1 |
|
|
2 |
|
|
3 |
|
|
4 |
|
|
5 |
|
|
6 |
|
|
7 |
|
|
8 |
|
|
9 |
|
|
10 |
|
|
11 |
|
|
12 |
|
|
13 |
|
|
14 |
|
|
15 |
|
|
16 |
|
|
17 |
|
|
18 |
|
|
19 |
|
|
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 |
|
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 715 (715) |
Complexity: 158 |
Complexity Density: 0.34 |
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 73 (73) |
Complexity: 9 |
Complexity Density: 0.15 |
|
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 |
|
|
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 |
|
|
201 |
|
|
202 |
|
|
203 |
|
|
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 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
212 |
0 |
@Override... |
213 |
|
public void print(String x) |
214 |
|
{ |
215 |
0 |
mappingDetails.append(x); |
216 |
|
} |
217 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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 |
|
|
250 |
|
|
251 |
0 |
this.pdb = pdb; |
252 |
0 |
this.prefsize = new Dimension(getSize().width, getSize().height); |
253 |
|
|
254 |
|
|
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 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 17 (17) |
Complexity: 4 |
Complexity Density: 0.36 |
|
294 |
0 |
void setupBonds()... |
295 |
|
{ |
296 |
0 |
seqColoursReady = false; |
297 |
|
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 76 (76) |
Complexity: 17 |
Complexity Density: 0.39 |
|
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 |
|
|
419 |
|
} |
420 |
|
|
|
|
| 0% |
Uncovered Elements: 16 (16) |
Complexity: 3 |
Complexity Density: 0.25 |
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 19 (19) |
Complexity: 3 |
Complexity Density: 0.2 |
|
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 |
|
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 39 (39) |
Complexity: 9 |
Complexity Density: 0.31 |
|
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 |
|
|
506 |
|
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
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 |
|
|
560 |
|
|
|
|
| 0% |
Uncovered Elements: 52 (52) |
Complexity: 13 |
Complexity Density: 0.43 |
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 73 (73) |
Complexity: 18 |
Complexity Density: 0.37 |
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 14 (14) |
Complexity: 3 |
Complexity Density: 0.3 |
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
756 |
0 |
public Dimension minimumsize()... |
757 |
|
{ |
758 |
0 |
return prefsize; |
759 |
|
} |
760 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
761 |
0 |
public Dimension preferredsize()... |
762 |
|
{ |
763 |
0 |
return prefsize; |
764 |
|
} |
765 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 33 (33) |
Complexity: 7 |
Complexity Density: 0.33 |
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 32 (32) |
Complexity: 6 |
Complexity Density: 0.27 |
|
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 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
870 |
0 |
@Override... |
871 |
|
public void mouseClicked(MouseEvent e) |
872 |
|
{ |
873 |
|
} |
874 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
875 |
0 |
@Override... |
876 |
|
public void mouseEntered(MouseEvent e) |
877 |
|
{ |
878 |
|
} |
879 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
880 |
0 |
@Override... |
881 |
|
public void mouseExited(MouseEvent e) |
882 |
|
{ |
883 |
|
} |
884 |
|
|
|
|
| 0% |
Uncovered Elements: 24 (24) |
Complexity: 2 |
Complexity Density: 0.09 |
|
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 |
|
|
907 |
0 |
for (PDBChain chain : pdb.getChains()) |
908 |
|
{ |
909 |
0 |
for (Bond tmpBond : chain.bonds) |
910 |
|
{ |
911 |
|
|
912 |
0 |
tmpBond.translate(-centre[0], -centre[1], -centre[2]); |
913 |
|
|
914 |
|
|
915 |
0 |
tmpBond.start = objmat.vectorMultiply(tmpBond.start); |
916 |
0 |
tmpBond.end = objmat.vectorMultiply(tmpBond.end); |
917 |
|
|
918 |
|
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
935 |
0 |
@Override... |
936 |
|
public void mouseReleased(MouseEvent evt) |
937 |
|
{ |
938 |
0 |
dragging = false; |
939 |
0 |
return; |
940 |
|
} |
941 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 4 |
Complexity Density: 0.57 |
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 3 |
Complexity Density: 0.27 |
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 43 (43) |
Complexity: 9 |
Complexity Density: 0.33 |
|
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 |
|
|
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) |
1052 |
|
{ |
1053 |
0 |
chain = pdb.getChains().elementAt(foundchain); |
1054 |
|
} |
1055 |
|
} |
1056 |
|
|
1057 |
0 |
return fatom; |
1058 |
|
} |
1059 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1060 |
0 |
@Override... |
1061 |
|
public void update(Graphics g) |
1062 |
|
{ |
1063 |
0 |
paint(g); |
1064 |
|
} |
1065 |
|
|
|
|
| 0% |
Uncovered Elements: 40 (40) |
Complexity: 10 |
Complexity Density: 0.42 |
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1132 |
0 |
@Override... |
1133 |
|
public String[] getStructureFiles() |
1134 |
|
{ |
1135 |
0 |
return new String[] { pdbentry.getFile() }; |
1136 |
|
} |
1137 |
|
|
1138 |
|
String lastMessage; |
1139 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
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 |
|
|
1156 |
|
|
1157 |
|
@param |
1158 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 4 |
Complexity Density: 0.44 |
|
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 |
1185 |
|
|
|
|
| 0% |
Uncovered Elements: 30 (30) |
Complexity: 7 |
Complexity Density: 0.39 |
|
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 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1225 |
0 |
public Color getColour(int atomIndex, int pdbResNum, String chain,... |
1226 |
|
String pdbfile) |
1227 |
|
{ |
1228 |
0 |
return Color.white; |
1229 |
|
|
1230 |
|
|
1231 |
|
|
1232 |
|
|
1233 |
|
} |
1234 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
1235 |
0 |
@Override... |
1236 |
|
public void updateColours(Object source) |
1237 |
|
{ |
1238 |
0 |
colourBySequence(); |
1239 |
0 |
redrawneeded = true; |
1240 |
0 |
repaint(); |
1241 |
|
} |
1242 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1243 |
0 |
@Override... |
1244 |
|
public void releaseReferences(Object svl) |
1245 |
|
{ |
1246 |
|
|
1247 |
|
|
1248 |
|
} |
1249 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
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 |
|
} |