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1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
7 | * Jalview is free software: you can redistribute it and/or | |
8 | * modify it under the terms of the GNU General Public License | |
9 | * as published by the Free Software Foundation, either version 3 | |
10 | * of the License, or (at your option) any later version. | |
11 | * | |
12 | * Jalview is distributed in the hope that it will be useful, but | |
13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
15 | * PURPOSE. See the GNU General Public License for more details. | |
16 | * | |
17 | * You should have received a copy of the GNU General Public License | |
18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
20 | */ | |
21 | package jalview.gui; | |
22 | ||
23 | import java.awt.BorderLayout; | |
24 | import java.awt.Color; | |
25 | import java.awt.Container; | |
26 | import java.awt.Dimension; | |
27 | import java.awt.Font; | |
28 | import java.awt.FontMetrics; | |
29 | import java.awt.Graphics; | |
30 | import java.awt.Graphics2D; | |
31 | import java.awt.event.AdjustmentEvent; | |
32 | import java.awt.event.AdjustmentListener; | |
33 | import java.awt.event.ComponentAdapter; | |
34 | import java.awt.event.ComponentEvent; | |
35 | import java.awt.print.PageFormat; | |
36 | import java.awt.print.Printable; | |
37 | import java.awt.print.PrinterException; | |
38 | import java.beans.PropertyChangeEvent; | |
39 | import java.beans.PropertyChangeListener; | |
40 | import java.io.File; | |
41 | import java.io.FileWriter; | |
42 | import java.io.PrintWriter; | |
43 | import java.util.List; | |
44 | ||
45 | import javax.swing.BoundedRangeModel; | |
46 | import javax.swing.SwingUtilities; | |
47 | ||
48 | import jalview.analysis.AnnotationSorter; | |
49 | import jalview.api.AlignViewportI; | |
50 | import jalview.api.AlignmentViewPanel; | |
51 | import jalview.bin.Cache; | |
52 | import jalview.bin.Console; | |
53 | import jalview.bin.Jalview; | |
54 | import jalview.datamodel.AlignmentAnnotation; | |
55 | import jalview.datamodel.AlignmentI; | |
56 | import jalview.datamodel.HiddenColumns; | |
57 | import jalview.datamodel.SearchResultsI; | |
58 | import jalview.datamodel.SequenceFeature; | |
59 | import jalview.datamodel.SequenceGroup; | |
60 | import jalview.datamodel.SequenceI; | |
61 | import jalview.gui.ImageExporter.ImageWriterI; | |
62 | import jalview.io.HTMLOutput; | |
63 | import jalview.io.exceptions.ImageOutputException; | |
64 | import jalview.jbgui.GAlignmentPanel; | |
65 | import jalview.math.AlignmentDimension; | |
66 | import jalview.schemes.ResidueProperties; | |
67 | import jalview.structure.StructureSelectionManager; | |
68 | import jalview.util.Comparison; | |
69 | import jalview.util.ImageMaker; | |
70 | import jalview.util.MessageManager; | |
71 | import jalview.util.imagemaker.BitmapImageSizing; | |
72 | import jalview.viewmodel.ViewportListenerI; | |
73 | import jalview.viewmodel.ViewportRanges; | |
74 | ||
75 | /** | |
76 | * DOCUMENT ME! | |
77 | * | |
78 | * @author $author$ | |
79 | * @version $Revision: 1.161 $ | |
80 | */ | |
81 | @SuppressWarnings("serial") | |
82 | public class AlignmentPanel extends GAlignmentPanel implements | |
83 | AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI | |
84 | { | |
85 | /* | |
86 | * spare space in pixels between sequence id and alignment panel | |
87 | */ | |
88 | private static final int ID_WIDTH_PADDING = 4; | |
89 | ||
90 | public AlignViewport av; | |
91 | ||
92 | OverviewPanel overviewPanel; | |
93 | ||
94 | private SeqPanel seqPanel; | |
95 | ||
96 | private IdPanel idPanel; | |
97 | ||
98 | IdwidthAdjuster idwidthAdjuster; | |
99 | ||
100 | public AlignFrame alignFrame; | |
101 | ||
102 | private ScalePanel scalePanel; | |
103 | ||
104 | private AnnotationPanel annotationPanel; | |
105 | ||
106 | private AnnotationLabels alabels; | |
107 | ||
108 | private int hextent = 0; | |
109 | ||
110 | private int vextent = 0; | |
111 | ||
112 | /* | |
113 | * Flag set while scrolling to follow complementary cDNA/protein scroll. When | |
114 | * false, suppresses invoking the same method recursively. | |
115 | */ | |
116 | private boolean scrollComplementaryPanel = true; | |
117 | ||
118 | private PropertyChangeListener propertyChangeListener; | |
119 | ||
120 | private CalculationChooser calculationDialog; | |
121 | ||
122 | /** | |
123 | * Creates a new AlignmentPanel object. | |
124 | * | |
125 | * @param af | |
126 | * @param av | |
127 | */ | |
128 | 478 | public AlignmentPanel(AlignFrame af, final AlignViewport av) |
129 | { | |
130 | // setBackground(Color.white); // BH 2019 | |
131 | 478 | alignFrame = af; |
132 | 478 | this.av = av; |
133 | 478 | setSeqPanel(new SeqPanel(av, this)); |
134 | 478 | setIdPanel(new IdPanel(av, this)); |
135 | ||
136 | 478 | setScalePanel(new ScalePanel(av, this)); |
137 | ||
138 | 478 | idPanelHolder.add(getIdPanel(), BorderLayout.CENTER); |
139 | 478 | idwidthAdjuster = new IdwidthAdjuster(this); |
140 | 478 | idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER); |
141 | ||
142 | 478 | setAnnotationPanel(new AnnotationPanel(this)); |
143 | 478 | setAlabels(new AnnotationLabels(this)); |
144 | ||
145 | 478 | annotationScroller.setViewportView(getAnnotationPanel()); |
146 | 478 | annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER); |
147 | ||
148 | 478 | scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER); |
149 | 478 | seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER); |
150 | ||
151 | 478 | setScrollValues(0, 0); |
152 | ||
153 | 478 | hscroll.addAdjustmentListener(this); |
154 | 478 | vscroll.addAdjustmentListener(this); |
155 | ||
156 | 478 | addComponentListener(new ComponentAdapter() |
157 | { | |
158 | 520 | @Override |
159 | public void componentResized(ComponentEvent evt) | |
160 | { | |
161 | // reset the viewport ranges when the alignment panel is resized | |
162 | // in particular, this initialises the end residue value when Jalview | |
163 | // is initialised | |
164 | 520 | ViewportRanges ranges = av.getRanges(); |
165 | 520 | if (av.getWrapAlignment()) |
166 | { | |
167 | 11 | int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth( |
168 | getSeqPanel().seqCanvas.getWidth()); | |
169 | 11 | ranges.setViewportWidth(widthInRes); |
170 | } | |
171 | else | |
172 | { | |
173 | 509 | int widthInRes = getSeqPanel().seqCanvas.getWidth() |
174 | / av.getCharWidth(); | |
175 | 509 | int heightInSeq = getSeqPanel().seqCanvas.getHeight() |
176 | / av.getCharHeight(); | |
177 | ||
178 | 509 | ranges.setViewportWidth(widthInRes); |
179 | 509 | ranges.setViewportHeight(heightInSeq); |
180 | } | |
181 | } | |
182 | ||
183 | }); | |
184 | ||
185 | 478 | final AlignmentPanel ap = this; |
186 | 478 | propertyChangeListener = new PropertyChangeListener() |
187 | { | |
188 | 67 | @Override |
189 | public void propertyChange(PropertyChangeEvent evt) | |
190 | { | |
191 | 67 | if (evt.getPropertyName().equals("alignment")) |
192 | { | |
193 | 67 | PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true); |
194 | 67 | alignmentChanged(); |
195 | } | |
196 | } | |
197 | }; | |
198 | 478 | av.addPropertyChangeListener(propertyChangeListener); |
199 | ||
200 | 478 | av.getRanges().addPropertyChangeListener(this); |
201 | 478 | fontChanged(); |
202 | 478 | adjustAnnotationHeight(); |
203 | 478 | updateLayout(); |
204 | } | |
205 | ||
206 | 619 | @Override |
207 | public AlignViewportI getAlignViewport() | |
208 | { | |
209 | 619 | return av; |
210 | } | |
211 | ||
212 | 549 | public void alignmentChanged() |
213 | { | |
214 | 549 | av.alignmentChanged(this); |
215 | ||
216 | 549 | if (getCalculationDialog() != null) |
217 | { | |
218 | 0 | getCalculationDialog().validateCalcTypes(); |
219 | } | |
220 | ||
221 | 549 | alignFrame.updateEditMenuBar(); |
222 | ||
223 | // no idea if we need to update structure | |
224 | 549 | paintAlignment(true, true); |
225 | ||
226 | } | |
227 | ||
228 | /** | |
229 | * DOCUMENT ME! | |
230 | */ | |
231 | 1491 | public void fontChanged() |
232 | { | |
233 | // set idCanvas bufferedImage to null | |
234 | // to prevent drawing old image | |
235 | 1491 | FontMetrics fm = getFontMetrics(av.getFont()); |
236 | ||
237 | // update the flag controlling whether the grid is too small to render the | |
238 | // font | |
239 | 1491 | av.validCharWidth = fm.charWidth('M') <= av.getCharWidth(); |
240 | ||
241 | 1491 | scalePanelHolder.setPreferredSize( |
242 | new Dimension(10, av.getCharHeight() + fm.getDescent())); | |
243 | 1491 | idSpaceFillerPanel1.setPreferredSize( |
244 | new Dimension(10, av.getCharHeight() + fm.getDescent())); | |
245 | 1491 | idwidthAdjuster.invalidate(); |
246 | 1491 | scalePanelHolder.invalidate(); |
247 | // BH 2018 getIdPanel().getIdCanvas().gg = null; | |
248 | 1491 | getSeqPanel().seqCanvas.img = null; |
249 | 1491 | getAnnotationPanel().adjustPanelHeight(); |
250 | ||
251 | 1491 | Dimension d = calculateIdWidth(); |
252 | 1491 | getIdPanel().getIdCanvas().setPreferredSize(d); |
253 | 1491 | hscrollFillerPanel.setPreferredSize(d); |
254 | ||
255 | 1491 | repaint(); |
256 | } | |
257 | ||
258 | /** | |
259 | * Calculates the width of the alignment labels based on the displayed names | |
260 | * and any bounds on label width set in preferences. | |
261 | * | |
262 | * The calculated width is set as a property of the viewport and the layout is | |
263 | * updated. | |
264 | * | |
265 | * @return Dimension giving the maximum width of the alignment label panel | |
266 | * that should be used. | |
267 | */ | |
268 | 1494 | public Dimension calculateIdWidth() |
269 | { | |
270 | 1494 | int oldWidth = av.getIdWidth(); |
271 | ||
272 | // calculate sensible default width when no preference is available | |
273 | 1494 | Dimension r = null; |
274 | 1494 | if (av.getIdWidth() < 0) |
275 | { | |
276 | 449 | r = calculateDefaultAlignmentIdWidth(); |
277 | 449 | av.setIdWidth(r.width); |
278 | } | |
279 | else | |
280 | { | |
281 | 1045 | r = new Dimension(); |
282 | 1045 | r.width = av.getIdWidth(); |
283 | 1045 | r.height = 0; |
284 | } | |
285 | ||
286 | /* | |
287 | * fudge: if desired width has changed, update layout | |
288 | * (see also paintComponent - updates layout on a repaint) | |
289 | */ | |
290 | 1494 | if (r.width != oldWidth) |
291 | { | |
292 | 449 | idPanelHolder.setPreferredSize(r); |
293 | 449 | validate(); |
294 | } | |
295 | 1494 | return r; |
296 | } | |
297 | ||
298 | 2649 | public Dimension calculateDefaultAlignmentIdWidth() |
299 | { | |
300 | 2649 | return calculateIdWidth(-1, false, false); |
301 | } | |
302 | ||
303 | /** | |
304 | * pre 2.11.3 Id width calculation - used when importing old projects only | |
305 | * | |
306 | * @return | |
307 | */ | |
308 | 43 | public int getLegacyIdWidth() |
309 | { | |
310 | 43 | int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); |
311 | 43 | int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3); |
312 | 43 | int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth); |
313 | 43 | Dimension w = calculateIdWidthOrLegacy(true, maxwidth, false, false); |
314 | 43 | return w.width; |
315 | } | |
316 | ||
317 | /** | |
318 | * Calculate the width of the alignment labels based on the displayed names | |
319 | * and any bounds on label width set in preferences. Also includes annotations | |
320 | * not actually visible. | |
321 | * | |
322 | * FIXME JAL-244 JAL-4091 - doesn't include sequence associated annotation | |
323 | * label decorators and only called during tests | |
324 | * | |
325 | * @param maxwidth | |
326 | * -1 or maximum width allowed for IdWidth | |
327 | * @return Dimension giving the maximum width of the alignment label panel | |
328 | * that should be used. | |
329 | */ | |
330 | 0 | protected Dimension calculateIdWidth(int maxwidth) |
331 | { | |
332 | 0 | return calculateIdWidth(maxwidth, true, false); |
333 | } | |
334 | ||
335 | /** | |
336 | * Calculate the width of the alignment labels based on the displayed names | |
337 | * and any bounds on label width set in preferences. | |
338 | * | |
339 | * @param maxwidth | |
340 | * -1 or maximum width allowed for IdWidth | |
341 | * @param includeAnnotations | |
342 | * - when true includes width of any additional marks in annotation | |
343 | * id panel | |
344 | * @param visibleOnly | |
345 | * - when true, ignore label widths for hidden annotation rows | |
346 | * @return Dimension giving the maximum width of the alignment label panel | |
347 | * that should be used. | |
348 | */ | |
349 | 2725 | public Dimension calculateIdWidth(int maxwidth, |
350 | boolean includeAnnotations, boolean visibleOnly) | |
351 | { | |
352 | 2725 | return calculateIdWidthOrLegacy(false, maxwidth, includeAnnotations, |
353 | visibleOnly); | |
354 | } | |
355 | ||
356 | /** | |
357 | * legacy mode or post 2.11.3 ID width calculation | |
358 | * | |
359 | * @param legacy | |
360 | * - uses annotation labels, not rendered label width (excludes | |
361 | * additional decorators) | |
362 | * @param maxwidth | |
363 | * @param includeAnnotations | |
364 | * @param visibleOnly | |
365 | * @return | |
366 | */ | |
367 | 2768 | private Dimension calculateIdWidthOrLegacy(boolean legacy, int maxwidth, |
368 | boolean includeAnnotations, boolean visibleOnly) | |
369 | { | |
370 | 2768 | Container c = new Container(); |
371 | ||
372 | 2768 | FontMetrics fm = c.getFontMetrics( |
373 | new Font(av.font.getName(), Font.ITALIC, av.font.getSize())); | |
374 | ||
375 | 2768 | AlignmentI al = av.getAlignment(); |
376 | 2768 | int i = 0; |
377 | 2768 | int idWidth = 0; |
378 | ||
379 | 32343 | while ((i < al.getHeight()) && (al.getSequenceAt(i) != null)) |
380 | { | |
381 | 29575 | SequenceI s = al.getSequenceAt(i); |
382 | 29575 | String id = s.getDisplayId(av.getShowJVSuffix()); |
383 | 29575 | int stringWidth = fm.stringWidth(id); |
384 | 29575 | idWidth = Math.max(idWidth, stringWidth); |
385 | 29575 | i++; |
386 | } | |
387 | ||
388 | // Also check annotation label widths | |
389 | 2768 | if (includeAnnotations && al.getAlignmentAnnotation() != null) |
390 | { | |
391 | 76 | if (legacy) |
392 | { | |
393 | 0 | fm = c.getFontMetrics(getAlabels().getFont()); |
394 | } | |
395 | ||
396 | 76 | if (!legacy || Jalview.isHeadlessMode()) |
397 | { | |
398 | 76 | AnnotationLabels aal = getAlabels(); |
399 | 76 | int stringWidth = aal.drawLabels(null, false, idWidth, false, false, |
400 | fm, !visibleOnly); | |
401 | 76 | idWidth = Math.max(idWidth, stringWidth); |
402 | } | |
403 | else | |
404 | { | |
405 | 0 | for (i = 0; i < al.getAlignmentAnnotation().length; i++) |
406 | { | |
407 | 0 | AlignmentAnnotation aa = al.getAlignmentAnnotation()[i]; |
408 | 0 | if (visibleOnly && !aa.visible) |
409 | { | |
410 | 0 | continue; |
411 | } | |
412 | 0 | String label = aa.label; |
413 | 0 | int stringWidth = fm.stringWidth(label); |
414 | 0 | idWidth = Math.max(idWidth, stringWidth); |
415 | } | |
416 | } | |
417 | } | |
418 | ||
419 | 2768 | int w = maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth); |
420 | 2768 | w += ID_WIDTH_PADDING; |
421 | ||
422 | 2768 | return new Dimension(w, 12); |
423 | } | |
424 | ||
425 | /** | |
426 | * Highlight the given results on the alignment | |
427 | * | |
428 | */ | |
429 | 1 | public void highlightSearchResults(SearchResultsI results) |
430 | { | |
431 | 1 | boolean scrolled = scrollToPosition(results, 0, false); |
432 | ||
433 | 1 | boolean fastPaint = !(scrolled && av.getWrapAlignment()); |
434 | ||
435 | 1 | getSeqPanel().seqCanvas.highlightSearchResults(results, fastPaint); |
436 | } | |
437 | ||
438 | /** | |
439 | * Scroll the view to show the position of the highlighted region in results | |
440 | * (if any) | |
441 | * | |
442 | * @param searchResults | |
443 | * @return | |
444 | */ | |
445 | 2 | public boolean scrollToPosition(SearchResultsI searchResults) |
446 | { | |
447 | 2 | return scrollToPosition(searchResults, 0, false); |
448 | } | |
449 | ||
450 | /** | |
451 | * Scrolls the view (if necessary) to show the position of the first | |
452 | * highlighted region in results (if any). Answers true if the view was | |
453 | * scrolled, or false if no matched region was found, or it is already | |
454 | * visible. | |
455 | * | |
456 | * @param results | |
457 | * @param verticalOffset | |
458 | * if greater than zero, allows scrolling to a position below the | |
459 | * first displayed sequence | |
460 | * @param centre | |
461 | * if true, try to centre the search results horizontally in the view | |
462 | * @return | |
463 | */ | |
464 | 7 | protected boolean scrollToPosition(SearchResultsI results, |
465 | int verticalOffset, boolean centre) | |
466 | { | |
467 | 7 | int startv, endv, starts, ends; |
468 | 7 | ViewportRanges ranges = av.getRanges(); |
469 | ||
470 | 7 | if (results == null || results.isEmpty() || av == null |
471 | || av.getAlignment() == null) | |
472 | { | |
473 | 0 | return false; |
474 | } | |
475 | 7 | int seqIndex = av.getAlignment().findIndex(results); |
476 | 7 | if (seqIndex == -1) |
477 | { | |
478 | 0 | return false; |
479 | } | |
480 | 7 | SequenceI seq = av.getAlignment().getSequenceAt(seqIndex); |
481 | ||
482 | 7 | int[] r = results.getResults(seq, 0, av.getAlignment().getWidth()); |
483 | 7 | if (r == null) |
484 | { | |
485 | 0 | return false; |
486 | } | |
487 | 7 | int start = r[0]; |
488 | 7 | int end = r[1]; |
489 | ||
490 | /* | |
491 | * To centre results, scroll to positions half the visible width | |
492 | * left/right of the start/end positions | |
493 | */ | |
494 | 7 | if (centre) |
495 | { | |
496 | 4 | int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1; |
497 | 4 | start = Math.max(start - offset, 0); |
498 | 4 | end = end + offset - 1; |
499 | } | |
500 | 7 | if (start < 0) |
501 | { | |
502 | 0 | return false; |
503 | } | |
504 | 7 | if (end == seq.getEnd()) |
505 | { | |
506 | 0 | return false; |
507 | } | |
508 | ||
509 | 7 | if (av.hasHiddenColumns()) |
510 | { | |
511 | 0 | HiddenColumns hidden = av.getAlignment().getHiddenColumns(); |
512 | 0 | start = hidden.absoluteToVisibleColumn(start); |
513 | 0 | end = hidden.absoluteToVisibleColumn(end); |
514 | 0 | if (start == end) |
515 | { | |
516 | 0 | if (!hidden.isVisible(r[0])) |
517 | { | |
518 | // don't scroll - position isn't visible | |
519 | 0 | return false; |
520 | } | |
521 | } | |
522 | } | |
523 | ||
524 | /* | |
525 | * allow for offset of target sequence (actually scroll to one above it) | |
526 | */ | |
527 | 7 | seqIndex = Math.max(0, seqIndex - verticalOffset); |
528 | 7 | boolean scrollNeeded = true; |
529 | ||
530 | 7 | if (!av.getWrapAlignment()) |
531 | { | |
532 | ? | if ((startv = ranges.getStartRes()) >= start) |
533 | { | |
534 | /* | |
535 | * Scroll left to make start of search results visible | |
536 | */ | |
537 | 4 | setScrollValues(start, seqIndex); |
538 | } | |
539 | ? | else if ((endv = ranges.getEndRes()) <= end) |
540 | { | |
541 | /* | |
542 | * Scroll right to make end of search results visible | |
543 | */ | |
544 | 2 | setScrollValues(startv + end - endv, seqIndex); |
545 | } | |
546 | 0 | else if ((starts = ranges.getStartSeq()) > seqIndex) |
547 | { | |
548 | /* | |
549 | * Scroll up to make start of search results visible | |
550 | */ | |
551 | 0 | setScrollValues(ranges.getStartRes(), seqIndex); |
552 | } | |
553 | 0 | else if ((ends = ranges.getEndSeq()) <= seqIndex) |
554 | { | |
555 | /* | |
556 | * Scroll down to make end of search results visible | |
557 | */ | |
558 | 0 | setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1); |
559 | } | |
560 | /* | |
561 | * Else results are already visible - no need to scroll | |
562 | */ | |
563 | 6 | scrollNeeded = false; |
564 | } | |
565 | else | |
566 | { | |
567 | 1 | scrollNeeded = ranges.scrollToWrappedVisible(start); |
568 | } | |
569 | ||
570 | 7 | paintAlignment(false, false); |
571 | ||
572 | 7 | return scrollNeeded; |
573 | } | |
574 | ||
575 | /** | |
576 | * DOCUMENT ME! | |
577 | * | |
578 | * @return DOCUMENT ME! | |
579 | */ | |
580 | 54 | public OverviewPanel getOverviewPanel() |
581 | { | |
582 | 54 | return overviewPanel; |
583 | } | |
584 | ||
585 | /** | |
586 | * DOCUMENT ME! | |
587 | * | |
588 | * @param op | |
589 | * DOCUMENT ME! | |
590 | */ | |
591 | 82 | public void setOverviewPanel(OverviewPanel op) |
592 | { | |
593 | 82 | overviewPanel = op; |
594 | } | |
595 | ||
596 | /** | |
597 | * | |
598 | * @param b | |
599 | * Hide or show annotation panel | |
600 | * | |
601 | */ | |
602 | 626 | public void setAnnotationVisible(boolean b) |
603 | { | |
604 | 626 | if (!av.getWrapAlignment()) |
605 | { | |
606 | 596 | annotationSpaceFillerHolder.setVisible(b); |
607 | 596 | annotationScroller.setVisible(b); |
608 | } | |
609 | 626 | repaint(); |
610 | } | |
611 | ||
612 | /** | |
613 | * automatically adjust annotation panel height for new annotation whilst | |
614 | * ensuring the alignment is still visible. | |
615 | */ | |
616 | 1750 | @Override |
617 | public void adjustAnnotationHeight() | |
618 | { | |
619 | // TODO: display vertical annotation scrollbar if necessary | |
620 | // this is called after loading new annotation onto alignment | |
621 | 1749 | if (alignFrame.getHeight() == 0) |
622 | { | |
623 | 10 | jalview.bin.Console.error( |
624 | "adjustAnnotationHeight called with zero height alignment window"); | |
625 | } | |
626 | 1750 | validateAnnotationDimensions(true); |
627 | 1750 | addNotify(); |
628 | // TODO: many places call this method and also paintAlignment with various | |
629 | // different settings. this means multiple redraws are triggered... | |
630 | 1750 | paintAlignment(true, av.needToUpdateStructureViews()); |
631 | } | |
632 | ||
633 | /** | |
634 | * calculate the annotation dimensions and refresh slider values accordingly. | |
635 | * need to do repaints/notifys afterwards. | |
636 | */ | |
637 | 2640 | protected void validateAnnotationDimensions(boolean adjustPanelHeight) |
638 | { | |
639 | // BH 2018.04.18 comment: addNotify() is not appropriate here. We | |
640 | // are not changing ancestors, and keyboard action listeners do | |
641 | // not need to be reset. addNotify() is a very expensive operation, | |
642 | // requiring a full re-layout of all parents and children. | |
643 | // Note in JComponent: | |
644 | // This method is called by the toolkit internally and should | |
645 | // not be called directly by programs. | |
646 | // I note that addNotify() is called in several areas of Jalview. | |
647 | ||
648 | 2640 | AnnotationPanel ap = getAnnotationPanel(); |
649 | 2640 | int annotationHeight = ap.adjustPanelHeight(); |
650 | 2640 | annotationHeight = ap.adjustForAlignFrame(adjustPanelHeight, |
651 | annotationHeight); | |
652 | ||
653 | 2640 | hscroll.addNotify(); |
654 | 2640 | Dimension e = idPanel.getSize(); |
655 | 2640 | int idWidth = e.width; |
656 | 2640 | boolean manuallyAdjusted = this.getIdPanel().getIdCanvas() |
657 | .isManuallyAdjusted(); | |
658 | 2640 | annotationScroller.setPreferredSize(new Dimension( |
659 | 2640 | manuallyAdjusted ? idWidth : annotationScroller.getWidth(), |
660 | annotationHeight)); | |
661 | ||
662 | 2640 | alabels.setPreferredSize(new Dimension(idWidth, annotationHeight)); |
663 | ||
664 | 2640 | annotationSpaceFillerHolder.setPreferredSize(new Dimension( |
665 | 2640 | manuallyAdjusted ? idWidth |
666 | : annotationSpaceFillerHolder.getWidth(), | |
667 | annotationHeight)); | |
668 | 2640 | annotationScroller.validate(); |
669 | 2640 | annotationScroller.addNotify(); |
670 | 2640 | ap.validate(); |
671 | } | |
672 | ||
673 | /** | |
674 | * update alignment layout for viewport settings | |
675 | * | |
676 | * @param wrap | |
677 | * DOCUMENT ME! | |
678 | */ | |
679 | 626 | public void updateLayout() |
680 | { | |
681 | 626 | fontChanged(); |
682 | 626 | setAnnotationVisible(av.isShowAnnotation()); |
683 | 626 | boolean wrap = av.getWrapAlignment(); |
684 | 626 | ViewportRanges ranges = av.getRanges(); |
685 | 626 | ranges.setStartSeq(0); |
686 | // scalePanelHolder.setVisible(!wrap); | |
687 | 626 | hscroll.setVisible(!wrap); |
688 | // Allow idPanel width adjustment in wrap mode | |
689 | 626 | idwidthAdjuster.setVisible(true); |
690 | ||
691 | 626 | if (wrap) |
692 | { | |
693 | 30 | annotationScroller.setVisible(false); |
694 | 30 | annotationSpaceFillerHolder.setVisible(false); |
695 | } | |
696 | 596 | else if (av.isShowAnnotation()) |
697 | { | |
698 | 586 | annotationScroller.setVisible(true); |
699 | 586 | annotationSpaceFillerHolder.setVisible(true); |
700 | 586 | validateAnnotationDimensions(false); |
701 | } | |
702 | ||
703 | 626 | int canvasWidth = getSeqPanel().seqCanvas.getWidth(); |
704 | 626 | if (canvasWidth > 0) |
705 | { // may not yet be laid out | |
706 | 31 | if (wrap) |
707 | { | |
708 | 10 | int widthInRes = getSeqPanel().seqCanvas |
709 | .getWrappedCanvasWidth(canvasWidth); | |
710 | 10 | ranges.setViewportWidth(widthInRes); |
711 | } | |
712 | else | |
713 | { | |
714 | 21 | int widthInRes = (canvasWidth / av.getCharWidth()); |
715 | 21 | int heightInSeq = (getSeqPanel().seqCanvas.getHeight() |
716 | / av.getCharHeight()); | |
717 | ||
718 | 21 | ranges.setViewportWidth(widthInRes); |
719 | 21 | ranges.setViewportHeight(heightInSeq); |
720 | } | |
721 | } | |
722 | ||
723 | // idSpaceFillerPanel1.setVisible(!wrap); | |
724 | ||
725 | 626 | repaint(); |
726 | } | |
727 | ||
728 | /** | |
729 | * Adjust row/column scrollers to show a visible position in the alignment. | |
730 | * | |
731 | * @param x | |
732 | * visible column to scroll to | |
733 | * @param y | |
734 | * visible row to scroll to | |
735 | * | |
736 | */ | |
737 | 3942 | public void setScrollValues(int xpos, int ypos) |
738 | { | |
739 | 3942 | int x = xpos; |
740 | 3942 | int y = ypos; |
741 | ||
742 | 3942 | if (av == null || av.getAlignment() == null) |
743 | { | |
744 | 0 | return; |
745 | } | |
746 | ||
747 | 3942 | if (av.getWrapAlignment()) |
748 | { | |
749 | 283 | setScrollingForWrappedPanel(x); |
750 | } | |
751 | else | |
752 | { | |
753 | 3659 | int width = av.getAlignment().getVisibleWidth(); |
754 | 3659 | int height = av.getAlignment().getHeight(); |
755 | ||
756 | 3659 | hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); |
757 | 3659 | vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); |
758 | ||
759 | 3659 | if (hextent > width) |
760 | { | |
761 | 729 | hextent = width; |
762 | } | |
763 | ||
764 | 3659 | if (vextent > height) |
765 | { | |
766 | 888 | vextent = height; |
767 | } | |
768 | ||
769 | 3659 | if ((hextent + x) > width) |
770 | { | |
771 | 2 | x = width - hextent; |
772 | } | |
773 | ||
774 | 3659 | if ((vextent + y) > height) |
775 | { | |
776 | 32 | y = height - vextent; |
777 | } | |
778 | ||
779 | 3659 | if (y < 0) |
780 | { | |
781 | 0 | y = 0; |
782 | } | |
783 | ||
784 | 3659 | if (x < 0) |
785 | { | |
786 | 1 | x = 0; |
787 | } | |
788 | ||
789 | // update the scroll values | |
790 | 3659 | hscroll.setValues(x, hextent, 0, width); |
791 | 3659 | vscroll.setValues(y, vextent, 0, height); |
792 | } | |
793 | } | |
794 | ||
795 | /** | |
796 | * Answers true if the panel has no horizontal scrollbar, or the scrollbar is | |
797 | * at its rightmost position, else false. | |
798 | * | |
799 | * @return | |
800 | */ | |
801 | 0 | boolean isScrolledFullyRight() |
802 | { | |
803 | 0 | if (hscroll == null) |
804 | { | |
805 | 0 | return true; |
806 | } | |
807 | 0 | BoundedRangeModel model = hscroll.getModel(); |
808 | 0 | return (model.getExtent() + model.getValue() >= model.getMaximum()); |
809 | } | |
810 | ||
811 | /** | |
812 | * Respond to adjustment event when horizontal or vertical scrollbar is | |
813 | * changed | |
814 | * | |
815 | * @param evt | |
816 | * adjustment event encoding whether hscroll or vscroll changed | |
817 | */ | |
818 | 744 | @Override |
819 | public void adjustmentValueChanged(AdjustmentEvent evt) | |
820 | { | |
821 | 744 | if (av.getWrapAlignment()) |
822 | { | |
823 | 26 | adjustScrollingWrapped(evt); |
824 | 26 | return; |
825 | } | |
826 | ||
827 | 718 | ViewportRanges ranges = av.getRanges(); |
828 | ||
829 | 718 | if (evt.getSource() == hscroll) |
830 | { | |
831 | 307 | int oldX = ranges.getStartRes(); |
832 | 307 | int oldwidth = ranges.getViewportWidth(); |
833 | 307 | int x = hscroll.getValue(); |
834 | 307 | int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); |
835 | ||
836 | // if we're scrolling to the position we're already at, stop | |
837 | // this prevents infinite recursion of events when the scroll/viewport | |
838 | // ranges values are the same | |
839 | 307 | if ((x == oldX) && (width == oldwidth)) |
840 | { | |
841 | 52 | return; |
842 | } | |
843 | 255 | ranges.setViewportStartAndWidth(x, width); |
844 | } | |
845 | 411 | else if (evt.getSource() == vscroll) |
846 | { | |
847 | 411 | int oldY = ranges.getStartSeq(); |
848 | 411 | int oldheight = ranges.getViewportHeight(); |
849 | 411 | int y = vscroll.getValue(); |
850 | 411 | int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); |
851 | ||
852 | // if we're scrolling to the position we're already at, stop | |
853 | // this prevents infinite recursion of events when the scroll/viewport | |
854 | // ranges values are the same | |
855 | 411 | if ((y == oldY) && (height == oldheight)) |
856 | { | |
857 | 36 | return; |
858 | } | |
859 | 375 | ranges.setViewportStartAndHeight(y, height); |
860 | } | |
861 | 630 | repaint(); |
862 | } | |
863 | ||
864 | /** | |
865 | * Responds to a scroll change by setting the start position of the viewport. | |
866 | * Does | |
867 | * | |
868 | * @param evt | |
869 | */ | |
870 | 26 | protected void adjustScrollingWrapped(AdjustmentEvent evt) |
871 | { | |
872 | 26 | if (evt.getSource() == hscroll) |
873 | { | |
874 | 0 | return; // no horizontal scroll when wrapped |
875 | } | |
876 | 26 | final ViewportRanges ranges = av.getRanges(); |
877 | ||
878 | 26 | if (evt.getSource() == vscroll) |
879 | { | |
880 | 26 | int newY = vscroll.getValue(); |
881 | ||
882 | /* | |
883 | * if we're scrolling to the position we're already at, stop | |
884 | * this prevents infinite recursion of events when the scroll/viewport | |
885 | * ranges values are the same | |
886 | */ | |
887 | 26 | int oldX = ranges.getStartRes(); |
888 | 26 | int oldY = ranges.getWrappedScrollPosition(oldX); |
889 | 26 | if (oldY == newY) |
890 | { | |
891 | 26 | return; |
892 | } | |
893 | 0 | if (newY > -1) |
894 | { | |
895 | /* | |
896 | * limit page up/down to one width's worth of positions | |
897 | */ | |
898 | 0 | int rowSize = ranges.getViewportWidth(); |
899 | 0 | int newX = newY > oldY ? oldX + rowSize : oldX - rowSize; |
900 | 0 | ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize); |
901 | } | |
902 | } | |
903 | else | |
904 | { | |
905 | // This is only called if file loaded is a jar file that | |
906 | // was wrapped when saved and user has wrap alignment true | |
907 | // as preference setting | |
908 | 0 | SwingUtilities.invokeLater(new Runnable() |
909 | { | |
910 | 0 | @Override |
911 | public void run() | |
912 | { | |
913 | // When updating scrolling to use ViewportChange events, this code | |
914 | // could not be validated and it is not clear if it is now being | |
915 | // called. Log warning here in case it is called and unforeseen | |
916 | // problems occur | |
917 | 0 | Console.warn( |
918 | "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences"); | |
919 | ||
920 | // scroll to start of panel | |
921 | 0 | ranges.setStartRes(0); |
922 | 0 | ranges.setStartSeq(0); |
923 | } | |
924 | }); | |
925 | } | |
926 | 0 | repaint(); |
927 | } | |
928 | ||
929 | /* (non-Javadoc) | |
930 | * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean) | |
931 | */ | |
932 | 5565 | @Override |
933 | public void paintAlignment(boolean updateOverview, | |
934 | boolean updateStructures) | |
935 | { | |
936 | 5565 | final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), |
937 | av.isShowAutocalculatedAbove()); | |
938 | 5565 | sorter.sort(getAlignment().getAlignmentAnnotation(), |
939 | av.getSortAnnotationsBy()); | |
940 | 5565 | repaint(); |
941 | ||
942 | 5565 | if (updateStructures) |
943 | { | |
944 | 3673 | av.getStructureSelectionManager().sequenceColoursChanged(this); |
945 | } | |
946 | 5562 | if (updateOverview) |
947 | { | |
948 | ||
949 | 5524 | if (overviewPanel != null) |
950 | { | |
951 | 493 | overviewPanel.updateOverviewImage(); |
952 | } | |
953 | } | |
954 | } | |
955 | ||
956 | 2807 | @Override |
957 | public void paintComponent(Graphics g) | |
958 | { | |
959 | 2807 | invalidate(); // needed so that the id width adjuster works correctly |
960 | 2807 | Dimension d = getIdPanel().getIdCanvas().getPreferredSize(); |
961 | 2807 | int idWidth = d.width; |
962 | ||
963 | // check wrapped alignment as at least 1 residue width | |
964 | 2807 | if (av.getWrapAlignment()) |
965 | { | |
966 | 257 | SeqCanvas sc = this.getSeqPanel().seqCanvas; |
967 | 257 | if (sc != null && sc.getWidth() < sc.getMinimumWrappedCanvasWidth()) |
968 | { | |
969 | // need to make some adjustments | |
970 | 0 | idWidth -= (sc.getMinimumWrappedCanvasWidth() - sc.getWidth()); |
971 | 0 | av.setIdWidth(idWidth); |
972 | 0 | av.getAlignPanel().getIdPanel().getIdCanvas() |
973 | .setManuallyAdjusted(true); | |
974 | ||
975 | 0 | validateAnnotationDimensions(false); |
976 | } | |
977 | } | |
978 | ||
979 | 2807 | idPanelHolder.setPreferredSize(new Dimension(idWidth, d.height)); |
980 | 2807 | hscrollFillerPanel.setPreferredSize(new Dimension(idWidth, 12)); |
981 | ||
982 | 2807 | validate(); // needed so that the id width adjuster works correctly |
983 | ||
984 | /* | |
985 | * set scroll bar positions - tried to remove but necessary for split panel to resize correctly | |
986 | * though I still think this call should be elsewhere. | |
987 | */ | |
988 | 2807 | ViewportRanges ranges = av.getRanges(); |
989 | 2806 | setScrollValues(ranges.getStartRes(), ranges.getStartSeq()); |
990 | 2806 | super.paintComponent(g); |
991 | } | |
992 | ||
993 | /** | |
994 | * Set vertical scroll bar position, and number of increments, for wrapped | |
995 | * panel | |
996 | * | |
997 | * @param topLeftColumn | |
998 | * the column position at top left (0..) | |
999 | */ | |
1000 | 283 | private void setScrollingForWrappedPanel(int topLeftColumn) |
1001 | { | |
1002 | 283 | ViewportRanges ranges = av.getRanges(); |
1003 | 283 | int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn); |
1004 | 283 | int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn); |
1005 | ||
1006 | /* | |
1007 | * a scrollbar's value can be set to at most (maximum-extent) | |
1008 | * so we add extent (1) to the maxScroll value | |
1009 | */ | |
1010 | 283 | vscroll.setUnitIncrement(1); |
1011 | 283 | vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1); |
1012 | } | |
1013 | ||
1014 | /** | |
1015 | * DOCUMENT ME! | |
1016 | * | |
1017 | * @param pg | |
1018 | * DOCUMENT ME! | |
1019 | * @param pf | |
1020 | * DOCUMENT ME! | |
1021 | * @param pi | |
1022 | * DOCUMENT ME! | |
1023 | * | |
1024 | * @return DOCUMENT ME! | |
1025 | * | |
1026 | * @throws PrinterException | |
1027 | * DOCUMENT ME! | |
1028 | */ | |
1029 | 0 | @Override |
1030 | public int print(Graphics pg, PageFormat pf, int pi) | |
1031 | throws PrinterException | |
1032 | { | |
1033 | 0 | pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); |
1034 | ||
1035 | 0 | int pwidth = (int) pf.getImageableWidth(); |
1036 | 0 | int pheight = (int) pf.getImageableHeight(); |
1037 | ||
1038 | 0 | if (av.getWrapAlignment()) |
1039 | { | |
1040 | 0 | return printWrappedAlignment(pwidth, pheight, pi, pg); |
1041 | } | |
1042 | else | |
1043 | { | |
1044 | 0 | return printUnwrapped(pwidth, pheight, pi, pg, pg); |
1045 | } | |
1046 | } | |
1047 | ||
1048 | /** | |
1049 | * Draws the alignment image, including sequence ids, sequences, and | |
1050 | * annotation labels and annotations if shown, on either one or two Graphics | |
1051 | * contexts. | |
1052 | * | |
1053 | * @param pageWidth | |
1054 | * in pixels | |
1055 | * @param pageHeight | |
1056 | * in pixels | |
1057 | * @param pageIndex | |
1058 | * (0, 1, ...) | |
1059 | * @param idGraphics | |
1060 | * the graphics context for sequence ids and annotation labels | |
1061 | * @param alignmentGraphics | |
1062 | * the graphics context for sequences and annotations (may or may not | |
1063 | * be the same context as idGraphics) | |
1064 | * @return | |
1065 | * @throws PrinterException | |
1066 | */ | |
1067 | 38 | public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex, |
1068 | Graphics idGraphics, Graphics alignmentGraphics) | |
1069 | throws PrinterException | |
1070 | { | |
1071 | 38 | final int idWidth, idWidthForGui; |
1072 | // otherwise calculate it | |
1073 | 38 | idWidth = getVisibleIdWidth(false); |
1074 | // if (getIdPanel()!=null && getIdPanel().getWidth()>0) | |
1075 | // { | |
1076 | // // use the current IdPanel's width, if its set and non-zero | |
1077 | // idWidthForGui = getIdPanel().getWidth(); | |
1078 | // } else { | |
1079 | // idWidthForGui=0; | |
1080 | // } | |
1081 | /* | |
1082 | * Get the horizontal offset to where we draw the sequences. | |
1083 | * This is idWidth if using a single Graphics context, else zero. | |
1084 | */ | |
1085 | 38 | final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 |
1086 | : idWidth; | |
1087 | ||
1088 | 38 | FontMetrics fm = getFontMetrics(av.getFont()); |
1089 | 38 | final int charHeight = av.getCharHeight(); |
1090 | 38 | final int scaleHeight = charHeight + fm.getDescent(); |
1091 | ||
1092 | 38 | idGraphics.setColor(Color.white); |
1093 | 38 | idGraphics.fillRect(0, 0, pageWidth, pageHeight); |
1094 | 38 | idGraphics.setFont(av.getFont()); |
1095 | ||
1096 | /* | |
1097 | * How many sequences and residues can we fit on a printable page? | |
1098 | */ | |
1099 | 38 | final int totalRes = (pageWidth - idWidth) / av.getCharWidth(); |
1100 | ||
1101 | 38 | final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; |
1102 | ||
1103 | 38 | final int alignmentWidth = av.getAlignment().getVisibleWidth(); |
1104 | 38 | int pagesWide = (alignmentWidth / totalRes) + 1; |
1105 | ||
1106 | 38 | final int startRes = (pageIndex % pagesWide) * totalRes; |
1107 | 38 | final int endRes = Math.min(startRes + totalRes - 1, |
1108 | alignmentWidth - 1); | |
1109 | ||
1110 | 38 | final int startSeq = (pageIndex / pagesWide) * totalSeq; |
1111 | 38 | final int alignmentHeight = av.getAlignment().getHeight(); |
1112 | 38 | final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight); |
1113 | ||
1114 | 38 | int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight; |
1115 | ||
1116 | 38 | if (av.isShowAnnotation()) |
1117 | { | |
1118 | 38 | pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3; |
1119 | } | |
1120 | ||
1121 | 38 | pagesHigh /= pageHeight; |
1122 | ||
1123 | 38 | if (pageIndex >= (pagesWide * pagesHigh)) |
1124 | { | |
1125 | 0 | return Printable.NO_SUCH_PAGE; |
1126 | } | |
1127 | 38 | final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3; |
1128 | ||
1129 | 38 | alignmentGraphics.setColor(Color.white); |
1130 | 38 | alignmentGraphics.fillRect(0, 0, pageWidth, pageHeight + scaleHeight); |
1131 | ||
1132 | /* | |
1133 | * draw the Scale at horizontal offset, then reset to top left (0, 0) | |
1134 | */ | |
1135 | 38 | alignmentGraphics.translate(alignmentGraphicsOffset, 0); |
1136 | 38 | getScalePanel().drawScale(alignmentGraphics, startRes, endRes, |
1137 | pageWidth - idWidth, scaleHeight); | |
1138 | 38 | alignmentGraphics.translate(-alignmentGraphicsOffset, 0); |
1139 | ||
1140 | /* | |
1141 | * Draw the sequence ids, offset for scale height, | |
1142 | * then reset to top left (0, 0) | |
1143 | */ | |
1144 | 38 | idGraphics.translate(0, scaleHeight); |
1145 | 38 | IdCanvas idCanvas = getIdPanel().getIdCanvas(); |
1146 | 38 | List<SequenceI> selection = av.getSelectionGroup() == null ? null |
1147 | : av.getSelectionGroup().getSequences(null); | |
1148 | ||
1149 | 38 | idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1, |
1150 | selection, false, idWidth); | |
1151 | ||
1152 | 38 | idGraphics.setFont(av.getFont()); |
1153 | 38 | idGraphics.translate(0, -scaleHeight); |
1154 | ||
1155 | /* | |
1156 | * draw the sequences, offset for scale height, and id width (if using a | |
1157 | * single graphics context), then reset to (0, scale height) | |
1158 | */ | |
1159 | 38 | alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); |
1160 | 38 | getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, |
1161 | startRes, endRes, startSeq, endSeq - 1); | |
1162 | 38 | alignmentGraphics.translate(-alignmentGraphicsOffset, 0); |
1163 | ||
1164 | 38 | if (av.isShowAnnotation() && (endSeq == alignmentHeight)) |
1165 | { | |
1166 | /* | |
1167 | * draw annotation labels; drawComponent() translates by | |
1168 | * getScrollOffset(), so compensate for that first; | |
1169 | * then reset to (0, scale height) | |
1170 | */ | |
1171 | 38 | int offset = getAlabels().getScrollOffset(); |
1172 | 38 | idGraphics.translate(0, -offset); |
1173 | 38 | idGraphics.translate(0, alignmentDrawnHeight); |
1174 | 38 | getAlabels().drawComponentNotGUI(idGraphics, idWidth); |
1175 | 38 | idGraphics.translate(0, -alignmentDrawnHeight); |
1176 | ||
1177 | /* | |
1178 | * draw the annotations starting at | |
1179 | * (idOffset, alignmentHeight) from (0, scaleHeight) | |
1180 | */ | |
1181 | 38 | alignmentGraphics.translate(alignmentGraphicsOffset, |
1182 | alignmentDrawnHeight); | |
1183 | 38 | updateLayout(); |
1184 | 38 | getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, |
1185 | alignmentGraphics, -1, startRes, endRes + 1); | |
1186 | } | |
1187 | ||
1188 | 38 | return Printable.PAGE_EXISTS; |
1189 | } | |
1190 | ||
1191 | /** | |
1192 | * Prints one page of an alignment in wrapped mode. Returns | |
1193 | * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if | |
1194 | * no page could be drawn (page number out of range). | |
1195 | * | |
1196 | * @param pageWidth | |
1197 | * @param pageHeight | |
1198 | * @param pageNumber | |
1199 | * (0, 1, ...) | |
1200 | * @param g | |
1201 | * | |
1202 | * @return | |
1203 | * | |
1204 | * @throws PrinterException | |
1205 | */ | |
1206 | 0 | public int printWrappedAlignment(int pageWidth, int pageHeight, |
1207 | int pageNumber, Graphics g) throws PrinterException | |
1208 | { | |
1209 | 0 | getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(), |
1210 | getHeight()); | |
1211 | 0 | int annotationHeight = 0; |
1212 | 0 | if (av.isShowAnnotation()) |
1213 | { | |
1214 | 0 | annotationHeight = getAnnotationPanel().adjustPanelHeight(); |
1215 | } | |
1216 | ||
1217 | 0 | int hgap = av.getCharHeight(); |
1218 | 0 | if (av.getScaleAboveWrapped()) |
1219 | { | |
1220 | 0 | hgap += av.getCharHeight(); |
1221 | } | |
1222 | ||
1223 | 0 | int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap |
1224 | + annotationHeight; | |
1225 | ||
1226 | 0 | int idWidth = getVisibleIdWidth(false); |
1227 | ||
1228 | 0 | int maxwidth = av.getAlignment().getVisibleWidth(); |
1229 | ||
1230 | 0 | int resWidth = getSeqPanel().seqCanvas |
1231 | .getWrappedCanvasWidth(pageWidth - idWidth); | |
1232 | 0 | av.getRanges().setViewportStartAndWidth(0, resWidth); |
1233 | ||
1234 | 0 | int totalHeight = cHeight * (maxwidth / resWidth + 1); |
1235 | ||
1236 | 0 | g.setColor(Color.white); |
1237 | 0 | g.fillRect(0, 0, pageWidth, pageHeight); |
1238 | 0 | g.setFont(av.getFont()); |
1239 | 0 | g.setColor(Color.black); |
1240 | ||
1241 | /* | |
1242 | * method: print the whole wrapped alignment, but with a clip region that | |
1243 | * is restricted to the requested page; this supports selective print of | |
1244 | * single pages or ranges, (at the cost of repeated processing in the | |
1245 | * 'normal' case, when all pages are printed) | |
1246 | */ | |
1247 | 0 | g.translate(0, -pageNumber * pageHeight); |
1248 | ||
1249 | 0 | g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight); |
1250 | ||
1251 | /* | |
1252 | * draw sequence ids and annotation labels (if shown) | |
1253 | */ | |
1254 | 0 | IdCanvas idCanvas = getIdPanel().getIdCanvas(); |
1255 | 0 | idCanvas.drawIdsWrappedNoGUI((Graphics2D) g, av, 0, totalHeight); |
1256 | ||
1257 | 0 | g.translate(idWidth, 0); |
1258 | ||
1259 | 0 | getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, |
1260 | pageWidth - idWidth, totalHeight, 0); | |
1261 | ||
1262 | 0 | if ((pageNumber * pageHeight) < totalHeight) |
1263 | { | |
1264 | 0 | return Printable.PAGE_EXISTS; |
1265 | } | |
1266 | else | |
1267 | { | |
1268 | 0 | return Printable.NO_SUCH_PAGE; |
1269 | } | |
1270 | } | |
1271 | ||
1272 | /** | |
1273 | * get current sequence ID panel width, or nominal value if panel were to be | |
1274 | * displayed using default settings | |
1275 | * | |
1276 | * @return | |
1277 | */ | |
1278 | 0 | public int getVisibleIdWidth() |
1279 | { | |
1280 | 0 | return getVisibleIdWidth(true); |
1281 | } | |
1282 | ||
1283 | /** | |
1284 | * get current sequence ID panel width, or nominal value if panel were to be | |
1285 | * displayed using default settings | |
1286 | * | |
1287 | * @param onscreen | |
1288 | * indicate if the Id width for onscreen or offscreen display should | |
1289 | * be returned | |
1290 | * @return | |
1291 | */ | |
1292 | 76 | protected int getVisibleIdWidth(boolean onscreen) |
1293 | { | |
1294 | // see if rendering offscreen - check preferences and calc width accordingly | |
1295 | 76 | if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false)) |
1296 | { | |
1297 | 0 | return calculateIdWidth(-1, true, true).width; |
1298 | } | |
1299 | 76 | Integer idwidth = onscreen ? null |
1300 | : Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"); | |
1301 | 76 | if (idwidth != null) |
1302 | { | |
1303 | 0 | return idwidth.intValue() + ID_WIDTH_PADDING; |
1304 | } | |
1305 | ||
1306 | // int w = getIdPanel().getWidth(); | |
1307 | // w = calculateIdWidth(-1, true, true).width; | |
1308 | 76 | int w = calculateIdWidth(-1, true, true).width; |
1309 | 76 | return (w > 0 ? w : calculateIdWidth().width); |
1310 | } | |
1311 | ||
1312 | 12 | void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer) |
1313 | throws ImageOutputException | |
1314 | { | |
1315 | 12 | makeAlignmentImage(type, file, renderer, |
1316 | BitmapImageSizing.defaultBitmapImageSizing()); | |
1317 | } | |
1318 | ||
1319 | /** | |
1320 | * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and | |
1321 | * writes it to the specified file | |
1322 | * | |
1323 | * @param type | |
1324 | * @param file | |
1325 | * @param textrenderer | |
1326 | * @param bitmapscale | |
1327 | */ | |
1328 | 36 | void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer, |
1329 | BitmapImageSizing userBis) throws ImageOutputException | |
1330 | { | |
1331 | 36 | final int borderBottomOffset = 5; |
1332 | ||
1333 | 36 | AlignmentDimension aDimension = getAlignmentDimension(); |
1334 | ||
1335 | // todo use a lambda function in place of callback here? | |
1336 | 36 | ImageWriterI writer = new ImageWriterI() |
1337 | { | |
1338 | 36 | @Override |
1339 | public void exportImage(Graphics graphics) throws Exception | |
1340 | { | |
1341 | 36 | if (av.getWrapAlignment()) |
1342 | { | |
1343 | 0 | printWrappedAlignment(aDimension.getWidth(), |
1344 | aDimension.getHeight() + borderBottomOffset, 0, graphics); | |
1345 | } | |
1346 | else | |
1347 | { | |
1348 | 36 | printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, |
1349 | graphics, graphics); | |
1350 | } | |
1351 | } | |
1352 | }; | |
1353 | ||
1354 | 36 | String fileTitle = alignFrame.getTitle(); |
1355 | 36 | ImageExporter exporter = new ImageExporter(writer, alignFrame, type, |
1356 | fileTitle); | |
1357 | 36 | int imageWidth = aDimension.getWidth(); |
1358 | 36 | int imageHeight = aDimension.getHeight() + borderBottomOffset; |
1359 | 36 | String of = MessageManager.getString("label.alignment"); |
1360 | 36 | exporter.doExport(file, this, imageWidth, imageHeight, of, renderer, |
1361 | userBis); | |
1362 | } | |
1363 | ||
1364 | /** | |
1365 | * Calculates and returns a suitable width and height (in pixels) for an | |
1366 | * exported image | |
1367 | * | |
1368 | * @return | |
1369 | */ | |
1370 | 38 | public AlignmentDimension getAlignmentDimension() |
1371 | { | |
1372 | 38 | int maxwidth = av.getAlignment().getVisibleWidth(); |
1373 | ||
1374 | 38 | int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) |
1375 | + getScalePanel().getHeight(); | |
1376 | 38 | int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth()); |
1377 | ||
1378 | 38 | if (av.getWrapAlignment()) |
1379 | { | |
1380 | 0 | height = getWrappedHeight(); |
1381 | 0 | if (Jalview.isHeadlessMode()) |
1382 | { | |
1383 | // need to obtain default alignment width and then add in any | |
1384 | // additional allowance for id margin | |
1385 | // this duplicates the calculation in getWrappedHeight but adjusts for | |
1386 | // offscreen idWidth | |
1387 | 0 | width = alignFrame.getWidth() - vscroll.getPreferredSize().width |
1388 | - alignFrame.getInsets().left - alignFrame.getInsets().right | |
1389 | - getVisibleIdWidth() + getVisibleIdWidth(false); | |
1390 | } | |
1391 | else | |
1392 | { | |
1393 | 0 | width = getSeqPanel().getWidth() + getVisibleIdWidth(false); |
1394 | } | |
1395 | ||
1396 | } | |
1397 | 38 | else if (av.isShowAnnotation()) |
1398 | { | |
1399 | 38 | height += getAnnotationPanel().adjustPanelHeight() + 3; |
1400 | } | |
1401 | 38 | return new AlignmentDimension(width, height); |
1402 | ||
1403 | } | |
1404 | ||
1405 | 0 | public void makePNGImageMap(File imgMapFile, String imageName) |
1406 | throws ImageOutputException | |
1407 | { | |
1408 | // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS | |
1409 | // //////////////////////////////////////////// | |
1410 | 0 | int idWidth = getVisibleIdWidth(false); |
1411 | 0 | FontMetrics fm = getFontMetrics(av.getFont()); |
1412 | 0 | int scaleHeight = av.getCharHeight() + fm.getDescent(); |
1413 | ||
1414 | // Gen image map | |
1415 | // //////////////////////////////// | |
1416 | 0 | if (imgMapFile != null) |
1417 | { | |
1418 | 0 | try |
1419 | { | |
1420 | 0 | int sSize = av.getAlignment().getHeight(); |
1421 | 0 | int alwidth = av.getAlignment().getWidth(); |
1422 | 0 | PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); |
1423 | 0 | out.println(HTMLOutput.getImageMapHTML()); |
1424 | 0 | out.println("<img src=\"" + imageName |
1425 | + "\" border=\"0\" usemap=\"#Map\" >" | |
1426 | + "<map name=\"Map\">"); | |
1427 | ||
1428 | 0 | for (int s = 0; s < sSize; s++) |
1429 | { | |
1430 | 0 | int sy = s * av.getCharHeight() + scaleHeight; |
1431 | ||
1432 | 0 | SequenceI seq = av.getAlignment().getSequenceAt(s); |
1433 | 0 | SequenceGroup[] groups = av.getAlignment().findAllGroups(seq); |
1434 | 0 | for (int column = 0; column < alwidth; column++) |
1435 | { | |
1436 | 0 | StringBuilder text = new StringBuilder(512); |
1437 | 0 | String triplet = null; |
1438 | 0 | if (av.getAlignment().isNucleotide()) |
1439 | { | |
1440 | 0 | triplet = ResidueProperties.nucleotideName |
1441 | .get(seq.getCharAt(column) + ""); | |
1442 | } | |
1443 | else | |
1444 | { | |
1445 | 0 | triplet = ResidueProperties.aa2Triplet |
1446 | .get(seq.getCharAt(column) + ""); | |
1447 | } | |
1448 | ||
1449 | 0 | if (triplet == null) |
1450 | { | |
1451 | 0 | continue; |
1452 | } | |
1453 | ||
1454 | 0 | int seqPos = seq.findPosition(column); |
1455 | 0 | int gSize = groups.length; |
1456 | 0 | for (int g = 0; g < gSize; g++) |
1457 | { | |
1458 | 0 | if (text.length() < 1) |
1459 | { | |
1460 | 0 | text.append("<area shape=\"rect\" coords=\"") |
1461 | .append((idWidth + column * av.getCharWidth())) | |
1462 | .append(",").append(sy).append(",") | |
1463 | .append((idWidth | |
1464 | + (column + 1) * av.getCharWidth())) | |
1465 | .append(",").append((av.getCharHeight() + sy)) | |
1466 | .append("\"").append(" onMouseOver=\"toolTip('") | |
1467 | .append(seqPos).append(" ").append(triplet); | |
1468 | } | |
1469 | ||
1470 | 0 | if (groups[g].getStartRes() < column |
1471 | && groups[g].getEndRes() > column) | |
1472 | { | |
1473 | 0 | text.append("<br><em>").append(groups[g].getName()) |
1474 | .append("</em>"); | |
1475 | } | |
1476 | } | |
1477 | ||
1478 | 0 | if (text.length() < 1) |
1479 | { | |
1480 | 0 | text.append("<area shape=\"rect\" coords=\"") |
1481 | .append((idWidth + column * av.getCharWidth())) | |
1482 | .append(",").append(sy).append(",") | |
1483 | .append((idWidth + (column + 1) * av.getCharWidth())) | |
1484 | .append(",").append((av.getCharHeight() + sy)) | |
1485 | .append("\"").append(" onMouseOver=\"toolTip('") | |
1486 | .append(seqPos).append(" ").append(triplet); | |
1487 | } | |
1488 | 0 | if (!Comparison.isGap(seq.getCharAt(column))) |
1489 | { | |
1490 | 0 | List<SequenceFeature> features = seq.findFeatures(column, |
1491 | column); | |
1492 | 0 | for (SequenceFeature sf : features) |
1493 | { | |
1494 | 0 | if (sf.isContactFeature()) |
1495 | { | |
1496 | 0 | text.append("<br>").append(sf.getType()).append(" ") |
1497 | .append(sf.getBegin()).append(":") | |
1498 | .append(sf.getEnd()); | |
1499 | } | |
1500 | else | |
1501 | { | |
1502 | 0 | text.append("<br>"); |
1503 | 0 | text.append(sf.getType()); |
1504 | 0 | String description = sf.getDescription(); |
1505 | 0 | if (description != null |
1506 | && !sf.getType().equals(description)) | |
1507 | { | |
1508 | 0 | description = description.replace("\"", """); |
1509 | 0 | text.append(" ").append(description); |
1510 | } | |
1511 | } | |
1512 | 0 | String status = sf.getStatus(); |
1513 | 0 | if (status != null && !"".equals(status)) |
1514 | { | |
1515 | 0 | text.append(" (").append(status).append(")"); |
1516 | } | |
1517 | } | |
1518 | 0 | if (text.length() > 1) |
1519 | { | |
1520 | 0 | text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">"); |
1521 | 0 | out.println(text.toString()); |
1522 | } | |
1523 | } | |
1524 | } | |
1525 | } | |
1526 | 0 | out.println("</map></body></html>"); |
1527 | 0 | out.close(); |
1528 | ||
1529 | } catch (Exception ex) | |
1530 | { | |
1531 | 0 | throw new ImageOutputException( |
1532 | "couldn't write ImageMap due to unexpected error", ex); | |
1533 | } | |
1534 | } // /////////END OF IMAGE MAP | |
1535 | ||
1536 | } | |
1537 | ||
1538 | /** | |
1539 | * Answers the height of the entire alignment in pixels, assuming it is in | |
1540 | * wrapped mode | |
1541 | * | |
1542 | * @return | |
1543 | */ | |
1544 | 0 | int getWrappedHeight() |
1545 | { | |
1546 | 0 | int seqPanelWidth = getSeqPanel().seqCanvas.getWidth(); |
1547 | ||
1548 | 0 | if (Jalview.isHeadlessMode()) |
1549 | { | |
1550 | 0 | seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth() |
1551 | - vscroll.getPreferredSize().width | |
1552 | - alignFrame.getInsets().left - alignFrame.getInsets().right; | |
1553 | } | |
1554 | ||
1555 | 0 | int chunkWidth = getSeqPanel().seqCanvas |
1556 | .getWrappedCanvasWidth(seqPanelWidth); | |
1557 | ||
1558 | 0 | int hgap = av.getCharHeight(); |
1559 | 0 | if (av.getScaleAboveWrapped()) |
1560 | { | |
1561 | 0 | hgap += av.getCharHeight(); |
1562 | } | |
1563 | ||
1564 | 0 | int annotationHeight = 0; |
1565 | 0 | if (av.isShowAnnotation()) |
1566 | { | |
1567 | 0 | hgap += SeqCanvas.SEQS_ANNOTATION_GAP; |
1568 | 0 | annotationHeight = getAnnotationPanel().adjustPanelHeight(); |
1569 | } | |
1570 | ||
1571 | 0 | int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap |
1572 | + annotationHeight; | |
1573 | ||
1574 | 0 | int maxwidth = av.getAlignment().getWidth(); |
1575 | 0 | if (av.hasHiddenColumns()) |
1576 | { | |
1577 | 0 | maxwidth = av.getAlignment().getHiddenColumns() |
1578 | .absoluteToVisibleColumn(maxwidth) - 1; | |
1579 | } | |
1580 | ||
1581 | 0 | int height = ((maxwidth / chunkWidth) + 1) * cHeight; |
1582 | ||
1583 | 0 | return height; |
1584 | } | |
1585 | ||
1586 | /** | |
1587 | * close the panel - deregisters all listeners and nulls any references to | |
1588 | * alignment data. | |
1589 | */ | |
1590 | 253 | public void closePanel() |
1591 | { | |
1592 | 253 | PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas); |
1593 | 253 | PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas()); |
1594 | 253 | PaintRefresher.RemoveComponent(this); |
1595 | ||
1596 | 253 | closeChildFrames(); |
1597 | ||
1598 | /* | |
1599 | * try to ensure references are nulled | |
1600 | */ | |
1601 | 253 | if (annotationPanel != null) |
1602 | { | |
1603 | 253 | annotationPanel.dispose(); |
1604 | 253 | annotationPanel = null; |
1605 | } | |
1606 | ||
1607 | 253 | if (av != null) |
1608 | { | |
1609 | 253 | av.removePropertyChangeListener(propertyChangeListener); |
1610 | 253 | propertyChangeListener = null; |
1611 | 253 | StructureSelectionManager ssm = av.getStructureSelectionManager(); |
1612 | 253 | ssm.removeStructureViewerListener(getSeqPanel(), null); |
1613 | 253 | ssm.removeSelectionListener(getSeqPanel()); |
1614 | 253 | ssm.removeCommandListener(av); |
1615 | 253 | ssm.removeStructureViewerListener(getSeqPanel(), null); |
1616 | 253 | ssm.removeSelectionListener(getSeqPanel()); |
1617 | 253 | av.dispose(); |
1618 | 253 | av = null; |
1619 | } | |
1620 | else | |
1621 | { | |
1622 | 0 | if (Console.isDebugEnabled()) |
1623 | { | |
1624 | 0 | Console.warn("Closing alignment panel which is already closed."); |
1625 | } | |
1626 | } | |
1627 | } | |
1628 | ||
1629 | /** | |
1630 | * Close any open dialogs that would be orphaned when this one is closed | |
1631 | */ | |
1632 | 253 | protected void closeChildFrames() |
1633 | { | |
1634 | 253 | if (overviewPanel != null) |
1635 | { | |
1636 | 1 | overviewPanel.dispose(); |
1637 | 1 | overviewPanel = null; |
1638 | } | |
1639 | 253 | if (calculationDialog != null) |
1640 | { | |
1641 | 0 | calculationDialog.closeFrame(); |
1642 | 0 | calculationDialog = null; |
1643 | } | |
1644 | } | |
1645 | ||
1646 | /** | |
1647 | * hides or shows dynamic annotation rows based on groups and av state flags | |
1648 | */ | |
1649 | 45 | public void updateAnnotation() |
1650 | { | |
1651 | 45 | updateAnnotation(false, false); |
1652 | } | |
1653 | ||
1654 | 0 | public void updateAnnotation(boolean applyGlobalSettings) |
1655 | { | |
1656 | 0 | updateAnnotation(applyGlobalSettings, false); |
1657 | } | |
1658 | ||
1659 | 130 | public void updateAnnotation(boolean applyGlobalSettings, |
1660 | boolean preserveNewGroupSettings) | |
1661 | { | |
1662 | 130 | av.updateGroupAnnotationSettings(applyGlobalSettings, |
1663 | preserveNewGroupSettings); | |
1664 | 130 | adjustAnnotationHeight(); |
1665 | } | |
1666 | ||
1667 | 12258 | @Override |
1668 | public AlignmentI getAlignment() | |
1669 | { | |
1670 | 12258 | return av == null ? null : av.getAlignment(); |
1671 | } | |
1672 | ||
1673 | 2795 | @Override |
1674 | public String getViewName() | |
1675 | { | |
1676 | 2795 | return av.getViewName(); |
1677 | } | |
1678 | ||
1679 | /** | |
1680 | * Make/Unmake this alignment panel the current input focus | |
1681 | * | |
1682 | * @param b | |
1683 | */ | |
1684 | 0 | public void setSelected(boolean b) |
1685 | { | |
1686 | 0 | try |
1687 | { | |
1688 | 0 | if (alignFrame.getSplitViewContainer() != null) |
1689 | { | |
1690 | /* | |
1691 | * bring enclosing SplitFrame to front first if there is one | |
1692 | */ | |
1693 | 0 | ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b); |
1694 | } | |
1695 | 0 | alignFrame.setSelected(b); |
1696 | } catch (Exception ex) | |
1697 | { | |
1698 | } | |
1699 | 0 | if (b) |
1700 | { | |
1701 | 0 | setAlignFrameView(); |
1702 | } | |
1703 | } | |
1704 | ||
1705 | 0 | public void setAlignFrameView() |
1706 | { | |
1707 | 0 | alignFrame.setDisplayedView(this); |
1708 | } | |
1709 | ||
1710 | 106 | @Override |
1711 | public StructureSelectionManager getStructureSelectionManager() | |
1712 | { | |
1713 | 106 | return av.getStructureSelectionManager(); |
1714 | } | |
1715 | ||
1716 | 0 | @Override |
1717 | public void raiseOOMWarning(String string, OutOfMemoryError error) | |
1718 | { | |
1719 | 0 | new OOMWarning(string, error, this); |
1720 | } | |
1721 | ||
1722 | 15 | @Override |
1723 | public jalview.api.FeatureRenderer cloneFeatureRenderer() | |
1724 | { | |
1725 | ||
1726 | 15 | return new FeatureRenderer(this); |
1727 | } | |
1728 | ||
1729 | 388 | @Override |
1730 | public jalview.api.FeatureRenderer getFeatureRenderer() | |
1731 | { | |
1732 | 388 | return seqPanel.seqCanvas.getFeatureRenderer(); |
1733 | } | |
1734 | ||
1735 | 0 | public void updateFeatureRenderer( |
1736 | jalview.renderer.seqfeatures.FeatureRenderer fr) | |
1737 | { | |
1738 | 0 | fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer()); |
1739 | } | |
1740 | ||
1741 | 0 | public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr) |
1742 | { | |
1743 | 0 | if (getSeqPanel().seqCanvas.getFeatureRenderer() != null) |
1744 | { | |
1745 | 0 | getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr); |
1746 | } | |
1747 | } | |
1748 | ||
1749 | 557 | public ScalePanel getScalePanel() |
1750 | { | |
1751 | 557 | return scalePanel; |
1752 | } | |
1753 | ||
1754 | 478 | public void setScalePanel(ScalePanel scalePanel) |
1755 | { | |
1756 | 478 | this.scalePanel = scalePanel; |
1757 | } | |
1758 | ||
1759 | 15270 | public SeqPanel getSeqPanel() |
1760 | { | |
1761 | 15270 | return seqPanel; |
1762 | } | |
1763 | ||
1764 | 478 | public void setSeqPanel(SeqPanel seqPanel) |
1765 | { | |
1766 | 478 | this.seqPanel = seqPanel; |
1767 | } | |
1768 | ||
1769 | 14388 | public AnnotationPanel getAnnotationPanel() |
1770 | { | |
1771 | 14389 | return annotationPanel; |
1772 | } | |
1773 | ||
1774 | 478 | public void setAnnotationPanel(AnnotationPanel annotationPanel) |
1775 | { | |
1776 | 478 | this.annotationPanel = annotationPanel; |
1777 | } | |
1778 | ||
1779 | 14727 | public AnnotationLabels getAlabels() |
1780 | { | |
1781 | 14727 | return alabels; |
1782 | } | |
1783 | ||
1784 | 478 | public void setAlabels(AnnotationLabels alabels) |
1785 | { | |
1786 | 478 | this.alabels = alabels; |
1787 | } | |
1788 | ||
1789 | 11210 | public IdPanel getIdPanel() |
1790 | { | |
1791 | 11210 | return idPanel; |
1792 | } | |
1793 | ||
1794 | 478 | public void setIdPanel(IdPanel idPanel) |
1795 | { | |
1796 | 478 | this.idPanel = idPanel; |
1797 | } | |
1798 | ||
1799 | /** | |
1800 | * Follow a scrolling change in the (cDNA/Protein) complementary alignment. | |
1801 | * The aim is to keep the two alignments 'lined up' on their centre columns. | |
1802 | * | |
1803 | * @param sr | |
1804 | * holds mapped region(s) of this alignment that we are scrolling | |
1805 | * 'to'; may be modified for sequence offset by this method | |
1806 | * @param verticalOffset | |
1807 | * the number of visible sequences to show above the mapped region | |
1808 | */ | |
1809 | 4 | protected void scrollToCentre(SearchResultsI sr, int verticalOffset) |
1810 | { | |
1811 | 4 | scrollToPosition(sr, verticalOffset, true); |
1812 | } | |
1813 | ||
1814 | /** | |
1815 | * Set a flag to say do not scroll any (cDNA/protein) complement. | |
1816 | * | |
1817 | * @param b | |
1818 | */ | |
1819 | 1284 | protected void setToScrollComplementPanel(boolean b) |
1820 | { | |
1821 | 1284 | this.scrollComplementaryPanel = b; |
1822 | } | |
1823 | ||
1824 | /** | |
1825 | * Get whether to scroll complement panel | |
1826 | * | |
1827 | * @return true if cDNA/protein complement panels should be scrolled | |
1828 | */ | |
1829 | 644 | protected boolean isSetToScrollComplementPanel() |
1830 | { | |
1831 | 644 | return this.scrollComplementaryPanel; |
1832 | } | |
1833 | ||
1834 | /** | |
1835 | * Redraw sensibly. | |
1836 | * | |
1837 | * @adjustHeight if true, try to recalculate panel height for visible | |
1838 | * annotations | |
1839 | */ | |
1840 | 0 | protected void refresh(boolean adjustHeight) |
1841 | { | |
1842 | 0 | validateAnnotationDimensions(adjustHeight); |
1843 | 0 | addNotify(); |
1844 | 0 | if (adjustHeight) |
1845 | { | |
1846 | // sort, repaint, update overview | |
1847 | 0 | paintAlignment(true, false); |
1848 | } | |
1849 | else | |
1850 | { | |
1851 | // lightweight repaint | |
1852 | 0 | repaint(); |
1853 | } | |
1854 | } | |
1855 | ||
1856 | 644 | @Override |
1857 | /** | |
1858 | * Property change event fired when a change is made to the viewport ranges | |
1859 | * object associated with this alignment panel's viewport | |
1860 | */ | |
1861 | public void propertyChange(PropertyChangeEvent evt) | |
1862 | { | |
1863 | // update this panel's scroll values based on the new viewport ranges values | |
1864 | 644 | ViewportRanges ranges = av.getRanges(); |
1865 | 644 | int x = ranges.getStartRes(); |
1866 | 644 | int y = ranges.getStartSeq(); |
1867 | 644 | setScrollValues(x, y); |
1868 | ||
1869 | // now update any complementary alignment (its viewport ranges object | |
1870 | // is different so does not get automatically updated) | |
1871 | 644 | if (isSetToScrollComplementPanel()) |
1872 | { | |
1873 | 637 | setToScrollComplementPanel(false); |
1874 | 637 | av.scrollComplementaryAlignment(); |
1875 | 637 | setToScrollComplementPanel(true); |
1876 | } | |
1877 | } | |
1878 | ||
1879 | /** | |
1880 | * Set the reference to the PCA/Tree chooser dialog for this panel. This | |
1881 | * reference should be nulled when the dialog is closed. | |
1882 | * | |
1883 | * @param calculationChooser | |
1884 | */ | |
1885 | 0 | public void setCalculationDialog(CalculationChooser calculationChooser) |
1886 | { | |
1887 | 0 | calculationDialog = calculationChooser; |
1888 | } | |
1889 | ||
1890 | /** | |
1891 | * Returns the reference to the PCA/Tree chooser dialog for this panel (null | |
1892 | * if none is open) | |
1893 | */ | |
1894 | 649 | public CalculationChooser getCalculationDialog() |
1895 | { | |
1896 | 649 | return calculationDialog; |
1897 | } | |
1898 | ||
1899 | /** | |
1900 | * Constructs and sets the title for the Overview window (if there is one), | |
1901 | * including the align frame's title, and view name (if applicable). Returns | |
1902 | * the title, or null if this panel has no Overview window open. | |
1903 | * | |
1904 | * @param alignFrame | |
1905 | * @return | |
1906 | */ | |
1907 | 469 | public String setOverviewTitle(AlignFrame alignFrame) |
1908 | { | |
1909 | 469 | if (this.overviewPanel == null) |
1910 | { | |
1911 | 367 | return null; |
1912 | } | |
1913 | 102 | String overviewTitle = MessageManager |
1914 | .formatMessage("label.overview_params", new Object[] | |
1915 | { alignFrame.getTitle() }); | |
1916 | 102 | String viewName = getViewName(); |
1917 | 102 | if (viewName != null) |
1918 | { | |
1919 | 65 | overviewTitle += (" " + viewName); |
1920 | } | |
1921 | 102 | overviewPanel.setTitle(overviewTitle); |
1922 | 102 | return overviewTitle; |
1923 | } | |
1924 | ||
1925 | /** | |
1926 | * If this alignment panel has an Overview panel open, closes it | |
1927 | */ | |
1928 | 32 | public void closeOverviewPanel() |
1929 | { | |
1930 | 32 | if (overviewPanel != null) |
1931 | { | |
1932 | 12 | overviewPanel.close(); |
1933 | 12 | overviewPanel = null; |
1934 | } | |
1935 | } | |
1936 | } |