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AppletPDBCanvas | 55 | 463 | 158 |
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 mc_view; | |
22 | ||
23 | import jalview.analysis.AlignSeq; | |
24 | import jalview.appletgui.AlignmentPanel; | |
25 | import jalview.appletgui.FeatureRenderer; | |
26 | import jalview.appletgui.SequenceRenderer; | |
27 | import jalview.datamodel.PDBEntry; | |
28 | import jalview.datamodel.SequenceI; | |
29 | import jalview.io.DataSourceType; | |
30 | import jalview.io.StructureFile; | |
31 | import jalview.renderer.seqfeatures.FeatureColourFinder; | |
32 | import jalview.structure.AtomSpec; | |
33 | import jalview.structure.StructureListener; | |
34 | import jalview.structure.StructureMapping; | |
35 | import jalview.structure.StructureSelectionManager; | |
36 | import jalview.util.MessageManager; | |
37 | ||
38 | import java.awt.Color; | |
39 | import java.awt.Dimension; | |
40 | import java.awt.Event; | |
41 | import java.awt.Font; | |
42 | import java.awt.Graphics; | |
43 | import java.awt.Image; | |
44 | // JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug | |
45 | import java.awt.Panel; | |
46 | import java.awt.event.KeyAdapter; | |
47 | import java.awt.event.KeyEvent; | |
48 | import java.awt.event.MouseEvent; | |
49 | import java.awt.event.MouseListener; | |
50 | import java.awt.event.MouseMotionListener; | |
51 | import java.io.PrintStream; | |
52 | import java.util.List; | |
53 | import java.util.Vector; | |
54 | ||
55 | public class AppletPDBCanvas extends Panel | |
56 | implements MouseListener, MouseMotionListener, StructureListener | |
57 | { | |
58 | ||
59 | MCMatrix idmat = new MCMatrix(3, 3); | |
60 | ||
61 | MCMatrix objmat = new MCMatrix(3, 3); | |
62 | ||
63 | boolean redrawneeded = true; | |
64 | ||
65 | int omx = 0; | |
66 | ||
67 | int mx = 0; | |
68 | ||
69 | int omy = 0; | |
70 | ||
71 | int my = 0; | |
72 | ||
73 | public StructureFile pdb; | |
74 | ||
75 | PDBEntry pdbentry; | |
76 | ||
77 | int bsize; | |
78 | ||
79 | Image img; | |
80 | ||
81 | Graphics ig; | |
82 | ||
83 | Dimension prefsize; | |
84 | ||
85 | float[] centre = new float[3]; | |
86 | ||
87 | float[] width = new float[3]; | |
88 | ||
89 | float maxwidth; | |
90 | ||
91 | float scale; | |
92 | ||
93 | String inStr; | |
94 | ||
95 | String inType; | |
96 | ||
97 | boolean bysequence = true; | |
98 | ||
99 | boolean depthcue = true; | |
100 | ||
101 | boolean wire = false; | |
102 | ||
103 | boolean bymolecule = false; | |
104 | ||
105 | boolean zbuffer = true; | |
106 | ||
107 | boolean dragging; | |
108 | ||
109 | int xstart; | |
110 | ||
111 | int xend; | |
112 | ||
113 | int ystart; | |
114 | ||
115 | int yend; | |
116 | ||
117 | int xmid; | |
118 | ||
119 | int ymid; | |
120 | ||
121 | Font font = new Font("Helvetica", Font.PLAIN, 10); | |
122 | ||
123 | public SequenceI[] sequence; | |
124 | ||
125 | final StringBuffer mappingDetails = new StringBuffer(); | |
126 | ||
127 | String appletToolTip = null; | |
128 | ||
129 | int toolx, tooly; | |
130 | ||
131 | PDBChain mainchain; | |
132 | ||
133 | Vector<String> highlightRes; | |
134 | ||
135 | boolean pdbAction = false; | |
136 | ||
137 | Bond highlightBond1, highlightBond2; | |
138 | ||
139 | boolean errorLoading = false; | |
140 | ||
141 | boolean seqColoursReady = false; | |
142 | ||
143 | FeatureRenderer fr; | |
144 | ||
145 | AlignmentPanel ap; | |
146 | ||
147 | StructureSelectionManager ssm; | |
148 | ||
149 | 0 | public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq, |
150 | String[] chains, AlignmentPanel ap, DataSourceType protocol) | |
151 | ||
152 | { | |
153 | 0 | this.ap = ap; |
154 | 0 | this.pdbentry = pdbentry; |
155 | 0 | this.sequence = seq; |
156 | ||
157 | 0 | ssm = StructureSelectionManager |
158 | .getStructureSelectionManager(ap.av.applet); | |
159 | ||
160 | 0 | try |
161 | { | |
162 | 0 | pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol, null); |
163 | ||
164 | 0 | if (protocol == DataSourceType.PASTE) |
165 | { | |
166 | 0 | pdbentry.setFile("INLINE" + pdb.getId()); |
167 | } | |
168 | ||
169 | } catch (Exception ex) | |
170 | { | |
171 | 0 | ex.printStackTrace(); |
172 | 0 | return; |
173 | } | |
174 | ||
175 | 0 | pdbentry.setId(pdb.getId()); |
176 | ||
177 | 0 | ssm.addStructureViewerListener(this); |
178 | ||
179 | 0 | colourBySequence(); |
180 | ||
181 | 0 | float max = -10; |
182 | 0 | int maxchain = -1; |
183 | 0 | int pdbstart = 0; |
184 | 0 | int pdbend = 0; |
185 | 0 | int seqstart = 0; |
186 | 0 | int seqend = 0; |
187 | ||
188 | // JUST DEAL WITH ONE SEQUENCE FOR NOW | |
189 | 0 | SequenceI sequence = seq[0]; |
190 | ||
191 | 0 | for (int i = 0; i < pdb.getChains().size(); i++) |
192 | { | |
193 | ||
194 | 0 | mappingDetails.append("\n\nPDB Sequence is :\nSequence = " |
195 | + pdb.getChains().elementAt(i).sequence | |
196 | .getSequenceAsString()); | |
197 | 0 | mappingDetails.append("\nNo of residues = " |
198 | + pdb.getChains().elementAt(i).residues.size() + "\n\n"); | |
199 | ||
200 | // Now lets compare the sequences to get | |
201 | // the start and end points. | |
202 | // Align the sequence to the pdb | |
203 | // TODO: DNa/Pep switch | |
204 | 0 | AlignSeq as = new AlignSeq(sequence, |
205 | pdb.getChains().elementAt(i).sequence, | |
206 | 0 | pdb.getChains().elementAt(i).isNa ? AlignSeq.DNA |
207 | : AlignSeq.PEP); | |
208 | 0 | as.calcScoreMatrix(); |
209 | 0 | as.traceAlignment(); |
210 | 0 | PrintStream ps = new PrintStream(System.out) |
211 | { | |
212 | 0 | @Override |
213 | public void print(String x) | |
214 | { | |
215 | 0 | mappingDetails.append(x); |
216 | } | |
217 | ||
218 | 0 | @Override |
219 | public void println() | |
220 | { | |
221 | 0 | mappingDetails.append("\n"); |
222 | } | |
223 | }; | |
224 | ||
225 | 0 | as.printAlignment(ps); |
226 | ||
227 | 0 | if (as.maxscore > max) |
228 | { | |
229 | 0 | max = as.maxscore; |
230 | 0 | maxchain = i; |
231 | ||
232 | 0 | pdbstart = as.seq2start; |
233 | 0 | pdbend = as.seq2end; |
234 | 0 | seqstart = as.seq1start + sequence.getStart() - 1; |
235 | 0 | seqend = as.seq1end + sequence.getEnd() - 1; |
236 | } | |
237 | ||
238 | 0 | mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend); |
239 | 0 | mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend); |
240 | } | |
241 | ||
242 | 0 | mainchain = pdb.getChains().elementAt(maxchain); |
243 | ||
244 | 0 | mainchain.pdbstart = pdbstart; |
245 | 0 | mainchain.pdbend = pdbend; |
246 | 0 | mainchain.seqstart = seqstart; |
247 | 0 | mainchain.seqend = seqend; |
248 | 0 | mainchain.isVisible = true; |
249 | // mainchain.makeExactMapping(maxAlignseq, sequence); | |
250 | // mainchain.transferRESNUMFeatures(sequence, null); | |
251 | 0 | this.pdb = pdb; |
252 | 0 | this.prefsize = new Dimension(getSize().width, getSize().height); |
253 | ||
254 | // Initialize the matrices to identity | |
255 | 0 | for (int i = 0; i < 3; i++) |
256 | { | |
257 | 0 | for (int j = 0; j < 3; j++) |
258 | { | |
259 | 0 | if (i != j) |
260 | { | |
261 | 0 | idmat.addElement(i, j, 0); |
262 | 0 | objmat.addElement(i, j, 0); |
263 | } | |
264 | else | |
265 | { | |
266 | 0 | idmat.addElement(i, j, 1); |
267 | 0 | objmat.addElement(i, j, 1); |
268 | } | |
269 | } | |
270 | } | |
271 | ||
272 | 0 | addMouseMotionListener(this); |
273 | 0 | addMouseListener(this); |
274 | ||
275 | 0 | addKeyListener(new KeyAdapter() |
276 | { | |
277 | 0 | @Override |
278 | public void keyPressed(KeyEvent evt) | |
279 | { | |
280 | 0 | doKeyPressed(evt); |
281 | } | |
282 | }); | |
283 | ||
284 | 0 | findCentre(); |
285 | 0 | findWidth(); |
286 | ||
287 | 0 | setupBonds(); |
288 | ||
289 | 0 | scale = findScale(); |
290 | } | |
291 | ||
292 | Vector<Bond> visiblebonds; | |
293 | ||
294 | 0 | void setupBonds() |
295 | { | |
296 | 0 | seqColoursReady = false; |
297 | // Sort the bonds by z coord | |
298 | 0 | visiblebonds = new Vector<Bond>(); |
299 | ||
300 | 0 | for (int ii = 0; ii < pdb.getChains().size(); ii++) |
301 | { | |
302 | 0 | if (pdb.getChains().elementAt(ii).isVisible) |
303 | { | |
304 | 0 | Vector<Bond> tmp = pdb.getChains().elementAt(ii).bonds; |
305 | ||
306 | 0 | for (int i = 0; i < tmp.size(); i++) |
307 | { | |
308 | 0 | visiblebonds.addElement(tmp.elementAt(i)); |
309 | } | |
310 | } | |
311 | } | |
312 | 0 | seqColoursReady = true; |
313 | 0 | colourBySequence(); |
314 | 0 | redrawneeded = true; |
315 | 0 | repaint(); |
316 | } | |
317 | ||
318 | 0 | public void findWidth() |
319 | { | |
320 | 0 | float[] max = new float[3]; |
321 | 0 | float[] min = new float[3]; |
322 | ||
323 | 0 | max[0] = (float) -1e30; |
324 | 0 | max[1] = (float) -1e30; |
325 | 0 | max[2] = (float) -1e30; |
326 | ||
327 | 0 | min[0] = (float) 1e30; |
328 | 0 | min[1] = (float) 1e30; |
329 | 0 | min[2] = (float) 1e30; |
330 | ||
331 | 0 | for (int ii = 0; ii < pdb.getChains().size(); ii++) |
332 | { | |
333 | 0 | if (pdb.getChains().elementAt(ii).isVisible) |
334 | { | |
335 | 0 | Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds; |
336 | ||
337 | 0 | for (Bond tmp : bonds) |
338 | { | |
339 | 0 | if (tmp.start[0] >= max[0]) |
340 | { | |
341 | 0 | max[0] = tmp.start[0]; |
342 | } | |
343 | ||
344 | 0 | if (tmp.start[1] >= max[1]) |
345 | { | |
346 | 0 | max[1] = tmp.start[1]; |
347 | } | |
348 | ||
349 | 0 | if (tmp.start[2] >= max[2]) |
350 | { | |
351 | 0 | max[2] = tmp.start[2]; |
352 | } | |
353 | ||
354 | 0 | if (tmp.start[0] <= min[0]) |
355 | { | |
356 | 0 | min[0] = tmp.start[0]; |
357 | } | |
358 | ||
359 | 0 | if (tmp.start[1] <= min[1]) |
360 | { | |
361 | 0 | min[1] = tmp.start[1]; |
362 | } | |
363 | ||
364 | 0 | if (tmp.start[2] <= min[2]) |
365 | { | |
366 | 0 | min[2] = tmp.start[2]; |
367 | } | |
368 | ||
369 | 0 | if (tmp.end[0] >= max[0]) |
370 | { | |
371 | 0 | max[0] = tmp.end[0]; |
372 | } | |
373 | ||
374 | 0 | if (tmp.end[1] >= max[1]) |
375 | { | |
376 | 0 | max[1] = tmp.end[1]; |
377 | } | |
378 | ||
379 | 0 | if (tmp.end[2] >= max[2]) |
380 | { | |
381 | 0 | max[2] = tmp.end[2]; |
382 | } | |
383 | ||
384 | 0 | if (tmp.end[0] <= min[0]) |
385 | { | |
386 | 0 | min[0] = tmp.end[0]; |
387 | } | |
388 | ||
389 | 0 | if (tmp.end[1] <= min[1]) |
390 | { | |
391 | 0 | min[1] = tmp.end[1]; |
392 | } | |
393 | ||
394 | 0 | if (tmp.end[2] <= min[2]) |
395 | { | |
396 | 0 | min[2] = tmp.end[2]; |
397 | } | |
398 | } | |
399 | } | |
400 | } | |
401 | ||
402 | 0 | width[0] = Math.abs(max[0] - min[0]); |
403 | 0 | width[1] = Math.abs(max[1] - min[1]); |
404 | 0 | width[2] = Math.abs(max[2] - min[2]); |
405 | ||
406 | 0 | maxwidth = width[0]; |
407 | ||
408 | 0 | if (width[1] > width[0]) |
409 | { | |
410 | 0 | maxwidth = width[1]; |
411 | } | |
412 | ||
413 | 0 | if (width[2] > width[1]) |
414 | { | |
415 | 0 | maxwidth = width[2]; |
416 | } | |
417 | ||
418 | // System.out.println("Maxwidth = " + maxwidth); | |
419 | } | |
420 | ||
421 | 0 | public float findScale() |
422 | { | |
423 | 0 | int dim; |
424 | 0 | int width; |
425 | 0 | int height; |
426 | ||
427 | 0 | if (getSize().width != 0) |
428 | { | |
429 | 0 | width = getSize().width; |
430 | 0 | height = getSize().height; |
431 | } | |
432 | else | |
433 | { | |
434 | 0 | width = prefsize.width; |
435 | 0 | height = prefsize.height; |
436 | } | |
437 | ||
438 | 0 | if (width < height) |
439 | { | |
440 | 0 | dim = width; |
441 | } | |
442 | else | |
443 | { | |
444 | 0 | dim = height; |
445 | } | |
446 | ||
447 | 0 | return (float) (dim / (1.5d * maxwidth)); |
448 | } | |
449 | ||
450 | 0 | public void findCentre() |
451 | { | |
452 | 0 | float xtot = 0; |
453 | 0 | float ytot = 0; |
454 | 0 | float ztot = 0; |
455 | ||
456 | 0 | int bsize = 0; |
457 | ||
458 | // Find centre coordinate | |
459 | 0 | for (int ii = 0; ii < pdb.getChains().size(); ii++) |
460 | { | |
461 | 0 | if (pdb.getChains().elementAt(ii).isVisible) |
462 | { | |
463 | 0 | Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds; |
464 | ||
465 | 0 | bsize += bonds.size(); |
466 | ||
467 | 0 | for (Bond b : bonds) |
468 | { | |
469 | 0 | xtot = xtot + b.start[0] + b.end[0]; |
470 | 0 | ytot = ytot + b.start[1] + b.end[1]; |
471 | 0 | ztot = ztot + b.start[2] + b.end[2]; |
472 | } | |
473 | } | |
474 | } | |
475 | ||
476 | 0 | centre[0] = xtot / (2 * (float) bsize); |
477 | 0 | centre[1] = ytot / (2 * (float) bsize); |
478 | 0 | centre[2] = ztot / (2 * (float) bsize); |
479 | } | |
480 | ||
481 | 0 | @Override |
482 | public void paint(Graphics g) | |
483 | { | |
484 | ||
485 | 0 | if (errorLoading) |
486 | { | |
487 | 0 | g.setColor(Color.white); |
488 | 0 | g.fillRect(0, 0, getSize().width, getSize().height); |
489 | 0 | g.setColor(Color.black); |
490 | 0 | g.setFont(new Font("Verdana", Font.BOLD, 14)); |
491 | 0 | g.drawString(MessageManager.getString("label.error_loading_pdb_data"), |
492 | 50, getSize().height / 2); | |
493 | 0 | return; |
494 | } | |
495 | ||
496 | 0 | if (!seqColoursReady) |
497 | { | |
498 | 0 | g.setColor(Color.black); |
499 | 0 | g.setFont(new Font("Verdana", Font.BOLD, 14)); |
500 | 0 | g.drawString(MessageManager.getString("label.fetching_pdb_data"), 50, |
501 | getSize().height / 2); | |
502 | 0 | return; |
503 | } | |
504 | ||
505 | // Only create the image at the beginning - | |
506 | // this saves much memory usage | |
507 | 0 | if ((img == null) || (prefsize.width != getSize().width) |
508 | || (prefsize.height != getSize().height)) | |
509 | { | |
510 | ||
511 | 0 | try |
512 | { | |
513 | 0 | prefsize.width = getSize().width; |
514 | 0 | prefsize.height = getSize().height; |
515 | ||
516 | 0 | scale = findScale(); |
517 | 0 | img = createImage(prefsize.width, prefsize.height); |
518 | 0 | ig = img.getGraphics(); |
519 | ||
520 | 0 | redrawneeded = true; |
521 | } catch (Exception ex) | |
522 | { | |
523 | 0 | ex.printStackTrace(); |
524 | } | |
525 | } | |
526 | ||
527 | 0 | if (redrawneeded) |
528 | { | |
529 | 0 | drawAll(ig, prefsize.width, prefsize.height); |
530 | 0 | redrawneeded = false; |
531 | } | |
532 | 0 | if (appletToolTip != null) |
533 | { | |
534 | 0 | ig.setColor(Color.red); |
535 | 0 | ig.drawString(appletToolTip, toolx, tooly); |
536 | } | |
537 | ||
538 | 0 | g.drawImage(img, 0, 0, this); |
539 | ||
540 | 0 | pdbAction = false; |
541 | } | |
542 | ||
543 | 0 | public void drawAll(Graphics g, int width, int height) |
544 | { | |
545 | 0 | ig.setColor(Color.black); |
546 | 0 | ig.fillRect(0, 0, width, height); |
547 | 0 | drawScene(ig); |
548 | 0 | drawLabels(ig); |
549 | } | |
550 | ||
551 | 0 | public void setColours(jalview.schemes.ColourSchemeI cs) |
552 | { | |
553 | 0 | bysequence = false; |
554 | 0 | pdb.setColours(cs); |
555 | 0 | redrawneeded = true; |
556 | 0 | repaint(); |
557 | } | |
558 | ||
559 | // This method has been taken out of PDBChain to allow | |
560 | // Applet and Application specific sequence renderers to be used | |
561 | 0 | void colourBySequence() |
562 | { | |
563 | 0 | SequenceRenderer sr = new SequenceRenderer(ap.av); |
564 | ||
565 | 0 | StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile()); |
566 | ||
567 | 0 | boolean showFeatures = false; |
568 | 0 | if (ap.av.isShowSequenceFeatures()) |
569 | { | |
570 | 0 | if (fr == null) |
571 | { | |
572 | 0 | fr = new jalview.appletgui.FeatureRenderer(ap.av); |
573 | } | |
574 | ||
575 | 0 | fr.transferSettings(ap.getFeatureRenderer()); |
576 | ||
577 | 0 | showFeatures = true; |
578 | } | |
579 | ||
580 | 0 | FeatureColourFinder finder = new FeatureColourFinder(fr); |
581 | ||
582 | 0 | PDBChain chain; |
583 | 0 | if (bysequence && pdb != null) |
584 | { | |
585 | 0 | for (int ii = 0; ii < pdb.getChains().size(); ii++) |
586 | { | |
587 | 0 | chain = pdb.getChains().elementAt(ii); |
588 | ||
589 | 0 | for (int i = 0; i < chain.bonds.size(); i++) |
590 | { | |
591 | 0 | Bond tmp = chain.bonds.elementAt(i); |
592 | 0 | tmp.startCol = Color.lightGray; |
593 | 0 | tmp.endCol = Color.lightGray; |
594 | 0 | if (chain != mainchain) |
595 | { | |
596 | 0 | continue; |
597 | } | |
598 | ||
599 | 0 | for (int s = 0; s < sequence.length; s++) |
600 | { | |
601 | 0 | for (int m = 0; m < mapping.length; m++) |
602 | { | |
603 | 0 | if (mapping[m].getSequence() == sequence[s]) |
604 | { | |
605 | 0 | int pos = mapping[m].getSeqPos(tmp.at1.resNumber) - 1; |
606 | 0 | if (pos > 0) |
607 | { | |
608 | 0 | pos = sequence[s].findIndex(pos); |
609 | 0 | tmp.startCol = sr.getResidueColour(sequence[s], pos, |
610 | finder); | |
611 | } | |
612 | 0 | pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1; |
613 | 0 | if (pos > 0) |
614 | { | |
615 | 0 | pos = sequence[s].findIndex(pos); |
616 | 0 | tmp.endCol = sr.getResidueColour(sequence[s], pos, |
617 | finder); | |
618 | } | |
619 | } | |
620 | } | |
621 | } | |
622 | } | |
623 | } | |
624 | } | |
625 | } | |
626 | ||
627 | Zsort zsort; | |
628 | ||
629 | 0 | public void drawScene(Graphics g) |
630 | { | |
631 | 0 | if (zbuffer) |
632 | { | |
633 | 0 | if (zsort == null) |
634 | { | |
635 | 0 | zsort = new Zsort(); |
636 | } | |
637 | ||
638 | 0 | zsort.sort(visiblebonds); |
639 | } | |
640 | ||
641 | 0 | Bond tmpBond = null; |
642 | 0 | for (int i = 0; i < visiblebonds.size(); i++) |
643 | { | |
644 | 0 | tmpBond = visiblebonds.elementAt(i); |
645 | ||
646 | 0 | xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) |
647 | + (getSize().width / 2)); | |
648 | 0 | ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) |
649 | + (getSize().height / 2)); | |
650 | ||
651 | 0 | xend = (int) (((tmpBond.end[0] - centre[0]) * scale) |
652 | + (getSize().width / 2)); | |
653 | 0 | yend = (int) (((centre[1] - tmpBond.end[1]) * scale) |
654 | + (getSize().height / 2)); | |
655 | ||
656 | 0 | xmid = (xend + xstart) / 2; |
657 | 0 | ymid = (yend + ystart) / 2; |
658 | ||
659 | 0 | if (depthcue && !bymolecule) |
660 | { | |
661 | 0 | if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) |
662 | { | |
663 | 0 | g.setColor(tmpBond.startCol.darker().darker()); |
664 | 0 | drawLine(g, xstart, ystart, xmid, ymid); |
665 | ||
666 | 0 | g.setColor(tmpBond.endCol.darker().darker()); |
667 | 0 | drawLine(g, xmid, ymid, xend, yend); |
668 | } | |
669 | 0 | else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) |
670 | { | |
671 | 0 | g.setColor(tmpBond.startCol.darker()); |
672 | 0 | drawLine(g, xstart, ystart, xmid, ymid); |
673 | ||
674 | 0 | g.setColor(tmpBond.endCol.darker()); |
675 | 0 | drawLine(g, xmid, ymid, xend, yend); |
676 | } | |
677 | else | |
678 | { | |
679 | 0 | g.setColor(tmpBond.startCol); |
680 | 0 | drawLine(g, xstart, ystart, xmid, ymid); |
681 | ||
682 | 0 | g.setColor(tmpBond.endCol); |
683 | 0 | drawLine(g, xmid, ymid, xend, yend); |
684 | } | |
685 | ||
686 | } | |
687 | 0 | else if (depthcue && bymolecule) |
688 | { | |
689 | 0 | if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) |
690 | { | |
691 | 0 | g.setColor(Color.green.darker().darker()); |
692 | 0 | drawLine(g, xstart, ystart, xend, yend); |
693 | } | |
694 | 0 | else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) |
695 | { | |
696 | 0 | g.setColor(Color.green.darker()); |
697 | 0 | drawLine(g, xstart, ystart, xend, yend); |
698 | } | |
699 | else | |
700 | { | |
701 | 0 | g.setColor(Color.green); |
702 | 0 | drawLine(g, xstart, ystart, xend, yend); |
703 | } | |
704 | } | |
705 | 0 | else if (!depthcue && !bymolecule) |
706 | { | |
707 | 0 | g.setColor(tmpBond.startCol); |
708 | 0 | drawLine(g, xstart, ystart, xmid, ymid); |
709 | 0 | g.setColor(tmpBond.endCol); |
710 | 0 | drawLine(g, xmid, ymid, xend, yend); |
711 | } | |
712 | else | |
713 | { | |
714 | 0 | drawLine(g, xstart, ystart, xend, yend); |
715 | } | |
716 | ||
717 | 0 | if (highlightBond1 != null && highlightBond1 == tmpBond) |
718 | { | |
719 | 0 | g.setColor(Color.white); |
720 | 0 | drawLine(g, xmid, ymid, xend, yend); |
721 | } | |
722 | ||
723 | 0 | if (highlightBond2 != null && highlightBond2 == tmpBond) |
724 | { | |
725 | 0 | g.setColor(Color.white); |
726 | 0 | drawLine(g, xstart, ystart, xmid, ymid); |
727 | } | |
728 | ||
729 | } | |
730 | } | |
731 | ||
732 | 0 | public void drawLine(Graphics g, int x1, int y1, int x2, int y2) |
733 | { | |
734 | 0 | if (!wire) |
735 | { | |
736 | 0 | if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5) |
737 | { | |
738 | 0 | g.drawLine(x1, y1, x2, y2); |
739 | 0 | g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1); |
740 | 0 | g.drawLine(x1, y1 - 1, x2, y2 - 1); |
741 | } | |
742 | else | |
743 | { | |
744 | 0 | g.setColor(g.getColor().brighter()); |
745 | 0 | g.drawLine(x1, y1, x2, y2); |
746 | 0 | g.drawLine(x1 + 1, y1, x2 + 1, y2); |
747 | 0 | g.drawLine(x1 - 1, y1, x2 - 1, y2); |
748 | } | |
749 | } | |
750 | else | |
751 | { | |
752 | 0 | g.drawLine(x1, y1, x2, y2); |
753 | } | |
754 | } | |
755 | ||
756 | 0 | public Dimension minimumsize() |
757 | { | |
758 | 0 | return prefsize; |
759 | } | |
760 | ||
761 | 0 | public Dimension preferredsize() |
762 | { | |
763 | 0 | return prefsize; |
764 | } | |
765 | ||
766 | 0 | public void doKeyPressed(KeyEvent evt) |
767 | { | |
768 | 0 | if (evt.getKeyCode() == KeyEvent.VK_UP) |
769 | { | |
770 | 0 | scale = (float) (scale * 1.1); |
771 | 0 | redrawneeded = true; |
772 | 0 | repaint(); |
773 | } | |
774 | 0 | else if (evt.getKeyCode() == KeyEvent.VK_DOWN) |
775 | { | |
776 | 0 | scale = (float) (scale * 0.9); |
777 | 0 | redrawneeded = true; |
778 | 0 | repaint(); |
779 | } | |
780 | } | |
781 | ||
782 | 0 | @Override |
783 | public void mousePressed(MouseEvent e) | |
784 | { | |
785 | 0 | pdbAction = true; |
786 | 0 | Atom fatom = findAtom(e.getX(), e.getY()); |
787 | 0 | if (fatom != null) |
788 | { | |
789 | 0 | fatom.isSelected = !fatom.isSelected; |
790 | ||
791 | 0 | redrawneeded = true; |
792 | 0 | repaint(); |
793 | 0 | if (foundchain != -1) |
794 | { | |
795 | 0 | PDBChain chain = pdb.getChains().elementAt(foundchain); |
796 | 0 | if (chain == mainchain) |
797 | { | |
798 | 0 | if (fatom.alignmentMapping != -1) |
799 | { | |
800 | 0 | if (highlightRes == null) |
801 | { | |
802 | 0 | highlightRes = new Vector<String>(); |
803 | } | |
804 | ||
805 | 0 | final String atomString = Integer |
806 | .toString(fatom.alignmentMapping); | |
807 | 0 | if (highlightRes.contains(atomString)) |
808 | { | |
809 | 0 | highlightRes.removeElement(atomString); |
810 | } | |
811 | else | |
812 | { | |
813 | 0 | highlightRes.addElement(atomString); |
814 | } | |
815 | } | |
816 | } | |
817 | } | |
818 | ||
819 | } | |
820 | 0 | mx = e.getX(); |
821 | 0 | my = e.getY(); |
822 | 0 | omx = mx; |
823 | 0 | omy = my; |
824 | 0 | dragging = false; |
825 | } | |
826 | ||
827 | 0 | @Override |
828 | public void mouseMoved(MouseEvent e) | |
829 | { | |
830 | 0 | pdbAction = true; |
831 | 0 | if (highlightBond1 != null) |
832 | { | |
833 | 0 | highlightBond1.at2.isSelected = false; |
834 | 0 | highlightBond2.at1.isSelected = false; |
835 | 0 | highlightBond1 = null; |
836 | 0 | highlightBond2 = null; |
837 | } | |
838 | ||
839 | 0 | Atom fatom = findAtom(e.getX(), e.getY()); |
840 | ||
841 | 0 | PDBChain chain = null; |
842 | 0 | if (foundchain != -1) |
843 | { | |
844 | 0 | chain = pdb.getChains().elementAt(foundchain); |
845 | 0 | if (chain == mainchain) |
846 | { | |
847 | 0 | mouseOverStructure(fatom.resNumber, chain.id); |
848 | } | |
849 | } | |
850 | ||
851 | 0 | if (fatom != null) |
852 | { | |
853 | 0 | toolx = e.getX(); |
854 | 0 | tooly = e.getY(); |
855 | ||
856 | 0 | appletToolTip = chain.id + ":" + fatom.resNumber + " " |
857 | + fatom.resName; | |
858 | 0 | redrawneeded = true; |
859 | 0 | repaint(); |
860 | } | |
861 | else | |
862 | { | |
863 | 0 | mouseOverStructure(-1, chain != null ? chain.id : null); |
864 | 0 | appletToolTip = null; |
865 | 0 | redrawneeded = true; |
866 | 0 | repaint(); |
867 | } | |
868 | } | |
869 | ||
870 | 0 | @Override |
871 | public void mouseClicked(MouseEvent e) | |
872 | { | |
873 | } | |
874 | ||
875 | 0 | @Override |
876 | public void mouseEntered(MouseEvent e) | |
877 | { | |
878 | } | |
879 | ||
880 | 0 | @Override |
881 | public void mouseExited(MouseEvent e) | |
882 | { | |
883 | } | |
884 | ||
885 | 0 | @Override |
886 | public void mouseDragged(MouseEvent evt) | |
887 | { | |
888 | 0 | int x = evt.getX(); |
889 | 0 | int y = evt.getY(); |
890 | 0 | mx = x; |
891 | 0 | my = y; |
892 | ||
893 | 0 | MCMatrix objmat = new MCMatrix(3, 3); |
894 | 0 | objmat.setIdentity(); |
895 | ||
896 | 0 | if ((evt.getModifiers() & Event.META_MASK) != 0) |
897 | { | |
898 | 0 | objmat.rotatez(((mx - omx))); |
899 | } | |
900 | else | |
901 | { | |
902 | 0 | objmat.rotatex(((omy - my))); |
903 | 0 | objmat.rotatey(((omx - mx))); |
904 | } | |
905 | ||
906 | // Alter the bonds | |
907 | 0 | for (PDBChain chain : pdb.getChains()) |
908 | { | |
909 | 0 | for (Bond tmpBond : chain.bonds) |
910 | { | |
911 | // Translate the bond so the centre is 0,0,0 | |
912 | 0 | tmpBond.translate(-centre[0], -centre[1], -centre[2]); |
913 | ||
914 | // Now apply the rotation matrix | |
915 | 0 | tmpBond.start = objmat.vectorMultiply(tmpBond.start); |
916 | 0 | tmpBond.end = objmat.vectorMultiply(tmpBond.end); |
917 | ||
918 | // Now translate back again | |
919 | 0 | tmpBond.translate(centre[0], centre[1], centre[2]); |
920 | } | |
921 | } | |
922 | ||
923 | 0 | objmat = null; |
924 | ||
925 | 0 | omx = mx; |
926 | 0 | omy = my; |
927 | ||
928 | 0 | dragging = true; |
929 | ||
930 | 0 | redrawneeded = true; |
931 | ||
932 | 0 | repaint(); |
933 | } | |
934 | ||
935 | 0 | @Override |
936 | public void mouseReleased(MouseEvent evt) | |
937 | { | |
938 | 0 | dragging = false; |
939 | 0 | return; |
940 | } | |
941 | ||
942 | 0 | void drawLabels(Graphics g) |
943 | { | |
944 | ||
945 | 0 | for (PDBChain chain : pdb.getChains()) |
946 | { | |
947 | 0 | if (chain.isVisible) |
948 | { | |
949 | 0 | for (Bond tmpBond : chain.bonds) |
950 | { | |
951 | 0 | if (tmpBond.at1.isSelected) |
952 | { | |
953 | 0 | labelAtom(g, tmpBond, 1); |
954 | } | |
955 | ||
956 | 0 | if (tmpBond.at2.isSelected) |
957 | { | |
958 | 0 | labelAtom(g, tmpBond, 2); |
959 | } | |
960 | } | |
961 | } | |
962 | } | |
963 | } | |
964 | ||
965 | 0 | public void labelAtom(Graphics g, Bond b, int n) |
966 | { | |
967 | 0 | g.setFont(font); |
968 | ||
969 | 0 | if (n == 1) |
970 | { | |
971 | 0 | int xstart = (int) (((b.start[0] - centre[0]) * scale) |
972 | + (getSize().width / 2)); | |
973 | 0 | int ystart = (int) (((centre[1] - b.start[1]) * scale) |
974 | + (getSize().height / 2)); | |
975 | ||
976 | 0 | g.setColor(Color.red); |
977 | 0 | g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart); |
978 | } | |
979 | ||
980 | 0 | if (n == 2) |
981 | { | |
982 | 0 | int xstart = (int) (((b.end[0] - centre[0]) * scale) |
983 | + (getSize().width / 2)); | |
984 | 0 | int ystart = (int) (((centre[1] - b.end[1]) * scale) |
985 | + (getSize().height / 2)); | |
986 | ||
987 | 0 | g.setColor(Color.red); |
988 | 0 | g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart); |
989 | } | |
990 | } | |
991 | ||
992 | int foundchain = -1; | |
993 | ||
994 | 0 | public Atom findAtom(int x, int y) |
995 | { | |
996 | 0 | Atom fatom = null; |
997 | ||
998 | 0 | foundchain = -1; |
999 | ||
1000 | 0 | for (int ii = 0; ii < pdb.getChains().size(); ii++) |
1001 | { | |
1002 | 0 | PDBChain chain = pdb.getChains().elementAt(ii); |
1003 | 0 | int truex; |
1004 | 0 | Bond tmpBond = null; |
1005 | ||
1006 | 0 | if (chain.isVisible) |
1007 | { | |
1008 | 0 | Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds; |
1009 | ||
1010 | 0 | for (int i = 0; i < bonds.size(); i++) |
1011 | { | |
1012 | 0 | tmpBond = bonds.elementAt(i); |
1013 | ||
1014 | 0 | truex = (int) (((tmpBond.start[0] - centre[0]) * scale) |
1015 | + (getSize().width / 2)); | |
1016 | ||
1017 | 0 | if (Math.abs(truex - x) <= 2) |
1018 | { | |
1019 | 0 | int truey = (int) (((centre[1] - tmpBond.start[1]) * scale) |
1020 | + (getSize().height / 2)); | |
1021 | ||
1022 | 0 | if (Math.abs(truey - y) <= 2) |
1023 | { | |
1024 | 0 | fatom = tmpBond.at1; |
1025 | 0 | foundchain = ii; |
1026 | 0 | break; |
1027 | } | |
1028 | } | |
1029 | } | |
1030 | ||
1031 | // Still here? Maybe its the last bond | |
1032 | ||
1033 | 0 | truex = (int) (((tmpBond.end[0] - centre[0]) * scale) |
1034 | + (getSize().width / 2)); | |
1035 | ||
1036 | 0 | if (Math.abs(truex - x) <= 2) |
1037 | { | |
1038 | 0 | int truey = (int) (((tmpBond.end[1] - centre[1]) * scale) |
1039 | + (getSize().height / 2)); | |
1040 | ||
1041 | 0 | if (Math.abs(truey - y) <= 2) |
1042 | { | |
1043 | 0 | fatom = tmpBond.at2; |
1044 | 0 | foundchain = ii; |
1045 | 0 | break; |
1046 | } | |
1047 | } | |
1048 | ||
1049 | } | |
1050 | ||
1051 | 0 | if (fatom != null) // )&& chain.ds != null) |
1052 | { | |
1053 | 0 | chain = pdb.getChains().elementAt(foundchain); |
1054 | } | |
1055 | } | |
1056 | ||
1057 | 0 | return fatom; |
1058 | } | |
1059 | ||
1060 | 0 | @Override |
1061 | public void update(Graphics g) | |
1062 | { | |
1063 | 0 | paint(g); |
1064 | } | |
1065 | ||
1066 | 0 | public void highlightRes(int ii) |
1067 | { | |
1068 | 0 | if (!seqColoursReady) |
1069 | { | |
1070 | 0 | return; |
1071 | } | |
1072 | ||
1073 | 0 | if (highlightRes != null && highlightRes.contains((ii - 1) + "")) |
1074 | { | |
1075 | 0 | return; |
1076 | } | |
1077 | ||
1078 | 0 | int index = -1; |
1079 | 0 | Bond tmpBond; |
1080 | 0 | for (index = 0; index < mainchain.bonds.size(); index++) |
1081 | { | |
1082 | 0 | tmpBond = mainchain.bonds.elementAt(index); |
1083 | 0 | if (tmpBond.at1.alignmentMapping == ii - 1) |
1084 | { | |
1085 | 0 | if (highlightBond1 != null) |
1086 | { | |
1087 | 0 | highlightBond1.at2.isSelected = false; |
1088 | } | |
1089 | ||
1090 | 0 | if (highlightBond2 != null) |
1091 | { | |
1092 | 0 | highlightBond2.at1.isSelected = false; |
1093 | } | |
1094 | ||
1095 | 0 | highlightBond1 = null; |
1096 | 0 | highlightBond2 = null; |
1097 | ||
1098 | 0 | if (index > 0) |
1099 | { | |
1100 | 0 | highlightBond1 = mainchain.bonds.elementAt(index - 1); |
1101 | 0 | highlightBond1.at2.isSelected = true; |
1102 | } | |
1103 | ||
1104 | 0 | if (index != mainchain.bonds.size()) |
1105 | { | |
1106 | 0 | highlightBond2 = mainchain.bonds.elementAt(index); |
1107 | 0 | highlightBond2.at1.isSelected = true; |
1108 | } | |
1109 | ||
1110 | 0 | break; |
1111 | } | |
1112 | } | |
1113 | ||
1114 | 0 | redrawneeded = true; |
1115 | 0 | repaint(); |
1116 | } | |
1117 | ||
1118 | 0 | public void setAllchainsVisible(boolean b) |
1119 | { | |
1120 | 0 | for (int ii = 0; ii < pdb.getChains().size(); ii++) |
1121 | { | |
1122 | 0 | PDBChain chain = pdb.getChains().elementAt(ii); |
1123 | 0 | chain.isVisible = b; |
1124 | } | |
1125 | 0 | mainchain.isVisible = true; |
1126 | 0 | findCentre(); |
1127 | 0 | setupBonds(); |
1128 | } | |
1129 | ||
1130 | // //////////////////////////////// | |
1131 | // /StructureListener | |
1132 | 0 | @Override |
1133 | public String[] getStructureFiles() | |
1134 | { | |
1135 | 0 | return new String[] { pdbentry.getFile() }; |
1136 | } | |
1137 | ||
1138 | String lastMessage; | |
1139 | ||
1140 | 0 | public void mouseOverStructure(int pdbResNum, String chain) |
1141 | { | |
1142 | 0 | if (lastMessage == null || !lastMessage.equals(pdbResNum + chain)) |
1143 | { | |
1144 | 0 | ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile()); |
1145 | } | |
1146 | ||
1147 | 0 | lastMessage = pdbResNum + chain; |
1148 | } | |
1149 | ||
1150 | StringBuffer resetLastRes = new StringBuffer(); | |
1151 | ||
1152 | StringBuffer eval = new StringBuffer(); | |
1153 | ||
1154 | /** | |
1155 | * Highlight the specified atoms in the structure. | |
1156 | * | |
1157 | * @param atoms | |
1158 | */ | |
1159 | 0 | @Override |
1160 | public void highlightAtoms(List<AtomSpec> atoms) | |
1161 | { | |
1162 | 0 | if (!seqColoursReady) |
1163 | { | |
1164 | 0 | return; |
1165 | } | |
1166 | 0 | for (AtomSpec atom : atoms) |
1167 | { | |
1168 | 0 | int atomIndex = atom.getAtomIndex(); |
1169 | ||
1170 | 0 | if (highlightRes != null |
1171 | && highlightRes.contains((atomIndex - 1) + "")) | |
1172 | { | |
1173 | 0 | continue; |
1174 | } | |
1175 | ||
1176 | 0 | highlightAtom(atomIndex); |
1177 | } | |
1178 | ||
1179 | 0 | redrawneeded = true; |
1180 | 0 | repaint(); |
1181 | } | |
1182 | ||
1183 | /** | |
1184 | * @param atomIndex | |
1185 | */ | |
1186 | 0 | protected void highlightAtom(int atomIndex) |
1187 | { | |
1188 | 0 | int index = -1; |
1189 | 0 | Bond tmpBond; |
1190 | 0 | for (index = 0; index < mainchain.bonds.size(); index++) |
1191 | { | |
1192 | 0 | tmpBond = mainchain.bonds.elementAt(index); |
1193 | 0 | if (tmpBond.at1.atomIndex == atomIndex) |
1194 | { | |
1195 | 0 | if (highlightBond1 != null) |
1196 | { | |
1197 | 0 | highlightBond1.at2.isSelected = false; |
1198 | } | |
1199 | ||
1200 | 0 | if (highlightBond2 != null) |
1201 | { | |
1202 | 0 | highlightBond2.at1.isSelected = false; |
1203 | } | |
1204 | ||
1205 | 0 | highlightBond1 = null; |
1206 | 0 | highlightBond2 = null; |
1207 | ||
1208 | 0 | if (index > 0) |
1209 | { | |
1210 | 0 | highlightBond1 = mainchain.bonds.elementAt(index - 1); |
1211 | 0 | highlightBond1.at2.isSelected = true; |
1212 | } | |
1213 | ||
1214 | 0 | if (index != mainchain.bonds.size()) |
1215 | { | |
1216 | 0 | highlightBond2 = mainchain.bonds.elementAt(index); |
1217 | 0 | highlightBond2.at1.isSelected = true; |
1218 | } | |
1219 | ||
1220 | 0 | break; |
1221 | } | |
1222 | } | |
1223 | } | |
1224 | ||
1225 | 0 | public Color getColour(int atomIndex, int pdbResNum, String chain, |
1226 | String pdbfile) | |
1227 | { | |
1228 | 0 | return Color.white; |
1229 | // if (!pdbfile.equals(pdbentry.getFile())) | |
1230 | // return null; | |
1231 | ||
1232 | // return new Color(viewer.getAtomArgb(atomIndex)); | |
1233 | } | |
1234 | ||
1235 | 0 | @Override |
1236 | public void updateColours(Object source) | |
1237 | { | |
1238 | 0 | colourBySequence(); |
1239 | 0 | redrawneeded = true; |
1240 | 0 | repaint(); |
1241 | } | |
1242 | ||
1243 | 0 | @Override |
1244 | public void releaseReferences(Object svl) | |
1245 | { | |
1246 | // TODO Auto-generated method stub | |
1247 | ||
1248 | } | |
1249 | ||
1250 | 0 | @Override |
1251 | public boolean isListeningFor(SequenceI seq) | |
1252 | { | |
1253 | 0 | if (sequence != null) |
1254 | { | |
1255 | 0 | for (SequenceI s : sequence) |
1256 | { | |
1257 | 0 | if (s == seq) |
1258 | { | |
1259 | 0 | return true; |
1260 | } | |
1261 | } | |
1262 | } | |
1263 | 0 | return false; |
1264 | } | |
1265 | } |