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TreeCanvas | 81 | 433 | 173 |
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.Color; | |
24 | import java.awt.Dimension; | |
25 | import java.awt.Font; | |
26 | import java.awt.FontMetrics; | |
27 | import java.awt.Graphics; | |
28 | import java.awt.Graphics2D; | |
29 | import java.awt.Point; | |
30 | import java.awt.Rectangle; | |
31 | import java.awt.RenderingHints; | |
32 | import java.awt.event.MouseEvent; | |
33 | import java.awt.event.MouseListener; | |
34 | import java.awt.event.MouseMotionListener; | |
35 | import java.awt.print.PageFormat; | |
36 | import java.awt.print.Printable; | |
37 | import java.awt.print.PrinterException; | |
38 | import java.awt.print.PrinterJob; | |
39 | import java.util.ArrayList; | |
40 | import java.util.BitSet; | |
41 | import java.util.HashMap; | |
42 | import java.util.Hashtable; | |
43 | import java.util.List; | |
44 | import java.util.Map; | |
45 | import java.util.Map.Entry; | |
46 | import java.util.Vector; | |
47 | ||
48 | import javax.swing.JPanel; | |
49 | import javax.swing.JScrollPane; | |
50 | import javax.swing.SwingUtilities; | |
51 | import javax.swing.ToolTipManager; | |
52 | ||
53 | import jalview.analysis.Conservation; | |
54 | import jalview.analysis.TreeModel; | |
55 | import jalview.api.AlignViewportI; | |
56 | import jalview.bin.Console; | |
57 | import jalview.datamodel.AlignmentAnnotation; | |
58 | import jalview.datamodel.Annotation; | |
59 | import jalview.datamodel.BinaryNode; | |
60 | import jalview.datamodel.ColumnSelection; | |
61 | import jalview.datamodel.ContactMatrixI; | |
62 | import jalview.datamodel.HiddenColumns; | |
63 | import jalview.datamodel.Sequence; | |
64 | import jalview.datamodel.SequenceGroup; | |
65 | import jalview.datamodel.SequenceI; | |
66 | import jalview.datamodel.SequenceNode; | |
67 | import jalview.gui.JalviewColourChooser.ColourChooserListener; | |
68 | import jalview.schemes.ColourSchemeI; | |
69 | import jalview.structure.SelectionSource; | |
70 | import jalview.util.ColorUtils; | |
71 | import jalview.util.Format; | |
72 | import jalview.util.MessageManager; | |
73 | import jalview.ws.datamodel.MappableContactMatrixI; | |
74 | ||
75 | /** | |
76 | * DOCUMENT ME! | |
77 | * | |
78 | * @author $author$ | |
79 | * @version $Revision$ | |
80 | */ | |
81 | public class TreeCanvas extends JPanel implements MouseListener, Runnable, | |
82 | Printable, MouseMotionListener, SelectionSource | |
83 | { | |
84 | /** DOCUMENT ME!! */ | |
85 | public static final String PLACEHOLDER = " * "; | |
86 | ||
87 | TreeModel tree; | |
88 | ||
89 | JScrollPane scrollPane; | |
90 | ||
91 | TreePanel tp; | |
92 | ||
93 | private AlignViewport av; | |
94 | ||
95 | private AlignmentPanel ap; | |
96 | ||
97 | Font font; | |
98 | ||
99 | FontMetrics fm; | |
100 | ||
101 | boolean fitToWindow = true; | |
102 | ||
103 | boolean showDistances = false; | |
104 | ||
105 | boolean showBootstrap = false; | |
106 | ||
107 | boolean markPlaceholders = false; | |
108 | ||
109 | int offx = 20; | |
110 | ||
111 | int offy; | |
112 | ||
113 | private float threshold; | |
114 | ||
115 | String longestName; | |
116 | ||
117 | int labelLength = -1; | |
118 | ||
119 | Map<Object, Rectangle> nameHash = new Hashtable<>(); | |
120 | ||
121 | Map<BinaryNode, Rectangle> nodeHash = new Hashtable<>(); | |
122 | ||
123 | BinaryNode highlightNode; | |
124 | ||
125 | boolean applyToAllViews = false; | |
126 | ||
127 | /** | |
128 | * Creates a new TreeCanvas object. | |
129 | * | |
130 | * @param av | |
131 | * DOCUMENT ME! | |
132 | * @param tree | |
133 | * DOCUMENT ME! | |
134 | * @param scroller | |
135 | * DOCUMENT ME! | |
136 | * @param label | |
137 | * DOCUMENT ME! | |
138 | */ | |
139 | 14 | public TreeCanvas(TreePanel tp, AlignmentPanel ap, JScrollPane scroller) |
140 | { | |
141 | 14 | this.tp = tp; |
142 | 14 | this.av = ap.av; |
143 | 14 | this.setAssociatedPanel(ap); |
144 | 14 | font = av.getFont(); |
145 | 14 | scrollPane = scroller; |
146 | 14 | addMouseListener(this); |
147 | 14 | addMouseMotionListener(this); |
148 | ||
149 | 14 | ToolTipManager.sharedInstance().registerComponent(this); |
150 | } | |
151 | ||
152 | 0 | public void clearSelectedLeaves() |
153 | { | |
154 | 0 | Vector<BinaryNode> leaves = tp.getTree() |
155 | .findLeaves(tp.getTree().getTopNode()); | |
156 | 0 | if (tp.isColumnWise()) |
157 | { | |
158 | 0 | markColumnsFor(getAssociatedPanels(), leaves, Color.white, true); |
159 | } | |
160 | else | |
161 | { | |
162 | 0 | for (AlignmentPanel ap : getAssociatedPanels()) |
163 | { | |
164 | 0 | SequenceGroup selected = ap.av.getSelectionGroup(); |
165 | 0 | if (selected != null) |
166 | { | |
167 | { | |
168 | 0 | for (int i = 0; i < leaves.size(); i++) |
169 | { | |
170 | 0 | SequenceI seq = (SequenceI) leaves.elementAt(i).element(); |
171 | 0 | if (selected.contains(seq)) |
172 | { | |
173 | 0 | selected.addOrRemove(seq, false); |
174 | } | |
175 | } | |
176 | 0 | selected.recalcConservation(); |
177 | } | |
178 | } | |
179 | 0 | ap.av.sendSelection(); |
180 | } | |
181 | } | |
182 | 0 | PaintRefresher.Refresh(tp, av.getSequenceSetId()); |
183 | 0 | repaint(); |
184 | } | |
185 | ||
186 | /** | |
187 | * DOCUMENT ME! | |
188 | * | |
189 | * @param sequence | |
190 | * DOCUMENT ME! | |
191 | */ | |
192 | 0 | public void treeSelectionChanged(SequenceI sequence) |
193 | { | |
194 | 0 | AlignmentPanel[] aps = getAssociatedPanels(); |
195 | ||
196 | 0 | for (int a = 0; a < aps.length; a++) |
197 | { | |
198 | 0 | SequenceGroup selected = aps[a].av.getSelectionGroup(); |
199 | ||
200 | 0 | if (selected == null) |
201 | { | |
202 | 0 | selected = new SequenceGroup(); |
203 | 0 | aps[a].av.setSelectionGroup(selected); |
204 | } | |
205 | ||
206 | 0 | selected.setEndRes(aps[a].av.getAlignment().getWidth() - 1); |
207 | 0 | selected.addOrRemove(sequence, true); |
208 | } | |
209 | } | |
210 | ||
211 | /** | |
212 | * DOCUMENT ME! | |
213 | * | |
214 | * @param tree | |
215 | * DOCUMENT ME! | |
216 | */ | |
217 | 14 | public void setTree(TreeModel tree) |
218 | { | |
219 | 14 | this.tree = tree; |
220 | 14 | tree.findHeight(tree.getTopNode()); |
221 | ||
222 | // Now have to calculate longest name based on the leaves | |
223 | 14 | Vector<BinaryNode> leaves = tree.findLeaves(tree.getTopNode()); |
224 | 14 | boolean has_placeholders = false; |
225 | 14 | longestName = ""; |
226 | ||
227 | 14 | AlignmentAnnotation aa = tp.getAssocAnnotation(); |
228 | 14 | ContactMatrixI cm = (aa != null) ? av.getContactMatrix(aa) : null; |
229 | 14 | if (cm != null && cm.hasCutHeight()) |
230 | { | |
231 | 0 | threshold = (float) cm.getCutHeight(); |
232 | } | |
233 | ||
234 | 184 | for (int i = 0; i < leaves.size(); i++) |
235 | { | |
236 | 170 | BinaryNode lf = leaves.elementAt(i); |
237 | ||
238 | 170 | if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder()) |
239 | { | |
240 | 0 | has_placeholders = true; |
241 | } | |
242 | ||
243 | 170 | if (longestName.length() < ((Sequence) lf.element()).getName() |
244 | .length()) | |
245 | { | |
246 | 22 | longestName = TreeCanvas.PLACEHOLDER |
247 | + ((Sequence) lf.element()).getName(); | |
248 | } | |
249 | 170 | if (tp.isColumnWise() && cm != null) |
250 | { | |
251 | // get color from group colours, if they are set for the matrix | |
252 | 0 | try |
253 | { | |
254 | 0 | Color col = cm.getGroupColorForPosition(parseColumnNode(lf)); |
255 | 0 | setColor(lf, col.brighter()); |
256 | } catch (NumberFormatException ex) | |
257 | { | |
258 | } | |
259 | 0 | ; |
260 | } | |
261 | } | |
262 | ||
263 | 14 | setMarkPlaceholders(has_placeholders); |
264 | } | |
265 | ||
266 | /** | |
267 | * DOCUMENT ME! | |
268 | * | |
269 | * @param g | |
270 | * DOCUMENT ME! | |
271 | * @param node | |
272 | * DOCUMENT ME! | |
273 | * @param chunk | |
274 | * DOCUMENT ME! | |
275 | * @param wscale | |
276 | * DOCUMENT ME! | |
277 | * @param width | |
278 | * DOCUMENT ME! | |
279 | * @param offx | |
280 | * DOCUMENT ME! | |
281 | * @param offy | |
282 | * DOCUMENT ME! | |
283 | */ | |
284 | 0 | public void drawNode(Graphics g, BinaryNode node, double chunk, |
285 | double wscale, int width, int offx, int offy) | |
286 | { | |
287 | 0 | if (node == null) |
288 | { | |
289 | 0 | return; |
290 | } | |
291 | ||
292 | 0 | if ((node.left() == null) && (node.right() == null)) |
293 | { | |
294 | // Drawing leaf node | |
295 | 0 | double height = node.height; |
296 | 0 | double dist = node.dist; |
297 | ||
298 | 0 | int xstart = (int) ((height - dist) * wscale) + offx; |
299 | 0 | int xend = (int) (height * wscale) + offx; |
300 | ||
301 | 0 | int ypos = (int) (node.ycount * chunk) + offy; |
302 | ||
303 | 0 | if (node.element() instanceof SequenceI) |
304 | { | |
305 | 0 | SequenceI seq = (SequenceI) node.element(); |
306 | ||
307 | 0 | if (av.getSequenceColour(seq) == Color.white) |
308 | { | |
309 | 0 | g.setColor(Color.black); |
310 | } | |
311 | else | |
312 | { | |
313 | 0 | g.setColor(av.getSequenceColour(seq).darker()); |
314 | } | |
315 | } | |
316 | else | |
317 | { | |
318 | 0 | g.setColor(Color.black); |
319 | } | |
320 | ||
321 | // Draw horizontal line | |
322 | 0 | g.drawLine(xstart, ypos, xend, ypos); |
323 | ||
324 | 0 | String nodeLabel = ""; |
325 | ||
326 | 0 | if (showDistances && (node.dist > 0)) |
327 | { | |
328 | 0 | nodeLabel = new Format("%g").form(node.dist); |
329 | } | |
330 | ||
331 | 0 | if (showBootstrap && node.bootstrap > -1) |
332 | { | |
333 | 0 | if (showDistances) |
334 | { | |
335 | 0 | nodeLabel = nodeLabel + " : "; |
336 | } | |
337 | ||
338 | 0 | nodeLabel = nodeLabel + String.valueOf(node.bootstrap); |
339 | } | |
340 | ||
341 | 0 | if (!nodeLabel.equals("")) |
342 | { | |
343 | 0 | g.drawString(nodeLabel, xstart + 2, ypos - 2); |
344 | } | |
345 | ||
346 | 0 | String name = (markPlaceholders && ((node instanceof SequenceNode |
347 | && ((SequenceNode) node).isPlaceholder()))) | |
348 | ? (PLACEHOLDER + node.getName()) | |
349 | : node.getName(); | |
350 | ||
351 | 0 | int charWidth = fm.stringWidth(name) + 3; |
352 | 0 | int charHeight = font.getSize(); |
353 | ||
354 | 0 | Rectangle rect = new Rectangle(xend + 10, ypos - charHeight / 2, |
355 | charWidth, charHeight); | |
356 | ||
357 | 0 | nameHash.put(node.element(), rect); |
358 | ||
359 | // Colour selected leaves differently | |
360 | 0 | boolean isSelected = false; |
361 | 0 | if (tp.isColumnWise()) |
362 | { | |
363 | 0 | isSelected = isColumnForNodeSelected(node); |
364 | } | |
365 | else | |
366 | { | |
367 | 0 | SequenceGroup selected = av.getSelectionGroup(); |
368 | ||
369 | 0 | if ((selected != null) |
370 | && selected.getSequences(null).contains(node.element())) | |
371 | { | |
372 | 0 | isSelected = true; |
373 | } | |
374 | } | |
375 | 0 | if (isSelected) |
376 | { | |
377 | 0 | g.setColor(Color.gray); |
378 | ||
379 | 0 | g.fillRect(xend + 10, ypos - charHeight / 2, charWidth, charHeight); |
380 | 0 | g.setColor(Color.white); |
381 | } | |
382 | ||
383 | 0 | g.drawString(name, xend + 10, ypos + fm.getDescent()); |
384 | 0 | g.setColor(Color.black); |
385 | } | |
386 | else | |
387 | { | |
388 | 0 | drawNode(g, (BinaryNode) node.left(), chunk, wscale, width, offx, |
389 | offy); | |
390 | 0 | drawNode(g, (BinaryNode) node.right(), chunk, wscale, width, offx, |
391 | offy); | |
392 | ||
393 | 0 | double height = node.height; |
394 | 0 | double dist = node.dist; |
395 | ||
396 | 0 | int xstart = (int) ((height - dist) * wscale) + offx; |
397 | 0 | int xend = (int) (height * wscale) + offx; |
398 | 0 | int ypos = (int) (node.ycount * chunk) + offy; |
399 | ||
400 | 0 | g.setColor(node.color.darker()); |
401 | ||
402 | // Draw horizontal line | |
403 | 0 | g.drawLine(xstart, ypos, xend, ypos); |
404 | 0 | if (node == highlightNode) |
405 | { | |
406 | 0 | g.fillRect(xend - 3, ypos - 3, 6, 6); |
407 | } | |
408 | else | |
409 | { | |
410 | 0 | g.fillRect(xend - 2, ypos - 2, 4, 4); |
411 | } | |
412 | ||
413 | 0 | int ystart = (node.left() == null ? 0 |
414 | : (int) (node.left().ycount * chunk)) + offy; | |
415 | 0 | int yend = (node.right() == null ? 0 |
416 | : (int) (node.right().ycount * chunk)) + offy; | |
417 | ||
418 | 0 | Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5); |
419 | 0 | nodeHash.put(node, pos); |
420 | ||
421 | 0 | g.drawLine((int) (height * wscale) + offx, ystart, |
422 | (int) (height * wscale) + offx, yend); | |
423 | ||
424 | 0 | String nodeLabel = ""; |
425 | ||
426 | 0 | if (showDistances && (node.dist > 0)) |
427 | { | |
428 | 0 | nodeLabel = new Format("%g").form(node.dist); |
429 | } | |
430 | ||
431 | 0 | if (showBootstrap && node.bootstrap > -1) |
432 | { | |
433 | 0 | if (showDistances) |
434 | { | |
435 | 0 | nodeLabel = nodeLabel + " : "; |
436 | } | |
437 | ||
438 | 0 | nodeLabel = nodeLabel + String.valueOf(node.bootstrap); |
439 | } | |
440 | ||
441 | 0 | if (!nodeLabel.equals("")) |
442 | { | |
443 | 0 | g.drawString(nodeLabel, xstart + 2, ypos - 2); |
444 | } | |
445 | } | |
446 | } | |
447 | ||
448 | /** | |
449 | * DOCUMENT ME! | |
450 | * | |
451 | * @param x | |
452 | * DOCUMENT ME! | |
453 | * @param y | |
454 | * DOCUMENT ME! | |
455 | * | |
456 | * @return DOCUMENT ME! | |
457 | */ | |
458 | 0 | public Object findElement(int x, int y) |
459 | { | |
460 | 0 | for (Entry<Object, Rectangle> entry : nameHash.entrySet()) |
461 | { | |
462 | 0 | Rectangle rect = entry.getValue(); |
463 | ||
464 | 0 | if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) |
465 | && (y <= (rect.y + rect.height))) | |
466 | { | |
467 | 0 | return entry.getKey(); |
468 | } | |
469 | } | |
470 | ||
471 | 0 | for (Entry<BinaryNode, Rectangle> entry : nodeHash.entrySet()) |
472 | { | |
473 | 0 | Rectangle rect = entry.getValue(); |
474 | ||
475 | 0 | if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) |
476 | && (y <= (rect.y + rect.height))) | |
477 | { | |
478 | 0 | return entry.getKey(); |
479 | } | |
480 | } | |
481 | ||
482 | 0 | return null; |
483 | } | |
484 | ||
485 | /** | |
486 | * DOCUMENT ME! | |
487 | * | |
488 | * @param pickBox | |
489 | * DOCUMENT ME! | |
490 | */ | |
491 | 0 | public void pickNodes(Rectangle pickBox) |
492 | { | |
493 | 0 | int width = getWidth(); |
494 | 0 | int height = getHeight(); |
495 | ||
496 | 0 | BinaryNode top = tree.getTopNode(); |
497 | ||
498 | 0 | double wscale = ((width * .8) - (offx * 2)) / tree.getMaxHeight(); |
499 | ||
500 | 0 | if (top.count == 0) |
501 | { | |
502 | 0 | top.count = ((BinaryNode) top.left()).count |
503 | + ((BinaryNode) top.right()).count; | |
504 | } | |
505 | ||
506 | 0 | float chunk = (float) (height - (offy)) / top.count; |
507 | ||
508 | 0 | pickNode(pickBox, top, chunk, wscale, width, offx, offy); |
509 | } | |
510 | ||
511 | /** | |
512 | * DOCUMENT ME! | |
513 | * | |
514 | * @param pickBox | |
515 | * DOCUMENT ME! | |
516 | * @param node | |
517 | * DOCUMENT ME! | |
518 | * @param chunk | |
519 | * DOCUMENT ME! | |
520 | * @param wscale | |
521 | * DOCUMENT ME! | |
522 | * @param width | |
523 | * DOCUMENT ME! | |
524 | * @param offx | |
525 | * DOCUMENT ME! | |
526 | * @param offy | |
527 | * DOCUMENT ME! | |
528 | */ | |
529 | 0 | public void pickNode(Rectangle pickBox, BinaryNode node, float chunk, |
530 | double wscale, int width, int offx, int offy) | |
531 | { | |
532 | 0 | if (node == null) |
533 | { | |
534 | 0 | return; |
535 | } | |
536 | ||
537 | 0 | if ((node.left() == null) && (node.right() == null)) |
538 | { | |
539 | 0 | double height = node.height; |
540 | // double dist = node.dist; | |
541 | // int xstart = (int) ((height - dist) * wscale) + offx; | |
542 | 0 | int xend = (int) (height * wscale) + offx; |
543 | ||
544 | 0 | int ypos = (int) (node.ycount * chunk) + offy; |
545 | ||
546 | 0 | if (pickBox.contains(new Point(xend, ypos))) |
547 | { | |
548 | 0 | if (node.element() instanceof SequenceI) |
549 | { | |
550 | 0 | SequenceI seq = (SequenceI) node.element(); |
551 | 0 | SequenceGroup sg = av.getSelectionGroup(); |
552 | ||
553 | 0 | if (sg != null) |
554 | { | |
555 | 0 | sg.addOrRemove(seq, true); |
556 | } | |
557 | } | |
558 | } | |
559 | } | |
560 | else | |
561 | { | |
562 | 0 | pickNode(pickBox, (BinaryNode) node.left(), chunk, wscale, width, |
563 | offx, offy); | |
564 | 0 | pickNode(pickBox, (BinaryNode) node.right(), chunk, wscale, width, |
565 | offx, offy); | |
566 | } | |
567 | } | |
568 | ||
569 | /** | |
570 | * DOCUMENT ME! | |
571 | * | |
572 | * @param node | |
573 | * DOCUMENT ME! | |
574 | * @param c | |
575 | * DOCUMENT ME! | |
576 | */ | |
577 | 0 | public void setColor(BinaryNode node, Color c) |
578 | { | |
579 | 0 | if (node == null) |
580 | { | |
581 | 0 | return; |
582 | } | |
583 | ||
584 | 0 | node.color = c; |
585 | 0 | if (node.element() instanceof SequenceI) |
586 | { | |
587 | 0 | final SequenceI seq = (SequenceI) node.element(); |
588 | 0 | AlignmentPanel[] aps = getAssociatedPanels(); |
589 | 0 | if (aps != null) |
590 | { | |
591 | 0 | for (int a = 0; a < aps.length; a++) |
592 | { | |
593 | 0 | aps[a].av.setSequenceColour(seq, c); |
594 | } | |
595 | } | |
596 | } | |
597 | 0 | setColor((BinaryNode) node.left(), c); |
598 | 0 | setColor((BinaryNode) node.right(), c); |
599 | } | |
600 | ||
601 | /** | |
602 | * DOCUMENT ME! | |
603 | */ | |
604 | 0 | void startPrinting() |
605 | { | |
606 | 0 | Thread thread = new Thread(this); |
607 | 0 | thread.start(); |
608 | } | |
609 | ||
610 | // put printing in a thread to avoid painting problems | |
611 | 0 | @Override |
612 | public void run() | |
613 | { | |
614 | 0 | PrinterJob printJob = PrinterJob.getPrinterJob(); |
615 | 0 | PageFormat defaultPage = printJob.defaultPage(); |
616 | 0 | PageFormat pf = printJob.pageDialog(defaultPage); |
617 | ||
618 | 0 | if (defaultPage == pf) |
619 | { | |
620 | /* | |
621 | * user cancelled | |
622 | */ | |
623 | 0 | return; |
624 | } | |
625 | ||
626 | 0 | printJob.setPrintable(this, pf); |
627 | ||
628 | 0 | if (printJob.printDialog()) |
629 | { | |
630 | 0 | try |
631 | { | |
632 | 0 | printJob.print(); |
633 | } catch (Exception PrintException) | |
634 | { | |
635 | 0 | PrintException.printStackTrace(); |
636 | } | |
637 | } | |
638 | } | |
639 | ||
640 | /** | |
641 | * DOCUMENT ME! | |
642 | * | |
643 | * @param pg | |
644 | * DOCUMENT ME! | |
645 | * @param pf | |
646 | * DOCUMENT ME! | |
647 | * @param pi | |
648 | * DOCUMENT ME! | |
649 | * | |
650 | * @return DOCUMENT ME! | |
651 | * | |
652 | * @throws PrinterException | |
653 | * DOCUMENT ME! | |
654 | */ | |
655 | 0 | @Override |
656 | public int print(Graphics pg, PageFormat pf, int pi) | |
657 | throws PrinterException | |
658 | { | |
659 | 0 | pg.setFont(font); |
660 | 0 | pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); |
661 | ||
662 | 0 | int pwidth = (int) pf.getImageableWidth(); |
663 | 0 | int pheight = (int) pf.getImageableHeight(); |
664 | ||
665 | 0 | int noPages = getHeight() / pheight; |
666 | ||
667 | 0 | if (pi > noPages) |
668 | { | |
669 | 0 | return Printable.NO_SUCH_PAGE; |
670 | } | |
671 | ||
672 | 0 | if (pwidth > getWidth()) |
673 | { | |
674 | 0 | pwidth = getWidth(); |
675 | } | |
676 | ||
677 | 0 | if (fitToWindow) |
678 | { | |
679 | 0 | if (pheight > getHeight()) |
680 | { | |
681 | 0 | pheight = getHeight(); |
682 | } | |
683 | ||
684 | 0 | noPages = 0; |
685 | } | |
686 | else | |
687 | { | |
688 | 0 | FontMetrics fm = pg.getFontMetrics(font); |
689 | 0 | int height = fm.getHeight() * nameHash.size(); |
690 | 0 | pg.translate(0, -pi * pheight); |
691 | 0 | pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight); |
692 | ||
693 | // translate number of pages, | |
694 | // height is screen size as this is the | |
695 | // non overlapping text size | |
696 | 0 | pheight = height; |
697 | } | |
698 | ||
699 | 0 | draw(pg, pwidth, pheight); |
700 | ||
701 | 0 | return Printable.PAGE_EXISTS; |
702 | } | |
703 | ||
704 | /** | |
705 | * DOCUMENT ME! | |
706 | * | |
707 | * @param g | |
708 | * DOCUMENT ME! | |
709 | */ | |
710 | 0 | @Override |
711 | public void paintComponent(Graphics g) | |
712 | { | |
713 | 0 | super.paintComponent(g); |
714 | 0 | g.setFont(font); |
715 | ||
716 | 0 | if (tree == null) |
717 | { | |
718 | 0 | g.drawString( |
719 | MessageManager.getString("label.calculating_tree") + "....", | |
720 | 20, getHeight() / 2); | |
721 | } | |
722 | else | |
723 | { | |
724 | 0 | fm = g.getFontMetrics(font); |
725 | ||
726 | 0 | int nameCount = nameHash.size(); |
727 | 0 | if (nameCount == 0) |
728 | { | |
729 | 0 | repaint(); |
730 | } | |
731 | ||
732 | 0 | if (fitToWindow || (!fitToWindow && (scrollPane |
733 | .getHeight() > ((fm.getHeight() * nameCount) + offy)))) | |
734 | { | |
735 | 0 | draw(g, scrollPane.getWidth(), scrollPane.getHeight()); |
736 | 0 | setPreferredSize(null); |
737 | } | |
738 | else | |
739 | { | |
740 | 0 | setPreferredSize(new Dimension(scrollPane.getWidth(), |
741 | fm.getHeight() * nameCount)); | |
742 | 0 | draw(g, scrollPane.getWidth(), fm.getHeight() * nameCount); |
743 | } | |
744 | ||
745 | 0 | scrollPane.revalidate(); |
746 | } | |
747 | } | |
748 | ||
749 | /** | |
750 | * DOCUMENT ME! | |
751 | * | |
752 | * @param fontSize | |
753 | * DOCUMENT ME! | |
754 | */ | |
755 | 26 | @Override |
756 | public void setFont(Font font) | |
757 | { | |
758 | 26 | this.font = font; |
759 | 26 | repaint(); |
760 | } | |
761 | ||
762 | /** | |
763 | * DOCUMENT ME! | |
764 | * | |
765 | * @param g1 | |
766 | * DOCUMENT ME! | |
767 | * @param width | |
768 | * DOCUMENT ME! | |
769 | * @param height | |
770 | * DOCUMENT ME! | |
771 | */ | |
772 | 0 | public void draw(Graphics g1, int width, int height) |
773 | { | |
774 | 0 | Graphics2D g2 = (Graphics2D) g1; |
775 | 0 | g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, |
776 | RenderingHints.VALUE_ANTIALIAS_ON); | |
777 | 0 | g2.setColor(Color.white); |
778 | 0 | g2.fillRect(0, 0, width, height); |
779 | 0 | g2.setFont(font); |
780 | ||
781 | 0 | if (longestName == null || tree == null) |
782 | { | |
783 | 0 | g2.drawString("Calculating tree.", 20, 20); |
784 | 0 | return; |
785 | } | |
786 | 0 | offy = font.getSize() + 10; |
787 | ||
788 | 0 | fm = g2.getFontMetrics(font); |
789 | ||
790 | 0 | labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar |
791 | ||
792 | 0 | double wscale = (width - labelLength - (offx * 2)) |
793 | / tree.getMaxHeight(); | |
794 | ||
795 | 0 | BinaryNode top = tree.getTopNode(); |
796 | ||
797 | 0 | if (top.count == 0) |
798 | { | |
799 | 0 | top.count = top.left().count + top.right().count; |
800 | } | |
801 | ||
802 | 0 | float chunk = (float) (height - (offy)) / top.count; |
803 | ||
804 | 0 | drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy); |
805 | ||
806 | 0 | if (threshold != 0) |
807 | { | |
808 | 0 | if (av.getCurrentTree() == tree) |
809 | { | |
810 | 0 | g2.setColor(Color.red); |
811 | } | |
812 | else | |
813 | { | |
814 | 0 | g2.setColor(Color.gray); |
815 | } | |
816 | ||
817 | 0 | int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) |
818 | + offx); | |
819 | ||
820 | 0 | g2.drawLine(x, 0, x, getHeight()); |
821 | } | |
822 | } | |
823 | ||
824 | /** | |
825 | * Empty method to satisfy the MouseListener interface | |
826 | * | |
827 | * @param e | |
828 | */ | |
829 | 0 | @Override |
830 | public void mouseReleased(MouseEvent e) | |
831 | { | |
832 | /* | |
833 | * isPopupTrigger is set on mouseReleased on Windows | |
834 | */ | |
835 | 0 | if (e.isPopupTrigger()) |
836 | { | |
837 | 0 | chooseSubtreeColour(); |
838 | 0 | e.consume(); // prevent mouseClicked happening |
839 | } | |
840 | } | |
841 | ||
842 | /** | |
843 | * Empty method to satisfy the MouseListener interface | |
844 | * | |
845 | * @param e | |
846 | */ | |
847 | 0 | @Override |
848 | public void mouseEntered(MouseEvent e) | |
849 | { | |
850 | } | |
851 | ||
852 | /** | |
853 | * Empty method to satisfy the MouseListener interface | |
854 | * | |
855 | * @param e | |
856 | */ | |
857 | 0 | @Override |
858 | public void mouseExited(MouseEvent e) | |
859 | { | |
860 | } | |
861 | ||
862 | /** | |
863 | * Handles a mouse click on a tree node (clicks elsewhere are handled in | |
864 | * mousePressed). Click selects the sub-tree, double-click swaps leaf nodes | |
865 | * order, right-click opens a dialogue to choose colour for the sub-tree. | |
866 | * | |
867 | * @param e | |
868 | */ | |
869 | 0 | @Override |
870 | public void mouseClicked(MouseEvent evt) | |
871 | { | |
872 | 0 | if (highlightNode == null) |
873 | { | |
874 | 0 | return; |
875 | } | |
876 | ||
877 | 0 | if (evt.getClickCount() > 1) |
878 | { | |
879 | 0 | tree.swapNodes(highlightNode); |
880 | 0 | tree.reCount(tree.getTopNode()); |
881 | 0 | tree.findHeight(tree.getTopNode()); |
882 | } | |
883 | else | |
884 | { | |
885 | 0 | Vector<BinaryNode> leaves = tree.findLeaves(highlightNode); |
886 | 0 | if (tp.isColumnWise()) |
887 | { | |
888 | 0 | markColumnsFor(getAssociatedPanels(), leaves, Color.red, false); |
889 | } | |
890 | else | |
891 | { | |
892 | 0 | for (int i = 0; i < leaves.size(); i++) |
893 | { | |
894 | 0 | SequenceI seq = (SequenceI) leaves.elementAt(i).element(); |
895 | 0 | treeSelectionChanged(seq); |
896 | } | |
897 | } | |
898 | 0 | av.sendSelection(); |
899 | } | |
900 | ||
901 | 0 | PaintRefresher.Refresh(tp, av.getSequenceSetId()); |
902 | 0 | repaint(); |
903 | } | |
904 | ||
905 | /** | |
906 | * Offer the user the option to choose a colour for the highlighted node and | |
907 | * its children; this colour is also applied to the corresponding sequence ids | |
908 | * in the alignment | |
909 | */ | |
910 | 0 | void chooseSubtreeColour() |
911 | { | |
912 | 0 | String ttl = MessageManager.getString("label.select_subtree_colour"); |
913 | 0 | ColourChooserListener listener = new ColourChooserListener() |
914 | { | |
915 | 0 | @Override |
916 | public void colourSelected(Color c) | |
917 | { | |
918 | 0 | setColor(highlightNode, c); |
919 | 0 | PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); |
920 | 0 | repaint(); |
921 | } | |
922 | }; | |
923 | 0 | JalviewColourChooser.showColourChooser(this, ttl, highlightNode.color, |
924 | listener); | |
925 | } | |
926 | ||
927 | 0 | @Override |
928 | public void mouseMoved(MouseEvent evt) | |
929 | { | |
930 | 0 | av.setCurrentTree(tree); |
931 | ||
932 | 0 | Object ob = findElement(evt.getX(), evt.getY()); |
933 | ||
934 | 0 | if (ob instanceof BinaryNode) |
935 | { | |
936 | 0 | highlightNode = (BinaryNode) ob; |
937 | 0 | this.setToolTipText( |
938 | "<html>" + MessageManager.getString("label.highlightnode")); | |
939 | 0 | repaint(); |
940 | ||
941 | } | |
942 | else | |
943 | { | |
944 | 0 | if (highlightNode != null) |
945 | { | |
946 | 0 | highlightNode = null; |
947 | 0 | setToolTipText(null); |
948 | 0 | repaint(); |
949 | } | |
950 | } | |
951 | } | |
952 | ||
953 | 0 | @Override |
954 | public void mouseDragged(MouseEvent ect) | |
955 | { | |
956 | } | |
957 | ||
958 | /** | |
959 | * Handles a mouse press on a sequence name or the tree background canvas | |
960 | * (click on a node is handled in mouseClicked). The action is to create | |
961 | * groups by partitioning the tree at the mouse position. Colours for the | |
962 | * groups (and sequence names) are generated randomly. | |
963 | * | |
964 | * @param e | |
965 | */ | |
966 | 0 | @Override |
967 | public void mousePressed(MouseEvent e) | |
968 | { | |
969 | 0 | av.setCurrentTree(tree); |
970 | ||
971 | /* | |
972 | * isPopupTrigger is set for mousePressed (Mac) | |
973 | * or mouseReleased (Windows) | |
974 | */ | |
975 | 0 | if (e.isPopupTrigger()) |
976 | { | |
977 | 0 | if (highlightNode != null) |
978 | { | |
979 | 0 | chooseSubtreeColour(); |
980 | } | |
981 | 0 | return; |
982 | } | |
983 | ||
984 | /* | |
985 | * defer right-click handling on Windows to | |
986 | * mouseClicked; note isRightMouseButton | |
987 | * also matches Cmd-click on Mac which should do | |
988 | * nothing here | |
989 | */ | |
990 | 0 | if (SwingUtilities.isRightMouseButton(e)) |
991 | { | |
992 | 0 | return; |
993 | } | |
994 | ||
995 | 0 | int x = e.getX(); |
996 | 0 | int y = e.getY(); |
997 | ||
998 | 0 | Object ob = findElement(x, y); |
999 | ||
1000 | 0 | if (ob instanceof SequenceI) |
1001 | { | |
1002 | 0 | treeSelectionChanged((Sequence) ob); |
1003 | 0 | PaintRefresher.Refresh(tp, |
1004 | getAssociatedPanel().av.getSequenceSetId()); | |
1005 | 0 | repaint(); |
1006 | 0 | av.sendSelection(); |
1007 | 0 | return; |
1008 | } | |
1009 | 0 | else if (!(ob instanceof BinaryNode)) |
1010 | { | |
1011 | // Find threshold | |
1012 | 0 | if (tree.getMaxHeight() != 0) |
1013 | { | |
1014 | 0 | threshold = (float) (x - offx) |
1015 | / (float) (getWidth() - labelLength - (2 * offx)); | |
1016 | ||
1017 | 0 | List<BinaryNode> groups = tree.groupNodes(threshold); |
1018 | 0 | setColor(tree.getTopNode(), Color.black); |
1019 | ||
1020 | 0 | AlignmentPanel[] aps = getAssociatedPanels(); |
1021 | ||
1022 | // TODO push calls below into a single AlignViewportI method? | |
1023 | // see also AlignViewController.deleteGroups | |
1024 | 0 | for (int a = 0; a < aps.length; a++) |
1025 | { | |
1026 | 0 | aps[a].av.setSelectionGroup(null); |
1027 | 0 | aps[a].av.getAlignment().deleteAllGroups(); |
1028 | 0 | aps[a].av.clearSequenceColours(); |
1029 | 0 | if (aps[a].av.getCodingComplement() != null) |
1030 | { | |
1031 | 0 | aps[a].av.getCodingComplement().setSelectionGroup(null); |
1032 | 0 | aps[a].av.getCodingComplement().getAlignment() |
1033 | .deleteAllGroups(); | |
1034 | 0 | aps[a].av.getCodingComplement().clearSequenceColours(); |
1035 | } | |
1036 | 0 | aps[a].av.setUpdateStructures(true); |
1037 | } | |
1038 | 0 | colourGroups(groups); |
1039 | ||
1040 | /* | |
1041 | * clear partition (don't show vertical line) if | |
1042 | * it is to the right of all nodes | |
1043 | */ | |
1044 | 0 | if (groups.isEmpty()) |
1045 | { | |
1046 | 0 | threshold = 0f; |
1047 | } | |
1048 | } | |
1049 | 0 | Console.log.debug("Tree cut threshold set at:" + threshold); |
1050 | 0 | PaintRefresher.Refresh(tp, |
1051 | getAssociatedPanel().av.getSequenceSetId()); | |
1052 | 0 | repaint(); |
1053 | } | |
1054 | ||
1055 | } | |
1056 | ||
1057 | 0 | void colourGroups(List<BinaryNode> groups) |
1058 | { | |
1059 | 0 | AlignmentPanel[] aps = getAssociatedPanels(); |
1060 | 0 | List<BitSet> colGroups = new ArrayList<>(); |
1061 | 0 | Map<BitSet, Color> colors = new HashMap(); |
1062 | 0 | for (int i = 0; i < groups.size(); i++) |
1063 | { | |
1064 | 0 | Color col = ColorUtils.getARandomColor(); |
1065 | ||
1066 | 0 | setColor(groups.get(i), col.brighter()); |
1067 | ||
1068 | 0 | Vector<BinaryNode> l = tree.findLeaves(groups.get(i)); |
1069 | 0 | if (!tp.isColumnWise()) |
1070 | { | |
1071 | 0 | createSeqGroupFor(aps, l, col); |
1072 | } | |
1073 | else | |
1074 | { | |
1075 | 0 | BitSet gp = createColumnGroupFor(l, col); |
1076 | ||
1077 | 0 | colGroups.add(gp); |
1078 | 0 | colors.put(gp, col); |
1079 | } | |
1080 | } | |
1081 | 0 | if (tp.isColumnWise()) |
1082 | { | |
1083 | 0 | AlignmentAnnotation aa = tp.getAssocAnnotation(); |
1084 | 0 | if (aa != null) |
1085 | { | |
1086 | 0 | ContactMatrixI cm = av.getContactMatrix(aa); |
1087 | 0 | if (cm != null) |
1088 | { | |
1089 | 0 | cm.updateGroups(colGroups); |
1090 | 0 | for (BitSet gp : colors.keySet()) |
1091 | { | |
1092 | 0 | cm.setColorForGroup(gp, colors.get(gp)); |
1093 | } | |
1094 | } | |
1095 | 0 | cm.transferGroupColorsTo(aa); |
1096 | } | |
1097 | } | |
1098 | ||
1099 | // notify the panel(s) to redo any group specific stuff | |
1100 | // also updates structure views if necessary | |
1101 | 0 | for (int a = 0; a < aps.length; a++) |
1102 | { | |
1103 | 0 | aps[a].updateAnnotation(); |
1104 | 0 | final AlignViewportI codingComplement = aps[a].av |
1105 | .getCodingComplement(); | |
1106 | 0 | if (codingComplement != null) |
1107 | { | |
1108 | 0 | ((AlignViewport) codingComplement).getAlignPanel() |
1109 | .updateAnnotation(); | |
1110 | } | |
1111 | } | |
1112 | } | |
1113 | ||
1114 | 0 | private int parseColumnNode(BinaryNode bn) throws NumberFormatException |
1115 | { | |
1116 | 0 | return Integer.parseInt( |
1117 | bn.getName().substring(bn.getName().indexOf("c") + 1)); | |
1118 | } | |
1119 | ||
1120 | 0 | private boolean isColumnForNodeSelected(BinaryNode bn) |
1121 | { | |
1122 | 0 | SequenceI rseq = tp.assocAnnotation.sequenceRef; |
1123 | 0 | int colm = -1; |
1124 | 0 | try |
1125 | { | |
1126 | 0 | colm = parseColumnNode(bn); |
1127 | } catch (Exception e) | |
1128 | { | |
1129 | 0 | return false; |
1130 | } | |
1131 | 0 | if (av == null || av.getAlignment() == null) |
1132 | { | |
1133 | // alignment is closed | |
1134 | 0 | return false; |
1135 | } | |
1136 | 0 | ColumnSelection cs = av.getColumnSelection(); |
1137 | 0 | HiddenColumns hc = av.getAlignment().getHiddenColumns(); |
1138 | 0 | AlignmentAnnotation aa = tp.getAssocAnnotation(); |
1139 | 0 | int offp = -1; |
1140 | 0 | if (aa != null) |
1141 | { | |
1142 | 0 | ContactMatrixI cm = av.getContactMatrix(aa); |
1143 | // generally, we assume cm has 1:1 mapping to annotation row - probably | |
1144 | // wrong | |
1145 | // but.. if | |
1146 | 0 | if (cm instanceof MappableContactMatrixI) |
1147 | { | |
1148 | 0 | int[] pos; |
1149 | // use the mappable's mapping - always the case for PAE Matrices so good | |
1150 | // for 2.11.3 | |
1151 | 0 | MappableContactMatrixI mcm = (MappableContactMatrixI) cm; |
1152 | 0 | pos = mcm.getMappedPositionsFor(rseq, colm + 1); |
1153 | // finally, look up the position of the column | |
1154 | 0 | if (pos != null) |
1155 | { | |
1156 | 0 | offp = rseq.findIndex(pos[0]); |
1157 | } | |
1158 | } | |
1159 | else | |
1160 | { | |
1161 | 0 | offp = colm; |
1162 | } | |
1163 | } | |
1164 | 0 | if (offp <= 0) |
1165 | { | |
1166 | 0 | return false; |
1167 | } | |
1168 | ||
1169 | 0 | offp -= 2; |
1170 | 0 | if (!av.hasHiddenColumns()) |
1171 | { | |
1172 | 0 | return cs.contains(offp); |
1173 | } | |
1174 | 0 | if (hc.isVisible(offp)) |
1175 | { | |
1176 | 0 | return cs.contains(offp); |
1177 | // return cs.contains(hc.absoluteToVisibleColumn(offp)); | |
1178 | } | |
1179 | 0 | return false; |
1180 | } | |
1181 | ||
1182 | 0 | private BitSet createColumnGroupFor(Vector<BinaryNode> l, Color col) |
1183 | { | |
1184 | 0 | BitSet gp = new BitSet(); |
1185 | 0 | for (BinaryNode bn : l) |
1186 | { | |
1187 | 0 | int colm = -1; |
1188 | 0 | if (bn.element() != null && bn.element() instanceof Integer) |
1189 | { | |
1190 | 0 | colm = (Integer) bn.element(); |
1191 | } | |
1192 | else | |
1193 | { | |
1194 | // parse out from nodename | |
1195 | 0 | try |
1196 | { | |
1197 | 0 | colm = parseColumnNode(bn); |
1198 | } catch (Exception e) | |
1199 | { | |
1200 | 0 | continue; |
1201 | } | |
1202 | } | |
1203 | 0 | gp.set(colm); |
1204 | } | |
1205 | 0 | return gp; |
1206 | } | |
1207 | ||
1208 | 0 | private void markColumnsFor(AlignmentPanel[] aps, Vector<BinaryNode> l, |
1209 | Color col, boolean clearSelected) | |
1210 | { | |
1211 | 0 | SequenceI rseq = tp.assocAnnotation.sequenceRef; |
1212 | 0 | if (av == null || av.getAlignment() == null) |
1213 | { | |
1214 | // alignment is closed | |
1215 | 0 | return; |
1216 | } | |
1217 | ||
1218 | // TODO - sort indices for faster lookup | |
1219 | 0 | ColumnSelection cs = av.getColumnSelection(); |
1220 | 0 | HiddenColumns hc = av.getAlignment().getHiddenColumns(); |
1221 | 0 | ContactMatrixI cm = av.getContactMatrix(tp.assocAnnotation); |
1222 | 0 | MappableContactMatrixI mcm = null; |
1223 | 0 | int offp; |
1224 | 0 | if (cm instanceof MappableContactMatrixI) |
1225 | { | |
1226 | 0 | mcm = (MappableContactMatrixI) cm; |
1227 | } | |
1228 | 0 | for (BinaryNode bn : l) |
1229 | { | |
1230 | 0 | int colm = -1; |
1231 | 0 | try |
1232 | { | |
1233 | 0 | colm = Integer.parseInt( |
1234 | bn.getName().substring(bn.getName().indexOf("c") + 1)); | |
1235 | } catch (Exception e) | |
1236 | { | |
1237 | 0 | continue; |
1238 | } | |
1239 | 0 | if (mcm != null) |
1240 | { | |
1241 | 0 | int[] seqpos = mcm.getMappedPositionsFor(rseq, colm); |
1242 | 0 | if (seqpos == null) |
1243 | { | |
1244 | // no mapping for this column. | |
1245 | 0 | continue; |
1246 | } | |
1247 | // TODO: handle ranges... | |
1248 | 0 | offp = rseq.findIndex(seqpos[0]) - 1; |
1249 | } | |
1250 | else | |
1251 | { | |
1252 | 0 | offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm) |
1253 | : colm; | |
1254 | } | |
1255 | 0 | if (!av.hasHiddenColumns() || hc.isVisible(offp)) |
1256 | { | |
1257 | 0 | if (clearSelected || cs.contains(offp)) |
1258 | { | |
1259 | 0 | cs.removeElement(offp); |
1260 | } | |
1261 | else | |
1262 | { | |
1263 | 0 | cs.addElement(offp); |
1264 | } | |
1265 | } | |
1266 | } | |
1267 | 0 | PaintRefresher.Refresh(tp, av.getSequenceSetId()); |
1268 | } | |
1269 | ||
1270 | 0 | public void createSeqGroupFor(AlignmentPanel[] aps, Vector<BinaryNode> l, |
1271 | Color col) | |
1272 | { | |
1273 | ||
1274 | 0 | Vector<SequenceI> sequences = new Vector<>(); |
1275 | ||
1276 | 0 | for (int j = 0; j < l.size(); j++) |
1277 | { | |
1278 | 0 | SequenceI s1 = (SequenceI) l.elementAt(j).element(); |
1279 | ||
1280 | 0 | if (!sequences.contains(s1)) |
1281 | { | |
1282 | 0 | sequences.addElement(s1); |
1283 | } | |
1284 | } | |
1285 | ||
1286 | 0 | ColourSchemeI cs = null; |
1287 | 0 | SequenceGroup _sg = new SequenceGroup(sequences, null, cs, true, true, |
1288 | false, 0, av.getAlignment().getWidth() - 1); | |
1289 | ||
1290 | 0 | _sg.setName("JTreeGroup:" + _sg.hashCode()); |
1291 | 0 | _sg.setIdColour(col); |
1292 | ||
1293 | 0 | for (int a = 0; a < aps.length; a++) |
1294 | { | |
1295 | 0 | SequenceGroup sg = new SequenceGroup(_sg); |
1296 | 0 | AlignViewport viewport = aps[a].av; |
1297 | ||
1298 | // Propagate group colours in each view | |
1299 | 0 | if (viewport.getGlobalColourScheme() != null) |
1300 | { | |
1301 | 0 | cs = viewport.getGlobalColourScheme().getInstance(viewport, sg); |
1302 | 0 | sg.setColourScheme(cs); |
1303 | 0 | sg.getGroupColourScheme().setThreshold( |
1304 | viewport.getResidueShading().getThreshold(), | |
1305 | viewport.isIgnoreGapsConsensus()); | |
1306 | ||
1307 | 0 | if (viewport.getResidueShading().conservationApplied()) |
1308 | { | |
1309 | 0 | Conservation c = new Conservation("Group", sg.getSequences(null), |
1310 | sg.getStartRes(), sg.getEndRes()); | |
1311 | 0 | c.calculate(); |
1312 | 0 | c.verdict(false, viewport.getConsPercGaps()); |
1313 | 0 | sg.cs.setConservation(c); |
1314 | } | |
1315 | } | |
1316 | // indicate that associated structure views will need an update | |
1317 | 0 | viewport.setUpdateStructures(true); |
1318 | // propagate structure view update and sequence group to complement view | |
1319 | 0 | viewport.addSequenceGroup(sg); |
1320 | } | |
1321 | } | |
1322 | ||
1323 | /** | |
1324 | * DOCUMENT ME! | |
1325 | * | |
1326 | * @param state | |
1327 | * DOCUMENT ME! | |
1328 | */ | |
1329 | 40 | public void setShowDistances(boolean state) |
1330 | { | |
1331 | 40 | this.showDistances = state; |
1332 | 40 | repaint(); |
1333 | } | |
1334 | ||
1335 | /** | |
1336 | * DOCUMENT ME! | |
1337 | * | |
1338 | * @param state | |
1339 | * DOCUMENT ME! | |
1340 | */ | |
1341 | 26 | public void setShowBootstrap(boolean state) |
1342 | { | |
1343 | 26 | this.showBootstrap = state; |
1344 | 26 | repaint(); |
1345 | } | |
1346 | ||
1347 | /** | |
1348 | * DOCUMENT ME! | |
1349 | * | |
1350 | * @param state | |
1351 | * DOCUMENT ME! | |
1352 | */ | |
1353 | 26 | public void setMarkPlaceholders(boolean state) |
1354 | { | |
1355 | 26 | this.markPlaceholders = state; |
1356 | 26 | repaint(); |
1357 | } | |
1358 | ||
1359 | 0 | AlignmentPanel[] getAssociatedPanels() |
1360 | { | |
1361 | 0 | if (applyToAllViews) |
1362 | { | |
1363 | 0 | return PaintRefresher.getAssociatedPanels(av.getSequenceSetId()); |
1364 | } | |
1365 | else | |
1366 | { | |
1367 | 0 | return new AlignmentPanel[] { getAssociatedPanel() }; |
1368 | } | |
1369 | } | |
1370 | ||
1371 | 32 | public AlignmentPanel getAssociatedPanel() |
1372 | { | |
1373 | 32 | return ap; |
1374 | } | |
1375 | ||
1376 | 14 | public void setAssociatedPanel(AlignmentPanel ap) |
1377 | { | |
1378 | 14 | this.ap = ap; |
1379 | } | |
1380 | ||
1381 | 4 | public AlignViewport getViewport() |
1382 | { | |
1383 | 4 | return av; |
1384 | } | |
1385 | ||
1386 | 0 | public void setViewport(AlignViewport av) |
1387 | { | |
1388 | 0 | this.av = av; |
1389 | } | |
1390 | ||
1391 | 4 | public float getThreshold() |
1392 | { | |
1393 | 4 | return threshold; |
1394 | } | |
1395 | ||
1396 | 12 | public void setThreshold(float threshold) |
1397 | { | |
1398 | 12 | this.threshold = threshold; |
1399 | } | |
1400 | ||
1401 | 4 | public boolean isApplyToAllViews() |
1402 | { | |
1403 | 4 | return this.applyToAllViews; |
1404 | } | |
1405 | ||
1406 | 12 | public void setApplyToAllViews(boolean applyToAllViews) |
1407 | { | |
1408 | 12 | this.applyToAllViews = applyToAllViews; |
1409 | } | |
1410 | } |