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ViewStyle | 36 | 163 | 93 |
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.viewmodel.styles; | |
22 | ||
23 | import java.awt.Color; | |
24 | ||
25 | import jalview.api.ViewStyleI; | |
26 | ||
27 | /** | |
28 | * A container for holding alignment view properties. View properties are | |
29 | * data-independent, which means they can be safely copied between views | |
30 | * involving different alignment data without causing exceptions in the | |
31 | * rendering system. | |
32 | * | |
33 | * @author jprocter | |
34 | * | |
35 | */ | |
36 | public class ViewStyle implements ViewStyleI | |
37 | { | |
38 | private boolean abovePIDThreshold = false; | |
39 | ||
40 | int charHeight; | |
41 | ||
42 | int charWidth; | |
43 | ||
44 | int idWidth = -1; | |
45 | ||
46 | /** | |
47 | * gui state - changes to colour scheme propagated to all groups | |
48 | */ | |
49 | private boolean colourAppliesToAllGroups; | |
50 | ||
51 | /** | |
52 | * centre columnar annotation labels in displayed alignment annotation | |
53 | */ | |
54 | boolean centreColumnLabels = false; | |
55 | ||
56 | private boolean showdbrefs; | |
57 | ||
58 | private boolean shownpfeats; | |
59 | ||
60 | // --------END Structure Conservation | |
61 | ||
62 | /** | |
63 | * colour according to the reference sequence defined on the alignment | |
64 | */ | |
65 | private boolean colourByReferenceSeq = false; | |
66 | ||
67 | boolean conservationColourSelected = false; | |
68 | ||
69 | /** | |
70 | * show the reference sequence in the alignment view | |
71 | */ | |
72 | private boolean displayReferenceSeq = false; | |
73 | ||
74 | private int increment; | |
75 | ||
76 | /** | |
77 | * display gap characters | |
78 | */ | |
79 | boolean renderGaps = true; | |
80 | ||
81 | private boolean rightAlignIds = false; | |
82 | ||
83 | boolean scaleAboveWrapped = false; | |
84 | ||
85 | boolean scaleLeftWrapped = true; | |
86 | ||
87 | boolean scaleRightWrapped = true; | |
88 | ||
89 | boolean seqNameItalics; | |
90 | ||
91 | /** | |
92 | * show annotation tracks on the alignment | |
93 | */ | |
94 | private boolean showAnnotation = true; | |
95 | ||
96 | /** | |
97 | * render each residue in a coloured box | |
98 | */ | |
99 | boolean showBoxes = true; | |
100 | ||
101 | /** | |
102 | * Colour sequence text | |
103 | */ | |
104 | boolean showColourText = false; | |
105 | ||
106 | /** | |
107 | * show blue triangles | |
108 | */ | |
109 | boolean showHiddenMarkers = true; | |
110 | ||
111 | /** | |
112 | * show /start-end in ID panel | |
113 | */ | |
114 | boolean showJVSuffix = true; | |
115 | ||
116 | /** | |
117 | * scale features height according to score | |
118 | */ | |
119 | boolean showSeqFeaturesHeight; | |
120 | ||
121 | /** | |
122 | * display setting for showing/hiding sequence features on alignment view | |
123 | */ | |
124 | boolean showSequenceFeatures = false; | |
125 | ||
126 | /** | |
127 | * display sequence symbols | |
128 | */ | |
129 | boolean showText = true; | |
130 | ||
131 | /** | |
132 | * show non-conserved residues only | |
133 | */ | |
134 | protected boolean showUnconserved = false; | |
135 | ||
136 | Color textColour = Color.black; | |
137 | ||
138 | Color textColour2 = Color.white; | |
139 | ||
140 | /** | |
141 | * PID or consensus threshold | |
142 | */ | |
143 | int threshold; | |
144 | ||
145 | /** | |
146 | * threshold for switching between textColour & textColour2 | |
147 | */ | |
148 | int thresholdTextColour = 0; | |
149 | ||
150 | /** | |
151 | * upper case characters in sequence are shown in bold | |
152 | */ | |
153 | boolean upperCasebold = false; | |
154 | ||
155 | /** | |
156 | * name of base font for view | |
157 | */ | |
158 | private String fontName; | |
159 | ||
160 | /** | |
161 | * size for base font | |
162 | */ | |
163 | private int fontSize; | |
164 | ||
165 | /* | |
166 | * If true, scale protein residues to 3 times width of cDNA bases (in | |
167 | * SplitFrame views only) | |
168 | */ | |
169 | private boolean scaleProteinAsCdna = true; | |
170 | ||
171 | /* | |
172 | * if true, font changes to protein or cDNA are applied to both | |
173 | * sides of a split screen | |
174 | */ | |
175 | private boolean proteinFontAsCdna = true; | |
176 | ||
177 | /** | |
178 | * Copy constructor | |
179 | * | |
180 | * @param vs | |
181 | */ | |
182 | 232 | public ViewStyle(ViewStyleI vs) |
183 | { | |
184 | 232 | setAbovePIDThreshold(vs.getAbovePIDThreshold()); |
185 | 232 | setCentreColumnLabels(vs.isCentreColumnLabels()); |
186 | 232 | setCharHeight(vs.getCharHeight()); |
187 | 232 | setCharWidth(vs.getCharWidth()); |
188 | 232 | setColourAppliesToAllGroups(vs.getColourAppliesToAllGroups()); |
189 | 232 | setColourByReferenceSeq(vs.isColourByReferenceSeq()); |
190 | 232 | setColourText(vs.getColourText()); |
191 | 232 | setConservationColourSelected(vs.isConservationColourSelected()); |
192 | 232 | setConservationSelected(vs.getConservationSelected()); |
193 | 232 | setDisplayReferenceSeq(vs.isDisplayReferenceSeq()); |
194 | 232 | setFontName(vs.getFontName()); |
195 | 232 | setFontSize(vs.getFontSize()); |
196 | 232 | setFontStyle(vs.getFontStyle()); |
197 | 232 | setIdWidth(vs.getIdWidth()); |
198 | 232 | setIncrement(vs.getIncrement()); |
199 | 232 | setRenderGaps(vs.isRenderGaps()); |
200 | 232 | setRightAlignIds(vs.isRightAlignIds()); |
201 | 232 | setScaleAboveWrapped(vs.getScaleAboveWrapped()); |
202 | 232 | setScaleLeftWrapped(vs.getScaleLeftWrapped()); |
203 | 232 | setScaleProteinAsCdna(vs.isScaleProteinAsCdna()); |
204 | 232 | setProteinFontAsCdna(vs.isProteinFontAsCdna()); |
205 | 232 | setScaleRightWrapped(vs.getScaleRightWrapped()); |
206 | 232 | setSeqNameItalics(vs.isSeqNameItalics()); |
207 | 232 | setShowAnnotation(vs.isShowAnnotation()); |
208 | 232 | setShowBoxes(vs.getShowBoxes()); |
209 | 232 | setShowColourText(vs.isShowColourText()); |
210 | 232 | setShowDBRefs(vs.isShowDBRefs()); |
211 | 232 | setShowHiddenMarkers(vs.getShowHiddenMarkers()); |
212 | 232 | setShowJVSuffix(vs.getShowJVSuffix()); |
213 | 232 | setShowNPFeats(vs.isShowNPFeats()); |
214 | 232 | setShowSequenceFeaturesHeight(vs.isShowSequenceFeaturesHeight()); |
215 | 232 | setShowSequenceFeatures(vs.isShowSequenceFeatures()); |
216 | 232 | setShowComplementFeatures(vs.isShowComplementFeatures()); |
217 | 232 | setShowComplementFeaturesOnTop(vs.isShowComplementFeaturesOnTop()); |
218 | 232 | setShowText(vs.getShowText()); |
219 | 232 | setShowUnconserved(vs.getShowUnconserved()); |
220 | 232 | setTextColour(vs.getTextColour()); |
221 | 232 | setTextColour2(vs.getTextColour2()); |
222 | 232 | setThreshold(vs.getThreshold()); |
223 | 232 | setThresholdTextColour(vs.getThresholdTextColour()); |
224 | 232 | setUpperCasebold(vs.isUpperCasebold()); |
225 | 232 | setWrapAlignment(vs.getWrapAlignment()); |
226 | 232 | setWrappedWidth(vs.getWrappedWidth()); |
227 | // ViewStyle.configureFrom(this, viewStyle); | |
228 | } | |
229 | ||
230 | 510 | public ViewStyle() |
231 | { | |
232 | } | |
233 | ||
234 | /** | |
235 | * Returns true if all attributes of the ViewStyles have the same value | |
236 | */ | |
237 | 48 | @Override |
238 | public boolean equals(Object other) | |
239 | { | |
240 | 48 | if (other == null || !(other instanceof ViewStyle)) |
241 | { | |
242 | 2 | return false; |
243 | } | |
244 | 46 | ViewStyle vs = (ViewStyle) other; |
245 | ||
246 | 46 | boolean match = (getAbovePIDThreshold() == vs.getAbovePIDThreshold() |
247 | && isCentreColumnLabels() == vs.isCentreColumnLabels() | |
248 | && getCharHeight() == vs.getCharHeight() | |
249 | && getCharWidth() == vs.getCharWidth() | |
250 | && getColourAppliesToAllGroups() == vs | |
251 | .getColourAppliesToAllGroups() | |
252 | && isColourByReferenceSeq() == vs.isColourByReferenceSeq() | |
253 | && getColourText() == vs.getColourText() | |
254 | && isConservationColourSelected() == vs | |
255 | .isConservationColourSelected() | |
256 | && getConservationSelected() == vs.getConservationSelected() | |
257 | && isDisplayReferenceSeq() == vs.isDisplayReferenceSeq() | |
258 | && getFontSize() == vs.getFontSize() | |
259 | && getFontStyle() == vs.getFontStyle() | |
260 | && getIdWidth() == vs.getIdWidth() | |
261 | && getIncrement() == vs.getIncrement() | |
262 | && isRenderGaps() == vs.isRenderGaps() | |
263 | && isRightAlignIds() == vs.isRightAlignIds() | |
264 | && getScaleAboveWrapped() == vs.getScaleAboveWrapped() | |
265 | && getScaleLeftWrapped() == vs.getScaleLeftWrapped() | |
266 | && isScaleProteinAsCdna() == vs.isScaleProteinAsCdna() | |
267 | && isProteinFontAsCdna() == vs.isProteinFontAsCdna() | |
268 | && getScaleRightWrapped() == vs.getScaleRightWrapped() | |
269 | && isSeqNameItalics() == vs.isSeqNameItalics() | |
270 | && isShowAnnotation() == vs.isShowAnnotation() | |
271 | && getShowBoxes() == vs.getShowBoxes() | |
272 | && isShowColourText() == vs.isShowColourText() | |
273 | && isShowDBRefs() == vs.isShowDBRefs() | |
274 | && getShowHiddenMarkers() == vs.getShowHiddenMarkers() | |
275 | && getShowJVSuffix() == vs.getShowJVSuffix() | |
276 | && isShowNPFeats() == vs.isShowNPFeats() | |
277 | && isShowSequenceFeaturesHeight() == vs | |
278 | .isShowSequenceFeaturesHeight() | |
279 | && isShowSequenceFeatures() == vs.isShowSequenceFeatures() | |
280 | && isShowComplementFeatures() == vs.isShowComplementFeatures() | |
281 | && isShowComplementFeaturesOnTop() == vs | |
282 | .isShowComplementFeaturesOnTop() | |
283 | && getShowText() == vs.getShowText() | |
284 | && getShowUnconserved() == vs.getShowUnconserved() | |
285 | && getThreshold() == vs.getThreshold() | |
286 | && getThresholdTextColour() == vs.getThresholdTextColour() | |
287 | && isUpperCasebold() == vs.isUpperCasebold() | |
288 | && getWrapAlignment() == vs.getWrapAlignment() | |
289 | && getWrappedWidth() == vs.getWrappedWidth()); | |
290 | /* | |
291 | * and compare non-primitive types; syntax below will match null with null | |
292 | * values | |
293 | */ | |
294 | 46 | match = match && String.valueOf(getFontName()) |
295 | .equals(String.valueOf(vs.getFontName())); | |
296 | 46 | match = match && String.valueOf(getTextColour()) |
297 | .equals(String.valueOf(vs.getTextColour())); | |
298 | 46 | match = match && String.valueOf(getTextColour2()) |
299 | .equals(String.valueOf(vs.getTextColour2())); | |
300 | 46 | return match; |
301 | // return equivalent(this, (ViewStyle) other); | |
302 | } | |
303 | ||
304 | /** | |
305 | * Overridden to ensure that whenever vs1.equals(vs2) then vs1.hashCode() == | |
306 | * vs2.hashCode() | |
307 | */ | |
308 | 84 | @Override |
309 | public int hashCode() | |
310 | { | |
311 | /* | |
312 | * No need to include all properties, just a selection... | |
313 | */ | |
314 | 84 | int hash = 0; |
315 | 84 | int m = 1; |
316 | // Boolean.hashCode returns 1231 or 1237 | |
317 | 84 | hash += m++ * Boolean.valueOf(this.abovePIDThreshold).hashCode(); |
318 | 84 | hash += m++ * Boolean.valueOf(this.centreColumnLabels).hashCode(); |
319 | 84 | hash += m++ * Boolean.valueOf(this.colourAppliesToAllGroups).hashCode(); |
320 | 84 | hash += m++ * Boolean.valueOf(this.displayReferenceSeq).hashCode(); |
321 | 84 | hash += m++ * Boolean.valueOf(this.renderGaps).hashCode(); |
322 | 84 | hash += m++ * Boolean.valueOf(this.rightAlignIds).hashCode(); |
323 | 84 | hash += m++ * Boolean.valueOf(this.scaleProteinAsCdna).hashCode(); |
324 | 84 | hash += m++ * Boolean.valueOf(this.scaleRightWrapped).hashCode(); |
325 | 84 | hash += m++ * Boolean.valueOf(this.seqNameItalics).hashCode(); |
326 | 84 | hash += m++ * Boolean.valueOf(this.showAnnotation).hashCode(); |
327 | 84 | hash += m++ * Boolean.valueOf(this.showBoxes).hashCode(); |
328 | 84 | hash += m++ * Boolean.valueOf(this.showdbrefs).hashCode(); |
329 | 84 | hash += m++ * Boolean.valueOf(this.showJVSuffix).hashCode(); |
330 | 84 | hash += m++ * Boolean.valueOf(this.showSequenceFeatures).hashCode(); |
331 | 84 | hash += m++ * Boolean.valueOf(this.showUnconserved).hashCode(); |
332 | 84 | hash += m++ * Boolean.valueOf(this.wrapAlignment).hashCode(); |
333 | 84 | hash += m++ * this.charHeight; |
334 | 84 | hash += m++ * this.charWidth; |
335 | 84 | hash += m++ * fontSize; |
336 | 84 | hash += m++ * fontStyle; |
337 | 84 | hash += m++ * idWidth; |
338 | 84 | hash += String.valueOf(this.fontName).hashCode(); |
339 | 84 | return hash; |
340 | } | |
341 | ||
342 | /** | |
343 | * @return the upperCasebold | |
344 | */ | |
345 | 250 | @Override |
346 | public boolean isUpperCasebold() | |
347 | { | |
348 | 250 | return upperCasebold; |
349 | } | |
350 | ||
351 | /** | |
352 | * @param upperCasebold | |
353 | * the upperCasebold to set | |
354 | */ | |
355 | 232 | @Override |
356 | public void setUpperCasebold(boolean upperCasebold) | |
357 | { | |
358 | 232 | this.upperCasebold = upperCasebold; |
359 | } | |
360 | ||
361 | /** | |
362 | * flag for wrapping | |
363 | */ | |
364 | boolean wrapAlignment = false; | |
365 | ||
366 | /** | |
367 | * number columns in wrapped alignment | |
368 | */ | |
369 | int wrappedWidth; | |
370 | ||
371 | private int fontStyle; | |
372 | ||
373 | private boolean showComplementFeatures; | |
374 | ||
375 | private boolean showComplementFeaturesOnTop; | |
376 | ||
377 | /** | |
378 | * GUI state | |
379 | * | |
380 | * @return true if percent identity threshold is applied to shading | |
381 | */ | |
382 | 1202 | @Override |
383 | public boolean getAbovePIDThreshold() | |
384 | { | |
385 | 1202 | return abovePIDThreshold; |
386 | } | |
387 | ||
388 | /** | |
389 | * DOCUMENT ME! | |
390 | * | |
391 | * @return DOCUMENT ME! | |
392 | */ | |
393 | 120187 | @Override |
394 | public int getCharHeight() | |
395 | { | |
396 | 120187 | return charHeight; |
397 | } | |
398 | ||
399 | /** | |
400 | * DOCUMENT ME! | |
401 | * | |
402 | * @return DOCUMENT ME! | |
403 | */ | |
404 | 1748184 | @Override |
405 | public int getCharWidth() | |
406 | { | |
407 | 1748184 | return charWidth; |
408 | } | |
409 | ||
410 | /** | |
411 | * | |
412 | * | |
413 | * @return flag indicating if colourchanges propagated to all groups | |
414 | */ | |
415 | 1274 | @Override |
416 | public boolean getColourAppliesToAllGroups() | |
417 | { | |
418 | 1274 | return colourAppliesToAllGroups; |
419 | } | |
420 | ||
421 | /** | |
422 | * DOCUMENT ME! | |
423 | * | |
424 | * @return DOCUMENT ME! | |
425 | */ | |
426 | 404492 | @Override |
427 | public boolean getColourText() | |
428 | { | |
429 | 404492 | return showColourText; |
430 | } | |
431 | ||
432 | /** | |
433 | * GUI state | |
434 | * | |
435 | * @return true if conservation based shading is enabled | |
436 | */ | |
437 | 1344 | @Override |
438 | public boolean getConservationSelected() | |
439 | { | |
440 | 1344 | return conservationColourSelected; |
441 | } | |
442 | ||
443 | /** | |
444 | * GUI State | |
445 | * | |
446 | * @return get scalar for bleaching colourschemes by conservation | |
447 | */ | |
448 | 296 | @Override |
449 | public int getIncrement() | |
450 | { | |
451 | 296 | return increment; |
452 | } | |
453 | ||
454 | /** | |
455 | * DOCUMENT ME! | |
456 | * | |
457 | * @return DOCUMENT ME! | |
458 | */ | |
459 | 1041 | @Override |
460 | public boolean getScaleAboveWrapped() | |
461 | { | |
462 | 1041 | return scaleAboveWrapped; |
463 | } | |
464 | ||
465 | /** | |
466 | * DOCUMENT ME! | |
467 | * | |
468 | * @return DOCUMENT ME! | |
469 | */ | |
470 | 1385 | @Override |
471 | public boolean getScaleLeftWrapped() | |
472 | { | |
473 | 1385 | return scaleLeftWrapped; |
474 | } | |
475 | ||
476 | /** | |
477 | * DOCUMENT ME! | |
478 | * | |
479 | * @return DOCUMENT ME! | |
480 | */ | |
481 | 2036 | @Override |
482 | public boolean getScaleRightWrapped() | |
483 | { | |
484 | 2036 | return scaleRightWrapped; |
485 | } | |
486 | ||
487 | /** | |
488 | * DOCUMENT ME! | |
489 | * | |
490 | * @return DOCUMENT ME! | |
491 | */ | |
492 | 437739 | @Override |
493 | public boolean getShowBoxes() | |
494 | { | |
495 | 437739 | return showBoxes; |
496 | } | |
497 | ||
498 | 7085 | @Override |
499 | public boolean getShowHiddenMarkers() | |
500 | { | |
501 | 7085 | return showHiddenMarkers; |
502 | } | |
503 | ||
504 | /** | |
505 | * DOCUMENT ME! | |
506 | * | |
507 | * @return DOCUMENT ME! | |
508 | */ | |
509 | 57126 | @Override |
510 | public boolean getShowJVSuffix() | |
511 | { | |
512 | 57126 | return showJVSuffix; |
513 | } | |
514 | ||
515 | /** | |
516 | * DOCUMENT ME! | |
517 | * | |
518 | * @return DOCUMENT ME! | |
519 | */ | |
520 | 405114 | @Override |
521 | public boolean getShowText() | |
522 | { | |
523 | 405114 | return showText; |
524 | } | |
525 | ||
526 | 402954 | @Override |
527 | public boolean getShowUnconserved() | |
528 | { | |
529 | 402954 | return showUnconserved; |
530 | } | |
531 | ||
532 | /** | |
533 | * @return the textColour | |
534 | */ | |
535 | 851139 | @Override |
536 | public Color getTextColour() | |
537 | { | |
538 | 851139 | return textColour; |
539 | } | |
540 | ||
541 | /** | |
542 | * @return the textColour2 | |
543 | */ | |
544 | 286 | @Override |
545 | public Color getTextColour2() | |
546 | { | |
547 | 286 | return textColour2; |
548 | } | |
549 | ||
550 | /** | |
551 | * DOCUMENT ME! | |
552 | * | |
553 | * @return DOCUMENT ME! | |
554 | */ | |
555 | 254 | @Override |
556 | public int getThreshold() | |
557 | { | |
558 | 254 | return threshold; |
559 | } | |
560 | ||
561 | /** | |
562 | * @return the thresholdTextColour | |
563 | */ | |
564 | 404436 | @Override |
565 | public int getThresholdTextColour() | |
566 | { | |
567 | 404436 | return thresholdTextColour; |
568 | } | |
569 | ||
570 | /** | |
571 | * DOCUMENT ME! | |
572 | * | |
573 | * @return DOCUMENT ME! | |
574 | */ | |
575 | 33350 | @Override |
576 | public boolean getWrapAlignment() | |
577 | { | |
578 | 33350 | return wrapAlignment; |
579 | } | |
580 | ||
581 | /** | |
582 | * DOCUMENT ME! | |
583 | * | |
584 | * @return DOCUMENT ME! | |
585 | */ | |
586 | 248 | @Override |
587 | public int getWrappedWidth() | |
588 | { | |
589 | 248 | return wrappedWidth; |
590 | } | |
591 | ||
592 | 315 | @Override |
593 | public boolean isColourByReferenceSeq() | |
594 | { | |
595 | 315 | return colourByReferenceSeq; |
596 | } | |
597 | ||
598 | /** | |
599 | * @return the conservationColourSelected | |
600 | */ | |
601 | 392 | @Override |
602 | public boolean isConservationColourSelected() | |
603 | { | |
604 | 392 | return conservationColourSelected; |
605 | } | |
606 | ||
607 | 832 | @Override |
608 | public boolean isDisplayReferenceSeq() | |
609 | { | |
610 | 832 | return displayReferenceSeq; |
611 | } | |
612 | ||
613 | /** | |
614 | * @return the renderGaps | |
615 | */ | |
616 | 4050 | @Override |
617 | public boolean isRenderGaps() | |
618 | { | |
619 | 4050 | return renderGaps; |
620 | } | |
621 | ||
622 | 21329 | @Override |
623 | public boolean isRightAlignIds() | |
624 | { | |
625 | 21329 | return rightAlignIds; |
626 | } | |
627 | ||
628 | /** | |
629 | * @return the seqNameItalics | |
630 | */ | |
631 | 3758 | @Override |
632 | public boolean isSeqNameItalics() | |
633 | { | |
634 | 3758 | return seqNameItalics; |
635 | } | |
636 | ||
637 | 4723 | @Override |
638 | public boolean isShowAnnotation() | |
639 | { | |
640 | 4723 | return showAnnotation; |
641 | } | |
642 | ||
643 | /** | |
644 | * @return the showColourText | |
645 | */ | |
646 | 946 | @Override |
647 | public boolean isShowColourText() | |
648 | { | |
649 | 946 | return showColourText; |
650 | } | |
651 | ||
652 | /** | |
653 | * @return the showSeqFeaturesHeight | |
654 | */ | |
655 | 266 | @Override |
656 | public boolean isShowSequenceFeaturesHeight() | |
657 | { | |
658 | 266 | return showSeqFeaturesHeight; |
659 | } | |
660 | ||
661 | 402651 | @Override |
662 | public boolean isShowSequenceFeatures() | |
663 | { | |
664 | 402679 | return showSequenceFeatures; |
665 | } | |
666 | ||
667 | /** | |
668 | * GUI state | |
669 | * | |
670 | * | |
671 | * @param b | |
672 | * indicate if percent identity threshold is applied to shading | |
673 | */ | |
674 | 326 | @Override |
675 | public void setAbovePIDThreshold(boolean b) | |
676 | { | |
677 | 326 | abovePIDThreshold = b; |
678 | } | |
679 | ||
680 | /** | |
681 | * DOCUMENT ME! | |
682 | * | |
683 | * @param h | |
684 | * DOCUMENT ME! | |
685 | */ | |
686 | 828 | @Override |
687 | public void setCharHeight(int h) | |
688 | { | |
689 | 828 | this.charHeight = h; |
690 | } | |
691 | ||
692 | /** | |
693 | * DOCUMENT ME! | |
694 | * | |
695 | * @param w | |
696 | * DOCUMENT ME! | |
697 | */ | |
698 | 831 | @Override |
699 | public void setCharWidth(int w) | |
700 | { | |
701 | 831 | this.charWidth = w; |
702 | } | |
703 | ||
704 | /** | |
705 | * @param value | |
706 | * indicating if subsequent colourscheme changes will be propagated | |
707 | * to all groups | |
708 | */ | |
709 | 925 | @Override |
710 | public void setColourAppliesToAllGroups(boolean b) | |
711 | { | |
712 | 925 | colourAppliesToAllGroups = b; |
713 | } | |
714 | ||
715 | 242 | @Override |
716 | public void setColourByReferenceSeq(boolean colourByReferenceSeq) | |
717 | { | |
718 | 242 | this.colourByReferenceSeq = colourByReferenceSeq; |
719 | } | |
720 | ||
721 | /** | |
722 | * DOCUMENT ME! | |
723 | * | |
724 | * @param state | |
725 | * DOCUMENT ME! | |
726 | */ | |
727 | 317 | @Override |
728 | public void setColourText(boolean state) | |
729 | { | |
730 | 317 | showColourText = state; |
731 | } | |
732 | ||
733 | /** | |
734 | * @param conservationColourSelected | |
735 | * the conservationColourSelected to set | |
736 | */ | |
737 | 232 | @Override |
738 | public void setConservationColourSelected( | |
739 | boolean conservationColourSelected) | |
740 | { | |
741 | 232 | this.conservationColourSelected = conservationColourSelected; |
742 | } | |
743 | ||
744 | /** | |
745 | * GUI state | |
746 | * | |
747 | * @param b | |
748 | * enable conservation based shading | |
749 | */ | |
750 | 325 | @Override |
751 | public void setConservationSelected(boolean b) | |
752 | { | |
753 | 325 | conservationColourSelected = b; |
754 | } | |
755 | ||
756 | 242 | @Override |
757 | public void setDisplayReferenceSeq(boolean displayReferenceSeq) | |
758 | { | |
759 | 242 | this.displayReferenceSeq = displayReferenceSeq; |
760 | } | |
761 | ||
762 | /** | |
763 | * | |
764 | * @param inc | |
765 | * set the scalar for bleaching colourschemes according to degree of | |
766 | * conservation | |
767 | */ | |
768 | 317 | @Override |
769 | public void setIncrement(int inc) | |
770 | { | |
771 | 317 | increment = inc; |
772 | } | |
773 | ||
774 | /** | |
775 | * DOCUMENT ME! | |
776 | * | |
777 | * @param state | |
778 | * DOCUMENT ME! | |
779 | */ | |
780 | 317 | @Override |
781 | public void setRenderGaps(boolean state) | |
782 | { | |
783 | 317 | renderGaps = state; |
784 | } | |
785 | ||
786 | 825 | @Override |
787 | public void setRightAlignIds(boolean rightAlignIds) | |
788 | { | |
789 | 825 | this.rightAlignIds = rightAlignIds; |
790 | } | |
791 | ||
792 | /** | |
793 | * DOCUMENT ME! | |
794 | * | |
795 | * @param b | |
796 | * DOCUMENT ME! | |
797 | */ | |
798 | 241 | @Override |
799 | public void setScaleAboveWrapped(boolean b) | |
800 | { | |
801 | 241 | scaleAboveWrapped = b; |
802 | } | |
803 | ||
804 | /** | |
805 | * DOCUMENT ME! | |
806 | * | |
807 | * @param b | |
808 | * DOCUMENT ME! | |
809 | */ | |
810 | 243 | @Override |
811 | public void setScaleLeftWrapped(boolean b) | |
812 | { | |
813 | 243 | scaleLeftWrapped = b; |
814 | } | |
815 | ||
816 | /** | |
817 | * | |
818 | * | |
819 | * @param scaleRightWrapped | |
820 | * - true or false | |
821 | */ | |
822 | ||
823 | 241 | @Override |
824 | public void setScaleRightWrapped(boolean b) | |
825 | { | |
826 | 241 | scaleRightWrapped = b; |
827 | } | |
828 | ||
829 | 740 | @Override |
830 | public void setSeqNameItalics(boolean italics) | |
831 | { | |
832 | 740 | seqNameItalics = italics; |
833 | } | |
834 | ||
835 | 912 | @Override |
836 | public void setShowAnnotation(boolean b) | |
837 | { | |
838 | 912 | showAnnotation = b; |
839 | } | |
840 | ||
841 | /** | |
842 | * DOCUMENT ME! | |
843 | * | |
844 | * @param state | |
845 | * DOCUMENT ME! | |
846 | */ | |
847 | 317 | @Override |
848 | public void setShowBoxes(boolean state) | |
849 | { | |
850 | 317 | showBoxes = state; |
851 | } | |
852 | ||
853 | /** | |
854 | * @param showColourText | |
855 | * the showColourText to set | |
856 | */ | |
857 | 232 | @Override |
858 | public void setShowColourText(boolean showColourText) | |
859 | { | |
860 | 232 | this.showColourText = showColourText; |
861 | } | |
862 | ||
863 | 232 | @Override |
864 | public void setShowHiddenMarkers(boolean show) | |
865 | { | |
866 | 232 | showHiddenMarkers = show; |
867 | } | |
868 | ||
869 | /** | |
870 | * DOCUMENT ME! | |
871 | * | |
872 | * @param b | |
873 | * DOCUMENT ME! | |
874 | */ | |
875 | 826 | @Override |
876 | public void setShowJVSuffix(boolean b) | |
877 | { | |
878 | 826 | showJVSuffix = b; |
879 | } | |
880 | ||
881 | 232 | @Override |
882 | public void setShowSequenceFeaturesHeight(boolean selected) | |
883 | { | |
884 | 232 | showSeqFeaturesHeight = selected; |
885 | ||
886 | } | |
887 | ||
888 | /** | |
889 | * set the flag | |
890 | * | |
891 | * @param b | |
892 | * features are displayed if true | |
893 | */ | |
894 | 373 | @Override |
895 | public void setShowSequenceFeatures(boolean b) | |
896 | { | |
897 | 373 | showSequenceFeatures = b; |
898 | } | |
899 | ||
900 | /** | |
901 | * DOCUMENT ME! | |
902 | * | |
903 | * @param state | |
904 | * DOCUMENT ME! | |
905 | */ | |
906 | 317 | @Override |
907 | public void setShowText(boolean state) | |
908 | { | |
909 | 317 | showText = state; |
910 | } | |
911 | ||
912 | 825 | @Override |
913 | public void setShowUnconserved(boolean showunconserved) | |
914 | { | |
915 | 825 | showUnconserved = showunconserved; |
916 | } | |
917 | ||
918 | /** | |
919 | * @param textColour | |
920 | * the textColour to set | |
921 | */ | |
922 | 317 | @Override |
923 | public void setTextColour(Color textColour) | |
924 | { | |
925 | 317 | this.textColour = textColour; |
926 | } | |
927 | ||
928 | /** | |
929 | * @param textColour2 | |
930 | * the textColour2 to set | |
931 | */ | |
932 | 317 | @Override |
933 | public void setTextColour2(Color textColour2) | |
934 | { | |
935 | 317 | this.textColour2 = textColour2; |
936 | } | |
937 | ||
938 | /** | |
939 | * DOCUMENT ME! | |
940 | * | |
941 | * @param thresh | |
942 | * DOCUMENT ME! | |
943 | */ | |
944 | 338 | @Override |
945 | public void setThreshold(int thresh) | |
946 | { | |
947 | 338 | threshold = thresh; |
948 | } | |
949 | ||
950 | /** | |
951 | * @param thresholdTextColour | |
952 | * the thresholdTextColour to set | |
953 | */ | |
954 | 317 | @Override |
955 | public void setThresholdTextColour(int thresholdTextColour) | |
956 | { | |
957 | 317 | this.thresholdTextColour = thresholdTextColour; |
958 | } | |
959 | ||
960 | /** | |
961 | * DOCUMENT ME! | |
962 | * | |
963 | * @param state | |
964 | * DOCUMENT ME! | |
965 | */ | |
966 | 837 | @Override |
967 | public void setWrapAlignment(boolean state) | |
968 | { | |
969 | 837 | wrapAlignment = state; |
970 | } | |
971 | ||
972 | /** | |
973 | * DOCUMENT ME! | |
974 | * | |
975 | * @param w | |
976 | * DOCUMENT ME! | |
977 | */ | |
978 | 912 | @Override |
979 | public void setWrappedWidth(int w) | |
980 | { | |
981 | 912 | this.wrappedWidth = w; |
982 | } | |
983 | ||
984 | 3 | @Override |
985 | public boolean sameStyle(ViewStyleI that) | |
986 | { | |
987 | 3 | return this.equals(that); |
988 | } | |
989 | ||
990 | 330 | @Override |
991 | public String getFontName() | |
992 | { | |
993 | 330 | return fontName; |
994 | } | |
995 | ||
996 | 388 | @Override |
997 | public int getFontSize() | |
998 | { | |
999 | 388 | return fontSize; |
1000 | } | |
1001 | ||
1002 | 386 | @Override |
1003 | public int getFontStyle() | |
1004 | { | |
1005 | 386 | return fontStyle; |
1006 | } | |
1007 | ||
1008 | 914 | @Override |
1009 | public void setFontName(String name) | |
1010 | { | |
1011 | 914 | fontName = name; |
1012 | } | |
1013 | ||
1014 | 914 | @Override |
1015 | public void setFontSize(int size) | |
1016 | { | |
1017 | 914 | fontSize = size; |
1018 | ||
1019 | } | |
1020 | ||
1021 | 914 | @Override |
1022 | public void setFontStyle(int style) | |
1023 | { | |
1024 | 914 | fontStyle = style; |
1025 | } | |
1026 | ||
1027 | 7044 | @Override |
1028 | public int getIdWidth() | |
1029 | { | |
1030 | 7044 | return idWidth; |
1031 | } | |
1032 | ||
1033 | /** | |
1034 | * @param idWidth | |
1035 | * the idWidth to set | |
1036 | */ | |
1037 | 1162 | @Override |
1038 | public void setIdWidth(int idWidth) | |
1039 | { | |
1040 | 1162 | this.idWidth = idWidth; |
1041 | } | |
1042 | ||
1043 | /** | |
1044 | * @return the centreColumnLabels | |
1045 | */ | |
1046 | 994 | @Override |
1047 | public boolean isCentreColumnLabels() | |
1048 | { | |
1049 | 994 | return centreColumnLabels; |
1050 | } | |
1051 | ||
1052 | /** | |
1053 | * @param centreColumnLabels | |
1054 | * the centreColumnLabels to set | |
1055 | */ | |
1056 | 825 | @Override |
1057 | public void setCentreColumnLabels(boolean centreColumnLabels) | |
1058 | { | |
1059 | 825 | this.centreColumnLabels = centreColumnLabels; |
1060 | } | |
1061 | ||
1062 | /** | |
1063 | * @return the showdbrefs | |
1064 | */ | |
1065 | 992 | @Override |
1066 | public boolean isShowDBRefs() | |
1067 | { | |
1068 | 992 | return showdbrefs; |
1069 | } | |
1070 | ||
1071 | /** | |
1072 | * @param showdbrefs | |
1073 | * the showdbrefs to set | |
1074 | */ | |
1075 | 825 | @Override |
1076 | public void setShowDBRefs(boolean showdbrefs) | |
1077 | { | |
1078 | 825 | this.showdbrefs = showdbrefs; |
1079 | } | |
1080 | ||
1081 | /** | |
1082 | * @return the shownpfeats | |
1083 | */ | |
1084 | 986 | @Override |
1085 | public boolean isShowNPFeats() | |
1086 | { | |
1087 | 986 | return shownpfeats; |
1088 | } | |
1089 | ||
1090 | /** | |
1091 | * @param shownpfeats | |
1092 | * the shownpfeats to set | |
1093 | */ | |
1094 | 825 | @Override |
1095 | public void setShowNPFeats(boolean shownpfeats) | |
1096 | { | |
1097 | 825 | this.shownpfeats = shownpfeats; |
1098 | } | |
1099 | ||
1100 | 335 | @Override |
1101 | public boolean isScaleProteinAsCdna() | |
1102 | { | |
1103 | 335 | return this.scaleProteinAsCdna; |
1104 | } | |
1105 | ||
1106 | 825 | @Override |
1107 | public void setScaleProteinAsCdna(boolean b) | |
1108 | { | |
1109 | 825 | this.scaleProteinAsCdna = b; |
1110 | } | |
1111 | ||
1112 | 284 | @Override |
1113 | public boolean isProteinFontAsCdna() | |
1114 | { | |
1115 | 284 | return proteinFontAsCdna; |
1116 | } | |
1117 | ||
1118 | 232 | @Override |
1119 | public void setProteinFontAsCdna(boolean b) | |
1120 | { | |
1121 | 232 | proteinFontAsCdna = b; |
1122 | } | |
1123 | ||
1124 | 317 | @Override |
1125 | public void setShowComplementFeatures(boolean b) | |
1126 | { | |
1127 | 317 | showComplementFeatures = b; |
1128 | } | |
1129 | ||
1130 | 395679 | @Override |
1131 | public boolean isShowComplementFeatures() | |
1132 | { | |
1133 | 395701 | return showComplementFeatures; |
1134 | } | |
1135 | ||
1136 | 317 | @Override |
1137 | public void setShowComplementFeaturesOnTop(boolean b) | |
1138 | { | |
1139 | 317 | showComplementFeaturesOnTop = b; |
1140 | } | |
1141 | ||
1142 | 307 | @Override |
1143 | public boolean isShowComplementFeaturesOnTop() | |
1144 | { | |
1145 | 307 | return showComplementFeaturesOnTop; |
1146 | } | |
1147 | } |