.intersect(av.getAlignment(), |
1828 | 0 | (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); |
1829 | 0 | if ((sgroup != null && sgroup.getSize() > 0)) |
1830 | { | |
1831 | 0 | copycolsel = true; |
1832 | } | |
1833 | } | |
1834 | 0 | if (sgroup != null && sgroup.getSize() > 0) |
1835 | { | |
1836 | 0 | av.setSelectionGroup(sgroup); |
1837 | } | |
1838 | else | |
1839 | { | |
1840 | 0 | av.setSelectionGroup(null); |
1841 | } | |
1842 | 0 | repaint = av.isSelectionGroupChanged(true); |
1843 | } | |
1844 | 0 | if (copycolsel && (av.getColumnSelection() == null |
1845 | || !av.isColSelChanged(true))) | |
1846 | { | |
1847 | // the current selection is unset or from a previous message | |
1848 | // so import the new colsel. | |
1849 | 0 | if (colsel == null || colsel.isEmpty()) |
1850 | { | |
1851 | 0 | if (av.getColumnSelection() != null) |
1852 | { | |
1853 | 0 | av.getColumnSelection().clear(); |
1854 | } | |
1855 | } | |
1856 | else | |
1857 | { | |
1858 | // TODO: shift colSel according to the intersecting sequences | |
1859 | 0 | if (av.getColumnSelection() == null) |
1860 | { | |
1861 | 0 | av.setColumnSelection(new ColumnSelection(colsel)); |
1862 | } | |
1863 | else | |
1864 | { | |
1865 | 0 | av.getColumnSelection().setElementsFrom(colsel, |
1866 | av.getAlignment().getHiddenColumns()); | |
1867 | } | |
1868 | } | |
1869 | 0 | repaint |= av.isColSelChanged(true); |
1870 | } | |
1871 | 0 | if (copycolsel && av.hasHiddenColumns() |
1872 | && (av.getColumnSelection() == null)) | |
1873 | { | |
1874 | 0 | jalview.bin.Console.errPrintln("Bad things"); |
1875 | } | |
1876 | 0 | if (repaint) |
1877 | { | |
1878 | 0 | ap.scalePanelHolder.repaint(); |
1879 | 0 | ap.repaint(); |
1880 | } | |
1881 | } | |
1882 | ||
1883 | /** | |
1884 | * scroll to the given row/column - or nearest visible location | |
1885 | * | |
1886 | * @param row | |
1887 | * @param column | |
1888 | */ | |
1889 | 0 | public void scrollTo(int row, int column) |
1890 | { | |
1891 | ||
1892 | 0 | row = row < 0 ? ap.av.getRanges().getStartSeq() : row; |
1893 | 0 | column = column < 0 ? ap.av.getRanges().getStartRes() : column; |
1894 | 0 | ap.scrollTo(column, column, row, true, true); |
1895 | } | |
1896 | ||
1897 | /** | |
1898 | * scroll to the given row - or nearest visible location | |
1899 | * | |
1900 | * @param row | |
1901 | */ | |
1902 | 0 | public void scrollToRow(int row) |
1903 | { | |
1904 | ||
1905 | 0 | row = row < 0 ? ap.av.getRanges().getStartSeq() : row; |
1906 | 0 | ap.scrollTo(ap.av.getRanges().getStartRes(), |
1907 | ap.av.getRanges().getStartRes(), row, true, true); | |
1908 | } | |
1909 | ||
1910 | /** | |
1911 | * scroll to the given column - or nearest visible location | |
1912 | * | |
1913 | * @param column | |
1914 | */ | |
1915 | 0 | public void scrollToColumn(int column) |
1916 | { | |
1917 | ||
1918 | 0 | column = column < 0 ? ap.av.getRanges().getStartRes() : column; |
1919 | 0 | ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true, |
1920 | true); | |
1921 | } | |
1922 | ||
1923 | /** | |
1924 | * If this panel is a cdna/protein translation view of the selection source, | |
1925 | * tries to map the source selection to a local one, and returns true. Else | |
1926 | * returns false. | |
1927 | * | |
1928 | * @param seqsel | |
1929 | * @param colsel | |
1930 | * @param source | |
1931 | */ | |
1932 | 0 | protected boolean selectionFromTranslation(SequenceGroup seqsel, |
1933 | ColumnSelection colsel, HiddenColumns hidden, | |
1934 | SelectionSource source) | |
1935 | { | |
1936 | 0 | if (!(source instanceof AlignViewportI)) |
1937 | { | |
1938 | 0 | return false; |
1939 | } | |
1940 | 0 | final AlignViewportI sourceAv = (AlignViewportI) source; |
1941 | 0 | if (sourceAv.getCodingComplement() != av |
1942 | && av.getCodingComplement() != sourceAv) | |
1943 | { | |
1944 | 0 | return false; |
1945 | } | |
1946 | ||
1947 | /* | |
1948 | * Map sequence selection | |
1949 | */ | |
1950 | 0 | SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av); |
1951 | 0 | av.setSelectionGroup(sg); |
1952 | 0 | av.isSelectionGroupChanged(true); |
1953 | ||
1954 | /* | |
1955 | * Map column selection | |
1956 | */ | |
1957 | // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv, | |
1958 | // av); | |
1959 | 0 | ColumnSelection cs = new ColumnSelection(); |
1960 | 0 | HiddenColumns hs = new HiddenColumns(); |
1961 | 0 | MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs); |
1962 | 0 | av.setColumnSelection(cs); |
1963 | 0 | av.getAlignment().setHiddenColumns(hs); |
1964 | ||
1965 | 0 | ap.scalePanelHolder.repaint(); |
1966 | 0 | ap.repaint(); |
1967 | ||
1968 | 0 | return true; |
1969 | } | |
1970 | ||
1971 | } |