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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.api; | |
22 | ||
23 | import java.awt.Color; | |
24 | import java.awt.Font; | |
25 | import java.util.Hashtable; | |
26 | import java.util.Iterator; | |
27 | import java.util.List; | |
28 | import java.util.Map; | |
29 | ||
30 | import jalview.analysis.Conservation; | |
31 | import jalview.analysis.TreeModel; | |
32 | import jalview.datamodel.AlignmentAnnotation; | |
33 | import jalview.datamodel.AlignmentExportData; | |
34 | import jalview.datamodel.AlignmentI; | |
35 | import jalview.datamodel.AlignmentView; | |
36 | import jalview.datamodel.ColumnSelection; | |
37 | import jalview.datamodel.ContactListI; | |
38 | import jalview.datamodel.ContactMatrixI; | |
39 | import jalview.datamodel.ProfilesI; | |
40 | import jalview.datamodel.SearchResultsI; | |
41 | import jalview.datamodel.SequenceCollectionI; | |
42 | import jalview.datamodel.SequenceGroup; | |
43 | import jalview.datamodel.SequenceI; | |
44 | import jalview.renderer.ResidueShaderI; | |
45 | import jalview.schemes.ColourSchemeI; | |
46 | import jalview.viewmodel.ViewportRanges; | |
47 | ||
48 | /** | |
49 | * @author jimp | |
50 | * | |
51 | */ | |
52 | public interface AlignViewportI extends ViewStyleI | |
53 | { | |
54 | ||
55 | /** | |
56 | * Get the ranges object containing details of the start and end sequences and | |
57 | * residues | |
58 | * | |
59 | * @return | |
60 | */ | |
61 | public ViewportRanges getRanges(); | |
62 | ||
63 | /** | |
64 | * calculate the height for visible annotation, revalidating bounds where | |
65 | * necessary ABSTRACT GUI METHOD | |
66 | * | |
67 | * @return total height of annotation | |
68 | */ | |
69 | public int calcPanelHeight(); | |
70 | ||
71 | /** | |
72 | * Answers true if the viewport has at least one column selected | |
73 | * | |
74 | * @return | |
75 | */ | |
76 | boolean hasSelectedColumns(); | |
77 | ||
78 | /** | |
79 | * Answers true if the viewport has at least one hidden column | |
80 | * | |
81 | * @return | |
82 | */ | |
83 | boolean hasHiddenColumns(); | |
84 | ||
85 | boolean isValidCharWidth(); | |
86 | ||
87 | boolean isShowConsensusHistogram(); | |
88 | ||
89 | boolean isShowSequenceLogo(); | |
90 | ||
91 | boolean isNormaliseSequenceLogo(); | |
92 | ||
93 | ColourSchemeI getGlobalColourScheme(); | |
94 | ||
95 | /** | |
96 | * Returns an object that describes colouring (including any thresholding or | |
97 | * fading) of the alignment | |
98 | * | |
99 | * @return | |
100 | */ | |
101 | ResidueShaderI getResidueShading(); | |
102 | ||
103 | AlignmentI getAlignment(); | |
104 | ||
105 | ColumnSelection getColumnSelection(); | |
106 | ||
107 | ProfilesI getSequenceConsensusHash(); | |
108 | ||
109 | /** | |
110 | * Get consensus data table for the cDNA complement of this alignment (if any) | |
111 | * | |
112 | * @return | |
113 | */ | |
114 | Hashtable<String, Object>[] getComplementConsensusHash(); | |
115 | ||
116 | Hashtable<String, Object>[] getRnaStructureConsensusHash(); | |
117 | ||
118 | boolean isIgnoreGapsConsensus(); | |
119 | ||
120 | boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation); | |
121 | ||
122 | AlignmentAnnotation getAlignmentQualityAnnot(); | |
123 | ||
124 | AlignmentAnnotation getAlignmentConservationAnnotation(); | |
125 | ||
126 | /** | |
127 | * get the container for alignment consensus annotation | |
128 | * | |
129 | * @return | |
130 | */ | |
131 | AlignmentAnnotation getAlignmentConsensusAnnotation(); | |
132 | ||
133 | List<AlignmentAnnotation> getAlignmentSecondaryStructureConsensusAnnotation(); | |
134 | ||
135 | /** | |
136 | * get the container for alignment gap annotation | |
137 | * | |
138 | * @return | |
139 | */ | |
140 | AlignmentAnnotation getAlignmentGapAnnotation(); | |
141 | ||
142 | /** | |
143 | * get the container for cDNA complement consensus annotation | |
144 | * | |
145 | * @return | |
146 | */ | |
147 | AlignmentAnnotation getComplementConsensusAnnotation(); | |
148 | ||
149 | /** | |
150 | * Test to see if viewport is still open and active | |
151 | * | |
152 | * @return true indicates that all references to viewport should be dropped | |
153 | */ | |
154 | boolean isClosed(); | |
155 | ||
156 | /** | |
157 | * Dispose of all references or resources held by the viewport | |
158 | */ | |
159 | void dispose(); | |
160 | ||
161 | /** | |
162 | * get the associated calculation thread manager for the view | |
163 | * | |
164 | * @return | |
165 | */ | |
166 | AlignCalcManagerI getCalcManager(); | |
167 | ||
168 | /** | |
169 | * get the percentage gaps allowed in a conservation calculation | |
170 | * | |
171 | */ | |
172 | public int getConsPercGaps(); | |
173 | ||
174 | /** | |
175 | * set the consensus result object for the viewport | |
176 | * | |
177 | * @param hconsensus | |
178 | */ | |
179 | void setSequenceConsensusHash(ProfilesI hconsensus); | |
180 | ||
181 | void setSequenceSSConsensusHash( | |
182 | Map<String, ProfilesI> hSSConsesnusProfileMap); | |
183 | ||
184 | /** | |
185 | * Set the cDNA complement consensus for the viewport | |
186 | * | |
187 | * @param hconsensus | |
188 | */ | |
189 | void setComplementConsensusHash(Hashtable<String, Object>[] hconsensus); | |
190 | ||
191 | /** | |
192 | * | |
193 | * @return the alignment annotation row for the structure consensus | |
194 | * calculation | |
195 | */ | |
196 | AlignmentAnnotation getAlignmentStrucConsensusAnnotation(); | |
197 | ||
198 | /** | |
199 | * set the Rna structure consensus result object for the viewport | |
200 | * | |
201 | * @param hStrucConsensus | |
202 | */ | |
203 | void setRnaStructureConsensusHash( | |
204 | Hashtable<String, Object>[] hStrucConsensus); | |
205 | ||
206 | /** | |
207 | * Sets the colour scheme for the background alignment (as distinct from | |
208 | * sub-groups, which may have their own colour schemes). A null value is used | |
209 | * for no residue colour (white). | |
210 | * | |
211 | * @param cs | |
212 | */ | |
213 | void setGlobalColourScheme(ColourSchemeI cs); | |
214 | ||
215 | Map<SequenceI, SequenceCollectionI> getHiddenRepSequences(); | |
216 | ||
217 | void setHiddenRepSequences( | |
218 | Map<SequenceI, SequenceCollectionI> hiddenRepSequences); | |
219 | ||
220 | /** | |
221 | * hides or shows dynamic annotation rows based on groups and group and | |
222 | * alignment associated auto-annotation state flags apply the current | |
223 | * group/autoannotation settings to the alignment view. Usually you should | |
224 | * call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to | |
225 | * ensure the annotation panel bounds are set correctly. | |
226 | * | |
227 | * @param applyGlobalSettings | |
228 | * - apply to all autoannotation rows or just the ones associated | |
229 | * with the current visible region | |
230 | * @param preserveNewGroupSettings | |
231 | * - don't apply global settings to groups which don't already have | |
232 | * group associated annotation | |
233 | */ | |
234 | void updateGroupAnnotationSettings(boolean applyGlobalSettings, | |
235 | boolean preserveNewGroupSettings); | |
236 | ||
237 | void setSequenceColour(SequenceI seq, Color col); | |
238 | ||
239 | Color getSequenceColour(SequenceI seq); | |
240 | ||
241 | void updateSequenceIdColours(); | |
242 | ||
243 | SequenceGroup getSelectionGroup(); | |
244 | ||
245 | /** | |
246 | * get the currently selected sequence objects or all the sequences in the | |
247 | * alignment. TODO: change to List<> | |
248 | * | |
249 | * @return array of references to sequence objects | |
250 | */ | |
251 | SequenceI[] getSequenceSelection(); | |
252 | ||
253 | void clearSequenceColours(); | |
254 | ||
255 | /** | |
256 | * return a compact representation of the current alignment selection to pass | |
257 | * to an analysis function | |
258 | * | |
259 | * @param selectedOnly | |
260 | * boolean true to just return the selected view | |
261 | * @return AlignmentView | |
262 | */ | |
263 | AlignmentView getAlignmentView(boolean selectedOnly); | |
264 | ||
265 | /** | |
266 | * return a compact representation of the current alignment selection to pass | |
267 | * to an analysis function | |
268 | * | |
269 | * @param selectedOnly | |
270 | * boolean true to just return the selected view | |
271 | * @param markGroups | |
272 | * boolean true to annotate the alignment view with groups on the | |
273 | * alignment (and intersecting with selected region if selectedOnly | |
274 | * is true) | |
275 | * @return AlignmentView | |
276 | */ | |
277 | AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups); | |
278 | ||
279 | /** | |
280 | * This method returns the visible alignment as text, as seen on the GUI, ie | |
281 | * if columns are hidden they will not be returned in the result. Use this for | |
282 | * calculating trees, PCA, redundancy etc on views which contain hidden | |
283 | * columns. This method doesn't exclude hidden sequences from the output. | |
284 | * | |
285 | * @param selectedRegionOnly | |
286 | * - determines if only the selected region or entire alignment is | |
287 | * exported | |
288 | * @return String[] | |
289 | */ | |
290 | String[] getViewAsString(boolean selectedRegionOnly); | |
291 | ||
292 | /** | |
293 | * This method returns the visible alignment as text, as seen on the GUI, ie | |
294 | * if columns are hidden they will not be returned in the result. Use this for | |
295 | * calculating trees, PCA, redundancy etc on views which contain hidden | |
296 | * columns. | |
297 | * | |
298 | * @param selectedRegionOnly | |
299 | * - determines if only the selected region or entire alignment is | |
300 | * exported | |
301 | * @param isExportHiddenSeqs | |
302 | * - determines if hidden sequences would be exported or not. | |
303 | * | |
304 | * @return String[] | |
305 | */ | |
306 | String[] getViewAsString(boolean selectedRegionOnly, | |
307 | boolean isExportHiddenSeqs); | |
308 | ||
309 | void setSelectionGroup(SequenceGroup sg); | |
310 | ||
311 | char getGapCharacter(); | |
312 | ||
313 | void setColumnSelection(ColumnSelection cs); | |
314 | ||
315 | void setConservation(Conservation cons); | |
316 | ||
317 | /** | |
318 | * get a copy of the currently visible alignment annotation | |
319 | * | |
320 | * @param selectedOnly | |
321 | * if true - trim to selected regions on the alignment | |
322 | * @return an empty list or new alignment annotation objects shown only | |
323 | * visible columns trimmed to selected region only | |
324 | */ | |
325 | List<AlignmentAnnotation> getVisibleAlignmentAnnotation( | |
326 | boolean selectedOnly); | |
327 | ||
328 | FeaturesDisplayedI getFeaturesDisplayed(); | |
329 | ||
330 | String getSequenceSetId(); | |
331 | ||
332 | boolean areFeaturesDisplayed(); | |
333 | ||
334 | void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI); | |
335 | ||
336 | void alignmentChanged(AlignmentViewPanel ap); | |
337 | ||
338 | /** | |
339 | * @return the padGaps | |
340 | */ | |
341 | boolean isPadGaps(); | |
342 | ||
343 | /** | |
344 | * @param padGaps | |
345 | * the padGaps to set | |
346 | */ | |
347 | void setPadGaps(boolean padGaps); | |
348 | ||
349 | /** | |
350 | * return visible region boundaries within given column range | |
351 | * | |
352 | * @param min | |
353 | * first column (inclusive, from 0) | |
354 | * @param max | |
355 | * last column (exclusive) | |
356 | * @return int[][] range of {start,end} visible positions | |
357 | */ | |
358 | List<int[]> getVisibleRegionBoundaries(int min, int max); | |
359 | ||
360 | /** | |
361 | * This method returns an array of new SequenceI objects derived from the | |
362 | * whole alignment or just the current selection with start and end points | |
363 | * adjusted | |
364 | * | |
365 | * @note if you need references to the actual SequenceI objects in the | |
366 | * alignment or currently selected then use getSequenceSelection() | |
367 | * @return selection as new sequenceI objects | |
368 | */ | |
369 | SequenceI[] getSelectionAsNewSequence(); | |
370 | ||
371 | void invertColumnSelection(); | |
372 | ||
373 | /** | |
374 | * broadcast selection to any interested parties | |
375 | */ | |
376 | void sendSelection(); | |
377 | ||
378 | /** | |
379 | * calculate the row position for alignmentIndex if all hidden sequences were | |
380 | * shown | |
381 | * | |
382 | * @param alignmentIndex | |
383 | * @return adjusted row position | |
384 | */ | |
385 | int adjustForHiddenSeqs(int alignmentIndex); | |
386 | ||
387 | boolean hasHiddenRows(); | |
388 | ||
389 | /** | |
390 | * | |
391 | * @return a copy of this view's current display settings | |
392 | */ | |
393 | public ViewStyleI getViewStyle(); | |
394 | ||
395 | /** | |
396 | * update the view's display settings with the given style set | |
397 | * | |
398 | * @param settingsForView | |
399 | */ | |
400 | public void setViewStyle(ViewStyleI settingsForView); | |
401 | ||
402 | /** | |
403 | * Returns a viewport which holds the cDna for this (protein), or vice versa, | |
404 | * or null if none is set. | |
405 | * | |
406 | * @return | |
407 | */ | |
408 | AlignViewportI getCodingComplement(); | |
409 | ||
410 | /** | |
411 | * Sets the viewport which holds the cDna for this (protein), or vice versa. | |
412 | * Implementation should guarantee that the reciprocal relationship is always | |
413 | * set, i.e. each viewport is the complement of the other. | |
414 | */ | |
415 | void setCodingComplement(AlignViewportI sl); | |
416 | ||
417 | /** | |
418 | * Answers true if viewport hosts DNA/RNA, else false. | |
419 | * | |
420 | * @return | |
421 | */ | |
422 | boolean isNucleotide(); | |
423 | ||
424 | /** | |
425 | * Returns an id guaranteed to be unique for this viewport. | |
426 | * | |
427 | * @return | |
428 | */ | |
429 | String getViewId(); | |
430 | ||
431 | /** | |
432 | * Return true if view should scroll to show the highlighted region of a | |
433 | * sequence | |
434 | * | |
435 | * @return | |
436 | */ | |
437 | boolean isFollowHighlight(); | |
438 | ||
439 | /** | |
440 | * Set whether view should scroll to show the highlighted region of a sequence | |
441 | */ | |
442 | void setFollowHighlight(boolean b); | |
443 | ||
444 | /** | |
445 | * configure the feature renderer with predefined feature settings | |
446 | * | |
447 | * @param featureSettings | |
448 | */ | |
449 | public void applyFeaturesStyle(FeatureSettingsModelI featureSettings); | |
450 | ||
451 | /** | |
452 | * Apply the given feature settings on top of existing feature settings. | |
453 | */ | |
454 | public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings); | |
455 | ||
456 | /** | |
457 | * check if current selection group is defined on the view, or is simply a | |
458 | * temporary group. | |
459 | * | |
460 | * @return true if group is defined on the alignment | |
461 | */ | |
462 | boolean isSelectionDefinedGroup(); | |
463 | ||
464 | /** | |
465 | * | |
466 | * @return true if there are search results on the view | |
467 | */ | |
468 | boolean hasSearchResults(); | |
469 | ||
470 | /** | |
471 | * set the search results for the view | |
472 | * | |
473 | * @param results | |
474 | * - or null to clear current results | |
475 | */ | |
476 | void setSearchResults(SearchResultsI results); | |
477 | ||
478 | /** | |
479 | * get search results for this view (if any) | |
480 | * | |
481 | * @return search results or null | |
482 | */ | |
483 | SearchResultsI getSearchResults(); | |
484 | ||
485 | /** | |
486 | * Retrieve a ContactListI corresponding to column in an annotation row in an | |
487 | * alignment. | |
488 | * | |
489 | * @param _aa | |
490 | * - annotation with associated matrix data | |
491 | * @param column | |
492 | * - column in alignment where _aa is associated | |
493 | */ | |
494 | ContactListI getContactList(AlignmentAnnotation _aa, int column); | |
495 | ||
496 | /** | |
497 | * Updates view settings with the given font. You may need to call | |
498 | * AlignmentPanel.fontChanged to update the layout geometry. | |
499 | * | |
500 | * @param setGrid | |
501 | * when true, charWidth/height is set according to font metrics | |
502 | */ | |
503 | void setFont(Font newFont, boolean b); | |
504 | ||
505 | /** | |
506 | * Answers true if split screen protein and cDNA use the same font | |
507 | * | |
508 | * @return | |
509 | */ | |
510 | @Override | |
511 | boolean isProteinFontAsCdna(); | |
512 | ||
513 | /** | |
514 | * Set the flag for whether split screen protein and cDNA use the same font | |
515 | * | |
516 | * @return | |
517 | */ | |
518 | @Override | |
519 | void setProteinFontAsCdna(boolean b); | |
520 | ||
521 | TreeModel getCurrentTree(); | |
522 | ||
523 | void setCurrentTree(TreeModel tree); | |
524 | ||
525 | /** | |
526 | * Answers a data bean containing data for export as configured by the | |
527 | * supplied options | |
528 | * | |
529 | * @param options | |
530 | * @return | |
531 | */ | |
532 | AlignmentExportData getAlignExportData(AlignExportSettingsI options); | |
533 | ||
534 | /** | |
535 | * @param update | |
536 | * - set the flag for updating structures on next repaint | |
537 | */ | |
538 | void setUpdateStructures(boolean update); | |
539 | ||
540 | /** | |
541 | * | |
542 | * @return true if structure views will be updated on next refresh | |
543 | */ | |
544 | boolean isUpdateStructures(); | |
545 | ||
546 | /** | |
547 | * check if structure views need to be updated, and clear the flag afterwards. | |
548 | * | |
549 | * @return if an update is needed | |
550 | */ | |
551 | boolean needToUpdateStructureViews(); | |
552 | ||
553 | /** | |
554 | * Adds sequencegroup to the alignment in the view. Also adds a group to the | |
555 | * complement view if one is defined. | |
556 | * | |
557 | * @param sequenceGroup | |
558 | * - a group defined on sequences in the alignment held by the view | |
559 | */ | |
560 | void addSequenceGroup(SequenceGroup sequenceGroup); | |
561 | ||
562 | /** | |
563 | * Returns an interator over the [start, end] column positions of the visible | |
564 | * regions of the alignment | |
565 | * | |
566 | * @param selectedRegionOnly | |
567 | * if true, and the view has a selection region, then only the | |
568 | * intersection of visible columns with the selection region is | |
569 | * returned | |
570 | * @return | |
571 | */ | |
572 | Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly); | |
573 | ||
574 | /** | |
575 | * notify all concerned that the alignment data has changed and derived data | |
576 | * needs to be recalculated | |
577 | */ | |
578 | public void notifyAlignmentChanged(); | |
579 | ||
580 | /** | |
581 | * retrieve a matrix associated with the view's alignment's annotation | |
582 | * | |
583 | * @param alignmentAnnotation | |
584 | * @return contact matrix or NULL | |
585 | */ | |
586 | ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation); | |
587 | ||
588 | Map<String, ProfilesI> getSequenceSSConsensusHash(); | |
589 | ||
590 | List<String> getSecondaryStructureSources(); | |
591 | ||
592 | void setSecondaryStructureSources(List<String> secondaryStructureSources); | |
593 | ||
594 | Color getAnnotationColour(AlignmentAnnotation annot); | |
595 | ||
596 | void setAnnotationColour(AlignmentAnnotation annot, Color col); | |
597 | ||
598 | void updateAnnotationColours(); | |
599 | ||
600 | void clearAnnotationColours(); | |
601 | ||
602 | Map<AlignmentAnnotation, Color> getAnnotationColours(); | |
603 | ||
604 | void setAnnotationColours( | |
605 | Map<AlignmentAnnotation, Color> annotationColours); | |
606 | ||
607 | } |