Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
FeatureRenderer | 42 | 160 | 70 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
7 | * Jalview is free software: you can redistribute it and/or | |
8 | * modify it under the terms of the GNU General Public License | |
9 | * as published by the Free Software Foundation, either version 3 | |
10 | * of the License, or (at your option) any later version. | |
11 | * | |
12 | * Jalview is distributed in the hope that it will be useful, but | |
13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
15 | * PURPOSE. See the GNU General Public License for more details. | |
16 | * | |
17 | * You should have received a copy of the GNU General Public License | |
18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
20 | */ | |
21 | package jalview.renderer.seqfeatures; | |
22 | ||
23 | import java.awt.AlphaComposite; | |
24 | import java.awt.Color; | |
25 | import java.awt.FontMetrics; | |
26 | import java.awt.Graphics; | |
27 | import java.awt.Graphics2D; | |
28 | import java.util.List; | |
29 | ||
30 | import jalview.api.AlignViewportI; | |
31 | import jalview.api.FeatureColourI; | |
32 | import jalview.datamodel.ContiguousI; | |
33 | import jalview.datamodel.MappedFeatures; | |
34 | import jalview.datamodel.SequenceFeature; | |
35 | import jalview.datamodel.SequenceI; | |
36 | import jalview.gui.AlignFrame; | |
37 | import jalview.gui.Desktop; | |
38 | import jalview.util.Comparison; | |
39 | import jalview.util.ReverseListIterator; | |
40 | import jalview.viewmodel.seqfeatures.FeatureRendererModel; | |
41 | ||
42 | public class FeatureRenderer extends FeatureRendererModel | |
43 | { | |
44 | private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite | |
45 | .getInstance(AlphaComposite.SRC_OVER, 1.0f); | |
46 | ||
47 | /** | |
48 | * Constructor given a viewport | |
49 | * | |
50 | * @param viewport | |
51 | */ | |
52 | 549 | public FeatureRenderer(AlignViewportI viewport) |
53 | { | |
54 | 549 | this.av = viewport; |
55 | } | |
56 | ||
57 | /** | |
58 | * Renders the sequence using the given feature colour between the given start | |
59 | * and end columns. Returns true if at least one column is drawn, else false | |
60 | * (the feature range does not overlap the start and end positions). | |
61 | * | |
62 | * @param g | |
63 | * @param seq | |
64 | * @param featureStart | |
65 | * @param featureEnd | |
66 | * @param featureColour | |
67 | * @param start | |
68 | * @param end | |
69 | * @param y1 | |
70 | * @param colourOnly | |
71 | * @return | |
72 | */ | |
73 | 17056 | boolean renderFeature(Graphics g, SequenceI seq, int featureStart, |
74 | int featureEnd, Color featureColour, int start, int end, int y1, | |
75 | boolean colourOnly) | |
76 | { | |
77 | 17056 | int charHeight = av.getCharHeight(); |
78 | 17056 | int charWidth = av.getCharWidth(); |
79 | 17056 | boolean validCharWidth = av.isValidCharWidth(); |
80 | ||
81 | 17056 | if (featureStart > end || featureEnd < start) |
82 | { | |
83 | 0 | return false; |
84 | } | |
85 | ||
86 | 17056 | if (featureStart < start) |
87 | { | |
88 | 0 | featureStart = start; |
89 | } | |
90 | 17056 | if (featureEnd >= end) |
91 | { | |
92 | 460 | featureEnd = end; |
93 | } | |
94 | 17056 | int pady = (y1 + charHeight) - charHeight / 5; |
95 | ||
96 | 17056 | FontMetrics fm = g.getFontMetrics(); |
97 | 45934 | for (int i = featureStart; i <= featureEnd; i++) |
98 | { | |
99 | 28878 | char s = seq.getCharAt(i); |
100 | ||
101 | 28878 | if (Comparison.isGap(s)) |
102 | { | |
103 | 0 | continue; |
104 | } | |
105 | ||
106 | 28878 | g.setColor(featureColour); |
107 | ||
108 | 28878 | g.fillRect((i - start) * charWidth, y1, charWidth, charHeight); |
109 | ||
110 | 28878 | if (colourOnly || !validCharWidth) |
111 | { | |
112 | 6 | continue; |
113 | } | |
114 | ||
115 | /* | |
116 | * JAL-3045 text is always drawn over features, even if | |
117 | * 'Show Text' is unchecked in the format menu | |
118 | */ | |
119 | 28872 | g.setColor(Color.white); |
120 | 28872 | int charOffset = (charWidth - fm.charWidth(s)) / 2; |
121 | 28872 | g.drawString(String.valueOf(s), |
122 | charOffset + (charWidth * (i - start)), pady); | |
123 | } | |
124 | 17056 | return true; |
125 | } | |
126 | ||
127 | /** | |
128 | * Renders the sequence using the given SCORE feature colour between the given | |
129 | * start and end columns. Returns true if at least one column is drawn, else | |
130 | * false (the feature range does not overlap the start and end positions). | |
131 | * | |
132 | * @param g | |
133 | * @param seq | |
134 | * @param fstart | |
135 | * @param fend | |
136 | * @param featureColour | |
137 | * @param start | |
138 | * @param end | |
139 | * @param y1 | |
140 | * @param bs | |
141 | * @param colourOnly | |
142 | * @return | |
143 | */ | |
144 | 0 | boolean renderScoreFeature(Graphics g, SequenceI seq, int fstart, |
145 | int fend, Color featureColour, int start, int end, int y1, | |
146 | byte[] bs, boolean colourOnly) | |
147 | { | |
148 | 0 | if (fstart > end || fend < start) |
149 | { | |
150 | 0 | return false; |
151 | } | |
152 | ||
153 | 0 | if (fstart < start) |
154 | { // fix for if the feature we have starts before the sequence start, | |
155 | 0 | fstart = start; // but the feature end is still valid!! |
156 | } | |
157 | ||
158 | 0 | if (fend >= end) |
159 | { | |
160 | 0 | fend = end; |
161 | } | |
162 | 0 | int charHeight = av.getCharHeight(); |
163 | 0 | int pady = (y1 + charHeight) - charHeight / 5; |
164 | 0 | int ystrt = 0, yend = charHeight; |
165 | 0 | if (bs[0] != 0) |
166 | { | |
167 | // signed - zero is always middle of residue line. | |
168 | 0 | if (bs[1] < 128) |
169 | { | |
170 | 0 | yend = charHeight * (128 - bs[1]) / 512; |
171 | 0 | ystrt = charHeight - yend / 2; |
172 | } | |
173 | else | |
174 | { | |
175 | 0 | ystrt = charHeight / 2; |
176 | 0 | yend = charHeight * (bs[1] - 128) / 512; |
177 | } | |
178 | } | |
179 | else | |
180 | { | |
181 | 0 | yend = charHeight * bs[1] / 255; |
182 | 0 | ystrt = charHeight - yend; |
183 | ||
184 | } | |
185 | ||
186 | 0 | FontMetrics fm = g.getFontMetrics(); |
187 | 0 | int charWidth = av.getCharWidth(); |
188 | ||
189 | 0 | for (int i = fstart; i <= fend; i++) |
190 | { | |
191 | 0 | char s = seq.getCharAt(i); |
192 | ||
193 | 0 | if (Comparison.isGap(s)) |
194 | { | |
195 | 0 | continue; |
196 | } | |
197 | ||
198 | 0 | g.setColor(featureColour); |
199 | 0 | int x = (i - start) * charWidth; |
200 | 0 | g.drawRect(x, y1, charWidth, charHeight); |
201 | 0 | g.fillRect(x, y1 + ystrt, charWidth, yend); |
202 | ||
203 | 0 | if (colourOnly || !av.isValidCharWidth()) |
204 | { | |
205 | 0 | continue; |
206 | } | |
207 | ||
208 | 0 | g.setColor(Color.black); |
209 | 0 | int charOffset = (charWidth - fm.charWidth(s)) / 2; |
210 | 0 | g.drawString(String.valueOf(s), |
211 | charOffset + (charWidth * (i - start)), pady); | |
212 | } | |
213 | 0 | return true; |
214 | } | |
215 | ||
216 | /** | |
217 | * {@inheritDoc} | |
218 | */ | |
219 | 28992 | @Override |
220 | public Color findFeatureColour(SequenceI seq, int column, Graphics g) | |
221 | { | |
222 | 28993 | if (!av.isShowSequenceFeatures()) |
223 | { | |
224 | 0 | return null; |
225 | } | |
226 | ||
227 | // column is 'base 1' but getCharAt is an array index (ie from 0) | |
228 | 28992 | if (Comparison.isGap(seq.getCharAt(column - 1))) |
229 | { | |
230 | /* | |
231 | * returning null allows the colour scheme to provide gap colour | |
232 | * - normally white, but can be customised | |
233 | */ | |
234 | 4008 | return null; |
235 | } | |
236 | ||
237 | 24984 | Color renderedColour = null; |
238 | 24984 | if (transparency == 1.0f) |
239 | { | |
240 | /* | |
241 | * simple case - just find the topmost rendered visible feature colour | |
242 | */ | |
243 | 24981 | renderedColour = findFeatureColour(seq, column); |
244 | } | |
245 | else | |
246 | { | |
247 | /* | |
248 | * transparency case - draw all visible features in render order to | |
249 | * build up a composite colour on the graphics context | |
250 | */ | |
251 | 4 | renderedColour = drawSequence(g, seq, column, column, 0, true); |
252 | } | |
253 | 24984 | return renderedColour; |
254 | } | |
255 | ||
256 | /** | |
257 | * Draws the sequence features on the graphics context, or just determines the | |
258 | * colour that would be drawn (if flag colourOnly is true). Returns the last | |
259 | * colour drawn (which may not be the effective colour if transparency | |
260 | * applies), or null if no feature is drawn in the range given. | |
261 | * | |
262 | * @param g | |
263 | * the graphics context to draw on (may be null if colourOnly==true) | |
264 | * @param seq | |
265 | * @param start | |
266 | * start column | |
267 | * @param end | |
268 | * end column | |
269 | * @param y1 | |
270 | * vertical offset at which to draw on the graphics | |
271 | * @param colourOnly | |
272 | * if true, only do enough to determine the colour for the position, | |
273 | * do not draw the character | |
274 | * @return | |
275 | */ | |
276 | 1098 | public synchronized Color drawSequence(final Graphics g, |
277 | final SequenceI seq, int start, int end, int y1, | |
278 | boolean colourOnly) | |
279 | { | |
280 | /* | |
281 | * if columns are all gapped, or sequence has no features, nothing to do | |
282 | */ | |
283 | 1098 | ContiguousI visiblePositions = seq.findPositions(start + 1, end + 1); |
284 | 1098 | if (visiblePositions == null || !seq.getFeatures().hasFeatures() |
285 | && !av.isShowComplementFeatures()) | |
286 | { | |
287 | 166 | return null; |
288 | } | |
289 | ||
290 | 932 | updateFeatures(); |
291 | ||
292 | 932 | if (transparency != 1f && g != null) |
293 | { | |
294 | 4 | Graphics2D g2 = (Graphics2D) g; |
295 | 4 | g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, |
296 | transparency)); | |
297 | } | |
298 | ||
299 | 932 | Color drawnColour = null; |
300 | ||
301 | /* | |
302 | * draw 'complement' features below ours if configured to do so | |
303 | */ | |
304 | 932 | if (av.isShowComplementFeatures() |
305 | && !av.isShowComplementFeaturesOnTop()) | |
306 | { | |
307 | 0 | drawnColour = drawComplementFeatures(g, seq, start, end, y1, |
308 | colourOnly, visiblePositions, drawnColour); | |
309 | } | |
310 | ||
311 | /* | |
312 | * iterate over features in ordering of their rendering (last is on top) | |
313 | */ | |
314 | 26491 | for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) |
315 | { | |
316 | 25559 | String type = renderOrder[renderIndex]; |
317 | 25559 | if (!showFeatureOfType(type)) |
318 | { | |
319 | 18693 | continue; |
320 | } | |
321 | ||
322 | 6866 | FeatureColourI fc = getFeatureStyle(type); |
323 | 6866 | List<SequenceFeature> overlaps = seq.getFeatures().findFeatures( |
324 | visiblePositions.getBegin(), visiblePositions.getEnd(), type); | |
325 | ||
326 | 6866 | if (overlaps.size() > 1 && fc.isSimpleColour()) |
327 | { | |
328 | 1408 | filterFeaturesForDisplay(overlaps); |
329 | } | |
330 | ||
331 | 6866 | for (SequenceFeature sf : overlaps) |
332 | { | |
333 | 17056 | Color featureColour = getColor(sf, fc); |
334 | 17056 | if (featureColour == null) |
335 | { | |
336 | /* | |
337 | * feature excluded by filters, or colour threshold | |
338 | */ | |
339 | 0 | continue; |
340 | } | |
341 | ||
342 | /* | |
343 | * if feature starts/ends outside the visible range, | |
344 | * restrict to visible positions (or if a contact feature, | |
345 | * to a single position) | |
346 | */ | |
347 | 17056 | int visibleStart = sf.getBegin(); |
348 | 17056 | if (visibleStart < visiblePositions.getBegin()) |
349 | { | |
350 | 108 | visibleStart = sf.isContactFeature() ? sf.getEnd() |
351 | : visiblePositions.getBegin(); | |
352 | } | |
353 | 17056 | int visibleEnd = sf.getEnd(); |
354 | 17056 | if (visibleEnd > visiblePositions.getEnd()) |
355 | { | |
356 | 16 | visibleEnd = sf.isContactFeature() ? sf.getBegin() |
357 | : visiblePositions.getEnd(); | |
358 | } | |
359 | ||
360 | 17056 | int featureStartCol = seq.findIndex(visibleStart); |
361 | 17056 | int featureEndCol = sf.begin == sf.end ? featureStartCol |
362 | : seq.findIndex(visibleEnd); | |
363 | ||
364 | // Color featureColour = getColour(sequenceFeature); | |
365 | ||
366 | 17056 | boolean isContactFeature = sf.isContactFeature(); |
367 | ||
368 | 17056 | if (isContactFeature) |
369 | { | |
370 | 0 | boolean drawn = renderFeature(g, seq, featureStartCol - 1, |
371 | featureStartCol - 1, featureColour, start, end, y1, | |
372 | colourOnly); | |
373 | 0 | drawn |= renderFeature(g, seq, featureEndCol - 1, |
374 | featureEndCol - 1, featureColour, start, end, y1, | |
375 | colourOnly); | |
376 | 0 | if (drawn) |
377 | { | |
378 | 0 | drawnColour = featureColour; |
379 | } | |
380 | } | |
381 | else | |
382 | { | |
383 | /* | |
384 | * showing feature score by height of colour | |
385 | * is not implemented as a selectable option | |
386 | * | |
387 | if (av.isShowSequenceFeaturesHeight() | |
388 | && !Float.isNaN(sequenceFeature.score)) | |
389 | { | |
390 | boolean drawn = renderScoreFeature(g, seq, | |
391 | seq.findIndex(sequenceFeature.begin) - 1, | |
392 | seq.findIndex(sequenceFeature.end) - 1, featureColour, | |
393 | start, end, y1, normaliseScore(sequenceFeature), | |
394 | colourOnly); | |
395 | if (drawn) | |
396 | { | |
397 | drawnColour = featureColour; | |
398 | } | |
399 | } | |
400 | else | |
401 | { | |
402 | */ | |
403 | 17056 | boolean drawn = renderFeature(g, seq, featureStartCol - 1, |
404 | featureEndCol - 1, featureColour, start, end, y1, | |
405 | colourOnly); | |
406 | 17056 | if (drawn) |
407 | { | |
408 | 17056 | drawnColour = featureColour; |
409 | } | |
410 | /*}*/ | |
411 | } | |
412 | } | |
413 | } | |
414 | ||
415 | /* | |
416 | * draw 'complement' features above ours if configured to do so | |
417 | */ | |
418 | 932 | if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop()) |
419 | { | |
420 | 0 | drawnColour = drawComplementFeatures(g, seq, start, end, y1, |
421 | colourOnly, visiblePositions, drawnColour); | |
422 | } | |
423 | ||
424 | 932 | if (transparency != 1.0f && g != null) |
425 | { | |
426 | /* | |
427 | * reset transparency | |
428 | */ | |
429 | 4 | Graphics2D g2 = (Graphics2D) g; |
430 | 4 | g2.setComposite(NO_TRANSPARENCY); |
431 | } | |
432 | ||
433 | 932 | return drawnColour; |
434 | } | |
435 | ||
436 | /** | |
437 | * Find any features on the CDS/protein complement of the sequence region and | |
438 | * draw them, with visibility and colouring as configured in the complementary | |
439 | * viewport | |
440 | * | |
441 | * @param g | |
442 | * @param seq | |
443 | * @param start | |
444 | * @param end | |
445 | * @param y1 | |
446 | * @param colourOnly | |
447 | * @param visiblePositions | |
448 | * @param drawnColour | |
449 | * @return | |
450 | */ | |
451 | 0 | Color drawComplementFeatures(final Graphics g, final SequenceI seq, |
452 | int start, int end, int y1, boolean colourOnly, | |
453 | ContiguousI visiblePositions, Color drawnColour) | |
454 | { | |
455 | 0 | AlignViewportI comp = av.getCodingComplement(); |
456 | 0 | FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp) |
457 | .getFeatureRenderer(); | |
458 | ||
459 | 0 | final int visibleStart = visiblePositions.getBegin(); |
460 | 0 | final int visibleEnd = visiblePositions.getEnd(); |
461 | ||
462 | 0 | for (int pos = visibleStart; pos <= visibleEnd; pos++) |
463 | { | |
464 | 0 | int column = seq.findIndex(pos); |
465 | 0 | MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq, pos); |
466 | 0 | if (mf != null) |
467 | { | |
468 | 0 | for (SequenceFeature sf : mf.features) |
469 | { | |
470 | 0 | FeatureColourI fc = fr2.getFeatureStyle(sf.getType()); |
471 | 0 | Color featureColour = fr2.getColor(sf, fc); |
472 | 0 | renderFeature(g, seq, column - 1, column - 1, featureColour, |
473 | start, end, y1, colourOnly); | |
474 | 0 | drawnColour = featureColour; |
475 | } | |
476 | } | |
477 | } | |
478 | 0 | return drawnColour; |
479 | } | |
480 | ||
481 | /** | |
482 | * Called when alignment in associated view has new/modified features to | |
483 | * discover and display. | |
484 | * | |
485 | */ | |
486 | 19 | @Override |
487 | public void featuresAdded() | |
488 | { | |
489 | 19 | findAllFeatures(); |
490 | } | |
491 | ||
492 | /** | |
493 | * Returns the sequence feature colour rendered at the given column position, | |
494 | * or null if none found. The feature of highest render order (i.e. on top) is | |
495 | * found, subject to both feature type and feature group being visible, and | |
496 | * its colour returned. This method is suitable when no feature transparency | |
497 | * applied (only the topmost visible feature colour is rendered). | |
498 | * <p> | |
499 | * Note this method does not check for a gap in the column so would return the | |
500 | * colour for features enclosing a gapped column. Check for gap before calling | |
501 | * if different behaviour is wanted. | |
502 | * | |
503 | * @param seq | |
504 | * @param column | |
505 | * (1..) | |
506 | * @return | |
507 | */ | |
508 | 24981 | Color findFeatureColour(SequenceI seq, int column) |
509 | { | |
510 | /* | |
511 | * check for new feature added while processing | |
512 | */ | |
513 | 24981 | updateFeatures(); |
514 | ||
515 | /* | |
516 | * show complement features on top (if configured to show them) | |
517 | */ | |
518 | 24980 | if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop()) |
519 | { | |
520 | 0 | Color col = findComplementFeatureColour(seq, column); |
521 | 0 | if (col != null) |
522 | { | |
523 | 0 | return col; |
524 | } | |
525 | } | |
526 | ||
527 | /* | |
528 | * inspect features in reverse renderOrder (the last in the array is | |
529 | * displayed on top) until we find one that is rendered at the position | |
530 | */ | |
531 | 24980 | for (int renderIndex = renderOrder.length |
532 | 738637 | - 1; renderIndex >= 0; renderIndex--) |
533 | { | |
534 | 721462 | String type = renderOrder[renderIndex]; |
535 | 722915 | if (!showFeatureOfType(type)) |
536 | { | |
537 | 462282 | continue; |
538 | } | |
539 | ||
540 | /* | |
541 | * find features of this type, and the colour of the _last_ one | |
542 | * (the one that would be drawn on top) that has a colour | |
543 | */ | |
544 | 260701 | List<SequenceFeature> overlaps = seq.findFeatures(column, column, |
545 | type); | |
546 | 260532 | for (int i = overlaps.size() - 1; i >= 0; i--) |
547 | { | |
548 | 7652 | SequenceFeature sequenceFeature = overlaps.get(i); |
549 | 7652 | if (!featureGroupNotShown(sequenceFeature)) |
550 | { | |
551 | 7651 | Color col = getColour(sequenceFeature); |
552 | 7651 | if (col != null) |
553 | { | |
554 | 7647 | return col; |
555 | } | |
556 | } | |
557 | } | |
558 | } | |
559 | ||
560 | /* | |
561 | * show complement features underneath (if configured to show them) | |
562 | */ | |
563 | 17334 | Color col = null; |
564 | 17334 | if (av.isShowComplementFeatures() |
565 | && !av.isShowComplementFeaturesOnTop()) | |
566 | { | |
567 | 0 | col = findComplementFeatureColour(seq, column); |
568 | } | |
569 | ||
570 | 17334 | return col; |
571 | } | |
572 | ||
573 | 0 | Color findComplementFeatureColour(SequenceI seq, int column) |
574 | { | |
575 | 0 | AlignViewportI complement = av.getCodingComplement(); |
576 | 0 | AlignFrame af = Desktop.getAlignFrameFor(complement); |
577 | 0 | FeatureRendererModel fr2 = af.getFeatureRenderer(); |
578 | 0 | MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq, |
579 | seq.findPosition(column - 1)); | |
580 | 0 | if (mf == null) |
581 | { | |
582 | 0 | return null; |
583 | } | |
584 | 0 | ReverseListIterator<SequenceFeature> it = new ReverseListIterator<>( |
585 | mf.features); | |
586 | 0 | while (it.hasNext()) |
587 | { | |
588 | 0 | SequenceFeature sf = it.next(); |
589 | 0 | if (!fr2.featureGroupNotShown(sf)) |
590 | { | |
591 | 0 | Color col = fr2.getColour(sf); |
592 | 0 | if (col != null) |
593 | { | |
594 | 0 | return col; |
595 | } | |
596 | } | |
597 | } | |
598 | 0 | return null; |
599 | } | |
600 | } |