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PDBCanvas | 58 | 442 | 149 |
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.datamodel.PDBEntry; | |
25 | import jalview.datamodel.SequenceI; | |
26 | import jalview.gui.AlignmentPanel; | |
27 | import jalview.gui.FeatureRenderer; | |
28 | import jalview.gui.SequenceRenderer; | |
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 | ||
37 | import java.awt.Color; | |
38 | import java.awt.Dimension; | |
39 | import java.awt.Event; | |
40 | import java.awt.Font; | |
41 | import java.awt.Graphics; | |
42 | import java.awt.Graphics2D; | |
43 | // JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug | |
44 | import java.awt.Image; | |
45 | import java.awt.RenderingHints; | |
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 | import javax.swing.JPanel; | |
56 | import javax.swing.ToolTipManager; | |
57 | ||
58 | public class PDBCanvas extends JPanel | |
59 | implements MouseListener, MouseMotionListener, StructureListener | |
60 | { | |
61 | boolean redrawneeded = true; | |
62 | ||
63 | int omx = 0; | |
64 | ||
65 | int mx = 0; | |
66 | ||
67 | int omy = 0; | |
68 | ||
69 | int my = 0; | |
70 | ||
71 | public StructureFile pdb; | |
72 | ||
73 | PDBEntry pdbentry; | |
74 | ||
75 | int bsize; | |
76 | ||
77 | Image img; | |
78 | ||
79 | Graphics ig; | |
80 | ||
81 | Dimension prefsize; | |
82 | ||
83 | float[] centre = new float[3]; | |
84 | ||
85 | float[] width = new float[3]; | |
86 | ||
87 | float maxwidth; | |
88 | ||
89 | float scale; | |
90 | ||
91 | String inStr; | |
92 | ||
93 | String inType; | |
94 | ||
95 | boolean bysequence = true; | |
96 | ||
97 | boolean depthcue = true; | |
98 | ||
99 | boolean wire = false; | |
100 | ||
101 | boolean bymolecule = false; | |
102 | ||
103 | boolean zbuffer = true; | |
104 | ||
105 | boolean dragging; | |
106 | ||
107 | int xstart; | |
108 | ||
109 | int xend; | |
110 | ||
111 | int ystart; | |
112 | ||
113 | int yend; | |
114 | ||
115 | int xmid; | |
116 | ||
117 | int ymid; | |
118 | ||
119 | Font font = new Font("Helvetica", Font.PLAIN, 10); | |
120 | ||
121 | jalview.gui.SeqCanvas seqcanvas; | |
122 | ||
123 | public SequenceI[] sequence; | |
124 | ||
125 | final StringBuffer mappingDetails = new StringBuffer(); | |
126 | ||
127 | PDBChain mainchain; | |
128 | ||
129 | Vector<String> highlightRes; | |
130 | ||
131 | boolean pdbAction = false; | |
132 | ||
133 | boolean seqColoursReady = false; | |
134 | ||
135 | jalview.renderer.seqfeatures.FeatureRenderer fr; | |
136 | ||
137 | Color backgroundColour = Color.black; | |
138 | ||
139 | AlignmentPanel ap; | |
140 | ||
141 | StructureSelectionManager ssm; | |
142 | ||
143 | String errorMessage; | |
144 | ||
145 | 0 | void init(PDBEntry pdbentry, SequenceI[] seq, String[] chains, |
146 | AlignmentPanel ap, DataSourceType protocol) | |
147 | { | |
148 | 0 | this.ap = ap; |
149 | 0 | this.pdbentry = pdbentry; |
150 | 0 | this.sequence = seq; |
151 | ||
152 | 0 | ssm = ap.av.getStructureSelectionManager(); |
153 | ||
154 | 0 | try |
155 | { | |
156 | 0 | pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol, |
157 | ap.alignFrame); | |
158 | ||
159 | 0 | if (protocol.equals(jalview.io.DataSourceType.PASTE)) |
160 | { | |
161 | 0 | pdbentry.setFile("INLINE" + pdb.getId()); |
162 | } | |
163 | ||
164 | } catch (Exception ex) | |
165 | { | |
166 | 0 | ex.printStackTrace(); |
167 | 0 | return; |
168 | } | |
169 | ||
170 | 0 | if (pdb == null) |
171 | { | |
172 | 0 | errorMessage = "Error loading file: " + pdbentry.getId(); |
173 | 0 | return; |
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 | 0 | AlignSeq as = new AlignSeq(sequence, |
204 | pdb.getChains().elementAt(i).sequence, "pep"); | |
205 | 0 | as.calcScoreMatrix(); |
206 | 0 | as.traceAlignment(); |
207 | 0 | PrintStream ps = new PrintStream(System.out) |
208 | { | |
209 | 0 | @Override |
210 | public void print(String x) | |
211 | { | |
212 | 0 | mappingDetails.append(x); |
213 | } | |
214 | ||
215 | 0 | @Override |
216 | public void println() | |
217 | { | |
218 | 0 | mappingDetails.append("\n"); |
219 | } | |
220 | }; | |
221 | ||
222 | 0 | as.printAlignment(ps); |
223 | ||
224 | 0 | if (as.maxscore > max) |
225 | { | |
226 | 0 | max = as.maxscore; |
227 | 0 | maxchain = i; |
228 | ||
229 | 0 | pdbstart = as.seq2start; |
230 | 0 | pdbend = as.seq2end; |
231 | 0 | seqstart = as.seq1start + sequence.getStart() - 1; |
232 | 0 | seqend = as.seq1end + sequence.getEnd() - 1; |
233 | } | |
234 | ||
235 | 0 | mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend); |
236 | 0 | mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend); |
237 | } | |
238 | ||
239 | 0 | mainchain = pdb.getChains().elementAt(maxchain); |
240 | ||
241 | 0 | mainchain.pdbstart = pdbstart; |
242 | 0 | mainchain.pdbend = pdbend; |
243 | 0 | mainchain.seqstart = seqstart; |
244 | 0 | mainchain.seqend = seqend; |
245 | 0 | mainchain.isVisible = true; |
246 | ||
247 | 0 | this.pdb = pdb; |
248 | 0 | this.prefsize = new Dimension(getSize().width, getSize().height); |
249 | ||
250 | 0 | addMouseMotionListener(this); |
251 | 0 | addMouseListener(this); |
252 | ||
253 | 0 | addKeyListener(new KeyAdapter() |
254 | { | |
255 | 0 | @Override |
256 | public void keyPressed(KeyEvent evt) | |
257 | { | |
258 | 0 | keyPressed(evt); |
259 | } | |
260 | }); | |
261 | ||
262 | 0 | findCentre(); |
263 | 0 | findWidth(); |
264 | ||
265 | 0 | setupBonds(); |
266 | ||
267 | 0 | scale = findScale(); |
268 | ||
269 | 0 | ToolTipManager.sharedInstance().registerComponent(this); |
270 | 0 | ToolTipManager.sharedInstance().setInitialDelay(0); |
271 | 0 | ToolTipManager.sharedInstance().setDismissDelay(10000); |
272 | } | |
273 | ||
274 | Vector<Bond> visiblebonds; | |
275 | ||
276 | 0 | void setupBonds() |
277 | { | |
278 | 0 | seqColoursReady = false; |
279 | // Sort the bonds by z coord | |
280 | 0 | visiblebonds = new Vector<Bond>(); |
281 | ||
282 | 0 | for (PDBChain chain : pdb.getChains()) |
283 | { | |
284 | 0 | if (chain.isVisible) |
285 | { | |
286 | 0 | for (Bond bond : chain.bonds) |
287 | { | |
288 | 0 | visiblebonds.addElement(bond); |
289 | } | |
290 | } | |
291 | } | |
292 | ||
293 | 0 | updateSeqColours(); |
294 | 0 | seqColoursReady = true; |
295 | 0 | redrawneeded = true; |
296 | 0 | repaint(); |
297 | } | |
298 | ||
299 | 0 | public void findWidth() |
300 | { | |
301 | 0 | float[] max = new float[3]; |
302 | 0 | float[] min = new float[3]; |
303 | ||
304 | 0 | max[0] = (float) -1e30; |
305 | 0 | max[1] = (float) -1e30; |
306 | 0 | max[2] = (float) -1e30; |
307 | ||
308 | 0 | min[0] = (float) 1e30; |
309 | 0 | min[1] = (float) 1e30; |
310 | 0 | min[2] = (float) 1e30; |
311 | ||
312 | 0 | for (PDBChain chain : pdb.getChains()) |
313 | { | |
314 | 0 | if (chain.isVisible) |
315 | { | |
316 | 0 | for (Bond tmp : chain.bonds) |
317 | { | |
318 | 0 | if (tmp.start[0] >= max[0]) |
319 | { | |
320 | 0 | max[0] = tmp.start[0]; |
321 | } | |
322 | ||
323 | 0 | if (tmp.start[1] >= max[1]) |
324 | { | |
325 | 0 | max[1] = tmp.start[1]; |
326 | } | |
327 | ||
328 | 0 | if (tmp.start[2] >= max[2]) |
329 | { | |
330 | 0 | max[2] = tmp.start[2]; |
331 | } | |
332 | ||
333 | 0 | if (tmp.start[0] <= min[0]) |
334 | { | |
335 | 0 | min[0] = tmp.start[0]; |
336 | } | |
337 | ||
338 | 0 | if (tmp.start[1] <= min[1]) |
339 | { | |
340 | 0 | min[1] = tmp.start[1]; |
341 | } | |
342 | ||
343 | 0 | if (tmp.start[2] <= min[2]) |
344 | { | |
345 | 0 | min[2] = tmp.start[2]; |
346 | } | |
347 | ||
348 | 0 | if (tmp.end[0] >= max[0]) |
349 | { | |
350 | 0 | max[0] = tmp.end[0]; |
351 | } | |
352 | ||
353 | 0 | if (tmp.end[1] >= max[1]) |
354 | { | |
355 | 0 | max[1] = tmp.end[1]; |
356 | } | |
357 | ||
358 | 0 | if (tmp.end[2] >= max[2]) |
359 | { | |
360 | 0 | max[2] = tmp.end[2]; |
361 | } | |
362 | ||
363 | 0 | if (tmp.end[0] <= min[0]) |
364 | { | |
365 | 0 | min[0] = tmp.end[0]; |
366 | } | |
367 | ||
368 | 0 | if (tmp.end[1] <= min[1]) |
369 | { | |
370 | 0 | min[1] = tmp.end[1]; |
371 | } | |
372 | ||
373 | 0 | if (tmp.end[2] <= min[2]) |
374 | { | |
375 | 0 | min[2] = tmp.end[2]; |
376 | } | |
377 | } | |
378 | } | |
379 | } | |
380 | /* | |
381 | * System.out.println("xmax " + max[0] + " min " + min[0]); | |
382 | * System.out.println("ymax " + max[1] + " min " + min[1]); | |
383 | * System.out.println("zmax " + max[2] + " min " + min[2]); | |
384 | */ | |
385 | ||
386 | 0 | width[0] = Math.abs(max[0] - min[0]); |
387 | 0 | width[1] = Math.abs(max[1] - min[1]); |
388 | 0 | width[2] = Math.abs(max[2] - min[2]); |
389 | ||
390 | 0 | maxwidth = width[0]; |
391 | ||
392 | 0 | if (width[1] > width[0]) |
393 | { | |
394 | 0 | maxwidth = width[1]; |
395 | } | |
396 | ||
397 | 0 | if (width[2] > width[1]) |
398 | { | |
399 | 0 | maxwidth = width[2]; |
400 | } | |
401 | ||
402 | // System.out.println("Maxwidth = " + maxwidth); | |
403 | } | |
404 | ||
405 | 0 | public float findScale() |
406 | { | |
407 | 0 | int dim; |
408 | 0 | int width; |
409 | 0 | int height; |
410 | ||
411 | 0 | if (getWidth() != 0) |
412 | { | |
413 | 0 | width = getWidth(); |
414 | 0 | height = getHeight(); |
415 | } | |
416 | else | |
417 | { | |
418 | 0 | width = prefsize.width; |
419 | 0 | height = prefsize.height; |
420 | } | |
421 | ||
422 | 0 | if (width < height) |
423 | { | |
424 | 0 | dim = width; |
425 | } | |
426 | else | |
427 | { | |
428 | 0 | dim = height; |
429 | } | |
430 | ||
431 | 0 | return (float) (dim / (1.5d * maxwidth)); |
432 | } | |
433 | ||
434 | 0 | public void findCentre() |
435 | { | |
436 | 0 | float xtot = 0; |
437 | 0 | float ytot = 0; |
438 | 0 | float ztot = 0; |
439 | ||
440 | 0 | int bsize = 0; |
441 | ||
442 | // Find centre coordinate | |
443 | 0 | for (PDBChain chain : pdb.getChains()) |
444 | { | |
445 | 0 | if (chain.isVisible) |
446 | { | |
447 | 0 | bsize += chain.bonds.size(); |
448 | ||
449 | 0 | for (Bond bond : chain.bonds) |
450 | { | |
451 | 0 | xtot = xtot + bond.start[0] + bond.end[0]; |
452 | 0 | ytot = ytot + bond.start[1] + bond.end[1]; |
453 | 0 | ztot = ztot + bond.start[2] + bond.end[2]; |
454 | } | |
455 | } | |
456 | } | |
457 | ||
458 | 0 | centre[0] = xtot / (2 * (float) bsize); |
459 | 0 | centre[1] = ytot / (2 * (float) bsize); |
460 | 0 | centre[2] = ztot / (2 * (float) bsize); |
461 | } | |
462 | ||
463 | 0 | @Override |
464 | public void paintComponent(Graphics g) | |
465 | { | |
466 | 0 | super.paintComponent(g); |
467 | ||
468 | 0 | if (!seqColoursReady || errorMessage != null) |
469 | { | |
470 | 0 | g.setColor(Color.black); |
471 | 0 | g.setFont(new Font("Verdana", Font.BOLD, 14)); |
472 | 0 | g.drawString(errorMessage == null ? "Retrieving PDB data...." |
473 | : errorMessage, 20, getHeight() / 2); | |
474 | 0 | return; |
475 | } | |
476 | ||
477 | // Only create the image at the beginning - | |
478 | // this saves much memory usage | |
479 | 0 | if ((img == null) || (prefsize.width != getWidth()) |
480 | || (prefsize.height != getHeight())) | |
481 | ||
482 | { | |
483 | 0 | prefsize.width = getWidth(); |
484 | 0 | prefsize.height = getHeight(); |
485 | ||
486 | 0 | scale = findScale(); |
487 | 0 | img = createImage(prefsize.width, prefsize.height); |
488 | 0 | ig = img.getGraphics(); |
489 | 0 | Graphics2D ig2 = (Graphics2D) ig; |
490 | ||
491 | 0 | ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, |
492 | RenderingHints.VALUE_ANTIALIAS_ON); | |
493 | ||
494 | 0 | redrawneeded = true; |
495 | } | |
496 | ||
497 | 0 | if (redrawneeded) |
498 | { | |
499 | 0 | drawAll(ig, prefsize.width, prefsize.height); |
500 | 0 | redrawneeded = false; |
501 | } | |
502 | ||
503 | 0 | g.drawImage(img, 0, 0, this); |
504 | ||
505 | 0 | pdbAction = false; |
506 | } | |
507 | ||
508 | 0 | public void drawAll(Graphics g, int width, int height) |
509 | { | |
510 | 0 | g.setColor(backgroundColour); |
511 | 0 | g.fillRect(0, 0, width, height); |
512 | 0 | drawScene(g); |
513 | 0 | drawLabels(g); |
514 | } | |
515 | ||
516 | 0 | public void updateSeqColours() |
517 | { | |
518 | 0 | if (pdbAction) |
519 | { | |
520 | 0 | return; |
521 | } | |
522 | ||
523 | 0 | colourBySequence(); |
524 | ||
525 | 0 | redrawneeded = true; |
526 | 0 | repaint(); |
527 | } | |
528 | ||
529 | // This method has been taken out of PDBChain to allow | |
530 | // Applet and Application specific sequence renderers to be used | |
531 | 0 | void colourBySequence() |
532 | { | |
533 | 0 | SequenceRenderer sr = new SequenceRenderer(ap.av); |
534 | ||
535 | 0 | StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile()); |
536 | ||
537 | 0 | boolean showFeatures = false; |
538 | 0 | if (ap.av.isShowSequenceFeatures()) |
539 | { | |
540 | 0 | if (fr == null) |
541 | { | |
542 | 0 | fr = new FeatureRenderer(ap); |
543 | } | |
544 | ||
545 | 0 | fr.transferSettings(ap.alignFrame.getFeatureRenderer()); |
546 | ||
547 | 0 | showFeatures = true; |
548 | } | |
549 | ||
550 | 0 | FeatureColourFinder finder = new FeatureColourFinder(fr); |
551 | 0 | PDBChain chain; |
552 | 0 | if (bysequence && pdb != null) |
553 | { | |
554 | 0 | for (int ii = 0; ii < pdb.getChains().size(); ii++) |
555 | { | |
556 | 0 | chain = pdb.getChains().elementAt(ii); |
557 | ||
558 | 0 | for (int i = 0; i < chain.bonds.size(); i++) |
559 | { | |
560 | 0 | Bond tmp = chain.bonds.elementAt(i); |
561 | 0 | tmp.startCol = Color.lightGray; |
562 | 0 | tmp.endCol = Color.lightGray; |
563 | 0 | if (chain != mainchain) |
564 | { | |
565 | 0 | continue; |
566 | } | |
567 | ||
568 | 0 | for (int s = 0; s < sequence.length; s++) |
569 | { | |
570 | 0 | for (int m = 0; m < mapping.length; m++) |
571 | { | |
572 | 0 | if (mapping[m].getSequence() == sequence[s]) |
573 | { | |
574 | 0 | int pos = mapping[m].getSeqPos(tmp.at1.resNumber) - 1; |
575 | 0 | if (pos > 0) |
576 | { | |
577 | 0 | pos = sequence[s].findIndex(pos); |
578 | 0 | tmp.startCol = sr.getResidueColour(sequence[s], pos, |
579 | finder); | |
580 | } | |
581 | 0 | pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1; |
582 | 0 | if (pos > 0) |
583 | { | |
584 | 0 | pos = sequence[s].findIndex(pos); |
585 | 0 | tmp.endCol = sr.getResidueColour(sequence[s], pos, |
586 | finder); | |
587 | } | |
588 | ||
589 | } | |
590 | } | |
591 | } | |
592 | } | |
593 | } | |
594 | } | |
595 | } | |
596 | ||
597 | Zsort zsort; | |
598 | ||
599 | 0 | public void drawScene(Graphics g) |
600 | { | |
601 | 0 | if (zbuffer) |
602 | { | |
603 | 0 | if (zsort == null) |
604 | { | |
605 | 0 | zsort = new Zsort(); |
606 | } | |
607 | ||
608 | 0 | zsort.sort(visiblebonds); |
609 | } | |
610 | ||
611 | 0 | Bond tmpBond = null; |
612 | 0 | for (int i = 0; i < visiblebonds.size(); i++) |
613 | { | |
614 | 0 | tmpBond = visiblebonds.elementAt(i); |
615 | ||
616 | 0 | xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) |
617 | + (getWidth() / 2)); | |
618 | 0 | ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) |
619 | + (getHeight() / 2)); | |
620 | ||
621 | 0 | xend = (int) (((tmpBond.end[0] - centre[0]) * scale) |
622 | + (getWidth() / 2)); | |
623 | 0 | yend = (int) (((centre[1] - tmpBond.end[1]) * scale) |
624 | + (getHeight() / 2)); | |
625 | ||
626 | 0 | xmid = (xend + xstart) / 2; |
627 | 0 | ymid = (yend + ystart) / 2; |
628 | 0 | if (depthcue && !bymolecule) |
629 | { | |
630 | 0 | if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) |
631 | { | |
632 | ||
633 | 0 | g.setColor(tmpBond.startCol.darker().darker()); |
634 | 0 | drawLine(g, xstart, ystart, xmid, ymid); |
635 | 0 | g.setColor(tmpBond.endCol.darker().darker()); |
636 | 0 | drawLine(g, xmid, ymid, xend, yend); |
637 | ||
638 | } | |
639 | 0 | else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) |
640 | { | |
641 | 0 | g.setColor(tmpBond.startCol.darker()); |
642 | 0 | drawLine(g, xstart, ystart, xmid, ymid); |
643 | ||
644 | 0 | g.setColor(tmpBond.endCol.darker()); |
645 | 0 | drawLine(g, xmid, ymid, xend, yend); |
646 | } | |
647 | else | |
648 | { | |
649 | 0 | g.setColor(tmpBond.startCol); |
650 | 0 | drawLine(g, xstart, ystart, xmid, ymid); |
651 | ||
652 | 0 | g.setColor(tmpBond.endCol); |
653 | 0 | drawLine(g, xmid, ymid, xend, yend); |
654 | } | |
655 | } | |
656 | 0 | else if (depthcue && bymolecule) |
657 | { | |
658 | 0 | if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) |
659 | { | |
660 | 0 | g.setColor(Color.green.darker().darker()); |
661 | 0 | drawLine(g, xstart, ystart, xend, yend); |
662 | } | |
663 | 0 | else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) |
664 | { | |
665 | 0 | g.setColor(Color.green.darker()); |
666 | 0 | drawLine(g, xstart, ystart, xend, yend); |
667 | } | |
668 | else | |
669 | { | |
670 | 0 | g.setColor(Color.green); |
671 | 0 | drawLine(g, xstart, ystart, xend, yend); |
672 | } | |
673 | } | |
674 | 0 | else if (!depthcue && !bymolecule) |
675 | { | |
676 | 0 | g.setColor(tmpBond.startCol); |
677 | 0 | drawLine(g, xstart, ystart, xmid, ymid); |
678 | 0 | g.setColor(tmpBond.endCol); |
679 | 0 | drawLine(g, xmid, ymid, xend, yend); |
680 | } | |
681 | else | |
682 | { | |
683 | 0 | drawLine(g, xstart, ystart, xend, yend); |
684 | } | |
685 | ||
686 | 0 | if (highlightBond1 != null && highlightBond1 == tmpBond) |
687 | { | |
688 | 0 | g.setColor( |
689 | tmpBond.endCol.brighter().brighter().brighter().brighter()); | |
690 | 0 | drawLine(g, xmid, ymid, xend, yend); |
691 | } | |
692 | ||
693 | 0 | if (highlightBond2 != null && highlightBond2 == tmpBond) |
694 | { | |
695 | 0 | g.setColor(tmpBond.startCol.brighter().brighter().brighter() |
696 | .brighter()); | |
697 | 0 | drawLine(g, xstart, ystart, xmid, ymid); |
698 | } | |
699 | ||
700 | } | |
701 | ||
702 | } | |
703 | ||
704 | 0 | public void drawLine(Graphics g, int x1, int y1, int x2, int y2) |
705 | { | |
706 | 0 | if (!wire) |
707 | { | |
708 | 0 | if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5) |
709 | { | |
710 | 0 | g.drawLine(x1, y1, x2, y2); |
711 | 0 | g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1); |
712 | 0 | g.drawLine(x1, y1 - 1, x2, y2 - 1); |
713 | } | |
714 | else | |
715 | { | |
716 | 0 | g.setColor(g.getColor().brighter()); |
717 | 0 | g.drawLine(x1, y1, x2, y2); |
718 | 0 | g.drawLine(x1 + 1, y1, x2 + 1, y2); |
719 | 0 | g.drawLine(x1 - 1, y1, x2 - 1, y2); |
720 | } | |
721 | } | |
722 | else | |
723 | { | |
724 | 0 | g.drawLine(x1, y1, x2, y2); |
725 | } | |
726 | } | |
727 | ||
728 | 0 | public Dimension minimumsize() |
729 | { | |
730 | 0 | return prefsize; |
731 | } | |
732 | ||
733 | 0 | public Dimension preferredsize() |
734 | { | |
735 | 0 | return prefsize; |
736 | } | |
737 | ||
738 | 0 | public void keyPressed(KeyEvent evt) |
739 | { | |
740 | 0 | if (evt.getKeyCode() == KeyEvent.VK_UP) |
741 | { | |
742 | 0 | scale = (float) (scale * 1.1); |
743 | 0 | redrawneeded = true; |
744 | 0 | repaint(); |
745 | } | |
746 | 0 | else if (evt.getKeyCode() == KeyEvent.VK_DOWN) |
747 | { | |
748 | 0 | scale = (float) (scale * 0.9); |
749 | 0 | redrawneeded = true; |
750 | 0 | repaint(); |
751 | } | |
752 | } | |
753 | ||
754 | 0 | @Override |
755 | public void mousePressed(MouseEvent e) | |
756 | { | |
757 | 0 | pdbAction = true; |
758 | 0 | Atom fatom = findAtom(e.getX(), e.getY()); |
759 | 0 | if (fatom != null) |
760 | { | |
761 | 0 | fatom.isSelected = !fatom.isSelected; |
762 | ||
763 | 0 | redrawneeded = true; |
764 | 0 | repaint(); |
765 | 0 | if (foundchain != -1) |
766 | { | |
767 | 0 | PDBChain chain = pdb.getChains().elementAt(foundchain); |
768 | 0 | if (chain == mainchain) |
769 | { | |
770 | 0 | if (fatom.alignmentMapping != -1) |
771 | { | |
772 | 0 | if (highlightRes == null) |
773 | { | |
774 | 0 | highlightRes = new Vector<String>(); |
775 | } | |
776 | ||
777 | 0 | final String atomString = Integer |
778 | .toString(fatom.alignmentMapping); | |
779 | 0 | if (highlightRes.contains(atomString)) |
780 | { | |
781 | 0 | highlightRes.remove(atomString); |
782 | } | |
783 | else | |
784 | { | |
785 | 0 | highlightRes.add(atomString); |
786 | } | |
787 | } | |
788 | } | |
789 | } | |
790 | ||
791 | } | |
792 | 0 | mx = e.getX(); |
793 | 0 | my = e.getY(); |
794 | 0 | omx = mx; |
795 | 0 | omy = my; |
796 | 0 | dragging = false; |
797 | } | |
798 | ||
799 | 0 | @Override |
800 | public void mouseMoved(MouseEvent e) | |
801 | { | |
802 | 0 | pdbAction = true; |
803 | 0 | if (highlightBond1 != null) |
804 | { | |
805 | 0 | highlightBond1.at2.isSelected = false; |
806 | 0 | highlightBond2.at1.isSelected = false; |
807 | 0 | highlightBond1 = null; |
808 | 0 | highlightBond2 = null; |
809 | } | |
810 | ||
811 | 0 | Atom fatom = findAtom(e.getX(), e.getY()); |
812 | ||
813 | 0 | PDBChain chain = null; |
814 | 0 | if (foundchain != -1) |
815 | { | |
816 | 0 | chain = pdb.getChains().elementAt(foundchain); |
817 | 0 | if (chain == mainchain) |
818 | { | |
819 | 0 | mouseOverStructure(fatom.resNumber, chain.id); |
820 | } | |
821 | } | |
822 | ||
823 | 0 | if (fatom != null) |
824 | { | |
825 | 0 | this.setToolTipText( |
826 | chain.id + ":" + fatom.resNumber + " " + fatom.resName); | |
827 | } | |
828 | else | |
829 | { | |
830 | 0 | mouseOverStructure(-1, chain != null ? chain.id : null); |
831 | 0 | this.setToolTipText(null); |
832 | } | |
833 | } | |
834 | ||
835 | 0 | @Override |
836 | public void mouseClicked(MouseEvent e) | |
837 | { | |
838 | } | |
839 | ||
840 | 0 | @Override |
841 | public void mouseEntered(MouseEvent e) | |
842 | { | |
843 | } | |
844 | ||
845 | 0 | @Override |
846 | public void mouseExited(MouseEvent e) | |
847 | { | |
848 | } | |
849 | ||
850 | 0 | @Override |
851 | public void mouseDragged(MouseEvent evt) | |
852 | { | |
853 | 0 | int x = evt.getX(); |
854 | 0 | int y = evt.getY(); |
855 | 0 | mx = x; |
856 | 0 | my = y; |
857 | ||
858 | 0 | MCMatrix objmat = new MCMatrix(3, 3); |
859 | 0 | objmat.setIdentity(); |
860 | ||
861 | 0 | if ((evt.getModifiers() & Event.META_MASK) != 0) |
862 | { | |
863 | 0 | objmat.rotatez(((mx - omx))); |
864 | } | |
865 | else | |
866 | { | |
867 | 0 | objmat.rotatex(((my - omy))); |
868 | 0 | objmat.rotatey(((omx - mx))); |
869 | } | |
870 | ||
871 | // Alter the bonds | |
872 | 0 | for (PDBChain chain : pdb.getChains()) |
873 | { | |
874 | 0 | for (Bond tmpBond : chain.bonds) |
875 | { | |
876 | // Translate the bond so the centre is 0,0,0 | |
877 | 0 | tmpBond.translate(-centre[0], -centre[1], -centre[2]); |
878 | ||
879 | // Now apply the rotation matrix | |
880 | 0 | tmpBond.start = objmat.vectorMultiply(tmpBond.start); |
881 | 0 | tmpBond.end = objmat.vectorMultiply(tmpBond.end); |
882 | ||
883 | // Now translate back again | |
884 | 0 | tmpBond.translate(centre[0], centre[1], centre[2]); |
885 | } | |
886 | } | |
887 | ||
888 | 0 | objmat = null; |
889 | ||
890 | 0 | omx = mx; |
891 | 0 | omy = my; |
892 | ||
893 | 0 | dragging = true; |
894 | ||
895 | 0 | redrawneeded = true; |
896 | ||
897 | 0 | repaint(); |
898 | } | |
899 | ||
900 | 0 | @Override |
901 | public void mouseReleased(MouseEvent evt) | |
902 | { | |
903 | 0 | dragging = false; |
904 | 0 | return; |
905 | } | |
906 | ||
907 | 0 | void drawLabels(Graphics g) |
908 | { | |
909 | ||
910 | 0 | for (PDBChain chain : pdb.getChains()) |
911 | { | |
912 | 0 | if (chain.isVisible) |
913 | { | |
914 | 0 | for (Bond tmpBond : chain.bonds) |
915 | { | |
916 | 0 | if (tmpBond.at1.isSelected) |
917 | { | |
918 | 0 | labelAtom(g, tmpBond, 1); |
919 | } | |
920 | ||
921 | 0 | if (tmpBond.at2.isSelected) |
922 | { | |
923 | 0 | labelAtom(g, tmpBond, 2); |
924 | } | |
925 | } | |
926 | } | |
927 | } | |
928 | } | |
929 | ||
930 | 0 | public void labelAtom(Graphics g, Bond b, int n) |
931 | { | |
932 | 0 | g.setFont(font); |
933 | 0 | g.setColor(Color.red); |
934 | 0 | if (n == 1) |
935 | { | |
936 | 0 | int xstart = (int) (((b.start[0] - centre[0]) * scale) |
937 | + (getWidth() / 2)); | |
938 | 0 | int ystart = (int) (((centre[1] - b.start[1]) * scale) |
939 | + (getHeight() / 2)); | |
940 | ||
941 | 0 | g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart); |
942 | } | |
943 | ||
944 | 0 | if (n == 2) |
945 | { | |
946 | 0 | int xstart = (int) (((b.end[0] - centre[0]) * scale) |
947 | + (getWidth() / 2)); | |
948 | 0 | int ystart = (int) (((centre[1] - b.end[1]) * scale) |
949 | + (getHeight() / 2)); | |
950 | ||
951 | 0 | g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart); |
952 | } | |
953 | } | |
954 | ||
955 | int foundchain = -1; | |
956 | ||
957 | 0 | public Atom findAtom(int x, int y) |
958 | { | |
959 | 0 | Atom fatom = null; |
960 | ||
961 | 0 | foundchain = -1; |
962 | ||
963 | 0 | for (int ii = 0; ii < pdb.getChains().size(); ii++) |
964 | { | |
965 | 0 | PDBChain chain = pdb.getChains().elementAt(ii); |
966 | 0 | int truex; |
967 | 0 | Bond tmpBond = null; |
968 | ||
969 | 0 | if (chain.isVisible) |
970 | { | |
971 | 0 | for (Bond bond : chain.bonds) |
972 | { | |
973 | 0 | tmpBond = bond; |
974 | ||
975 | 0 | truex = (int) (((tmpBond.start[0] - centre[0]) * scale) |
976 | + (getWidth() / 2)); | |
977 | ||
978 | 0 | if (Math.abs(truex - x) <= 2) |
979 | { | |
980 | 0 | int truey = (int) (((centre[1] - tmpBond.start[1]) * scale) |
981 | + (getHeight() / 2)); | |
982 | ||
983 | 0 | if (Math.abs(truey - y) <= 2) |
984 | { | |
985 | 0 | fatom = tmpBond.at1; |
986 | 0 | foundchain = ii; |
987 | 0 | break; |
988 | } | |
989 | } | |
990 | } | |
991 | ||
992 | // Still here? Maybe its the last bond | |
993 | ||
994 | 0 | truex = (int) (((tmpBond.end[0] - centre[0]) * scale) |
995 | + (getWidth() / 2)); | |
996 | ||
997 | 0 | if (Math.abs(truex - x) <= 2) |
998 | { | |
999 | 0 | int truey = (int) (((tmpBond.end[1] - centre[1]) * scale) |
1000 | + (getHeight() / 2)); | |
1001 | ||
1002 | 0 | if (Math.abs(truey - y) <= 2) |
1003 | { | |
1004 | 0 | fatom = tmpBond.at2; |
1005 | 0 | foundchain = ii; |
1006 | 0 | break; |
1007 | } | |
1008 | } | |
1009 | ||
1010 | } | |
1011 | ||
1012 | 0 | if (fatom != null) // )&& chain.ds != null) |
1013 | { // dead code? value of chain is either overwritten or discarded | |
1014 | 0 | chain = pdb.getChains().elementAt(foundchain); |
1015 | } | |
1016 | } | |
1017 | ||
1018 | 0 | return fatom; |
1019 | } | |
1020 | ||
1021 | Bond highlightBond1, highlightBond2; | |
1022 | ||
1023 | 0 | public void highlightRes(int ii) |
1024 | { | |
1025 | 0 | if (!seqColoursReady) |
1026 | { | |
1027 | 0 | return; |
1028 | } | |
1029 | ||
1030 | 0 | if (highlightRes != null && highlightRes.contains((ii - 1) + "")) |
1031 | { | |
1032 | 0 | return; |
1033 | } | |
1034 | ||
1035 | 0 | int index = -1; |
1036 | 0 | Bond tmpBond; |
1037 | 0 | for (index = 0; index < mainchain.bonds.size(); index++) |
1038 | { | |
1039 | 0 | tmpBond = mainchain.bonds.elementAt(index); |
1040 | 0 | if (tmpBond.at1.alignmentMapping == ii - 1) |
1041 | { | |
1042 | 0 | if (highlightBond1 != null) |
1043 | { | |
1044 | 0 | highlightBond1.at2.isSelected = false; |
1045 | } | |
1046 | ||
1047 | 0 | if (highlightBond2 != null) |
1048 | { | |
1049 | 0 | highlightBond2.at1.isSelected = false; |
1050 | } | |
1051 | ||
1052 | 0 | highlightBond1 = null; |
1053 | 0 | highlightBond2 = null; |
1054 | ||
1055 | 0 | if (index > 0) |
1056 | { | |
1057 | 0 | highlightBond1 = mainchain.bonds.elementAt(index - 1); |
1058 | 0 | highlightBond1.at2.isSelected = true; |
1059 | } | |
1060 | ||
1061 | 0 | if (index != mainchain.bonds.size()) |
1062 | { | |
1063 | 0 | highlightBond2 = mainchain.bonds.elementAt(index); |
1064 | 0 | highlightBond2.at1.isSelected = true; |
1065 | } | |
1066 | ||
1067 | 0 | break; |
1068 | } | |
1069 | } | |
1070 | ||
1071 | 0 | redrawneeded = true; |
1072 | 0 | repaint(); |
1073 | } | |
1074 | ||
1075 | 0 | public void setAllchainsVisible(boolean b) |
1076 | { | |
1077 | 0 | for (int ii = 0; ii < pdb.getChains().size(); ii++) |
1078 | { | |
1079 | 0 | PDBChain chain = pdb.getChains().elementAt(ii); |
1080 | 0 | chain.isVisible = b; |
1081 | } | |
1082 | 0 | mainchain.isVisible = true; |
1083 | 0 | findCentre(); |
1084 | 0 | setupBonds(); |
1085 | } | |
1086 | ||
1087 | // //////////////////////////////// | |
1088 | // /StructureListener | |
1089 | 0 | @Override |
1090 | public String[] getStructureFiles() | |
1091 | { | |
1092 | 0 | return new String[] { pdbentry.getFile() }; |
1093 | } | |
1094 | ||
1095 | String lastMessage; | |
1096 | ||
1097 | 0 | public void mouseOverStructure(int pdbResNum, String chain) |
1098 | { | |
1099 | 0 | if (lastMessage == null || !lastMessage.equals(pdbResNum + chain)) |
1100 | { | |
1101 | 0 | ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile()); |
1102 | } | |
1103 | ||
1104 | 0 | lastMessage = pdbResNum + chain; |
1105 | } | |
1106 | ||
1107 | StringBuffer resetLastRes = new StringBuffer(); | |
1108 | ||
1109 | StringBuffer eval = new StringBuffer(); | |
1110 | ||
1111 | /** | |
1112 | * Highlight the specified atoms in the structure. | |
1113 | * | |
1114 | * @param atoms | |
1115 | */ | |
1116 | 0 | @Override |
1117 | public void highlightAtoms(List<AtomSpec> atoms) | |
1118 | { | |
1119 | 0 | if (!seqColoursReady) |
1120 | { | |
1121 | 0 | return; |
1122 | } | |
1123 | ||
1124 | 0 | for (AtomSpec atom : atoms) |
1125 | { | |
1126 | 0 | int atomIndex = atom.getAtomIndex(); |
1127 | 0 | if (highlightRes != null |
1128 | && highlightRes.contains((atomIndex - 1) + "")) | |
1129 | { | |
1130 | 0 | continue; |
1131 | } | |
1132 | ||
1133 | 0 | highlightAtom(atomIndex); |
1134 | } | |
1135 | ||
1136 | 0 | redrawneeded = true; |
1137 | 0 | repaint(); |
1138 | } | |
1139 | ||
1140 | /** | |
1141 | * Highlight the atom at the specified index. | |
1142 | * | |
1143 | * @param atomIndex | |
1144 | */ | |
1145 | 0 | protected void highlightAtom(int atomIndex) |
1146 | { | |
1147 | 0 | int index = -1; |
1148 | 0 | Bond tmpBond; |
1149 | 0 | for (index = 0; index < mainchain.bonds.size(); index++) |
1150 | { | |
1151 | 0 | tmpBond = mainchain.bonds.elementAt(index); |
1152 | 0 | if (tmpBond.at1.atomIndex == atomIndex) |
1153 | { | |
1154 | 0 | if (highlightBond1 != null) |
1155 | { | |
1156 | 0 | highlightBond1.at2.isSelected = false; |
1157 | } | |
1158 | ||
1159 | 0 | if (highlightBond2 != null) |
1160 | { | |
1161 | 0 | highlightBond2.at1.isSelected = false; |
1162 | } | |
1163 | ||
1164 | 0 | highlightBond1 = null; |
1165 | 0 | highlightBond2 = null; |
1166 | ||
1167 | 0 | if (index > 0) |
1168 | { | |
1169 | 0 | highlightBond1 = mainchain.bonds.elementAt(index - 1); |
1170 | 0 | highlightBond1.at2.isSelected = true; |
1171 | } | |
1172 | ||
1173 | 0 | if (index != mainchain.bonds.size()) |
1174 | { | |
1175 | 0 | highlightBond2 = mainchain.bonds.elementAt(index); |
1176 | 0 | highlightBond2.at1.isSelected = true; |
1177 | } | |
1178 | ||
1179 | 0 | break; |
1180 | } | |
1181 | } | |
1182 | } | |
1183 | ||
1184 | 0 | public Color getColour(int atomIndex, int pdbResNum, String chain, |
1185 | String pdbfile) | |
1186 | { | |
1187 | 0 | return Color.white; |
1188 | // if (!pdbfile.equals(pdbentry.getFile())) | |
1189 | // return null; | |
1190 | ||
1191 | // return new Color(viewer.getAtomArgb(atomIndex)); | |
1192 | } | |
1193 | ||
1194 | 0 | @Override |
1195 | public void updateColours(Object source) | |
1196 | { | |
1197 | 0 | colourBySequence(); |
1198 | 0 | redrawneeded = true; |
1199 | 0 | repaint(); |
1200 | } | |
1201 | ||
1202 | 0 | @Override |
1203 | public void releaseReferences(Object svl) | |
1204 | { | |
1205 | // TODO Auto-generated method stub | |
1206 | ||
1207 | } | |
1208 | ||
1209 | 0 | @Override |
1210 | public boolean isListeningFor(SequenceI seq) | |
1211 | { | |
1212 | 0 | if (sequence != null) |
1213 | { | |
1214 | 0 | for (SequenceI s : sequence) |
1215 | { | |
1216 | 0 | if (s == seq) |
1217 | { | |
1218 | 0 | return true; |
1219 | } | |
1220 | } | |
1221 | } | |
1222 | 0 | return false; |
1223 | } | |
1224 | } |