Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
AnnotationRenderer | 64 | 776 | 426 |
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; | |
22 | ||
23 | import java.awt.BasicStroke; | |
24 | import java.awt.Color; | |
25 | import java.awt.Font; | |
26 | import java.awt.FontMetrics; | |
27 | import java.awt.Graphics; | |
28 | import java.awt.Graphics2D; | |
29 | import java.awt.Image; | |
30 | import java.awt.RenderingHints; | |
31 | import java.awt.Stroke; | |
32 | import java.awt.geom.AffineTransform; | |
33 | import java.awt.image.ImageObserver; | |
34 | import java.util.BitSet; | |
35 | import java.util.Hashtable; | |
36 | import java.util.List; | |
37 | import java.util.Map; | |
38 | ||
39 | import org.jfree.graphics2d.svg.SVGGraphics2D; | |
40 | import org.jibble.epsgraphics.EpsGraphics2D; | |
41 | ||
42 | import jalview.analysis.AAFrequency; | |
43 | import jalview.analysis.AlignmentUtils; | |
44 | import jalview.analysis.CodingUtils; | |
45 | import jalview.analysis.Rna; | |
46 | import jalview.analysis.StructureFrequency; | |
47 | import jalview.api.AlignViewportI; | |
48 | import jalview.bin.Cache; | |
49 | import jalview.bin.Console; | |
50 | import jalview.datamodel.AlignmentAnnotation; | |
51 | import jalview.datamodel.Annotation; | |
52 | import jalview.datamodel.ColumnSelection; | |
53 | import jalview.datamodel.HiddenColumns; | |
54 | import jalview.datamodel.ProfilesI; | |
55 | import jalview.renderer.api.AnnotationRendererFactoryI; | |
56 | import jalview.renderer.api.AnnotationRowRendererI; | |
57 | import jalview.schemes.ColourSchemeI; | |
58 | import jalview.schemes.NucleotideColourScheme; | |
59 | import jalview.schemes.ResidueProperties; | |
60 | import jalview.schemes.ZappoColourScheme; | |
61 | import jalview.util.Constants; | |
62 | import jalview.util.Platform; | |
63 | ||
64 | public class AnnotationRenderer | |
65 | { | |
66 | private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32 | |
67 | ||
68 | private static final int CHAR_A = 'A'; // 65 | |
69 | ||
70 | private static final int CHAR_Z = 'Z'; // 90 | |
71 | ||
72 | /** | |
73 | * flag indicating if timing and redraw parameter info should be output | |
74 | */ | |
75 | private final boolean debugRedraw; | |
76 | ||
77 | private int charWidth, endRes, charHeight; | |
78 | ||
79 | private boolean validCharWidth, hasHiddenColumns; | |
80 | ||
81 | private FontMetrics fm; | |
82 | ||
83 | private final boolean USE_FILL_ROUND_RECT = Platform.isAMacAndNotJS(); | |
84 | ||
85 | boolean av_renderHistogram = true, av_renderProfile = true, | |
86 | av_normaliseProfile = false; | |
87 | ||
88 | ResidueShaderI profcolour = null; | |
89 | ||
90 | private ColumnSelection columnSelection; | |
91 | ||
92 | private HiddenColumns hiddenColumns; | |
93 | ||
94 | private ProfilesI hconsensus; | |
95 | ||
96 | private Map<String, ProfilesI> hSSconsensus; | |
97 | ||
98 | private Hashtable<String, Object>[] complementConsensus; | |
99 | ||
100 | private Hashtable<String, Object>[] hStrucConsensus; | |
101 | ||
102 | private boolean av_ignoreGapsConsensus; | |
103 | ||
104 | private boolean renderingVectors = false; | |
105 | ||
106 | private boolean glyphLineDrawn = false; | |
107 | ||
108 | /** | |
109 | * attributes set from AwtRenderPanelI | |
110 | */ | |
111 | /** | |
112 | * old image used when data is currently being calculated and cannot be | |
113 | * rendered | |
114 | */ | |
115 | private Image fadedImage; | |
116 | ||
117 | /** | |
118 | * panel being rendered into | |
119 | */ | |
120 | private ImageObserver annotationPanel; | |
121 | ||
122 | /** | |
123 | * width of image to render in panel | |
124 | */ | |
125 | private int imgWidth; | |
126 | ||
127 | /** | |
128 | * offset to beginning of visible area | |
129 | */ | |
130 | private int sOffset; | |
131 | ||
132 | /** | |
133 | * offset to end of visible area | |
134 | */ | |
135 | private int visHeight; | |
136 | ||
137 | /** | |
138 | * indicate if the renderer should only render the visible portion of the | |
139 | * annotation given the current view settings | |
140 | */ | |
141 | private boolean useClip = true; | |
142 | ||
143 | /** | |
144 | * master flag indicating if renderer should ever try to clip. not enabled for | |
145 | * jalview 2.8.1 | |
146 | */ | |
147 | private boolean canClip = false; | |
148 | ||
149 | 491 | public AnnotationRenderer() |
150 | { | |
151 | 491 | this(false); |
152 | } | |
153 | ||
154 | /** | |
155 | * Create a new annotation Renderer | |
156 | * | |
157 | * @param debugRedraw | |
158 | * flag indicating if timing and redraw parameter info should be | |
159 | * output | |
160 | */ | |
161 | 491 | public AnnotationRenderer(boolean debugRedraw) |
162 | { | |
163 | 491 | this.debugRedraw = debugRedraw; |
164 | } | |
165 | ||
166 | /** | |
167 | * Remove any references and resources when this object is no longer required | |
168 | */ | |
169 | 253 | public void dispose() |
170 | { | |
171 | 253 | hiddenColumns = null; |
172 | 253 | hconsensus = null; |
173 | 253 | hSSconsensus = null; |
174 | 253 | complementConsensus = null; |
175 | 253 | hStrucConsensus = null; |
176 | 253 | fadedImage = null; |
177 | 253 | annotationPanel = null; |
178 | 253 | rendererFactoryI = null; |
179 | } | |
180 | ||
181 | 0 | void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX, |
182 | int x, int y, int iconOffset, int startRes, int column, | |
183 | boolean validRes, boolean validEnd) | |
184 | { | |
185 | 0 | int sCol = (lastSSX / charWidth) |
186 | + hiddenColumns.visibleToAbsoluteColumn(startRes); | |
187 | 0 | int x1 = lastSSX; |
188 | 0 | int x2 = (x * charWidth); |
189 | ||
190 | 0 | char dc = (column == 0 || row_annotations[column - 1] == null) ? ' ' |
191 | : row_annotations[column - 1].secondaryStructure; | |
192 | ||
193 | 0 | boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null |
194 | || dc != row_annotations[sCol - 1].secondaryStructure | |
195 | || !validEnd; | |
196 | 0 | boolean diffdownstream = !validRes || !validEnd |
197 | || row_annotations[column] == null | |
198 | || dc != row_annotations[column].secondaryStructure; | |
199 | ||
200 | 0 | if (diffupstream || diffdownstream) |
201 | { | |
202 | // draw glyphline under arrow | |
203 | 0 | drawGlyphLine(g, lastSSX, x, y, iconOffset); |
204 | } | |
205 | 0 | g.setColor(STEM_COLOUR); |
206 | ||
207 | 0 | if (column > 0 && Rna.isClosingParenthesis(dc)) |
208 | { | |
209 | 0 | if (diffupstream) |
210 | // if (validRes && column>1 && row_annotations[column-2]!=null && | |
211 | // dc.equals(row_annotations[column-2].displayCharacter)) | |
212 | { | |
213 | /* | |
214 | * if new annotation with a closing base pair half of the stem, | |
215 | * display a backward arrow | |
216 | */ | |
217 | 0 | fillPolygon(g, new int[] { lastSSX + 5, lastSSX + 5, lastSSX }, |
218 | new int[] | |
219 | { y + iconOffset + 1, y + 13 + iconOffset, | |
220 | y + 7 + iconOffset }, | |
221 | 3); | |
222 | 0 | x1 += 5; |
223 | } | |
224 | 0 | if (diffdownstream) |
225 | { | |
226 | 0 | x2 -= 1; |
227 | } | |
228 | } | |
229 | else | |
230 | { | |
231 | // display a forward arrow | |
232 | 0 | if (diffdownstream) |
233 | { | |
234 | /* | |
235 | * if annotation ending with an opeing base pair half of the stem, | |
236 | * display a forward arrow | |
237 | */ | |
238 | 0 | fillPolygon(g, new int[] { x2 - 6, x2 - 6, x2 - 1 }, |
239 | new int[] | |
240 | { y + iconOffset + 1, y + 13 + iconOffset, | |
241 | y + 7 + iconOffset }, | |
242 | 3); | |
243 | 0 | x2 -= 5; |
244 | } | |
245 | 0 | if (diffupstream) |
246 | { | |
247 | 0 | x1 += 1; |
248 | } | |
249 | } | |
250 | // draw arrow body | |
251 | 0 | unsetAntialias(g); |
252 | 0 | fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6); |
253 | } | |
254 | ||
255 | 0 | void drawNotCanonicalAnnot(Graphics g, Color nonCanColor, |
256 | Annotation[] row_annotations, int lastSSX, int x, int y, | |
257 | int iconOffset, int startRes, int column, boolean validRes, | |
258 | boolean validEnd) | |
259 | { | |
260 | // Console.info(nonCanColor); | |
261 | ||
262 | 0 | int sCol = (lastSSX / charWidth) |
263 | + hiddenColumns.visibleToAbsoluteColumn(startRes); | |
264 | 0 | int x1 = lastSSX; |
265 | 0 | int x2 = (x * charWidth); |
266 | ||
267 | 0 | String dc = (column == 0 || row_annotations[column - 1] == null) ? "" |
268 | : row_annotations[column - 1].displayCharacter; | |
269 | ||
270 | 0 | boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null |
271 | || !dc.equals(row_annotations[sCol - 1].displayCharacter) | |
272 | || !validEnd; | |
273 | 0 | boolean diffdownstream = !validRes || !validEnd |
274 | || row_annotations[column] == null | |
275 | || !dc.equals(row_annotations[column].displayCharacter); | |
276 | // Console.info("Column "+column+" diff up: | |
277 | // "+diffupstream+" | |
278 | // down:"+diffdownstream); | |
279 | // If a closing base pair half of the stem, display a backward arrow | |
280 | 0 | if (diffupstream || diffdownstream) |
281 | { | |
282 | // draw glyphline under arrow | |
283 | 0 | drawGlyphLine(g, lastSSX, x, y, iconOffset); |
284 | } | |
285 | 0 | g.setColor(nonCanColor); |
286 | 0 | if (column > 0 && Rna.isClosingParenthesis(dc)) |
287 | { | |
288 | ||
289 | 0 | if (diffupstream) |
290 | // if (validRes && column>1 && row_annotations[column-2]!=null && | |
291 | // dc.equals(row_annotations[column-2].displayCharacter)) | |
292 | { | |
293 | 0 | fillPolygon(g, new int[] { lastSSX + 5, lastSSX + 5, lastSSX }, |
294 | new int[] | |
295 | { y + iconOffset + 1, y + 13 + iconOffset, | |
296 | y + 7 + iconOffset }, | |
297 | 3); | |
298 | 0 | x1 += 5; |
299 | } | |
300 | 0 | if (diffdownstream) |
301 | { | |
302 | 0 | x2 -= 1; |
303 | } | |
304 | } | |
305 | else | |
306 | { | |
307 | ||
308 | // display a forward arrow | |
309 | 0 | if (diffdownstream) |
310 | { | |
311 | 0 | fillPolygon(g, new int[] { x2 - 6, x2 - 6, x2 - 1 }, |
312 | new int[] | |
313 | { y + iconOffset + 1, y + 13 + iconOffset, | |
314 | y + 7 + iconOffset }, | |
315 | 3); | |
316 | 0 | x2 -= 5; |
317 | } | |
318 | 0 | if (diffupstream) |
319 | { | |
320 | 0 | x1 += 1; |
321 | } | |
322 | } | |
323 | // draw arrow body | |
324 | 0 | unsetAntialias(g); |
325 | 0 | fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6); |
326 | } | |
327 | ||
328 | // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI | |
329 | // av) | |
330 | 2374 | public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel, |
331 | AlignViewportI av) | |
332 | { | |
333 | 2374 | fm = annotPanel.getFontMetrics(); |
334 | 2374 | annotationPanel = annotPanel; |
335 | 2374 | fadedImage = annotPanel.getFadedImage(); |
336 | 2374 | imgWidth = annotPanel.getFadedImageWidth(); |
337 | // visible area for rendering | |
338 | 2374 | int[] bounds = annotPanel.getVisibleVRange(); |
339 | 2374 | if (bounds != null) |
340 | { | |
341 | 2120 | sOffset = bounds[0]; |
342 | 2120 | visHeight = bounds[1]; |
343 | 2120 | if (visHeight == 0) |
344 | { | |
345 | 0 | useClip = false; |
346 | } | |
347 | else | |
348 | { | |
349 | 2120 | useClip = canClip; |
350 | } | |
351 | } | |
352 | else | |
353 | { | |
354 | 254 | useClip = false; |
355 | } | |
356 | ||
357 | 2374 | rendererFactoryI = AnnotationRendererFactory.getRendererFactory(); |
358 | 2374 | updateFromAlignViewport(av); |
359 | } | |
360 | ||
361 | 2374 | public void updateFromAlignViewport(AlignViewportI av) |
362 | { | |
363 | 2374 | charWidth = av.getCharWidth(); |
364 | 2374 | endRes = av.getRanges().getEndRes(); |
365 | 2374 | charHeight = av.getCharHeight(); |
366 | 2374 | hasHiddenColumns = av.hasHiddenColumns(); |
367 | 2374 | validCharWidth = av.isValidCharWidth(); |
368 | 2374 | av_renderHistogram = av.isShowConsensusHistogram(); |
369 | 2374 | av_renderProfile = av.isShowSequenceLogo(); |
370 | 2374 | av_normaliseProfile = av.isNormaliseSequenceLogo(); |
371 | 2374 | profcolour = av.getResidueShading(); |
372 | 2374 | if (profcolour == null || profcolour.getColourScheme() == null) |
373 | { | |
374 | /* | |
375 | * Use default colour for sequence logo if | |
376 | * the alignment has no colourscheme set | |
377 | * (would like to use user preference but n/a for applet) | |
378 | */ | |
379 | 2111 | ColourSchemeI col = av.getAlignment().isNucleotide() |
380 | ? new NucleotideColourScheme() | |
381 | : new ZappoColourScheme(); | |
382 | 2111 | profcolour = new ResidueShader(col); |
383 | } | |
384 | 2374 | columnSelection = av.getColumnSelection(); |
385 | 2374 | hiddenColumns = av.getAlignment().getHiddenColumns(); |
386 | 2374 | hconsensus = av.getSequenceConsensusHash(); |
387 | 2374 | hSSconsensus = av.getSequenceSSConsensusHash(); |
388 | 2374 | complementConsensus = av.getComplementConsensusHash(); |
389 | 2374 | hStrucConsensus = av.getRnaStructureConsensusHash(); |
390 | 2374 | av_ignoreGapsConsensus = av.isIgnoreGapsConsensus(); |
391 | } | |
392 | ||
393 | /** | |
394 | * Returns profile data; the first element is the profile type, the second is | |
395 | * the number of distinct values, the third the total count, and the remainder | |
396 | * depend on the profile type. | |
397 | * | |
398 | * @param aa | |
399 | * @param column | |
400 | * @return | |
401 | */ | |
402 | 104407 | int[] getProfileFor(AlignmentAnnotation aa, int column) |
403 | { | |
404 | // TODO : consider refactoring the global alignment calculation | |
405 | // properties/rendering attributes as a global 'alignment group' which holds | |
406 | // all vis settings for the alignment as a whole rather than a subset | |
407 | // | |
408 | 104407 | if (aa.autoCalculated && (aa.label.startsWith("Consensus") |
409 | || aa.label.startsWith("cDNA Consensus"))) | |
410 | { | |
411 | 104407 | boolean forComplement = aa.label.startsWith("cDNA Consensus"); |
412 | 104407 | if (aa.groupRef != null && aa.groupRef.consensusData != null |
413 | && aa.groupRef.isShowSequenceLogo()) | |
414 | { | |
415 | // TODO? group consensus for cDNA complement | |
416 | 39816 | return AAFrequency.extractProfile( |
417 | aa.groupRef.consensusData.get(column), | |
418 | aa.groupRef.getIgnoreGapsConsensus()); | |
419 | } | |
420 | // TODO extend annotation row to enable dynamic and static profile data to | |
421 | // be stored | |
422 | 64591 | if (aa.groupRef == null && aa.sequenceRef == null) |
423 | { | |
424 | 64591 | if (forComplement) |
425 | { | |
426 | 0 | return AAFrequency.extractCdnaProfile(complementConsensus[column], |
427 | av_ignoreGapsConsensus); | |
428 | } | |
429 | else | |
430 | { | |
431 | 64591 | return AAFrequency.extractProfile(hconsensus.get(column), |
432 | av_ignoreGapsConsensus); | |
433 | } | |
434 | } | |
435 | } | |
436 | ||
437 | 0 | if (aa.autoCalculated && aa.label |
438 | .startsWith(Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL)) | |
439 | { | |
440 | ||
441 | 0 | if (aa.groupRef != null && aa.groupRef.hSSConsensusProfileMap != null |
442 | && aa.groupRef.isShowSequenceLogo()) | |
443 | { | |
444 | 0 | for (String source : aa.groupRef.hSSConsensusProfileMap.keySet()) |
445 | { | |
446 | 0 | if (aa.description.startsWith(source)) |
447 | { | |
448 | ||
449 | 0 | return AAFrequency |
450 | .extractProfile( | |
451 | aa.groupRef.hSSConsensusProfileMap.get(source) | |
452 | .get(column), | |
453 | aa.groupRef.getIgnoreGapsConsensus()); | |
454 | } | |
455 | } | |
456 | } | |
457 | ||
458 | 0 | if (hSSconsensus != null && aa.groupRef == null) |
459 | { | |
460 | 0 | for (String source : hSSconsensus.keySet()) |
461 | { | |
462 | 0 | if (aa.description.startsWith(source)) |
463 | { | |
464 | ||
465 | 0 | return AAFrequency.extractProfile( |
466 | hSSconsensus.get(source).get(column), | |
467 | av_ignoreGapsConsensus); | |
468 | } | |
469 | } | |
470 | } | |
471 | ||
472 | } | |
473 | ||
474 | 0 | if (aa.autoCalculated && aa.label.startsWith("StrucConsensus")) |
475 | { | |
476 | // TODO implement group structure consensus | |
477 | /* | |
478 | * if (aa.groupRef != null && aa.groupRef.consensusData != null && | |
479 | * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for | |
480 | * group selections return StructureFrequency.extractProfile( | |
481 | * aa.groupRef.consensusData[column], aa.groupRef | |
482 | * .getIgnoreGapsConsensus()); } | |
483 | */ | |
484 | // TODO extend annotation row to enable dynamic and static profile data | |
485 | // to | |
486 | // be stored | |
487 | 0 | if (aa.groupRef == null && aa.sequenceRef == null |
488 | && hStrucConsensus != null && hStrucConsensus.length > column) | |
489 | { | |
490 | 0 | return StructureFrequency.extractProfile(hStrucConsensus[column], |
491 | av_ignoreGapsConsensus); | |
492 | } | |
493 | } | |
494 | ||
495 | 0 | return null; |
496 | } | |
497 | ||
498 | boolean rna = false; | |
499 | ||
500 | private AnnotationRendererFactoryI rendererFactoryI; | |
501 | ||
502 | /** | |
503 | * Render the annotation rows associated with an alignment. | |
504 | * | |
505 | * @param annotPanel | |
506 | * container frame | |
507 | * @param av | |
508 | * data and view settings to render | |
509 | * @param g | |
510 | * destination for graphics | |
511 | * @param activeRow | |
512 | * row where a mouse event occured (or -1) | |
513 | * @param startRes | |
514 | * first column that will be drawn | |
515 | * @param endRes | |
516 | * last column that will be drawn | |
517 | * @return true if the fadedImage was used for any alignment annotation rows | |
518 | * currently being calculated | |
519 | */ | |
520 | 2374 | public boolean drawComponent(AwtRenderPanelI annotPanel, |
521 | AlignViewportI av, Graphics g, int activeRow, int startRes, | |
522 | int endRes) | |
523 | { | |
524 | 2374 | if (g instanceof EpsGraphics2D || g instanceof SVGGraphics2D) |
525 | { | |
526 | 14 | this.setVectorRendering(true); |
527 | } | |
528 | 2374 | Graphics2D g2d = (Graphics2D) g; |
529 | ||
530 | 2374 | long stime = System.currentTimeMillis(); |
531 | 2374 | boolean usedFaded = false; |
532 | // NOTES: | |
533 | // AnnotationPanel needs to implement: ImageObserver, access to | |
534 | // AlignViewport | |
535 | 2374 | updateFromAwtRenderPanel(annotPanel, av); |
536 | 2374 | fm = g.getFontMetrics(); |
537 | 2374 | AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); |
538 | // int temp = 0; | |
539 | 2374 | if (aa == null) |
540 | { | |
541 | 0 | return false; |
542 | } | |
543 | 2374 | int x = 0, y = 0; |
544 | 2374 | int column = 0; |
545 | 2374 | char lastSS; |
546 | 2374 | int lastSSX; |
547 | 2374 | int iconOffset = 0; |
548 | 2374 | boolean validRes = false; |
549 | 2374 | boolean validEnd = false; |
550 | 2374 | boolean labelAllCols = false; |
551 | // boolean centreColLabels; | |
552 | // boolean centreColLabelsDef = av.isCentreColumnLabels(); | |
553 | 2374 | boolean scaleColLabel = false; |
554 | 2374 | final AlignmentAnnotation consensusAnnot = av |
555 | .getAlignmentConsensusAnnotation(); | |
556 | 2374 | final AlignmentAnnotation structConsensusAnnot = av |
557 | .getAlignmentStrucConsensusAnnotation(); | |
558 | 2374 | final AlignmentAnnotation complementConsensusAnnot = av |
559 | .getComplementConsensusAnnotation(); | |
560 | 2374 | final List<AlignmentAnnotation> ssConsensusAnnot = av |
561 | .getAlignmentSecondaryStructureConsensusAnnotation(); | |
562 | ||
563 | 2374 | BitSet graphGroupDrawn = new BitSet(); |
564 | 2374 | int charOffset = 0; // offset for a label |
565 | // \u03B2 \u03B1 | |
566 | // debug ints | |
567 | 2374 | int yfrom = 0, f_i = 0, yto = 0, f_to = 0; |
568 | 2374 | boolean clipst = false, clipend = false; |
569 | 15263 | for (int i = 0; i < aa.length; i++) |
570 | { | |
571 | 12889 | AlignmentAnnotation row = aa[i]; |
572 | 12889 | boolean renderHistogram = true; |
573 | 12889 | boolean renderProfile = false; |
574 | 12889 | boolean normaliseProfile = false; |
575 | 12889 | boolean isRNA = row.isRNA(); |
576 | ||
577 | // check if this is a consensus annotation row and set the display | |
578 | // settings appropriately | |
579 | // TODO: generalise this to have render styles for consensus/profile | |
580 | // data | |
581 | 12889 | if (row.groupRef != null && (row == row.groupRef.getConsensus() |
582 | || (row.groupRef.getSSConsensus(null) != null | |
583 | && row.groupRef.getSSConsensus(null).contains(row)))) | |
584 | { | |
585 | 634 | renderHistogram = row.groupRef.isShowConsensusHistogram(); |
586 | 634 | renderProfile = row.groupRef.isShowSequenceLogo(); |
587 | 634 | normaliseProfile = row.groupRef.isNormaliseSequenceLogo(); |
588 | } | |
589 | 12255 | else if (row == consensusAnnot || row == structConsensusAnnot |
590 | || row == complementConsensusAnnot | |
591 | || (ssConsensusAnnot != null | |
592 | && ssConsensusAnnot.contains(row))) | |
593 | { | |
594 | 2374 | renderHistogram = av_renderHistogram; |
595 | 2374 | renderProfile = av_renderProfile; |
596 | 2374 | normaliseProfile = av_normaliseProfile; |
597 | } | |
598 | ||
599 | 12889 | Annotation[] row_annotations = row.annotations; |
600 | 12889 | if (!row.visible) |
601 | { | |
602 | 1133 | continue; |
603 | } | |
604 | // centreColLabels = row.centreColLabels || centreColLabelsDef; | |
605 | 11756 | labelAllCols = row.showAllColLabels; |
606 | 11756 | scaleColLabel = row.scaleColLabel; |
607 | 11756 | lastSS = ' '; |
608 | 11756 | lastSSX = 0; |
609 | ||
610 | 11756 | if (!useClip || ((y - charHeight) < visHeight |
611 | && (y + row.height + charHeight * 2) >= sOffset)) | |
612 | {// if_in_visible_region | |
613 | 11756 | if (!clipst) |
614 | { | |
615 | 2364 | clipst = true; |
616 | 2364 | yfrom = y; |
617 | 2364 | f_i = i; |
618 | } | |
619 | 11756 | yto = y; |
620 | 11756 | f_to = i; |
621 | 11756 | if (row.graph > 0) |
622 | { | |
623 | 9991 | if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup)) |
624 | { | |
625 | 0 | continue; |
626 | } | |
627 | ||
628 | // this is so that we draw the characters below the graph | |
629 | 9991 | y += row.height; |
630 | ||
631 | 9991 | if (row.hasText) |
632 | { | |
633 | 9353 | iconOffset = charHeight - fm.getDescent(); |
634 | 9353 | y -= charHeight; |
635 | } | |
636 | } | |
637 | 1765 | else if (row.hasText) |
638 | { | |
639 | 1516 | iconOffset = charHeight - fm.getDescent(); |
640 | ||
641 | } | |
642 | else | |
643 | { | |
644 | 249 | iconOffset = 0; |
645 | } | |
646 | ||
647 | 11756 | if (row.autoCalculated && av.isCalculationInProgress(row)) |
648 | { | |
649 | 386 | y += charHeight; |
650 | 386 | usedFaded = true; |
651 | 386 | g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, |
652 | y - row.height, imgWidth, y, annotationPanel); | |
653 | 386 | g.setColor(Color.black); |
654 | // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2); | |
655 | ||
656 | 386 | continue; |
657 | } | |
658 | ||
659 | /* | |
660 | * else if (annotationPanel.av.updatingConservation && | |
661 | * aa[i].label.equals("Conservation")) { | |
662 | * | |
663 | * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y - | |
664 | * row.height, annotationPanel.imgWidth, y, 0, y - row.height, | |
665 | * annotationPanel.imgWidth, y, annotationPanel); | |
666 | * | |
667 | * g.setColor(Color.black); // | |
668 | * g.drawString("Calculating Conservation.....",20, y-row.height/2); | |
669 | * | |
670 | * continue; } else if (annotationPanel.av.updatingConservation && | |
671 | * aa[i].label.equals("Quality")) { | |
672 | * | |
673 | * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y - | |
674 | * row.height, annotationPanel.imgWidth, y, 0, y - row.height, | |
675 | * annotationPanel.imgWidth, y, annotationPanel); | |
676 | * g.setColor(Color.black); // / | |
677 | * g.drawString("Calculating Quality....",20, y-row.height/2); | |
678 | * | |
679 | * continue; } | |
680 | */ | |
681 | ||
682 | // first pass sets up state for drawing continuation from left-hand | |
683 | // column | |
684 | // of startRes | |
685 | ||
686 | // flag used for vector rendition | |
687 | 11370 | this.glyphLineDrawn = false; |
688 | 11370 | x = (startRes == 0) ? 0 : -1; |
689 | 589635 | while (x < endRes - startRes) |
690 | { | |
691 | 578264 | if (hasHiddenColumns) |
692 | { | |
693 | 130167 | column = hiddenColumns.visibleToAbsoluteColumn(startRes + x); |
694 | 130167 | if (column > row_annotations.length - 1) |
695 | { | |
696 | 0 | break; |
697 | } | |
698 | } | |
699 | else | |
700 | { | |
701 | 448097 | column = startRes + x; |
702 | } | |
703 | ||
704 | 578264 | if ((row_annotations == null) |
705 | || (row_annotations.length <= column) | |
706 | || (row_annotations[column] == null)) | |
707 | { | |
708 | 101028 | validRes = false; |
709 | } | |
710 | else | |
711 | { | |
712 | 477235 | validRes = true; |
713 | } | |
714 | 578263 | final String displayChar = validRes |
715 | ? row_annotations[column].displayCharacter | |
716 | : null; | |
717 | 578265 | if (x > -1) |
718 | { | |
719 | 573257 | unsetAntialias(g); |
720 | 573259 | if (activeRow == i) |
721 | { | |
722 | 0 | g.setColor(Color.red); |
723 | ||
724 | 0 | if (columnSelection != null) |
725 | { | |
726 | 0 | if (columnSelection.contains(column)) |
727 | { | |
728 | 0 | fillRect(g, x * charWidth, y, charWidth, charHeight); |
729 | } | |
730 | } | |
731 | } | |
732 | 573259 | if (row.getInvalidStrucPos() > x) |
733 | { | |
734 | 0 | g.setColor(Color.orange); |
735 | 0 | fillRect(g, x * charWidth, y, charWidth, charHeight); |
736 | } | |
737 | 573259 | else if (row.getInvalidStrucPos() == x) |
738 | { | |
739 | 0 | g.setColor(Color.orange.darker()); |
740 | 0 | fillRect(g, x * charWidth, y, charWidth, charHeight); |
741 | } | |
742 | 573258 | if (validCharWidth && validRes && displayChar != null |
743 | && (displayChar.length() > 0)) | |
744 | { | |
745 | // Graphics2D gg = (g); | |
746 | 340386 | float fmWidth = fm.charsWidth(displayChar.toCharArray(), 0, |
747 | displayChar.length()); | |
748 | ||
749 | /* | |
750 | * shrink label width to fit in column, if that is | |
751 | * both configured and necessary | |
752 | */ | |
753 | 340388 | boolean scaledToFit = false; |
754 | 340386 | float fmScaling = 1f; |
755 | 340386 | if (scaleColLabel && fmWidth > charWidth) |
756 | { | |
757 | 0 | scaledToFit = true; |
758 | 0 | fmScaling = charWidth; |
759 | 0 | fmScaling /= fmWidth; |
760 | // and update the label's width to reflect the scaling. | |
761 | 0 | fmWidth = charWidth; |
762 | } | |
763 | ||
764 | 340386 | charOffset = (int) ((charWidth - fmWidth) / 2f); |
765 | ||
766 | 340387 | if (row_annotations[column].colour == null) |
767 | { | |
768 | 144871 | g2d.setColor(Color.black); |
769 | } | |
770 | else | |
771 | { | |
772 | 195516 | g2d.setColor(row_annotations[column].colour); |
773 | } | |
774 | ||
775 | /* | |
776 | * draw the label, unless it is the same secondary structure | |
777 | * symbol (excluding RNA Helix) as the previous column | |
778 | */ | |
779 | 340386 | final int xPos = (x * charWidth) + charOffset; |
780 | 340386 | final int yPos = y + iconOffset; |
781 | ||
782 | /* | |
783 | * translate to drawing position _before_ applying any scaling | |
784 | */ | |
785 | 340386 | g2d.translate(xPos, yPos); |
786 | 340385 | if (scaledToFit) |
787 | { | |
788 | /* | |
789 | * use a scaling transform to make the label narrower | |
790 | * (JalviewJS doesn't have Font.deriveFont(AffineTransform)) | |
791 | */ | |
792 | 0 | g2d.transform( |
793 | AffineTransform.getScaleInstance(fmScaling, 1.0)); | |
794 | } | |
795 | 340385 | setAntialias(g); |
796 | 340387 | if (column == 0 || row.graph > 0) |
797 | { | |
798 | 332153 | g2d.drawString(displayChar, 0, 0); |
799 | } | |
800 | 8233 | else if (row_annotations[column - 1] == null || (labelAllCols |
801 | || !displayChar.equals( | |
802 | row_annotations[column - 1].displayCharacter) | |
803 | || (displayChar.length() < 2 | |
804 | && row_annotations[column].secondaryStructure == ' '))) | |
805 | { | |
806 | 8233 | g2d.drawString(displayChar, 0, 0); |
807 | } | |
808 | 340385 | if (scaledToFit) |
809 | { | |
810 | /* | |
811 | * undo scaling before translating back | |
812 | * (restoring saved transform does NOT work in JS PDFGraphics!) | |
813 | */ | |
814 | 0 | g2d.transform(AffineTransform |
815 | .getScaleInstance(1D / fmScaling, 1.0)); | |
816 | } | |
817 | 340385 | g2d.translate(-xPos, -yPos); |
818 | } | |
819 | } | |
820 | 578266 | if (row.hasIcons) |
821 | { | |
822 | 60525 | char ss = validRes ? row_annotations[column].secondaryStructure |
823 | : '-'; | |
824 | ||
825 | 60525 | if (ss == '(') |
826 | { | |
827 | // distinguish between forward/backward base-pairing | |
828 | 0 | if (displayChar.indexOf(')') > -1) |
829 | { | |
830 | ||
831 | 0 | ss = ')'; |
832 | ||
833 | } | |
834 | } | |
835 | 60525 | if (ss == '[') |
836 | { | |
837 | 0 | if ((displayChar.indexOf(']') > -1)) |
838 | { | |
839 | 0 | ss = ']'; |
840 | ||
841 | } | |
842 | } | |
843 | 60525 | if (ss == '{') |
844 | { | |
845 | // distinguish between forward/backward base-pairing | |
846 | 0 | if (displayChar.indexOf('}') > -1) |
847 | { | |
848 | 0 | ss = '}'; |
849 | ||
850 | } | |
851 | } | |
852 | 60525 | if (ss == '<') |
853 | { | |
854 | // distinguish between forward/backward base-pairing | |
855 | 0 | if (displayChar.indexOf('<') > -1) |
856 | { | |
857 | 0 | ss = '>'; |
858 | ||
859 | } | |
860 | } | |
861 | 60525 | if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z)) |
862 | { | |
863 | // distinguish between forward/backward base-pairing | |
864 | 0 | int ssLowerCase = ss + UPPER_TO_LOWER; |
865 | // TODO would .equals() be safer here? or charAt(0)? | |
866 | 0 | if (displayChar.indexOf(ssLowerCase) > -1) |
867 | { | |
868 | 0 | ss = (char) ssLowerCase; |
869 | } | |
870 | } | |
871 | ||
872 | 60525 | if (!validRes || (ss != lastSS)) |
873 | { | |
874 | ||
875 | 46561 | if (x > -1) |
876 | { | |
877 | ||
878 | // int nb_annot = x - temp; | |
879 | // Console.info("\t type :"+lastSS+"\t x | |
880 | // :"+x+"\t nbre | |
881 | // annot :"+nb_annot); | |
882 | 45800 | switch (lastSS) |
883 | { | |
884 | 0 | case '(': // Stem case for RNA secondary structure |
885 | 0 | case ')': // and opposite direction |
886 | 0 | drawStemAnnot(g, row_annotations, lastSSX, x, y, |
887 | iconOffset, startRes, column, validRes, validEnd); | |
888 | // temp = x; | |
889 | 0 | break; |
890 | ||
891 | 802 | case 'H': |
892 | 802 | if (!isRNA) |
893 | { | |
894 | 802 | drawHelixAnnot(g, row_annotations, lastSSX, x, y, |
895 | iconOffset, startRes, column, validRes, | |
896 | validEnd); | |
897 | 802 | break; |
898 | } | |
899 | // no break if isRNA - falls through to drawNotCanonicalAnnot! | |
900 | 4069 | case 'E': |
901 | 4069 | if (!isRNA) |
902 | { | |
903 | 4069 | drawSheetAnnot(g, row_annotations, lastSSX, x, y, |
904 | iconOffset, startRes, column, validRes, | |
905 | validEnd); | |
906 | 4069 | break; |
907 | } | |
908 | // no break if isRNA - fall through to drawNotCanonicalAnnot! | |
909 | ||
910 | 0 | case '{': |
911 | 0 | case '}': |
912 | 0 | case '[': |
913 | 0 | case ']': |
914 | 0 | case '>': |
915 | 0 | case '<': |
916 | 0 | case 'A': |
917 | 0 | case 'a': |
918 | 0 | case 'B': |
919 | 0 | case 'b': |
920 | 0 | case 'C': |
921 | 0 | case 'c': |
922 | 0 | case 'D': |
923 | 0 | case 'd': |
924 | 0 | case 'e': |
925 | 0 | case 'F': |
926 | 0 | case 'f': |
927 | 0 | case 'G': |
928 | 0 | case 'g': |
929 | 0 | case 'h': |
930 | 0 | case 'I': |
931 | 0 | case 'i': |
932 | 0 | case 'J': |
933 | 0 | case 'j': |
934 | 0 | case 'K': |
935 | 0 | case 'k': |
936 | 0 | case 'L': |
937 | 0 | case 'l': |
938 | 0 | case 'M': |
939 | 0 | case 'm': |
940 | 0 | case 'N': |
941 | 0 | case 'n': |
942 | 0 | case 'O': |
943 | 0 | case 'o': |
944 | 0 | case 'P': |
945 | 0 | case 'p': |
946 | 0 | case 'Q': |
947 | 0 | case 'q': |
948 | 0 | case 'R': |
949 | 0 | case 'r': |
950 | 0 | case 'S': |
951 | 0 | case 's': |
952 | 0 | case 'T': |
953 | 0 | case 't': |
954 | 0 | case 'U': |
955 | 0 | case 'u': |
956 | 0 | case 'V': |
957 | 0 | case 'v': |
958 | 0 | case 'W': |
959 | 0 | case 'w': |
960 | 0 | case 'X': |
961 | 0 | case 'x': |
962 | 0 | case 'Y': |
963 | 0 | case 'y': |
964 | 0 | case 'Z': |
965 | 0 | case 'z': |
966 | ||
967 | 0 | Color nonCanColor = getNotCanonicalColor(lastSS); |
968 | 0 | drawNotCanonicalAnnot(g, nonCanColor, row_annotations, |
969 | lastSSX, x, y, iconOffset, startRes, column, | |
970 | validRes, validEnd); | |
971 | // temp = x; | |
972 | 0 | break; |
973 | 40929 | default: |
974 | 40929 | if (isVectorRendering()) |
975 | { | |
976 | // draw single full width glyphline | |
977 | 0 | drawGlyphLine(g, lastSSX, endRes - x, y, iconOffset); |
978 | // disable more glyph lines | |
979 | 0 | this.glyphLineDrawn = true; |
980 | } | |
981 | else | |
982 | { | |
983 | 40929 | drawGlyphLine(g, lastSSX, x, y, iconOffset); |
984 | } | |
985 | 40929 | break; |
986 | } | |
987 | } | |
988 | 46561 | if (validRes) |
989 | { | |
990 | 4970 | lastSS = ss; |
991 | } | |
992 | else | |
993 | { | |
994 | 41591 | lastSS = ' '; |
995 | } | |
996 | 46561 | if (x > -1) |
997 | { | |
998 | 45800 | lastSSX = (x * charWidth); |
999 | } | |
1000 | } | |
1001 | } | |
1002 | 578264 | column++; |
1003 | 578265 | x++; |
1004 | } | |
1005 | 11370 | if (column >= row_annotations.length) |
1006 | { | |
1007 | 1724 | column = row_annotations.length - 1; |
1008 | 1724 | validEnd = false; |
1009 | } | |
1010 | else | |
1011 | { | |
1012 | 9646 | validEnd = true; |
1013 | } | |
1014 | 11370 | if ((row_annotations == null) || (row_annotations.length <= column) |
1015 | || (row_annotations[column] == null)) | |
1016 | { | |
1017 | 2178 | validRes = false; |
1018 | } | |
1019 | else | |
1020 | { | |
1021 | 9192 | validRes = true; |
1022 | } | |
1023 | // x ++; | |
1024 | ||
1025 | 11370 | if (row.hasIcons) |
1026 | { | |
1027 | 1007 | switch (lastSS) |
1028 | { | |
1029 | ||
1030 | 0 | case 'H': |
1031 | 0 | if (!isRNA) |
1032 | { | |
1033 | 0 | drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, |
1034 | startRes, column, validRes, validEnd); | |
1035 | 0 | break; |
1036 | } | |
1037 | // no break if isRNA - fall through to drawNotCanonicalAnnot! | |
1038 | ||
1039 | 99 | case 'E': |
1040 | 99 | if (!isRNA) |
1041 | { | |
1042 | 99 | drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, |
1043 | startRes, column, validRes, validEnd); | |
1044 | 99 | break; |
1045 | } | |
1046 | // no break if isRNA - fall through to drawNotCanonicalAnnot! | |
1047 | ||
1048 | 0 | case '(': |
1049 | 0 | case ')': // Stem case for RNA secondary structure |
1050 | ||
1051 | 0 | drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, |
1052 | startRes, column, validRes, validEnd); | |
1053 | ||
1054 | 0 | break; |
1055 | 0 | case '{': |
1056 | 0 | case '}': |
1057 | 0 | case '[': |
1058 | 0 | case ']': |
1059 | 0 | case '>': |
1060 | 0 | case '<': |
1061 | 0 | case 'A': |
1062 | 0 | case 'a': |
1063 | 0 | case 'B': |
1064 | 0 | case 'b': |
1065 | 0 | case 'C': |
1066 | 0 | case 'c': |
1067 | 0 | case 'D': |
1068 | 0 | case 'd': |
1069 | 0 | case 'e': |
1070 | 0 | case 'F': |
1071 | 0 | case 'f': |
1072 | 0 | case 'G': |
1073 | 0 | case 'g': |
1074 | 0 | case 'h': |
1075 | 0 | case 'I': |
1076 | 0 | case 'i': |
1077 | 0 | case 'J': |
1078 | 0 | case 'j': |
1079 | 0 | case 'K': |
1080 | 0 | case 'k': |
1081 | 0 | case 'L': |
1082 | 0 | case 'l': |
1083 | 0 | case 'M': |
1084 | 0 | case 'm': |
1085 | 0 | case 'N': |
1086 | 0 | case 'n': |
1087 | 0 | case 'O': |
1088 | 0 | case 'o': |
1089 | 0 | case 'P': |
1090 | 0 | case 'p': |
1091 | 0 | case 'Q': |
1092 | 0 | case 'q': |
1093 | 0 | case 'R': |
1094 | 0 | case 'r': |
1095 | 0 | case 'T': |
1096 | 0 | case 't': |
1097 | 0 | case 'U': |
1098 | 0 | case 'u': |
1099 | 0 | case 'V': |
1100 | 0 | case 'v': |
1101 | 0 | case 'W': |
1102 | 0 | case 'w': |
1103 | 0 | case 'X': |
1104 | 0 | case 'x': |
1105 | 0 | case 'Y': |
1106 | 0 | case 'y': |
1107 | 0 | case 'Z': |
1108 | 0 | case 'z': |
1109 | // Console.info(lastSS); | |
1110 | 0 | Color nonCanColor = getNotCanonicalColor(lastSS); |
1111 | 0 | drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX, |
1112 | x, y, iconOffset, startRes, column, validRes, validEnd); | |
1113 | 0 | break; |
1114 | 908 | default: |
1115 | 908 | if (isVectorRendering()) |
1116 | { | |
1117 | // draw single full width glyphline | |
1118 | 0 | drawGlyphLine(g, lastSSX, endRes - x, y, iconOffset); |
1119 | // disable more glyph lines | |
1120 | 0 | this.glyphLineDrawn = true; |
1121 | } | |
1122 | else | |
1123 | { | |
1124 | 908 | drawGlyphLine(g, lastSSX, x, y, iconOffset); |
1125 | } | |
1126 | 908 | break; |
1127 | } | |
1128 | } | |
1129 | ||
1130 | 11370 | if (row.graph > 0 && row.graphHeight > 0) |
1131 | { | |
1132 | 9605 | if (row.graph == AlignmentAnnotation.LINE_GRAPH) |
1133 | { | |
1134 | 499 | if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup)) |
1135 | { | |
1136 | // TODO: JAL-1291 revise rendering model so the graphGroup map is | |
1137 | // computed efficiently for all visible labels | |
1138 | 0 | float groupmax = -999999, groupmin = 9999999; |
1139 | 0 | for (int gg = 0; gg < aa.length; gg++) |
1140 | { | |
1141 | 0 | if (aa[gg].graphGroup != row.graphGroup) |
1142 | { | |
1143 | 0 | continue; |
1144 | } | |
1145 | ||
1146 | 0 | if (aa[gg] != row) |
1147 | { | |
1148 | 0 | aa[gg].visible = false; |
1149 | } | |
1150 | 0 | if (aa[gg].graphMax > groupmax) |
1151 | { | |
1152 | 0 | groupmax = aa[gg].graphMax; |
1153 | } | |
1154 | 0 | if (aa[gg].graphMin < groupmin) |
1155 | { | |
1156 | 0 | groupmin = aa[gg].graphMin; |
1157 | } | |
1158 | } | |
1159 | ||
1160 | 0 | for (int gg = 0; gg < aa.length; gg++) |
1161 | { | |
1162 | 0 | if (aa[gg].graphGroup == row.graphGroup) |
1163 | { | |
1164 | 0 | drawLineGraph(g, aa[gg], aa[gg].annotations, startRes, |
1165 | endRes, y, groupmin, groupmax, row.graphHeight); | |
1166 | } | |
1167 | } | |
1168 | ||
1169 | 0 | graphGroupDrawn.set(row.graphGroup); |
1170 | } | |
1171 | else | |
1172 | { | |
1173 | 499 | drawLineGraph(g, row, row_annotations, startRes, endRes, y, |
1174 | row.graphMin, row.graphMax, row.graphHeight); | |
1175 | } | |
1176 | } | |
1177 | 9106 | else if (row.graph == AlignmentAnnotation.BAR_GRAPH) |
1178 | { | |
1179 | 8967 | drawBarGraph(g, row, row_annotations, startRes, endRes, |
1180 | row.graphMin, row.graphMax, y, renderHistogram, | |
1181 | renderProfile, normaliseProfile); | |
1182 | } | |
1183 | else | |
1184 | { | |
1185 | 139 | AnnotationRowRendererI renderer = rendererFactoryI |
1186 | .getRendererFor(row); | |
1187 | 139 | if (renderer != null) |
1188 | { | |
1189 | 139 | renderer.renderRow(g, charWidth, charHeight, hasHiddenColumns, |
1190 | av, hiddenColumns, columnSelection, row, | |
1191 | row_annotations, startRes, endRes, row.graphMin, | |
1192 | row.graphMax, y); | |
1193 | } | |
1194 | 139 | if (debugRedraw) |
1195 | { | |
1196 | 0 | if (renderer == null) |
1197 | { | |
1198 | 0 | System.err |
1199 | .println("No renderer found for " + row.toString()); | |
1200 | } | |
1201 | else | |
1202 | { | |
1203 | 0 | Console.warn( |
1204 | "rendered with " + renderer.getClass().toString()); | |
1205 | } | |
1206 | } | |
1207 | ||
1208 | } | |
1209 | } | |
1210 | } | |
1211 | else | |
1212 | { | |
1213 | 0 | if (clipst && !clipend) |
1214 | { | |
1215 | 0 | clipend = true; |
1216 | } | |
1217 | } // end if_in_visible_region | |
1218 | 11370 | if (row.graph > 0 && row.hasText) |
1219 | { | |
1220 | 8967 | y += charHeight; |
1221 | } | |
1222 | ||
1223 | 11370 | if (row.graph == 0) |
1224 | { | |
1225 | 1765 | y += aa[i].height; |
1226 | } | |
1227 | } | |
1228 | 2374 | if (debugRedraw) |
1229 | { | |
1230 | 0 | if (canClip) |
1231 | { | |
1232 | 0 | if (clipst) |
1233 | { | |
1234 | 0 | Console.warn("Start clip at : " + yfrom + " (index " + f_i + ")"); |
1235 | } | |
1236 | 0 | if (clipend) |
1237 | { | |
1238 | 0 | Console.warn("End clip at : " + yto + " (index " + f_to + ")"); |
1239 | } | |
1240 | } | |
1241 | 0 | ; |
1242 | 0 | Console.warn("Annotation Rendering time:" |
1243 | + (System.currentTimeMillis() - stime)); | |
1244 | } | |
1245 | 2374 | ; |
1246 | ||
1247 | 2374 | return !usedFaded; |
1248 | } | |
1249 | ||
1250 | public static final Color GLYPHLINE_COLOR = Color.gray; | |
1251 | ||
1252 | public static final Color SHEET_COLOUR = Color.green; | |
1253 | ||
1254 | public static final Color HELIX_COLOUR = Color.red; | |
1255 | ||
1256 | public static final Color STEM_COLOUR = Color.blue; | |
1257 | ||
1258 | // private Color sdNOTCANONICAL_COLOUR; | |
1259 | ||
1260 | 46805 | void drawGlyphLine(Graphics g, int lastSSX, int x, int y, int iconOffset) |
1261 | { | |
1262 | 46805 | if (glyphLineDrawn) |
1263 | { | |
1264 | // if we've drawn a single long glyphline for an export, don't draw the | |
1265 | // bits | |
1266 | 0 | return; |
1267 | } | |
1268 | 46805 | unsetAntialias(g); |
1269 | 46805 | g.setColor(GLYPHLINE_COLOR); |
1270 | 46805 | g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2); |
1271 | } | |
1272 | ||
1273 | 4168 | void drawSheetAnnot(Graphics g, Annotation[] row, |
1274 | ||
1275 | int lastSSX, int x, int y, int iconOffset, int startRes, | |
1276 | int column, boolean validRes, boolean validEnd) | |
1277 | { | |
1278 | 4168 | if (!validEnd || !validRes || row == null || row[column] == null |
1279 | || row[column].secondaryStructure != 'E') | |
1280 | { | |
1281 | // draw the glyphline underneath | |
1282 | 4166 | drawGlyphLine(g, lastSSX, x, y, iconOffset); |
1283 | ||
1284 | 4166 | g.setColor(SHEET_COLOUR); |
1285 | 4166 | fillRect(g, lastSSX, y + 4 + iconOffset, |
1286 | (x * charWidth) - lastSSX - 4, 6); | |
1287 | 4166 | fillPolygon(g, |
1288 | new int[] | |
1289 | { (x * charWidth) - 6, (x * charWidth) - 6, | |
1290 | (x * charWidth - 1) }, | |
1291 | new int[] | |
1292 | { y + iconOffset + 1, y + 13 + iconOffset, | |
1293 | y + 7 + iconOffset }, | |
1294 | 3); | |
1295 | } | |
1296 | else | |
1297 | { | |
1298 | 2 | g.setColor(SHEET_COLOUR); |
1299 | 2 | fillRect(g, lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX, |
1300 | 6); | |
1301 | } | |
1302 | } | |
1303 | ||
1304 | 802 | void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x, |
1305 | int y, int iconOffset, int startRes, int column, boolean validRes, | |
1306 | boolean validEnd) | |
1307 | { | |
1308 | 802 | int sCol = (lastSSX / charWidth) |
1309 | + hiddenColumns.visibleToAbsoluteColumn(startRes); | |
1310 | 802 | int x1 = lastSSX; |
1311 | 802 | int x2 = (x * charWidth); |
1312 | ||
1313 | 802 | if (USE_FILL_ROUND_RECT || isVectorRendering()) |
1314 | { | |
1315 | // draw glyph line behind helix (visible in EPS or SVG output) | |
1316 | 0 | drawGlyphLine(g, lastSSX, x, y, iconOffset); |
1317 | ||
1318 | 0 | g.setColor(HELIX_COLOUR); |
1319 | 0 | setAntialias(g); |
1320 | 0 | int ofs = charWidth / 2; |
1321 | // Off by 1 offset when drawing rects and ovals | |
1322 | // to offscreen image on the MAC | |
1323 | 0 | fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - 1, 8, 8, 8); |
1324 | 0 | if (sCol == 0 || row[sCol - 1] == null |
1325 | || row[sCol - 1].secondaryStructure != 'H') | |
1326 | { | |
1327 | } | |
1328 | else | |
1329 | { | |
1330 | 0 | fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - ofs, 8, 0, |
1331 | 0); | |
1332 | } | |
1333 | 0 | if (!validRes || row[column] == null |
1334 | || row[column].secondaryStructure != 'H') | |
1335 | { | |
1336 | ||
1337 | } | |
1338 | else | |
1339 | { | |
1340 | 0 | fillRoundRect(g, lastSSX + ofs, y + 3 + iconOffset, x2 - x1 - ofs, |
1341 | 8, 0, 0); | |
1342 | } | |
1343 | ||
1344 | 0 | return; |
1345 | } | |
1346 | ||
1347 | 802 | boolean leftEnd = sCol == 0 || row[sCol - 1] == null |
1348 | || row[sCol - 1].secondaryStructure != 'H'; | |
1349 | 802 | boolean rightEnd = !validRes || row[column] == null |
1350 | || row[column].secondaryStructure != 'H'; | |
1351 | ||
1352 | 802 | if (leftEnd || rightEnd) |
1353 | { | |
1354 | 802 | drawGlyphLine(g, lastSSX, x, y, iconOffset); |
1355 | } | |
1356 | 802 | g.setColor(HELIX_COLOUR); |
1357 | ||
1358 | 802 | if (leftEnd) |
1359 | { | |
1360 | 802 | fillArc(g, lastSSX, y + 3 + iconOffset, charWidth, 8, 90, 180); |
1361 | 802 | x1 += charWidth / 2; |
1362 | } | |
1363 | ||
1364 | 802 | if (rightEnd) |
1365 | { | |
1366 | 802 | fillArc(g, ((x - 1) * charWidth), y + 3 + iconOffset, charWidth, 8, |
1367 | 270, 180); | |
1368 | 802 | x2 -= charWidth / 2; |
1369 | } | |
1370 | ||
1371 | 802 | fillRect(g, x1, y + 3 + iconOffset, x2 - x1, 8); |
1372 | } | |
1373 | ||
1374 | 499 | void drawLineGraph(Graphics g, AlignmentAnnotation _aa, |
1375 | Annotation[] aa_annotations, int sRes, int eRes, int y, float min, | |
1376 | float max, int graphHeight) | |
1377 | { | |
1378 | 499 | if (sRes > aa_annotations.length) |
1379 | { | |
1380 | 1 | return; |
1381 | } | |
1382 | 498 | Stroke roundStroke = new BasicStroke(1, BasicStroke.CAP_ROUND, |
1383 | BasicStroke.JOIN_ROUND); | |
1384 | 498 | Stroke squareStroke = new BasicStroke(1, BasicStroke.CAP_SQUARE, |
1385 | BasicStroke.JOIN_MITER); | |
1386 | 498 | Graphics2D g2d = (Graphics2D) g; |
1387 | 498 | Stroke prevStroke = g2d.getStroke(); |
1388 | 498 | g2d.setStroke(roundStroke); |
1389 | ||
1390 | 498 | int x = 0; |
1391 | ||
1392 | // Adjustment for fastpaint to left | |
1393 | 498 | if (eRes < endRes) |
1394 | { | |
1395 | 0 | eRes++; |
1396 | } | |
1397 | ||
1398 | 498 | eRes = Math.min(eRes, aa_annotations.length); |
1399 | ||
1400 | 498 | if (sRes == 0) |
1401 | { | |
1402 | 496 | x++; |
1403 | } | |
1404 | ||
1405 | 498 | int y1 = y, y2 = y; |
1406 | 498 | float range = max - min; |
1407 | ||
1408 | // //Draw origin | |
1409 | 498 | if (min < 0) |
1410 | { | |
1411 | 0 | y2 = y - (int) ((0 - min / range) * graphHeight); |
1412 | } | |
1413 | ||
1414 | 498 | g.setColor(Color.gray); |
1415 | 498 | drawLine(g, squareStroke, x * charWidth - charWidth, y2, |
1416 | (eRes - sRes) * charWidth, y2); | |
1417 | ||
1418 | 498 | eRes = Math.min(eRes, aa_annotations.length); |
1419 | ||
1420 | 498 | int column; |
1421 | 498 | int aaMax = aa_annotations.length - 1; |
1422 | ||
1423 | 22292 | while (x < eRes - sRes) |
1424 | { | |
1425 | 21794 | column = sRes + x; |
1426 | 21794 | if (hasHiddenColumns) |
1427 | { | |
1428 | 8000 | column = hiddenColumns.visibleToAbsoluteColumn(column); |
1429 | } | |
1430 | ||
1431 | 21794 | if (column > aaMax) |
1432 | { | |
1433 | 0 | break; |
1434 | } | |
1435 | ||
1436 | 21794 | if (aa_annotations[column] == null) |
1437 | { | |
1438 | 7618 | x++; |
1439 | 7618 | continue; |
1440 | } | |
1441 | ||
1442 | 14176 | if (aa_annotations[column].colour == null) |
1443 | { | |
1444 | 3276 | g.setColor(Color.black); |
1445 | } | |
1446 | else | |
1447 | { | |
1448 | 10900 | g.setColor(aa_annotations[column].colour); |
1449 | } | |
1450 | ||
1451 | 14176 | if (aa_annotations[column - 1] == null |
1452 | && aa_annotations.length > column + 1 | |
1453 | && aa_annotations[column + 1] == null) | |
1454 | { | |
1455 | // standalone value | |
1456 | 1545 | y1 = y - (int) (((aa_annotations[column].value - min) / range) |
1457 | * graphHeight); | |
1458 | 1545 | drawLine(g, x * charWidth + charWidth / 4, y1, |
1459 | x * charWidth + 3 * charWidth / 4, y1); | |
1460 | 1545 | x++; |
1461 | 1545 | continue; |
1462 | } | |
1463 | ||
1464 | 12631 | if (aa_annotations[column - 1] == null) |
1465 | { | |
1466 | 210 | x++; |
1467 | 210 | continue; |
1468 | } | |
1469 | ||
1470 | 12421 | y1 = y - (int) (((aa_annotations[column - 1].value - min) / range) |
1471 | * graphHeight); | |
1472 | 12421 | y2 = y - (int) (((aa_annotations[column].value - min) / range) |
1473 | * graphHeight); | |
1474 | ||
1475 | 12421 | drawLine(g, (x - 1) * charWidth + charWidth / 2, y1, |
1476 | x * charWidth + charWidth / 2, y2); | |
1477 | 12421 | x++; |
1478 | } | |
1479 | ||
1480 | 498 | if (_aa.threshold != null) |
1481 | { | |
1482 | 0 | g.setColor(_aa.threshold.colour); |
1483 | 0 | Graphics2D g2 = (Graphics2D) g; |
1484 | 0 | Stroke s = new BasicStroke(1, BasicStroke.CAP_SQUARE, |
1485 | BasicStroke.JOIN_ROUND, 3f, new float[] | |
1486 | { 5f, 3f }, 0f); | |
1487 | ||
1488 | 0 | y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight); |
1489 | 0 | drawLine(g, s, 0, y2, (eRes - sRes) * charWidth, y2); |
1490 | } | |
1491 | 498 | g2d.setStroke(prevStroke); |
1492 | } | |
1493 | ||
1494 | 8967 | @SuppressWarnings("unused") |
1495 | void drawBarGraph(Graphics g, AlignmentAnnotation _aa, | |
1496 | Annotation[] aa_annotations, int sRes, int eRes, float min, | |
1497 | float max, int y, boolean renderHistogram, boolean renderProfile, | |
1498 | boolean normaliseProfile) | |
1499 | { | |
1500 | 8967 | if (sRes > aa_annotations.length) |
1501 | { | |
1502 | 0 | return; |
1503 | } | |
1504 | 8967 | Font ofont = g.getFont(); |
1505 | 8967 | eRes = Math.min(eRes, aa_annotations.length); |
1506 | ||
1507 | 8967 | int x = 0, y1 = y, y2 = y; |
1508 | ||
1509 | 8967 | float range = max - min; |
1510 | ||
1511 | 8967 | if (min < 0) |
1512 | { | |
1513 | 0 | y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight); |
1514 | } | |
1515 | ||
1516 | 8967 | g.setColor(Color.gray); |
1517 | ||
1518 | 8967 | drawLine(g, x, y2, (eRes - sRes) * charWidth, y2); |
1519 | ||
1520 | 8967 | int column; |
1521 | 8967 | int aaMax = aa_annotations.length - 1; |
1522 | ||
1523 | /** | |
1524 | * TODO Should really set this using a constant local to AlignmentAnnotation | |
1525 | * in the same way as the cDNA and rna structure profiles are typed | |
1526 | */ | |
1527 | 8967 | boolean _aa_is_dssp3 = _aa.autoCalculated && _aa.label |
1528 | .startsWith(Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL); | |
1529 | ||
1530 | 446236 | while (x < eRes - sRes) |
1531 | { | |
1532 | 437269 | column = sRes + x; |
1533 | 437269 | if (hasHiddenColumns) |
1534 | { | |
1535 | 121917 | column = hiddenColumns.visibleToAbsoluteColumn(column); |
1536 | } | |
1537 | ||
1538 | 437269 | if (column > aaMax) |
1539 | { | |
1540 | 0 | break; |
1541 | } | |
1542 | ||
1543 | 437269 | if (aa_annotations[column] == null) |
1544 | { | |
1545 | 2825 | x++; |
1546 | 2825 | continue; |
1547 | } | |
1548 | 434443 | if (aa_annotations[column].colour == null) |
1549 | { | |
1550 | 144935 | g.setColor(Color.black); |
1551 | } | |
1552 | else | |
1553 | { | |
1554 | 289508 | g.setColor(aa_annotations[column].colour); |
1555 | } | |
1556 | ||
1557 | 434442 | y1 = y - (int) (((aa_annotations[column].value - min) / (range)) |
1558 | * _aa.graphHeight); | |
1559 | ||
1560 | 434441 | if (renderHistogram) |
1561 | { | |
1562 | 434441 | if (y1 - y2 > 0) |
1563 | { | |
1564 | 0 | fillRect(g, x * charWidth, y2, charWidth, y1 - y2); |
1565 | } | |
1566 | else | |
1567 | { | |
1568 | 434441 | fillRect(g, x * charWidth, y1, charWidth, y2 - y1); |
1569 | } | |
1570 | } | |
1571 | // draw profile if available | |
1572 | 434444 | if (renderProfile) |
1573 | { | |
1574 | ||
1575 | /* | |
1576 | * {profile type, #values, total count, char1, pct1, char2, pct2...} | |
1577 | */ | |
1578 | 104407 | int profl[] = getProfileFor(_aa, column); |
1579 | ||
1580 | // just try to draw the logo if profl is not null | |
1581 | 104407 | if (profl != null && profl[2] != 0) |
1582 | { | |
1583 | // TODO do we ever have different profiles for different columns ? | |
1584 | // Move up to where we set _aa_is_dssp3 | |
1585 | 104407 | boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE; |
1586 | 104407 | boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE; |
1587 | 104407 | float ht = normaliseProfile ? y - _aa.graphHeight : y1; |
1588 | 104407 | final double normaliseFactor = normaliseProfile ? _aa.graphHeight |
1589 | : (y2 - y1); | |
1590 | ||
1591 | /** | |
1592 | * Render a single base for a sequence profile, a base pair for | |
1593 | * structure profile, and a triplet for a cdna profile | |
1594 | */ | |
1595 | 104407 | char[] dc = new char[isStructureProfile ? 2 |
1596 | 104407 | : (isCdnaProfile ? 3 : 1)]; |
1597 | ||
1598 | // lm is not necessary - we can just use fm - could be off by no more | |
1599 | // than 0.5 px | |
1600 | // LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g); | |
1601 | // Console.info(asc + " " + dec + " " + (asc - | |
1602 | // lm.getAscent()) | |
1603 | // + " " + (dec - lm.getDescent())); | |
1604 | ||
1605 | 104407 | double asc = fm.getAscent(); |
1606 | 104407 | double dec = fm.getDescent(); |
1607 | 104407 | double fht = fm.getHeight(); |
1608 | ||
1609 | 104407 | double scale = 1f / (normaliseProfile ? profl[2] : 100f); |
1610 | // float ofontHeight = 1f / fm.getAscent();// magnify to fill box | |
1611 | ||
1612 | /* | |
1613 | * Traverse the character(s)/percentage data in the array | |
1614 | */ | |
1615 | ||
1616 | 104407 | float ht2 = ht; |
1617 | ||
1618 | // profl[1] is the number of values in the profile | |
1619 | 295918 | for (int i = 0, c = 3, last = profl[1]; i < last; i++) |
1620 | { | |
1621 | ||
1622 | 191511 | String s; |
1623 | 191510 | if (isStructureProfile) |
1624 | { | |
1625 | // todo can we encode a structure pair as an int, like codons? | |
1626 | 0 | dc[0] = (char) profl[c++]; |
1627 | 0 | dc[1] = (char) profl[c++]; |
1628 | 0 | s = new String(dc); |
1629 | } | |
1630 | 191510 | else if (isCdnaProfile) |
1631 | { | |
1632 | 0 | CodingUtils.decodeCodon2(profl[c++], dc); |
1633 | 0 | s = new String(dc); |
1634 | } | |
1635 | else | |
1636 | { | |
1637 | 191510 | dc[0] = (char) profl[c++]; |
1638 | 191511 | s = new String(dc); |
1639 | } | |
1640 | // next profl[] position is profile % for the character(s) | |
1641 | ||
1642 | 191512 | int percent = profl[c++]; |
1643 | 191512 | if (percent == 0) |
1644 | { | |
1645 | // failsafe in case a count rounds down to 0% | |
1646 | 0 | continue; |
1647 | } | |
1648 | 191512 | double newHeight = normaliseFactor * scale * percent; |
1649 | ||
1650 | /* | |
1651 | * Set character colour as per alignment colour scheme; use the | |
1652 | * codon translation if a cDNA profile | |
1653 | */ | |
1654 | 191512 | Color colour = null; |
1655 | 191512 | if (isCdnaProfile) |
1656 | { | |
1657 | 0 | final String codonTranslation = ResidueProperties |
1658 | .codonTranslate(s); | |
1659 | 0 | colour = profcolour.findColour(codonTranslation.charAt(0), |
1660 | column, null); | |
1661 | } | |
1662 | 191512 | else if (_aa_is_dssp3) |
1663 | { | |
1664 | // TODO - would be nice to get rid of the special 'findSSColour' | |
1665 | // here ? | |
1666 | 0 | colour = profcolour.findSSColour(dc[0], column); |
1667 | } | |
1668 | else | |
1669 | { | |
1670 | ||
1671 | 191512 | colour = profcolour.findColour(dc[0], column, null); |
1672 | } | |
1673 | 191513 | g.setColor(colour == Color.white ? Color.lightGray : colour); |
1674 | ||
1675 | // Debug - render boxes around characters | |
1676 | // g.setColor(Color.red); | |
1677 | // g.drawRect(x*av.charWidth, (int)ht, av.charWidth, | |
1678 | // (int)(scl)); | |
1679 | // g.setColor(profcolour.findColour(dc[0]).darker()); | |
1680 | ||
1681 | 191512 | double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length); |
1682 | 191512 | double sy = newHeight / asc; |
1683 | 191512 | double newAsc = asc * sy; |
1684 | 191512 | double newDec = dec * sy; |
1685 | // it is not necessary to recalculate lm for the new font. | |
1686 | // note: lm.getBaselineOffsets()[lm.getBaselineIndex()]) must be 0 | |
1687 | // by definition. Was: | |
1688 | // int hght = (int) (ht + (newAsc - newDec); | |
1689 | // - lm.getBaselineOffsets()[lm.getBaselineIndex()])); | |
1690 | ||
1691 | 191513 | if (Platform.isJS()) |
1692 | { | |
1693 | /* | |
1694 | * SwingJS does not implement font.deriveFont() | |
1695 | * so use a scaling transform to draw instead, | |
1696 | * this is off by a very small amount | |
1697 | */ | |
1698 | 0 | final int hght = (int) (ht2 + (newAsc - newDec)); |
1699 | 0 | Graphics2D gg = (Graphics2D) g; |
1700 | 0 | int xShift = (int) Math.round(x * charWidth / sx); |
1701 | 0 | int yShift = (int) Math.round(hght / sy); |
1702 | 0 | gg.transform(AffineTransform.getScaleInstance(sx, sy)); |
1703 | 0 | gg.drawString(s, xShift, yShift); |
1704 | 0 | gg.transform( |
1705 | AffineTransform.getScaleInstance(1D / sx, 1D / sy)); | |
1706 | 0 | ht2 += newHeight; |
1707 | } | |
1708 | else | |
1709 | /** | |
1710 | * Java only | |
1711 | * | |
1712 | * @j2sIgnore | |
1713 | */ | |
1714 | { | |
1715 | // Java ('normal') method is to scale the font to fit | |
1716 | ||
1717 | 191513 | final int hght = (int) (ht + (newAsc - newDec)); |
1718 | 191513 | Font font = ofont |
1719 | .deriveFont(AffineTransform.getScaleInstance(sx, sy)); | |
1720 | 191512 | g.setFont(font); |
1721 | 191512 | g.drawChars(dc, 0, dc.length, x * charWidth, hght); |
1722 | 191512 | g.setFont(ofont); |
1723 | ||
1724 | 191512 | ht += newHeight; |
1725 | } | |
1726 | } | |
1727 | } | |
1728 | } | |
1729 | 434444 | x++; |
1730 | } | |
1731 | 8967 | if (_aa.threshold != null) |
1732 | { | |
1733 | 0 | g.setColor(_aa.threshold.colour); |
1734 | 0 | Stroke s = new BasicStroke(1, BasicStroke.CAP_SQUARE, |
1735 | BasicStroke.JOIN_ROUND, 3f, new float[] | |
1736 | { 5f, 3f }, 0f); | |
1737 | ||
1738 | 0 | y2 = (int) (y |
1739 | - ((_aa.threshold.value - min) / range) * _aa.graphHeight); | |
1740 | 0 | drawLine(g, s, 0, y2, (eRes - sRes) * charWidth, y2); |
1741 | } | |
1742 | } | |
1743 | ||
1744 | // used by overview window | |
1745 | 0 | public void drawGraph(Graphics g, AlignmentAnnotation _aa, |
1746 | Annotation[] aa_annotations, int width, int y, int sRes, int eRes) | |
1747 | { | |
1748 | 0 | eRes = Math.min(eRes, aa_annotations.length); |
1749 | 0 | g.setColor(Color.white); |
1750 | 0 | fillRect(g, 0, 0, width, y); |
1751 | 0 | g.setColor(new Color(0, 0, 180)); |
1752 | ||
1753 | 0 | int x = 0, height; |
1754 | ||
1755 | 0 | for (int j = sRes; j < eRes; j++) |
1756 | { | |
1757 | 0 | if (aa_annotations[j] != null) |
1758 | { | |
1759 | 0 | if (aa_annotations[j].colour == null) |
1760 | { | |
1761 | 0 | g.setColor(Color.black); |
1762 | } | |
1763 | else | |
1764 | { | |
1765 | 0 | g.setColor(aa_annotations[j].colour); |
1766 | } | |
1767 | ||
1768 | 0 | height = (int) ((aa_annotations[j].value / _aa.graphMax) * y); |
1769 | 0 | if (height > y) |
1770 | { | |
1771 | 0 | height = y; |
1772 | } | |
1773 | ||
1774 | 0 | fillRect(g, x, y - height, charWidth, height); |
1775 | } | |
1776 | 0 | x += charWidth; |
1777 | } | |
1778 | } | |
1779 | ||
1780 | 0 | Color getNotCanonicalColor(char lastss) |
1781 | { | |
1782 | 0 | switch (lastss) |
1783 | { | |
1784 | 0 | case '{': |
1785 | 0 | case '}': |
1786 | 0 | return new Color(255, 125, 5); |
1787 | ||
1788 | 0 | case '[': |
1789 | 0 | case ']': |
1790 | 0 | return new Color(245, 115, 10); |
1791 | ||
1792 | 0 | case '>': |
1793 | 0 | case '<': |
1794 | 0 | return new Color(235, 135, 15); |
1795 | ||
1796 | 0 | case 'A': |
1797 | 0 | case 'a': |
1798 | 0 | return new Color(225, 105, 20); |
1799 | ||
1800 | 0 | case 'B': |
1801 | 0 | case 'b': |
1802 | 0 | return new Color(215, 145, 30); |
1803 | ||
1804 | 0 | case 'C': |
1805 | 0 | case 'c': |
1806 | 0 | return new Color(205, 95, 35); |
1807 | ||
1808 | 0 | case 'D': |
1809 | 0 | case 'd': |
1810 | 0 | return new Color(195, 155, 45); |
1811 | ||
1812 | 0 | case 'E': |
1813 | 0 | case 'e': |
1814 | 0 | return new Color(185, 85, 55); |
1815 | ||
1816 | 0 | case 'F': |
1817 | 0 | case 'f': |
1818 | 0 | return new Color(175, 165, 65); |
1819 | ||
1820 | 0 | case 'G': |
1821 | 0 | case 'g': |
1822 | 0 | return new Color(170, 75, 75); |
1823 | ||
1824 | 0 | case 'H': |
1825 | 0 | case 'h': |
1826 | 0 | return new Color(160, 175, 85); |
1827 | ||
1828 | 0 | case 'I': |
1829 | 0 | case 'i': |
1830 | 0 | return new Color(150, 65, 95); |
1831 | ||
1832 | 0 | case 'J': |
1833 | 0 | case 'j': |
1834 | 0 | return new Color(140, 185, 105); |
1835 | ||
1836 | 0 | case 'K': |
1837 | 0 | case 'k': |
1838 | 0 | return new Color(130, 55, 110); |
1839 | ||
1840 | 0 | case 'L': |
1841 | 0 | case 'l': |
1842 | 0 | return new Color(120, 195, 120); |
1843 | ||
1844 | 0 | case 'M': |
1845 | 0 | case 'm': |
1846 | 0 | return new Color(110, 45, 130); |
1847 | ||
1848 | 0 | case 'N': |
1849 | 0 | case 'n': |
1850 | 0 | return new Color(100, 205, 140); |
1851 | ||
1852 | 0 | case 'O': |
1853 | 0 | case 'o': |
1854 | 0 | return new Color(90, 35, 150); |
1855 | ||
1856 | 0 | case 'P': |
1857 | 0 | case 'p': |
1858 | 0 | return new Color(85, 215, 160); |
1859 | ||
1860 | 0 | case 'Q': |
1861 | 0 | case 'q': |
1862 | 0 | return new Color(75, 25, 170); |
1863 | ||
1864 | 0 | case 'R': |
1865 | 0 | case 'r': |
1866 | 0 | return new Color(65, 225, 180); |
1867 | ||
1868 | 0 | case 'S': |
1869 | 0 | case 's': |
1870 | 0 | return new Color(55, 15, 185); |
1871 | ||
1872 | 0 | case 'T': |
1873 | 0 | case 't': |
1874 | 0 | return new Color(45, 235, 195); |
1875 | ||
1876 | 0 | case 'U': |
1877 | 0 | case 'u': |
1878 | 0 | return new Color(35, 5, 205); |
1879 | ||
1880 | 0 | case 'V': |
1881 | 0 | case 'v': |
1882 | 0 | return new Color(25, 245, 215); |
1883 | ||
1884 | 0 | case 'W': |
1885 | 0 | case 'w': |
1886 | 0 | return new Color(15, 0, 225); |
1887 | ||
1888 | 0 | case 'X': |
1889 | 0 | case 'x': |
1890 | 0 | return new Color(10, 255, 235); |
1891 | ||
1892 | 0 | case 'Y': |
1893 | 0 | case 'y': |
1894 | 0 | return new Color(5, 150, 245); |
1895 | ||
1896 | 0 | case 'Z': |
1897 | 0 | case 'z': |
1898 | 0 | return new Color(0, 80, 255); |
1899 | ||
1900 | 0 | default: |
1901 | 0 | Console.info("This is not a interaction : " + lastss); |
1902 | 0 | return null; |
1903 | ||
1904 | } | |
1905 | } | |
1906 | ||
1907 | 4166 | private void fillPolygon(Graphics g, int[] xpoints, int[] ypoints, int n) |
1908 | { | |
1909 | 4166 | setAntialias(g); |
1910 | 4166 | g.fillPolygon(xpoints, ypoints, n); |
1911 | } | |
1912 | ||
1913 | /* | |
1914 | private void fillRect(Graphics g, int a, int b, int c, int d) | |
1915 | { | |
1916 | fillRect(g, false, a, b, c, d); | |
1917 | }*/ | |
1918 | ||
1919 | 439411 | private void fillRect(Graphics g, int a, int b, int c, int d) |
1920 | { | |
1921 | 439411 | unsetAntialias(g); |
1922 | 439414 | g.fillRect(a, b, c, d); |
1923 | } | |
1924 | ||
1925 | 0 | private void fillRoundRect(Graphics g, int a, int b, int c, int d, int e, |
1926 | int f) | |
1927 | { | |
1928 | 0 | setAntialias(g); |
1929 | 0 | g.fillRoundRect(a, b, c, d, e, f); |
1930 | } | |
1931 | ||
1932 | 1604 | private void fillArc(Graphics g, int a, int b, int c, int d, int e, int f) |
1933 | { | |
1934 | 1604 | setAntialias(g); |
1935 | 1604 | g.fillArc(a, b, c, d, e, f); |
1936 | } | |
1937 | ||
1938 | 498 | private void drawLine(Graphics g, Stroke s, int a, int b, int c, int d) |
1939 | { | |
1940 | 498 | Graphics2D g2d = (Graphics2D) g; |
1941 | 498 | Stroke p = g2d.getStroke(); |
1942 | 498 | g2d.setStroke(s); |
1943 | 498 | drawLine(g, a, b, c, d); |
1944 | 498 | g2d.setStroke(p); |
1945 | } | |
1946 | ||
1947 | 23431 | private void drawLine(Graphics g, int a, int b, int c, int d) |
1948 | { | |
1949 | 23431 | setAntialias(g); |
1950 | 23431 | g.drawLine(a, b, c, d); |
1951 | } | |
1952 | ||
1953 | 369584 | private void setAntialias(Graphics g) |
1954 | { | |
1955 | 369585 | if (isVectorRendering()) |
1956 | { | |
1957 | // no need to antialias vector drawings | |
1958 | 6650 | return; |
1959 | } | |
1960 | 362933 | if (Cache.getDefault("ANTI_ALIAS", true)) |
1961 | { | |
1962 | 47645 | Graphics2D g2d = (Graphics2D) g; |
1963 | 47646 | g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, |
1964 | RenderingHints.VALUE_ANTIALIAS_ON); | |
1965 | } | |
1966 | } | |
1967 | ||
1968 | 1059467 | private void unsetAntialias(Graphics g) |
1969 | { | |
1970 | 1059468 | if (isVectorRendering()) |
1971 | { | |
1972 | // no need to antialias vector drawings | |
1973 | 17584 | return; |
1974 | } | |
1975 | 1041885 | Graphics2D g2d = (Graphics2D) g; |
1976 | 1041885 | g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, |
1977 | RenderingHints.VALUE_ANTIALIAS_OFF); | |
1978 | } | |
1979 | ||
1980 | 14 | public void setVectorRendering(boolean b) |
1981 | { | |
1982 | 14 | renderingVectors = b; |
1983 | } | |
1984 | ||
1985 | 1471669 | public boolean isVectorRendering() |
1986 | { | |
1987 | 1471669 | return renderingVectors; |
1988 | } | |
1989 | } |