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ViewStyle | 37 | 175 | 101 |
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 | import java.util.List; | |
25 | ||
26 | import jalview.api.ViewStyleI; | |
27 | ||
28 | /** | |
29 | * A container for holding alignment view properties. View properties are | |
30 | * data-independent, which means they can be safely copied between views | |
31 | * involving different alignment data without causing exceptions in the | |
32 | * rendering system. | |
33 | * | |
34 | * @author jprocter | |
35 | * | |
36 | */ | |
37 | public class ViewStyle implements ViewStyleI | |
38 | { | |
39 | private boolean abovePIDThreshold = false; | |
40 | ||
41 | int charHeight; | |
42 | ||
43 | int charWidth; | |
44 | ||
45 | int idWidth = -1; | |
46 | ||
47 | /** | |
48 | * gui state - changes to colour scheme propagated to all groups | |
49 | */ | |
50 | private boolean colourAppliesToAllGroups; | |
51 | ||
52 | /** | |
53 | * centre columnar annotation labels in displayed alignment annotation | |
54 | */ | |
55 | boolean centreColumnLabels = false; | |
56 | ||
57 | private boolean showdbrefs; | |
58 | ||
59 | private boolean shownpfeats; | |
60 | ||
61 | // --------END Structure Conservation | |
62 | ||
63 | /** | |
64 | * colour according to the reference sequence defined on the alignment | |
65 | */ | |
66 | private boolean colourByReferenceSeq = false; | |
67 | ||
68 | boolean conservationColourSelected = false; | |
69 | ||
70 | boolean byConsensusSecondaryStructureSelected = false; | |
71 | ||
72 | /** | |
73 | * show the reference sequence in the alignment view | |
74 | */ | |
75 | private boolean displayReferenceSeq = false; | |
76 | ||
77 | private int increment; | |
78 | ||
79 | private int consensusSecondaryStructureThreshold; | |
80 | ||
81 | /** | |
82 | * display gap characters | |
83 | */ | |
84 | boolean renderGaps = true; | |
85 | ||
86 | private boolean rightAlignIds = false; | |
87 | ||
88 | boolean scaleAboveWrapped = false; | |
89 | ||
90 | boolean scaleLeftWrapped = true; | |
91 | ||
92 | boolean scaleRightWrapped = true; | |
93 | ||
94 | boolean seqNameItalics; | |
95 | ||
96 | /** | |
97 | * show annotation tracks on the alignment | |
98 | */ | |
99 | private boolean showAnnotation = true; | |
100 | ||
101 | /** | |
102 | * render each residue in a coloured box | |
103 | */ | |
104 | boolean showBoxes = true; | |
105 | ||
106 | /** | |
107 | * Colour sequence text | |
108 | */ | |
109 | boolean showColourText = false; | |
110 | ||
111 | /** | |
112 | * show blue triangles | |
113 | */ | |
114 | boolean showHiddenMarkers = true; | |
115 | ||
116 | /** | |
117 | * show /start-end in ID panel | |
118 | */ | |
119 | boolean showJVSuffix = true; | |
120 | ||
121 | /** | |
122 | * scale features height according to score | |
123 | */ | |
124 | boolean showSeqFeaturesHeight; | |
125 | ||
126 | /** | |
127 | * display setting for showing/hiding sequence features on alignment view | |
128 | */ | |
129 | boolean showSequenceFeatures = false; | |
130 | ||
131 | /** | |
132 | * display sequence symbols | |
133 | */ | |
134 | boolean showText = true; | |
135 | ||
136 | /** | |
137 | * show non-conserved residues only | |
138 | */ | |
139 | protected boolean showUnconserved = false; | |
140 | ||
141 | Color textColour = Color.black; | |
142 | ||
143 | Color textColour2 = Color.white; | |
144 | ||
145 | /** | |
146 | * PID or consensus threshold | |
147 | */ | |
148 | int threshold; | |
149 | ||
150 | /** | |
151 | * threshold for switching between textColour & textColour2 | |
152 | */ | |
153 | int thresholdTextColour = 0; | |
154 | ||
155 | /** | |
156 | * upper case characters in sequence are shown in bold | |
157 | */ | |
158 | boolean upperCasebold = false; | |
159 | ||
160 | /** | |
161 | * name of base font for view | |
162 | */ | |
163 | private String fontName; | |
164 | ||
165 | /** | |
166 | * size for base font | |
167 | */ | |
168 | private int fontSize; | |
169 | ||
170 | /* | |
171 | * If true, scale protein residues to 3 times width of cDNA bases (in | |
172 | * SplitFrame views only) | |
173 | */ | |
174 | private boolean scaleProteinAsCdna = true; | |
175 | ||
176 | /* | |
177 | * if true, font changes to protein or cDNA are applied to both | |
178 | * sides of a split screen | |
179 | */ | |
180 | private boolean proteinFontAsCdna = true; | |
181 | ||
182 | /** | |
183 | * Copy constructor | |
184 | * | |
185 | * @param vs | |
186 | */ | |
187 | 232 | public ViewStyle(ViewStyleI vs) |
188 | { | |
189 | 232 | setAbovePIDThreshold(vs.getAbovePIDThreshold()); |
190 | 232 | setCentreColumnLabels(vs.isCentreColumnLabels()); |
191 | 232 | setCharHeight(vs.getCharHeight()); |
192 | 232 | setCharWidth(vs.getCharWidth()); |
193 | 232 | setColourAppliesToAllGroups(vs.getColourAppliesToAllGroups()); |
194 | 232 | setColourByReferenceSeq(vs.isColourByReferenceSeq()); |
195 | 232 | setColourText(vs.getColourText()); |
196 | 232 | setByConsensusSecondaryStructureSelected( |
197 | vs.getByConsensusSecondaryStructureSelected()); | |
198 | 232 | setConsensusSecondaryStructureThreshold( |
199 | vs.getConsensusSecondaryStructureThreshold()); | |
200 | 232 | setConservationColourSelected(vs.isConservationColourSelected()); |
201 | 232 | setConservationSelected(vs.getConservationSelected()); |
202 | 232 | setDisplayReferenceSeq(vs.isDisplayReferenceSeq()); |
203 | 232 | setFontName(vs.getFontName()); |
204 | 232 | setFontSize(vs.getFontSize()); |
205 | 232 | setFontStyle(vs.getFontStyle()); |
206 | 232 | setIdWidth(vs.getIdWidth()); |
207 | 232 | setIncrement(vs.getIncrement()); |
208 | 232 | setRenderGaps(vs.isRenderGaps()); |
209 | 232 | setRightAlignIds(vs.isRightAlignIds()); |
210 | 232 | setScaleAboveWrapped(vs.getScaleAboveWrapped()); |
211 | 232 | setScaleLeftWrapped(vs.getScaleLeftWrapped()); |
212 | 232 | setScaleProteinAsCdna(vs.isScaleProteinAsCdna()); |
213 | 232 | setProteinFontAsCdna(vs.isProteinFontAsCdna()); |
214 | 232 | setScaleRightWrapped(vs.getScaleRightWrapped()); |
215 | 232 | setSeqNameItalics(vs.isSeqNameItalics()); |
216 | 232 | setShowAnnotation(vs.isShowAnnotation()); |
217 | 232 | setShowBoxes(vs.getShowBoxes()); |
218 | 232 | setShowColourText(vs.isShowColourText()); |
219 | 232 | setShowDBRefs(vs.isShowDBRefs()); |
220 | 232 | setShowHiddenMarkers(vs.getShowHiddenMarkers()); |
221 | 232 | setShowJVSuffix(vs.getShowJVSuffix()); |
222 | 232 | setShowNPFeats(vs.isShowNPFeats()); |
223 | 232 | setShowSequenceFeaturesHeight(vs.isShowSequenceFeaturesHeight()); |
224 | 232 | setShowSequenceFeatures(vs.isShowSequenceFeatures()); |
225 | 232 | setShowComplementFeatures(vs.isShowComplementFeatures()); |
226 | 232 | setShowComplementFeaturesOnTop(vs.isShowComplementFeaturesOnTop()); |
227 | 232 | setShowText(vs.getShowText()); |
228 | 232 | setShowUnconserved(vs.getShowUnconserved()); |
229 | 232 | setTextColour(vs.getTextColour()); |
230 | 232 | setTextColour2(vs.getTextColour2()); |
231 | 232 | setThreshold(vs.getThreshold()); |
232 | 232 | setThresholdTextColour(vs.getThresholdTextColour()); |
233 | 232 | setUpperCasebold(vs.isUpperCasebold()); |
234 | 232 | setWrapAlignment(vs.getWrapAlignment()); |
235 | 232 | setWrappedWidth(vs.getWrappedWidth()); |
236 | 232 | setSecondaryStructureSources(vs.getSecondaryStructureSources()); |
237 | 232 | setShowStructureProvider(vs.isShowStructureProvider()); |
238 | // ViewStyle.configureFrom(this, viewStyle); | |
239 | } | |
240 | ||
241 | 510 | public ViewStyle() |
242 | { | |
243 | } | |
244 | ||
245 | /** | |
246 | * Returns true if all attributes of the ViewStyles have the same value | |
247 | */ | |
248 | 52 | @Override |
249 | public boolean equals(Object other) | |
250 | { | |
251 | 52 | if (other == null || !(other instanceof ViewStyle)) |
252 | { | |
253 | 2 | return false; |
254 | } | |
255 | 50 | ViewStyle vs = (ViewStyle) other; |
256 | ||
257 | 50 | boolean match = (getAbovePIDThreshold() == vs.getAbovePIDThreshold() |
258 | && isCentreColumnLabels() == vs.isCentreColumnLabels() | |
259 | && getCharHeight() == vs.getCharHeight() | |
260 | && getCharWidth() == vs.getCharWidth() | |
261 | && getColourAppliesToAllGroups() == vs | |
262 | .getColourAppliesToAllGroups() | |
263 | && isColourByReferenceSeq() == vs.isColourByReferenceSeq() | |
264 | && getColourText() == vs.getColourText() | |
265 | && isConservationColourSelected() == vs | |
266 | .isConservationColourSelected() | |
267 | && getByConsensusSecondaryStructureSelected() == vs | |
268 | .getByConsensusSecondaryStructureSelected() | |
269 | && getConservationSelected() == vs.getConservationSelected() | |
270 | && isDisplayReferenceSeq() == vs.isDisplayReferenceSeq() | |
271 | && getFontSize() == vs.getFontSize() | |
272 | && getFontStyle() == vs.getFontStyle() | |
273 | && getIdWidth() == vs.getIdWidth() | |
274 | && getIncrement() == vs.getIncrement() | |
275 | && getConsensusSecondaryStructureThreshold() == vs | |
276 | .getConsensusSecondaryStructureThreshold() | |
277 | && isRenderGaps() == vs.isRenderGaps() | |
278 | && isRightAlignIds() == vs.isRightAlignIds() | |
279 | && getScaleAboveWrapped() == vs.getScaleAboveWrapped() | |
280 | && getScaleLeftWrapped() == vs.getScaleLeftWrapped() | |
281 | && isScaleProteinAsCdna() == vs.isScaleProteinAsCdna() | |
282 | && isProteinFontAsCdna() == vs.isProteinFontAsCdna() | |
283 | && getScaleRightWrapped() == vs.getScaleRightWrapped() | |
284 | && isSeqNameItalics() == vs.isSeqNameItalics() | |
285 | && isShowAnnotation() == vs.isShowAnnotation() | |
286 | && getShowBoxes() == vs.getShowBoxes() | |
287 | && isShowColourText() == vs.isShowColourText() | |
288 | && isShowDBRefs() == vs.isShowDBRefs() | |
289 | && getShowHiddenMarkers() == vs.getShowHiddenMarkers() | |
290 | && getShowJVSuffix() == vs.getShowJVSuffix() | |
291 | && isShowNPFeats() == vs.isShowNPFeats() | |
292 | && isShowSequenceFeaturesHeight() == vs | |
293 | .isShowSequenceFeaturesHeight() | |
294 | && isShowSequenceFeatures() == vs.isShowSequenceFeatures() | |
295 | && isShowComplementFeatures() == vs.isShowComplementFeatures() | |
296 | && isShowComplementFeaturesOnTop() == vs | |
297 | .isShowComplementFeaturesOnTop() | |
298 | && getShowText() == vs.getShowText() | |
299 | && getShowUnconserved() == vs.getShowUnconserved() | |
300 | && getThreshold() == vs.getThreshold() | |
301 | && getThresholdTextColour() == vs.getThresholdTextColour() | |
302 | && isUpperCasebold() == vs.isUpperCasebold() | |
303 | && getWrapAlignment() == vs.getWrapAlignment() | |
304 | && getWrappedWidth() == vs.getWrappedWidth() | |
305 | && getSecondaryStructureSources() == vs | |
306 | .getSecondaryStructureSources() | |
307 | && isShowStructureProvider() == vs.isShowStructureProvider()); | |
308 | /* | |
309 | * and compare non-primitive types; syntax below will match null with null | |
310 | * values | |
311 | */ | |
312 | 50 | match = match && String.valueOf(getFontName()) |
313 | .equals(String.valueOf(vs.getFontName())); | |
314 | 50 | match = match && String.valueOf(getTextColour()) |
315 | .equals(String.valueOf(vs.getTextColour())); | |
316 | 50 | match = match && String.valueOf(getTextColour2()) |
317 | .equals(String.valueOf(vs.getTextColour2())); | |
318 | 50 | return match; |
319 | // return equivalent(this, (ViewStyle) other); | |
320 | } | |
321 | ||
322 | /** | |
323 | * Overridden to ensure that whenever vs1.equals(vs2) then vs1.hashCode() == | |
324 | * vs2.hashCode() | |
325 | */ | |
326 | 92 | @Override |
327 | public int hashCode() | |
328 | { | |
329 | /* | |
330 | * No need to include all properties, just a selection... | |
331 | */ | |
332 | 92 | int hash = 0; |
333 | 92 | int m = 1; |
334 | // Boolean.hashCode returns 1231 or 1237 | |
335 | 92 | hash += m++ * Boolean.valueOf(this.abovePIDThreshold).hashCode(); |
336 | 92 | hash += m++ * Boolean.valueOf(this.centreColumnLabels).hashCode(); |
337 | 92 | hash += m++ * Boolean.valueOf(this.colourAppliesToAllGroups).hashCode(); |
338 | 92 | hash += m++ * Boolean.valueOf(this.displayReferenceSeq).hashCode(); |
339 | 92 | hash += m++ * Boolean.valueOf(this.renderGaps).hashCode(); |
340 | 92 | hash += m++ * Boolean.valueOf(this.rightAlignIds).hashCode(); |
341 | 92 | hash += m++ * Boolean.valueOf(this.scaleProteinAsCdna).hashCode(); |
342 | 92 | hash += m++ * Boolean.valueOf(this.scaleRightWrapped).hashCode(); |
343 | 92 | hash += m++ * Boolean.valueOf(this.seqNameItalics).hashCode(); |
344 | 92 | hash += m++ * Boolean.valueOf(this.showAnnotation).hashCode(); |
345 | 92 | hash += m++ * Boolean.valueOf(this.showBoxes).hashCode(); |
346 | 92 | hash += m++ * Boolean.valueOf(this.showdbrefs).hashCode(); |
347 | 92 | hash += m++ * Boolean.valueOf(this.showJVSuffix).hashCode(); |
348 | 92 | hash += m++ * Boolean.valueOf(this.showSequenceFeatures).hashCode(); |
349 | 92 | hash += m++ * Boolean.valueOf(this.showUnconserved).hashCode(); |
350 | 92 | hash += m++ * Boolean.valueOf(this.wrapAlignment).hashCode(); |
351 | 92 | hash += m++ * this.charHeight; |
352 | 92 | hash += m++ * this.charWidth; |
353 | 92 | hash += m++ * fontSize; |
354 | 92 | hash += m++ * fontStyle; |
355 | 92 | hash += m++ * idWidth; |
356 | 92 | hash += String.valueOf(this.fontName).hashCode(); |
357 | 92 | return hash; |
358 | } | |
359 | ||
360 | /** | |
361 | * @return the upperCasebold | |
362 | */ | |
363 | 254 | @Override |
364 | public boolean isUpperCasebold() | |
365 | { | |
366 | 254 | return upperCasebold; |
367 | } | |
368 | ||
369 | /** | |
370 | * @param upperCasebold | |
371 | * the upperCasebold to set | |
372 | */ | |
373 | 232 | @Override |
374 | public void setUpperCasebold(boolean upperCasebold) | |
375 | { | |
376 | 232 | this.upperCasebold = upperCasebold; |
377 | } | |
378 | ||
379 | /** | |
380 | * flag for wrapping | |
381 | */ | |
382 | boolean wrapAlignment = false; | |
383 | ||
384 | /** | |
385 | * number columns in wrapped alignment | |
386 | */ | |
387 | int wrappedWidth; | |
388 | ||
389 | private int fontStyle; | |
390 | ||
391 | private boolean showComplementFeatures; | |
392 | ||
393 | private boolean showComplementFeaturesOnTop; | |
394 | ||
395 | /** | |
396 | * secondary structure annotation rows shown in the view | |
397 | */ | |
398 | private List<String> secondaryStructureSources = List.of(new String[0]); | |
399 | ||
400 | private boolean showStructureProvider; | |
401 | ||
402 | /** | |
403 | * GUI state | |
404 | * | |
405 | * @return true if percent identity threshold is applied to shading | |
406 | */ | |
407 | 1210 | @Override |
408 | public boolean getAbovePIDThreshold() | |
409 | { | |
410 | 1210 | return abovePIDThreshold; |
411 | } | |
412 | ||
413 | 1190 | @Override |
414 | public boolean getByConsensusSecondaryStructureSelected() | |
415 | { | |
416 | 1190 | return byConsensusSecondaryStructureSelected; |
417 | } | |
418 | ||
419 | /** | |
420 | * DOCUMENT ME! | |
421 | * | |
422 | * @return DOCUMENT ME! | |
423 | */ | |
424 | 115575 | @Override |
425 | public int getCharHeight() | |
426 | { | |
427 | 115575 | return charHeight; |
428 | } | |
429 | ||
430 | /** | |
431 | * DOCUMENT ME! | |
432 | * | |
433 | * @return DOCUMENT ME! | |
434 | */ | |
435 | 1521435 | @Override |
436 | public int getCharWidth() | |
437 | { | |
438 | 1521435 | return charWidth; |
439 | } | |
440 | ||
441 | /** | |
442 | * | |
443 | * | |
444 | * @return flag indicating if colourchanges propagated to all groups | |
445 | */ | |
446 | 1282 | @Override |
447 | public boolean getColourAppliesToAllGroups() | |
448 | { | |
449 | 1282 | return colourAppliesToAllGroups; |
450 | } | |
451 | ||
452 | /** | |
453 | * DOCUMENT ME! | |
454 | * | |
455 | * @return DOCUMENT ME! | |
456 | */ | |
457 | 433100 | @Override |
458 | public boolean getColourText() | |
459 | { | |
460 | 433100 | return showColourText; |
461 | } | |
462 | ||
463 | /** | |
464 | * GUI state | |
465 | * | |
466 | * @return true if conservation based shading is enabled | |
467 | */ | |
468 | 1350 | @Override |
469 | public boolean getConservationSelected() | |
470 | { | |
471 | 1350 | return conservationColourSelected; |
472 | } | |
473 | ||
474 | /** | |
475 | * GUI State | |
476 | * | |
477 | * @return get scalar for bleaching colourschemes by conservation | |
478 | */ | |
479 | 302 | @Override |
480 | public int getIncrement() | |
481 | { | |
482 | 302 | return increment; |
483 | } | |
484 | ||
485 | /** | |
486 | * DOCUMENT ME! | |
487 | * | |
488 | * @return DOCUMENT ME! | |
489 | */ | |
490 | 1207 | @Override |
491 | public boolean getScaleAboveWrapped() | |
492 | { | |
493 | 1207 | return scaleAboveWrapped; |
494 | } | |
495 | ||
496 | /** | |
497 | * DOCUMENT ME! | |
498 | * | |
499 | * @return DOCUMENT ME! | |
500 | */ | |
501 | 1600 | @Override |
502 | public boolean getScaleLeftWrapped() | |
503 | { | |
504 | 1600 | return scaleLeftWrapped; |
505 | } | |
506 | ||
507 | /** | |
508 | * DOCUMENT ME! | |
509 | * | |
510 | * @return DOCUMENT ME! | |
511 | */ | |
512 | 2408 | @Override |
513 | public boolean getScaleRightWrapped() | |
514 | { | |
515 | 2408 | return scaleRightWrapped; |
516 | } | |
517 | ||
518 | /** | |
519 | * DOCUMENT ME! | |
520 | * | |
521 | * @return DOCUMENT ME! | |
522 | */ | |
523 | 471546 | @Override |
524 | public boolean getShowBoxes() | |
525 | { | |
526 | 471546 | return showBoxes; |
527 | } | |
528 | ||
529 | 7366 | @Override |
530 | public boolean getShowHiddenMarkers() | |
531 | { | |
532 | 7366 | return showHiddenMarkers; |
533 | } | |
534 | ||
535 | /** | |
536 | * DOCUMENT ME! | |
537 | * | |
538 | * @return DOCUMENT ME! | |
539 | */ | |
540 | 49117 | @Override |
541 | public boolean getShowJVSuffix() | |
542 | { | |
543 | 49117 | return showJVSuffix; |
544 | } | |
545 | ||
546 | /** | |
547 | * DOCUMENT ME! | |
548 | * | |
549 | * @return DOCUMENT ME! | |
550 | */ | |
551 | 433718 | @Override |
552 | public boolean getShowText() | |
553 | { | |
554 | 433718 | return showText; |
555 | } | |
556 | ||
557 | 431226 | @Override |
558 | public boolean getShowUnconserved() | |
559 | { | |
560 | 431226 | return showUnconserved; |
561 | } | |
562 | ||
563 | /** | |
564 | * @return the textColour | |
565 | */ | |
566 | 737024 | @Override |
567 | public Color getTextColour() | |
568 | { | |
569 | 737024 | return textColour; |
570 | } | |
571 | ||
572 | /** | |
573 | * @return the textColour2 | |
574 | */ | |
575 | 286 | @Override |
576 | public Color getTextColour2() | |
577 | { | |
578 | 286 | return textColour2; |
579 | } | |
580 | ||
581 | /** | |
582 | * DOCUMENT ME! | |
583 | * | |
584 | * @return DOCUMENT ME! | |
585 | */ | |
586 | 258 | @Override |
587 | public int getThreshold() | |
588 | { | |
589 | 258 | return threshold; |
590 | } | |
591 | ||
592 | 300 | @Override |
593 | public int getConsensusSecondaryStructureThreshold() | |
594 | { | |
595 | 300 | return consensusSecondaryStructureThreshold; |
596 | } | |
597 | ||
598 | /** | |
599 | * @return the thresholdTextColour | |
600 | */ | |
601 | 433040 | @Override |
602 | public int getThresholdTextColour() | |
603 | { | |
604 | 433040 | return thresholdTextColour; |
605 | } | |
606 | ||
607 | /** | |
608 | * DOCUMENT ME! | |
609 | * | |
610 | * @return DOCUMENT ME! | |
611 | */ | |
612 | 30884 | @Override |
613 | public boolean getWrapAlignment() | |
614 | { | |
615 | 30884 | return wrapAlignment; |
616 | } | |
617 | ||
618 | /** | |
619 | * DOCUMENT ME! | |
620 | * | |
621 | * @return DOCUMENT ME! | |
622 | */ | |
623 | 252 | @Override |
624 | public int getWrappedWidth() | |
625 | { | |
626 | 252 | return wrappedWidth; |
627 | } | |
628 | ||
629 | 323 | @Override |
630 | public boolean isColourByReferenceSeq() | |
631 | { | |
632 | 323 | return colourByReferenceSeq; |
633 | } | |
634 | ||
635 | /** | |
636 | * @return the conservationColourSelected | |
637 | */ | |
638 | 400 | @Override |
639 | public boolean isConservationColourSelected() | |
640 | { | |
641 | 400 | return conservationColourSelected; |
642 | } | |
643 | ||
644 | 961 | @Override |
645 | public boolean isDisplayReferenceSeq() | |
646 | { | |
647 | 961 | return displayReferenceSeq; |
648 | } | |
649 | ||
650 | /** | |
651 | * @return the renderGaps | |
652 | */ | |
653 | 3731 | @Override |
654 | public boolean isRenderGaps() | |
655 | { | |
656 | 3731 | return renderGaps; |
657 | } | |
658 | ||
659 | 19564 | @Override |
660 | public boolean isRightAlignIds() | |
661 | { | |
662 | 19564 | return rightAlignIds; |
663 | } | |
664 | ||
665 | /** | |
666 | * @return the seqNameItalics | |
667 | */ | |
668 | 3471 | @Override |
669 | public boolean isSeqNameItalics() | |
670 | { | |
671 | 3471 | return seqNameItalics; |
672 | } | |
673 | ||
674 | 5196 | @Override |
675 | public boolean isShowAnnotation() | |
676 | { | |
677 | 5196 | return showAnnotation; |
678 | } | |
679 | ||
680 | /** | |
681 | * @return the showColourText | |
682 | */ | |
683 | 950 | @Override |
684 | public boolean isShowColourText() | |
685 | { | |
686 | 950 | return showColourText; |
687 | } | |
688 | ||
689 | /** | |
690 | * @return the showSeqFeaturesHeight | |
691 | */ | |
692 | 270 | @Override |
693 | public boolean isShowSequenceFeaturesHeight() | |
694 | { | |
695 | 270 | return showSeqFeaturesHeight; |
696 | } | |
697 | ||
698 | 459590 | @Override |
699 | public boolean isShowSequenceFeatures() | |
700 | { | |
701 | 459621 | return showSequenceFeatures; |
702 | } | |
703 | ||
704 | /** | |
705 | * GUI state | |
706 | * | |
707 | * | |
708 | * @param b | |
709 | * indicate if percent identity threshold is applied to shading | |
710 | */ | |
711 | 326 | @Override |
712 | public void setAbovePIDThreshold(boolean b) | |
713 | { | |
714 | 326 | abovePIDThreshold = b; |
715 | } | |
716 | ||
717 | 317 | @Override |
718 | public void setByConsensusSecondaryStructureSelected(boolean b) | |
719 | { | |
720 | 317 | byConsensusSecondaryStructureSelected = b; |
721 | } | |
722 | ||
723 | /** | |
724 | * DOCUMENT ME! | |
725 | * | |
726 | * @param h | |
727 | * DOCUMENT ME! | |
728 | */ | |
729 | 828 | @Override |
730 | public void setCharHeight(int h) | |
731 | { | |
732 | 828 | this.charHeight = h; |
733 | } | |
734 | ||
735 | /** | |
736 | * DOCUMENT ME! | |
737 | * | |
738 | * @param w | |
739 | * DOCUMENT ME! | |
740 | */ | |
741 | 831 | @Override |
742 | public void setCharWidth(int w) | |
743 | { | |
744 | 831 | this.charWidth = w; |
745 | } | |
746 | ||
747 | /** | |
748 | * @param value | |
749 | * indicating if subsequent colourscheme changes will be propagated | |
750 | * to all groups | |
751 | */ | |
752 | 925 | @Override |
753 | public void setColourAppliesToAllGroups(boolean b) | |
754 | { | |
755 | 925 | colourAppliesToAllGroups = b; |
756 | } | |
757 | ||
758 | 242 | @Override |
759 | public void setColourByReferenceSeq(boolean colourByReferenceSeq) | |
760 | { | |
761 | 242 | this.colourByReferenceSeq = colourByReferenceSeq; |
762 | } | |
763 | ||
764 | /** | |
765 | * DOCUMENT ME! | |
766 | * | |
767 | * @param state | |
768 | * DOCUMENT ME! | |
769 | */ | |
770 | 317 | @Override |
771 | public void setColourText(boolean state) | |
772 | { | |
773 | 317 | showColourText = state; |
774 | } | |
775 | ||
776 | /** | |
777 | * @param conservationColourSelected | |
778 | * the conservationColourSelected to set | |
779 | */ | |
780 | 232 | @Override |
781 | public void setConservationColourSelected( | |
782 | boolean conservationColourSelected) | |
783 | { | |
784 | 232 | this.conservationColourSelected = conservationColourSelected; |
785 | } | |
786 | ||
787 | /** | |
788 | * GUI state | |
789 | * | |
790 | * @param b | |
791 | * enable conservation based shading | |
792 | */ | |
793 | 325 | @Override |
794 | public void setConservationSelected(boolean b) | |
795 | { | |
796 | 325 | conservationColourSelected = b; |
797 | } | |
798 | ||
799 | 242 | @Override |
800 | public void setDisplayReferenceSeq(boolean displayReferenceSeq) | |
801 | { | |
802 | 242 | this.displayReferenceSeq = displayReferenceSeq; |
803 | } | |
804 | ||
805 | /** | |
806 | * | |
807 | * @param inc | |
808 | * set the scalar for bleaching colourschemes according to degree of | |
809 | * conservation | |
810 | */ | |
811 | 317 | @Override |
812 | public void setIncrement(int inc) | |
813 | { | |
814 | 317 | increment = inc; |
815 | } | |
816 | ||
817 | /** | |
818 | * | |
819 | * @param val | |
820 | * set the scalar for bleaching colourschemes according to degree of | |
821 | * secondary structure conservation | |
822 | */ | |
823 | 317 | @Override |
824 | public void setConsensusSecondaryStructureThreshold(int val) | |
825 | { | |
826 | 317 | consensusSecondaryStructureThreshold = val; |
827 | } | |
828 | ||
829 | /** | |
830 | * DOCUMENT ME! | |
831 | * | |
832 | * @param state | |
833 | * DOCUMENT ME! | |
834 | */ | |
835 | 317 | @Override |
836 | public void setRenderGaps(boolean state) | |
837 | { | |
838 | 317 | renderGaps = state; |
839 | } | |
840 | ||
841 | 825 | @Override |
842 | public void setRightAlignIds(boolean rightAlignIds) | |
843 | { | |
844 | 825 | this.rightAlignIds = rightAlignIds; |
845 | } | |
846 | ||
847 | /** | |
848 | * DOCUMENT ME! | |
849 | * | |
850 | * @param b | |
851 | * DOCUMENT ME! | |
852 | */ | |
853 | 241 | @Override |
854 | public void setScaleAboveWrapped(boolean b) | |
855 | { | |
856 | 241 | scaleAboveWrapped = b; |
857 | } | |
858 | ||
859 | /** | |
860 | * DOCUMENT ME! | |
861 | * | |
862 | * @param b | |
863 | * DOCUMENT ME! | |
864 | */ | |
865 | 243 | @Override |
866 | public void setScaleLeftWrapped(boolean b) | |
867 | { | |
868 | 243 | scaleLeftWrapped = b; |
869 | } | |
870 | ||
871 | /** | |
872 | * | |
873 | * | |
874 | * @param scaleRightWrapped | |
875 | * - true or false | |
876 | */ | |
877 | ||
878 | 241 | @Override |
879 | public void setScaleRightWrapped(boolean b) | |
880 | { | |
881 | 241 | scaleRightWrapped = b; |
882 | } | |
883 | ||
884 | 740 | @Override |
885 | public void setSeqNameItalics(boolean italics) | |
886 | { | |
887 | 740 | seqNameItalics = italics; |
888 | } | |
889 | ||
890 | 912 | @Override |
891 | public void setShowAnnotation(boolean b) | |
892 | { | |
893 | 912 | showAnnotation = b; |
894 | } | |
895 | ||
896 | /** | |
897 | * DOCUMENT ME! | |
898 | * | |
899 | * @param state | |
900 | * DOCUMENT ME! | |
901 | */ | |
902 | 317 | @Override |
903 | public void setShowBoxes(boolean state) | |
904 | { | |
905 | 317 | showBoxes = state; |
906 | } | |
907 | ||
908 | /** | |
909 | * @param showColourText | |
910 | * the showColourText to set | |
911 | */ | |
912 | 232 | @Override |
913 | public void setShowColourText(boolean showColourText) | |
914 | { | |
915 | 232 | this.showColourText = showColourText; |
916 | } | |
917 | ||
918 | 232 | @Override |
919 | public void setShowHiddenMarkers(boolean show) | |
920 | { | |
921 | 232 | showHiddenMarkers = show; |
922 | } | |
923 | ||
924 | /** | |
925 | * DOCUMENT ME! | |
926 | * | |
927 | * @param b | |
928 | * DOCUMENT ME! | |
929 | */ | |
930 | 826 | @Override |
931 | public void setShowJVSuffix(boolean b) | |
932 | { | |
933 | 826 | showJVSuffix = b; |
934 | } | |
935 | ||
936 | 232 | @Override |
937 | public void setShowSequenceFeaturesHeight(boolean selected) | |
938 | { | |
939 | 232 | showSeqFeaturesHeight = selected; |
940 | ||
941 | } | |
942 | ||
943 | /** | |
944 | * set the flag | |
945 | * | |
946 | * @param b | |
947 | * features are displayed if true | |
948 | */ | |
949 | 373 | @Override |
950 | public void setShowSequenceFeatures(boolean b) | |
951 | { | |
952 | 373 | showSequenceFeatures = b; |
953 | } | |
954 | ||
955 | /** | |
956 | * DOCUMENT ME! | |
957 | * | |
958 | * @param state | |
959 | * DOCUMENT ME! | |
960 | */ | |
961 | 317 | @Override |
962 | public void setShowText(boolean state) | |
963 | { | |
964 | 317 | showText = state; |
965 | } | |
966 | ||
967 | 825 | @Override |
968 | public void setShowUnconserved(boolean showunconserved) | |
969 | { | |
970 | 825 | showUnconserved = showunconserved; |
971 | } | |
972 | ||
973 | /** | |
974 | * @param textColour | |
975 | * the textColour to set | |
976 | */ | |
977 | 317 | @Override |
978 | public void setTextColour(Color textColour) | |
979 | { | |
980 | 317 | this.textColour = textColour; |
981 | } | |
982 | ||
983 | /** | |
984 | * @param textColour2 | |
985 | * the textColour2 to set | |
986 | */ | |
987 | 317 | @Override |
988 | public void setTextColour2(Color textColour2) | |
989 | { | |
990 | 317 | this.textColour2 = textColour2; |
991 | } | |
992 | ||
993 | /** | |
994 | * DOCUMENT ME! | |
995 | * | |
996 | * @param thresh | |
997 | * DOCUMENT ME! | |
998 | */ | |
999 | 338 | @Override |
1000 | public void setThreshold(int thresh) | |
1001 | { | |
1002 | 338 | threshold = thresh; |
1003 | } | |
1004 | ||
1005 | /** | |
1006 | * @param thresholdTextColour | |
1007 | * the thresholdTextColour to set | |
1008 | */ | |
1009 | 317 | @Override |
1010 | public void setThresholdTextColour(int thresholdTextColour) | |
1011 | { | |
1012 | 317 | this.thresholdTextColour = thresholdTextColour; |
1013 | } | |
1014 | ||
1015 | /** | |
1016 | * DOCUMENT ME! | |
1017 | * | |
1018 | * @param state | |
1019 | * DOCUMENT ME! | |
1020 | */ | |
1021 | 837 | @Override |
1022 | public void setWrapAlignment(boolean state) | |
1023 | { | |
1024 | 837 | wrapAlignment = state; |
1025 | } | |
1026 | ||
1027 | /** | |
1028 | * DOCUMENT ME! | |
1029 | * | |
1030 | * @param w | |
1031 | * DOCUMENT ME! | |
1032 | */ | |
1033 | 1074 | @Override |
1034 | public void setWrappedWidth(int w) | |
1035 | { | |
1036 | 1074 | this.wrappedWidth = w; |
1037 | } | |
1038 | ||
1039 | 3 | @Override |
1040 | public boolean sameStyle(ViewStyleI that) | |
1041 | { | |
1042 | 3 | return this.equals(that); |
1043 | } | |
1044 | ||
1045 | 330 | @Override |
1046 | public String getFontName() | |
1047 | { | |
1048 | 330 | return fontName; |
1049 | } | |
1050 | ||
1051 | 394 | @Override |
1052 | public int getFontSize() | |
1053 | { | |
1054 | 394 | return fontSize; |
1055 | } | |
1056 | ||
1057 | 392 | @Override |
1058 | public int getFontStyle() | |
1059 | { | |
1060 | 392 | return fontStyle; |
1061 | } | |
1062 | ||
1063 | 914 | @Override |
1064 | public void setFontName(String name) | |
1065 | { | |
1066 | 914 | fontName = name; |
1067 | } | |
1068 | ||
1069 | 914 | @Override |
1070 | public void setFontSize(int size) | |
1071 | { | |
1072 | 914 | fontSize = size; |
1073 | ||
1074 | } | |
1075 | ||
1076 | 914 | @Override |
1077 | public void setFontStyle(int style) | |
1078 | { | |
1079 | 914 | fontStyle = style; |
1080 | } | |
1081 | ||
1082 | 6605 | @Override |
1083 | public int getIdWidth() | |
1084 | { | |
1085 | 6605 | return idWidth; |
1086 | } | |
1087 | ||
1088 | /** | |
1089 | * @param idWidth | |
1090 | * the idWidth to set | |
1091 | */ | |
1092 | 1202 | @Override |
1093 | public void setIdWidth(int idWidth) | |
1094 | { | |
1095 | 1202 | this.idWidth = idWidth; |
1096 | } | |
1097 | ||
1098 | /** | |
1099 | * @return the centreColumnLabels | |
1100 | */ | |
1101 | 1002 | @Override |
1102 | public boolean isCentreColumnLabels() | |
1103 | { | |
1104 | 1002 | return centreColumnLabels; |
1105 | } | |
1106 | ||
1107 | /** | |
1108 | * @param centreColumnLabels | |
1109 | * the centreColumnLabels to set | |
1110 | */ | |
1111 | 825 | @Override |
1112 | public void setCentreColumnLabels(boolean centreColumnLabels) | |
1113 | { | |
1114 | 825 | this.centreColumnLabels = centreColumnLabels; |
1115 | } | |
1116 | ||
1117 | /** | |
1118 | * @return the showdbrefs | |
1119 | */ | |
1120 | 996 | @Override |
1121 | public boolean isShowDBRefs() | |
1122 | { | |
1123 | 996 | return showdbrefs; |
1124 | } | |
1125 | ||
1126 | /** | |
1127 | * @param showdbrefs | |
1128 | * the showdbrefs to set | |
1129 | */ | |
1130 | 825 | @Override |
1131 | public void setShowDBRefs(boolean showdbrefs) | |
1132 | { | |
1133 | 825 | this.showdbrefs = showdbrefs; |
1134 | } | |
1135 | ||
1136 | /** | |
1137 | * @return the shownpfeats | |
1138 | */ | |
1139 | 990 | @Override |
1140 | public boolean isShowNPFeats() | |
1141 | { | |
1142 | 990 | return shownpfeats; |
1143 | } | |
1144 | ||
1145 | /** | |
1146 | * @param shownpfeats | |
1147 | * the shownpfeats to set | |
1148 | */ | |
1149 | 825 | @Override |
1150 | public void setShowNPFeats(boolean shownpfeats) | |
1151 | { | |
1152 | 825 | this.shownpfeats = shownpfeats; |
1153 | } | |
1154 | ||
1155 | 339 | @Override |
1156 | public boolean isScaleProteinAsCdna() | |
1157 | { | |
1158 | 339 | return this.scaleProteinAsCdna; |
1159 | } | |
1160 | ||
1161 | 825 | @Override |
1162 | public void setScaleProteinAsCdna(boolean b) | |
1163 | { | |
1164 | 825 | this.scaleProteinAsCdna = b; |
1165 | } | |
1166 | ||
1167 | 288 | @Override |
1168 | public boolean isProteinFontAsCdna() | |
1169 | { | |
1170 | 288 | return proteinFontAsCdna; |
1171 | } | |
1172 | ||
1173 | 232 | @Override |
1174 | public void setProteinFontAsCdna(boolean b) | |
1175 | { | |
1176 | 232 | proteinFontAsCdna = b; |
1177 | } | |
1178 | ||
1179 | 317 | @Override |
1180 | public void setShowComplementFeatures(boolean b) | |
1181 | { | |
1182 | 317 | showComplementFeatures = b; |
1183 | } | |
1184 | ||
1185 | 460976 | @Override |
1186 | public boolean isShowComplementFeatures() | |
1187 | { | |
1188 | 460987 | return showComplementFeatures; |
1189 | } | |
1190 | ||
1191 | 317 | @Override |
1192 | public void setShowComplementFeaturesOnTop(boolean b) | |
1193 | { | |
1194 | 317 | showComplementFeaturesOnTop = b; |
1195 | } | |
1196 | ||
1197 | 311 | @Override |
1198 | public boolean isShowComplementFeaturesOnTop() | |
1199 | { | |
1200 | 311 | return showComplementFeaturesOnTop; |
1201 | } | |
1202 | ||
1203 | 2726 | @Override |
1204 | public List<String> getSecondaryStructureSources() | |
1205 | { | |
1206 | 2726 | return secondaryStructureSources; |
1207 | } | |
1208 | ||
1209 | 1609 | @Override |
1210 | public void setSecondaryStructureSources( | |
1211 | List<String> secondaryStructureSources) | |
1212 | { | |
1213 | 1609 | this.secondaryStructureSources = secondaryStructureSources; |
1214 | } | |
1215 | ||
1216 | 825 | @Override |
1217 | public void setShowStructureProvider(boolean showStructureProvider) | |
1218 | { | |
1219 | 825 | this.showStructureProvider = showStructureProvider; |
1220 | } | |
1221 | ||
1222 | 6971 | @Override |
1223 | public boolean isShowStructureProvider() | |
1224 | { | |
1225 | 6971 | return showStructureProvider; |
1226 | } | |
1227 | } |