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Alignment | 51 | 622 | 318 |
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.datamodel; | |
22 | ||
23 | import java.util.ArrayList; | |
24 | import java.util.Arrays; | |
25 | import java.util.BitSet; | |
26 | import java.util.Collection; | |
27 | import java.util.Collections; | |
28 | import java.util.Enumeration; | |
29 | import java.util.HashSet; | |
30 | import java.util.Hashtable; | |
31 | import java.util.Iterator; | |
32 | import java.util.List; | |
33 | import java.util.Map; | |
34 | import java.util.Set; | |
35 | import java.util.Vector; | |
36 | ||
37 | import jalview.analysis.AlignmentUtils; | |
38 | import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; | |
39 | import jalview.io.FastaFile; | |
40 | import jalview.util.Comparison; | |
41 | import jalview.util.LinkedIdentityHashSet; | |
42 | import jalview.util.MessageManager; | |
43 | ||
44 | /** | |
45 | * Data structure to hold and manipulate a multiple sequence alignment | |
46 | */ | |
47 | /** | |
48 | * @author JimP | |
49 | * | |
50 | */ | |
51 | public class Alignment implements AlignmentI, AutoCloseable | |
52 | { | |
53 | private Alignment dataset; | |
54 | ||
55 | private List<SequenceI> sequences; | |
56 | ||
57 | protected List<SequenceGroup> groups; | |
58 | ||
59 | protected char gapCharacter = '-'; | |
60 | ||
61 | private boolean nucleotide = true; | |
62 | ||
63 | public boolean hasRNAStructure = false; | |
64 | ||
65 | public AlignmentAnnotation[] annotations; | |
66 | ||
67 | HiddenSequences hiddenSequences; | |
68 | ||
69 | HiddenColumns hiddenCols; | |
70 | ||
71 | public Hashtable alignmentProperties; | |
72 | ||
73 | private List<AlignedCodonFrame> codonFrameList; | |
74 | ||
75 | 1766 | private void initAlignment(SequenceI[] seqs) |
76 | { | |
77 | 1766 | groups = Collections.synchronizedList(new ArrayList<SequenceGroup>()); |
78 | 1766 | hiddenSequences = new HiddenSequences(this); |
79 | 1766 | hiddenCols = new HiddenColumns(); |
80 | 1766 | codonFrameList = new ArrayList<>(); |
81 | ||
82 | 1766 | nucleotide = Comparison.isNucleotide(seqs); |
83 | ||
84 | 1766 | sequences = Collections.synchronizedList(new ArrayList<SequenceI>()); |
85 | ||
86 | 34303 | for (int i = 0; i < seqs.length; i++) |
87 | { | |
88 | 32537 | sequences.add(seqs[i]); |
89 | } | |
90 | ||
91 | } | |
92 | ||
93 | /** | |
94 | * Make a 'copy' alignment - sequences have new copies of features and | |
95 | * annotations, but share the original dataset sequences. | |
96 | */ | |
97 | 4 | public Alignment(AlignmentI al) |
98 | { | |
99 | 4 | SequenceI[] seqs = al.getSequencesArray(); |
100 | 19 | for (int i = 0; i < seqs.length; i++) |
101 | { | |
102 | 15 | seqs[i] = new Sequence(seqs[i]); |
103 | } | |
104 | ||
105 | 4 | initAlignment(seqs); |
106 | ||
107 | /* | |
108 | * Share the same dataset sequence mappings (if any). | |
109 | */ | |
110 | 4 | if (dataset == null && al.getDataset() == null) |
111 | { | |
112 | 1 | this.setCodonFrames(al.getCodonFrames()); |
113 | } | |
114 | } | |
115 | ||
116 | /** | |
117 | * Make an alignment from an array of Sequences. | |
118 | * | |
119 | * @param sequences | |
120 | */ | |
121 | 1760 | public Alignment(SequenceI[] seqs) |
122 | { | |
123 | 1760 | initAlignment(seqs); |
124 | } | |
125 | ||
126 | /** | |
127 | * Make a new alignment from an array of SeqCigars | |
128 | * | |
129 | * @param seqs | |
130 | * SeqCigar[] | |
131 | */ | |
132 | 2 | public Alignment(SeqCigar[] alseqs) |
133 | { | |
134 | 2 | SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, |
135 | gapCharacter, new HiddenColumns(), null); | |
136 | 2 | initAlignment(seqs); |
137 | } | |
138 | ||
139 | /** | |
140 | * Make a new alignment from an CigarArray JBPNote - can only do this when | |
141 | * compactAlignment does not contain hidden regions. JBPNote - must also check | |
142 | * that compactAlignment resolves to a set of SeqCigars - or construct them | |
143 | * appropriately. | |
144 | * | |
145 | * @param compactAlignment | |
146 | * CigarArray | |
147 | */ | |
148 | 0 | public static AlignmentI createAlignment(CigarArray compactAlignment) |
149 | { | |
150 | 0 | throw new Error(MessageManager |
151 | .getString("error.alignment_cigararray_not_implemented")); | |
152 | // this(compactAlignment.refCigars); | |
153 | } | |
154 | ||
155 | 70320 | @Override |
156 | public List<SequenceI> getSequences() | |
157 | { | |
158 | 70320 | return sequences; |
159 | } | |
160 | ||
161 | 13 | @Override |
162 | public List<SequenceI> getSequences( | |
163 | Map<SequenceI, SequenceCollectionI> hiddenReps) | |
164 | { | |
165 | // TODO: in jalview 2.8 we don't do anything with hiddenreps - fix design to | |
166 | // work on this. | |
167 | 13 | return sequences; |
168 | } | |
169 | ||
170 | 31823 | @Override |
171 | public SequenceI[] getSequencesArray() | |
172 | { | |
173 | 31823 | if (sequences == null) |
174 | { | |
175 | 0 | return null; |
176 | } | |
177 | 31823 | synchronized (sequences) |
178 | { | |
179 | 31823 | return sequences.toArray(new SequenceI[sequences.size()]); |
180 | } | |
181 | } | |
182 | ||
183 | /** | |
184 | * Returns a map of lists of sequences keyed by sequence name. | |
185 | * | |
186 | * @return | |
187 | */ | |
188 | 0 | @Override |
189 | public Map<String, List<SequenceI>> getSequencesByName() | |
190 | { | |
191 | 0 | return AlignmentUtils.getSequencesByName(this); |
192 | } | |
193 | ||
194 | 1037146 | @Override |
195 | public SequenceI getSequenceAt(int i) | |
196 | { | |
197 | 1037153 | synchronized (sequences) |
198 | { | |
199 | ||
200 | 1037147 | if (i > -1 && i < sequences.size()) |
201 | { | |
202 | 1037141 | return sequences.get(i); |
203 | } | |
204 | } | |
205 | ||
206 | 7 | return null; |
207 | } | |
208 | ||
209 | 2580 | @Override |
210 | public SequenceI getSequenceAtAbsoluteIndex(int i) | |
211 | { | |
212 | 2580 | SequenceI seq = null; |
213 | 2580 | if (getHiddenSequences().getSize() > 0) |
214 | { | |
215 | 1716 | seq = getHiddenSequences().getHiddenSequence(i); |
216 | 1716 | if (seq == null) |
217 | { | |
218 | // didn't find the sequence in the hidden sequences, get it from the | |
219 | // alignment | |
220 | 1716 | int index = getHiddenSequences().findIndexWithoutHiddenSeqs(i); |
221 | 1716 | seq = getSequenceAt(index); |
222 | } | |
223 | } | |
224 | else | |
225 | { | |
226 | 864 | seq = getSequenceAt(i); |
227 | } | |
228 | 2580 | return seq; |
229 | } | |
230 | ||
231 | /** | |
232 | * Adds a sequence to the alignment. Recalculates maxLength and size. Note | |
233 | * this currently does not recalculate whether or not the alignment is | |
234 | * nucleotide, so mixed alignments may have undefined behaviour. | |
235 | * | |
236 | * @param snew | |
237 | */ | |
238 | 251 | @Override |
239 | public void addSequence(SequenceI snew) | |
240 | { | |
241 | 251 | if (dataset != null) |
242 | { | |
243 | ||
244 | // maintain dataset integrity | |
245 | 68 | SequenceI dsseq = snew.getDatasetSequence(); |
246 | 68 | if (dsseq == null) |
247 | { | |
248 | // derive new sequence | |
249 | 5 | SequenceI adding = snew.deriveSequence(); |
250 | 5 | snew = adding; |
251 | 5 | dsseq = snew.getDatasetSequence(); |
252 | } | |
253 | 68 | if (getDataset().findIndex(dsseq) == -1) |
254 | { | |
255 | 65 | getDataset().addSequence(dsseq); |
256 | } | |
257 | ||
258 | } | |
259 | 251 | if (sequences == null) |
260 | { | |
261 | 0 | initAlignment(new SequenceI[] { snew }); |
262 | } | |
263 | else | |
264 | { | |
265 | 251 | synchronized (sequences) |
266 | { | |
267 | 251 | sequences.add(snew); |
268 | } | |
269 | } | |
270 | 251 | if (hiddenSequences != null) |
271 | { | |
272 | 251 | hiddenSequences.adjustHeightSequenceAdded(); |
273 | } | |
274 | } | |
275 | ||
276 | 50 | @Override |
277 | public SequenceI replaceSequenceAt(int i, SequenceI snew) | |
278 | { | |
279 | 50 | synchronized (sequences) |
280 | { | |
281 | 50 | if (sequences.size() > i) |
282 | { | |
283 | 50 | return sequences.set(i, snew); |
284 | ||
285 | } | |
286 | else | |
287 | { | |
288 | 0 | sequences.add(snew); |
289 | 0 | hiddenSequences.adjustHeightSequenceAdded(); |
290 | } | |
291 | 0 | return null; |
292 | } | |
293 | } | |
294 | ||
295 | /** | |
296 | * DOCUMENT ME! | |
297 | * | |
298 | * @return DOCUMENT ME! | |
299 | */ | |
300 | 9412 | @Override |
301 | public List<SequenceGroup> getGroups() | |
302 | { | |
303 | 9412 | return groups; |
304 | } | |
305 | ||
306 | 0 | @Override |
307 | public void close() | |
308 | { | |
309 | 0 | if (getDataset() != null) |
310 | { | |
311 | 0 | try |
312 | { | |
313 | 0 | getDataset().removeAlignmentRef(); |
314 | } catch (Throwable e) | |
315 | { | |
316 | 0 | e.printStackTrace(); |
317 | } | |
318 | } | |
319 | ||
320 | 0 | nullReferences(); |
321 | } | |
322 | ||
323 | /** | |
324 | * Defensively nulls out references in case this object is not garbage | |
325 | * collected | |
326 | */ | |
327 | 0 | void nullReferences() |
328 | { | |
329 | 0 | dataset = null; |
330 | 0 | sequences = null; |
331 | 0 | groups = null; |
332 | 0 | annotations = null; |
333 | 0 | hiddenSequences = null; |
334 | } | |
335 | ||
336 | /** | |
337 | * decrement the alignmentRefs counter by one and null references if it goes | |
338 | * to zero. | |
339 | * | |
340 | * @throws Throwable | |
341 | */ | |
342 | 0 | private void removeAlignmentRef() throws Throwable |
343 | { | |
344 | 0 | if (--alignmentRefs == 0) |
345 | { | |
346 | 0 | nullReferences(); |
347 | } | |
348 | } | |
349 | ||
350 | 70 | @Override |
351 | public void deleteSequence(SequenceI s) | |
352 | { | |
353 | 70 | synchronized (sequences) |
354 | { | |
355 | 70 | deleteSequence(findIndex(s)); |
356 | } | |
357 | } | |
358 | ||
359 | 75 | @Override |
360 | public void deleteSequence(int i) | |
361 | { | |
362 | 75 | synchronized (sequences) |
363 | { | |
364 | 75 | if (i > -1 && i < getHeight()) |
365 | { | |
366 | 73 | sequences.remove(i); |
367 | 73 | hiddenSequences.adjustHeightSequenceDeleted(i); |
368 | } | |
369 | } | |
370 | } | |
371 | ||
372 | 530 | @Override |
373 | public void deleteHiddenSequence(int i) | |
374 | { | |
375 | 530 | synchronized (sequences) |
376 | { | |
377 | 530 | if (i > -1 && i < getHeight()) |
378 | { | |
379 | 530 | sequences.remove(i); |
380 | } | |
381 | } | |
382 | } | |
383 | ||
384 | /* | |
385 | * (non-Javadoc) | |
386 | * | |
387 | * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI) | |
388 | */ | |
389 | 19 | @Override |
390 | public SequenceGroup findGroup(SequenceI seq, int position) | |
391 | { | |
392 | 19 | synchronized (groups) |
393 | { | |
394 | 19 | for (SequenceGroup sg : groups) |
395 | { | |
396 | 23 | if (sg.getSequences(null).contains(seq)) |
397 | { | |
398 | 16 | if (position >= sg.getStartRes() && position <= sg.getEndRes()) |
399 | { | |
400 | 10 | return sg; |
401 | } | |
402 | } | |
403 | } | |
404 | } | |
405 | 9 | return null; |
406 | } | |
407 | ||
408 | /* | |
409 | * (non-Javadoc) | |
410 | * | |
411 | * @see | |
412 | * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI) | |
413 | */ | |
414 | 53356 | @Override |
415 | public SequenceGroup[] findAllGroups(SequenceI s) | |
416 | { | |
417 | 53356 | ArrayList<SequenceGroup> temp = new ArrayList<>(); |
418 | ||
419 | 53356 | synchronized (groups) |
420 | { | |
421 | 53356 | int gSize = groups.size(); |
422 | 62675 | for (int i = 0; i < gSize; i++) |
423 | { | |
424 | 9319 | SequenceGroup sg = groups.get(i); |
425 | 9319 | if (sg == null || sg.getSequences() == null) |
426 | { | |
427 | 0 | this.deleteGroup(sg); |
428 | 0 | gSize--; |
429 | 0 | continue; |
430 | } | |
431 | ||
432 | 9319 | if (sg.getSequences().contains(s)) |
433 | { | |
434 | 6625 | temp.add(sg); |
435 | } | |
436 | } | |
437 | } | |
438 | 53356 | SequenceGroup[] ret = new SequenceGroup[temp.size()]; |
439 | 53356 | return temp.toArray(ret); |
440 | } | |
441 | ||
442 | /** */ | |
443 | 109 | @Override |
444 | public void addGroup(SequenceGroup sg) | |
445 | { | |
446 | 109 | synchronized (groups) |
447 | { | |
448 | 109 | if (!groups.contains(sg)) |
449 | { | |
450 | 100 | if (hiddenSequences.getSize() > 0) |
451 | { | |
452 | 0 | int i, iSize = sg.getSize(); |
453 | 0 | for (i = 0; i < iSize; i++) |
454 | { | |
455 | 0 | if (!sequences.contains(sg.getSequenceAt(i))) |
456 | { | |
457 | 0 | sg.deleteSequence(sg.getSequenceAt(i), false); |
458 | 0 | iSize--; |
459 | 0 | i--; |
460 | } | |
461 | } | |
462 | ||
463 | 0 | if (sg.getSize() < 1) |
464 | { | |
465 | 0 | return; |
466 | } | |
467 | } | |
468 | 100 | sg.setContext(this, true); |
469 | 100 | groups.add(sg); |
470 | } | |
471 | } | |
472 | } | |
473 | ||
474 | /** | |
475 | * remove any annotation that references gp | |
476 | * | |
477 | * @param gp | |
478 | * (if null, removes all group associated annotation) | |
479 | */ | |
480 | 0 | private void removeAnnotationForGroup(SequenceGroup gp) |
481 | { | |
482 | 0 | if (annotations == null || annotations.length == 0) |
483 | { | |
484 | 0 | return; |
485 | } | |
486 | // remove annotation very quickly | |
487 | 0 | AlignmentAnnotation[] t, |
488 | todelete = new AlignmentAnnotation[annotations.length], | |
489 | tokeep = new AlignmentAnnotation[annotations.length]; | |
490 | 0 | int i, p, k; |
491 | 0 | if (gp == null) |
492 | { | |
493 | 0 | for (i = 0, p = 0, k = 0; i < annotations.length; i++) |
494 | { | |
495 | 0 | if (annotations[i].groupRef != null) |
496 | { | |
497 | 0 | todelete[p++] = annotations[i]; |
498 | } | |
499 | else | |
500 | { | |
501 | 0 | tokeep[k++] = annotations[i]; |
502 | } | |
503 | } | |
504 | } | |
505 | else | |
506 | { | |
507 | 0 | for (i = 0, p = 0, k = 0; i < annotations.length; i++) |
508 | { | |
509 | 0 | if (annotations[i].groupRef == gp) |
510 | { | |
511 | 0 | todelete[p++] = annotations[i]; |
512 | } | |
513 | else | |
514 | { | |
515 | 0 | tokeep[k++] = annotations[i]; |
516 | } | |
517 | } | |
518 | } | |
519 | 0 | if (p > 0) |
520 | { | |
521 | // clear out the group associated annotation. | |
522 | 0 | for (i = 0; i < p; i++) |
523 | { | |
524 | 0 | unhookAnnotation(todelete[i]); |
525 | 0 | todelete[i] = null; |
526 | } | |
527 | 0 | t = new AlignmentAnnotation[k]; |
528 | 0 | for (i = 0; i < k; i++) |
529 | { | |
530 | 0 | t[i] = tokeep[i]; |
531 | } | |
532 | 0 | annotations = t; |
533 | } | |
534 | } | |
535 | ||
536 | 0 | @Override |
537 | public void deleteAllGroups() | |
538 | { | |
539 | 0 | synchronized (groups) |
540 | { | |
541 | 0 | if (annotations != null) |
542 | { | |
543 | 0 | removeAnnotationForGroup(null); |
544 | } | |
545 | 0 | for (SequenceGroup sg : groups) |
546 | { | |
547 | 0 | sg.setContext(null, false); |
548 | } | |
549 | 0 | groups.clear(); |
550 | } | |
551 | } | |
552 | ||
553 | /** */ | |
554 | 0 | @Override |
555 | public void deleteGroup(SequenceGroup g) | |
556 | { | |
557 | 0 | synchronized (groups) |
558 | { | |
559 | 0 | if (groups.contains(g)) |
560 | { | |
561 | 0 | removeAnnotationForGroup(g); |
562 | 0 | groups.remove(g); |
563 | 0 | g.setContext(null, false); |
564 | } | |
565 | } | |
566 | } | |
567 | ||
568 | /** */ | |
569 | 309 | @Override |
570 | public SequenceI findName(String name) | |
571 | { | |
572 | 309 | return findName(name, false); |
573 | } | |
574 | ||
575 | /* | |
576 | * (non-Javadoc) | |
577 | * | |
578 | * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean) | |
579 | */ | |
580 | 1415 | @Override |
581 | public SequenceI findName(String token, boolean b) | |
582 | { | |
583 | 1415 | return findName(null, token, b); |
584 | } | |
585 | ||
586 | /* | |
587 | * (non-Javadoc) | |
588 | * | |
589 | * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String, | |
590 | * boolean) | |
591 | */ | |
592 | 2154 | @Override |
593 | public SequenceI findName(SequenceI startAfter, String token, boolean b) | |
594 | { | |
595 | ||
596 | 2154 | int i = 0; |
597 | 2154 | SequenceI sq = null; |
598 | 2154 | String sqname = null; |
599 | 2154 | int nseq = sequences.size(); |
600 | 2154 | if (startAfter != null) |
601 | { | |
602 | // try to find the sequence in the alignment | |
603 | 739 | boolean matched = false; |
604 | 6502 | while (i < nseq) |
605 | { | |
606 | 6487 | if (getSequenceAt(i++) == startAfter) |
607 | { | |
608 | 724 | matched = true; |
609 | 724 | break; |
610 | } | |
611 | } | |
612 | 739 | if (!matched) |
613 | { | |
614 | 15 | i = 0; |
615 | } | |
616 | } | |
617 | 17964 | while (i < nseq) |
618 | { | |
619 | 17192 | sq = getSequenceAt(i); |
620 | 17192 | sqname = sq.getName(); |
621 | 17192 | if (sqname.equals(token) // exact match |
622 | || (b && // allow imperfect matches - case varies | |
623 | (sqname.equalsIgnoreCase(token)))) | |
624 | { | |
625 | 1382 | return getSequenceAt(i); |
626 | } | |
627 | ||
628 | 15810 | i++; |
629 | } | |
630 | ||
631 | 772 | return null; |
632 | } | |
633 | ||
634 | 22 | @Override |
635 | public SequenceI[] findSequenceMatch(String name) | |
636 | { | |
637 | 22 | Vector matches = new Vector(); |
638 | 22 | int i = 0; |
639 | ||
640 | 493 | while (i < sequences.size()) |
641 | { | |
642 | 471 | if (getSequenceAt(i).getName().equals(name)) |
643 | { | |
644 | 5 | matches.addElement(getSequenceAt(i)); |
645 | } | |
646 | 471 | i++; |
647 | } | |
648 | ||
649 | 22 | SequenceI[] result = new SequenceI[matches.size()]; |
650 | 27 | for (i = 0; i < result.length; i++) |
651 | { | |
652 | 5 | result[i] = (SequenceI) matches.elementAt(i); |
653 | } | |
654 | ||
655 | 22 | return result; |
656 | ||
657 | } | |
658 | ||
659 | /* | |
660 | * (non-Javadoc) | |
661 | * | |
662 | * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI) | |
663 | */ | |
664 | 2431 | @Override |
665 | public int findIndex(SequenceI s) | |
666 | { | |
667 | 2431 | int i = 0; |
668 | ||
669 | 74695 | while (i < sequences.size()) |
670 | { | |
671 | 74602 | if (s == getSequenceAt(i)) |
672 | { | |
673 | 2338 | return i; |
674 | } | |
675 | ||
676 | 72264 | i++; |
677 | } | |
678 | ||
679 | 93 | return -1; |
680 | } | |
681 | ||
682 | /* | |
683 | * (non-Javadoc) | |
684 | * | |
685 | * @see | |
686 | * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults) | |
687 | */ | |
688 | 8 | @Override |
689 | public int findIndex(SearchResultsI results) | |
690 | { | |
691 | 8 | int i = 0; |
692 | ||
693 | 55 | while (i < sequences.size()) |
694 | { | |
695 | 55 | if (results.involvesSequence(getSequenceAt(i))) |
696 | { | |
697 | 8 | return i; |
698 | } | |
699 | 47 | i++; |
700 | } | |
701 | 0 | return -1; |
702 | } | |
703 | ||
704 | 59634 | @Override |
705 | public int getHeight() | |
706 | { | |
707 | 59634 | return sequences.size(); |
708 | } | |
709 | ||
710 | 10 | @Override |
711 | public int getAbsoluteHeight() | |
712 | { | |
713 | 10 | return sequences.size() + getHiddenSequences().getSize(); |
714 | } | |
715 | ||
716 | 17871 | @Override |
717 | public int getWidth() | |
718 | { | |
719 | 17871 | int maxLength = -1; |
720 | ||
721 | 687258 | for (int i = 0; i < sequences.size(); i++) |
722 | { | |
723 | 669390 | maxLength = Math.max(maxLength, getSequenceAt(i).getLength()); |
724 | } | |
725 | 17871 | return maxLength; |
726 | } | |
727 | ||
728 | 8441 | @Override |
729 | public int getVisibleWidth() | |
730 | { | |
731 | 8441 | int w = getWidth(); |
732 | 8441 | if (hiddenCols != null) |
733 | { | |
734 | 8441 | w -= hiddenCols.getSize(); |
735 | } | |
736 | 8441 | return w; |
737 | } | |
738 | ||
739 | /** | |
740 | * DOCUMENT ME! | |
741 | * | |
742 | * @param gc | |
743 | * DOCUMENT ME! | |
744 | */ | |
745 | 539 | @Override |
746 | public void setGapCharacter(char gc) | |
747 | { | |
748 | 539 | gapCharacter = gc; |
749 | 539 | synchronized (sequences) |
750 | { | |
751 | 539 | for (SequenceI seq : sequences) |
752 | { | |
753 | 4455 | seq.setSequence(seq.getSequenceAsString().replace('.', gc) |
754 | .replace('-', gc).replace(' ', gc)); | |
755 | } | |
756 | } | |
757 | } | |
758 | ||
759 | /** | |
760 | * DOCUMENT ME! | |
761 | * | |
762 | * @return DOCUMENT ME! | |
763 | */ | |
764 | 431 | @Override |
765 | public char getGapCharacter() | |
766 | { | |
767 | 431 | return gapCharacter; |
768 | } | |
769 | ||
770 | /* | |
771 | * (non-Javadoc) | |
772 | * | |
773 | * @see jalview.datamodel.AlignmentI#isAligned() | |
774 | */ | |
775 | 0 | @Override |
776 | public boolean isAligned() | |
777 | { | |
778 | 0 | return isAligned(false); |
779 | } | |
780 | ||
781 | /* | |
782 | * (non-Javadoc) | |
783 | * | |
784 | * @see jalview.datamodel.AlignmentI#isAligned(boolean) | |
785 | */ | |
786 | 0 | @Override |
787 | public boolean isAligned(boolean includeHidden) | |
788 | { | |
789 | 0 | int width = getWidth(); |
790 | 0 | if (hiddenSequences == null || hiddenSequences.getSize() == 0) |
791 | { | |
792 | 0 | includeHidden = true; // no hidden sequences to check against. |
793 | } | |
794 | 0 | for (int i = 0; i < sequences.size(); i++) |
795 | { | |
796 | 0 | if (includeHidden || !hiddenSequences.isHidden(getSequenceAt(i))) |
797 | { | |
798 | 0 | if (getSequenceAt(i).getLength() != width) |
799 | { | |
800 | 0 | return false; |
801 | } | |
802 | } | |
803 | } | |
804 | ||
805 | 0 | return true; |
806 | } | |
807 | ||
808 | 0 | @Override |
809 | public boolean isHidden(int alignmentIndex) | |
810 | { | |
811 | 0 | return (getHiddenSequences().getHiddenSequence(alignmentIndex) != null); |
812 | } | |
813 | ||
814 | /** | |
815 | * Delete all annotations, including auto-calculated if the flag is set true. | |
816 | * Returns true if at least one annotation was deleted, else false. | |
817 | * | |
818 | * @param includingAutoCalculated | |
819 | * @return | |
820 | */ | |
821 | 2 | @Override |
822 | public boolean deleteAllAnnotations(boolean includingAutoCalculated) | |
823 | { | |
824 | 2 | boolean result = false; |
825 | 2 | for (AlignmentAnnotation alan : getAlignmentAnnotation()) |
826 | { | |
827 | 8 | if (!alan.autoCalculated || includingAutoCalculated) |
828 | { | |
829 | 7 | deleteAnnotation(alan); |
830 | 7 | result = true; |
831 | } | |
832 | } | |
833 | 2 | return result; |
834 | } | |
835 | ||
836 | /* | |
837 | * (non-Javadoc) | |
838 | * | |
839 | * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel. | |
840 | * AlignmentAnnotation) | |
841 | */ | |
842 | 7 | @Override |
843 | public boolean deleteAnnotation(AlignmentAnnotation aa) | |
844 | { | |
845 | 7 | return deleteAnnotation(aa, true); |
846 | } | |
847 | ||
848 | 233 | @Override |
849 | public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook) | |
850 | { | |
851 | 233 | int aSize = 1; |
852 | ||
853 | 233 | if (annotations != null) |
854 | { | |
855 | 233 | aSize = annotations.length; |
856 | } | |
857 | ||
858 | 233 | if (aSize < 1) |
859 | { | |
860 | 0 | return false; |
861 | } | |
862 | ||
863 | 233 | AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1]; |
864 | ||
865 | 233 | boolean swap = false; |
866 | 233 | int tIndex = 0; |
867 | ||
868 | 1500 | for (int i = 0; i < aSize; i++) |
869 | { | |
870 | 1267 | if (annotations[i] == aa) |
871 | { | |
872 | 233 | swap = true; |
873 | 233 | continue; |
874 | } | |
875 | 1034 | if (tIndex < temp.length) |
876 | { | |
877 | 1034 | temp[tIndex++] = annotations[i]; |
878 | } | |
879 | } | |
880 | ||
881 | 233 | if (swap) |
882 | { | |
883 | 233 | annotations = temp; |
884 | 233 | if (unhook) |
885 | { | |
886 | 7 | unhookAnnotation(aa); |
887 | } | |
888 | } | |
889 | 233 | return swap; |
890 | } | |
891 | ||
892 | /** | |
893 | * remove any object references associated with this annotation | |
894 | * | |
895 | * @param aa | |
896 | */ | |
897 | 7 | private void unhookAnnotation(AlignmentAnnotation aa) |
898 | { | |
899 | 7 | if (aa.sequenceRef != null) |
900 | { | |
901 | 6 | aa.sequenceRef.removeAlignmentAnnotation(aa); |
902 | } | |
903 | 7 | if (aa.groupRef != null) |
904 | { | |
905 | // probably need to do more here in the future (post 2.5.0) | |
906 | 0 | aa.groupRef = null; |
907 | } | |
908 | } | |
909 | ||
910 | /* | |
911 | * (non-Javadoc) | |
912 | * | |
913 | * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel. | |
914 | * AlignmentAnnotation) | |
915 | */ | |
916 | 3154 | @Override |
917 | public void addAnnotation(AlignmentAnnotation aa) | |
918 | { | |
919 | 3153 | addAnnotation(aa, -1); |
920 | } | |
921 | ||
922 | /* | |
923 | * (non-Javadoc) | |
924 | * | |
925 | * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel. | |
926 | * AlignmentAnnotation, int) | |
927 | */ | |
928 | 3404 | @Override |
929 | public void addAnnotation(AlignmentAnnotation aa, int pos) | |
930 | { | |
931 | 3403 | if (aa.getRNAStruc() != null) |
932 | { | |
933 | 419 | hasRNAStructure = true; |
934 | } | |
935 | ||
936 | 3404 | int aSize = 1; |
937 | 3404 | if (annotations != null) |
938 | { | |
939 | 2769 | aSize = annotations.length + 1; |
940 | } | |
941 | ||
942 | 3404 | AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize]; |
943 | 3404 | int i = 0; |
944 | 3404 | if (pos == -1 || pos >= aSize) |
945 | { | |
946 | 3154 | temp[aSize - 1] = aa; |
947 | } | |
948 | else | |
949 | { | |
950 | 250 | temp[pos] = aa; |
951 | } | |
952 | 3404 | if (aSize > 1) |
953 | { | |
954 | 2749 | int p = 0; |
955 | 23970 | for (i = 0; i < (aSize - 1); i++, p++) |
956 | { | |
957 | 21222 | if (p == pos) |
958 | { | |
959 | 91 | p++; |
960 | } | |
961 | 21222 | if (p < temp.length) |
962 | { | |
963 | 21222 | temp[p] = annotations[i]; |
964 | } | |
965 | } | |
966 | } | |
967 | ||
968 | 3404 | annotations = temp; |
969 | } | |
970 | ||
971 | 210 | @Override |
972 | public void setAnnotationIndex(AlignmentAnnotation aa, int index) | |
973 | { | |
974 | 210 | if (aa == null || annotations == null || annotations.length - 1 < index) |
975 | { | |
976 | 0 | return; |
977 | } | |
978 | ||
979 | 210 | int aSize = annotations.length; |
980 | 210 | AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize]; |
981 | ||
982 | 210 | temp[index] = aa; |
983 | ||
984 | 3251 | for (int i = 0; i < aSize; i++) |
985 | { | |
986 | 3041 | if (i == index) |
987 | { | |
988 | 210 | continue; |
989 | } | |
990 | ||
991 | 2831 | if (i < index) |
992 | { | |
993 | 2663 | temp[i] = annotations[i]; |
994 | } | |
995 | else | |
996 | { | |
997 | 168 | temp[i] = annotations[i - 1]; |
998 | } | |
999 | } | |
1000 | ||
1001 | 210 | annotations = temp; |
1002 | } | |
1003 | ||
1004 | 48334 | @Override |
1005 | /** | |
1006 | * returns all annotation on the alignment | |
1007 | */ | |
1008 | public AlignmentAnnotation[] getAlignmentAnnotation() | |
1009 | { | |
1010 | 48335 | return annotations; |
1011 | } | |
1012 | ||
1013 | 16616 | @Override |
1014 | public boolean isNucleotide() | |
1015 | { | |
1016 | 16616 | return nucleotide; |
1017 | } | |
1018 | ||
1019 | 978 | @Override |
1020 | public boolean hasRNAStructure() | |
1021 | { | |
1022 | // TODO can it happen that structure is removed from alignment? | |
1023 | 978 | return hasRNAStructure; |
1024 | } | |
1025 | ||
1026 | 643 | @Override |
1027 | public void setDataset(AlignmentI data) | |
1028 | { | |
1029 | 643 | if (dataset == null && data == null) |
1030 | { | |
1031 | 562 | createDatasetAlignment(); |
1032 | } | |
1033 | 81 | else if (dataset == null && data != null) |
1034 | { | |
1035 | 66 | if (data == this) |
1036 | { | |
1037 | 1 | throw new IllegalArgumentException("Circular dataset reference"); |
1038 | } | |
1039 | 65 | if (!(data instanceof Alignment)) |
1040 | { | |
1041 | 0 | throw new Error( |
1042 | "Implementation Error: jalview.datamodel.Alignment does not yet support other implementations of AlignmentI as its dataset reference"); | |
1043 | } | |
1044 | 65 | dataset = (Alignment) data; |
1045 | 846 | for (int i = 0; i < getHeight(); i++) |
1046 | { | |
1047 | 781 | SequenceI currentSeq = getSequenceAt(i); |
1048 | 781 | SequenceI dsq = currentSeq.getDatasetSequence(); |
1049 | 781 | if (dsq == null) |
1050 | { | |
1051 | 0 | dsq = currentSeq.createDatasetSequence(); |
1052 | 0 | dataset.addSequence(dsq); |
1053 | } | |
1054 | else | |
1055 | { | |
1056 | 781 | while (dsq.getDatasetSequence() != null) |
1057 | { | |
1058 | 0 | dsq = dsq.getDatasetSequence(); |
1059 | } | |
1060 | 781 | if (dataset.findIndex(dsq) == -1) |
1061 | { | |
1062 | 0 | dataset.addSequence(dsq); |
1063 | } | |
1064 | } | |
1065 | } | |
1066 | } | |
1067 | 642 | dataset.addAlignmentRef(); |
1068 | } | |
1069 | ||
1070 | /** | |
1071 | * add dataset sequences to seq for currentSeq and any sequences it references | |
1072 | */ | |
1073 | 3991 | private void resolveAndAddDatasetSeq(SequenceI currentSeq, |
1074 | Set<SequenceI> seqs, boolean createDatasetSequence) | |
1075 | { | |
1076 | 3991 | SequenceI alignedSeq = currentSeq; |
1077 | 3991 | if (currentSeq.getDatasetSequence() != null) |
1078 | { | |
1079 | 822 | currentSeq = currentSeq.getDatasetSequence(); |
1080 | } | |
1081 | else | |
1082 | { | |
1083 | 3169 | if (createDatasetSequence) |
1084 | { | |
1085 | 3169 | currentSeq = currentSeq.createDatasetSequence(); |
1086 | } | |
1087 | } | |
1088 | ||
1089 | 3991 | List<SequenceI> toProcess = new ArrayList<>(); |
1090 | 3991 | toProcess.add(currentSeq); |
1091 | 7988 | while (toProcess.size() > 0) |
1092 | { | |
1093 | // use a queue ? | |
1094 | 3997 | SequenceI curDs = toProcess.remove(0); |
1095 | ||
1096 | 3997 | if (!seqs.add(curDs)) |
1097 | { | |
1098 | 109 | continue; |
1099 | } | |
1100 | // iterate over database references, making sure we add forward referenced | |
1101 | // sequences | |
1102 | 3888 | if (curDs.getDBRefs() != null) |
1103 | { | |
1104 | 569 | for (DBRefEntry dbr : curDs.getDBRefs()) |
1105 | { | |
1106 | 772 | if (dbr.getMap() != null && dbr.getMap().getTo() != null) |
1107 | { | |
1108 | 6 | if (dbr.getMap().getTo() == alignedSeq) |
1109 | { | |
1110 | /* | |
1111 | * update mapping to be to the newly created dataset sequence | |
1112 | */ | |
1113 | 2 | dbr.getMap().setTo(currentSeq); |
1114 | } | |
1115 | 6 | if (dbr.getMap().getTo().getDatasetSequence() != null) |
1116 | { | |
1117 | 0 | throw new Error("Implementation error: Map.getTo() for dbref " |
1118 | + dbr + " from " + curDs.getName() | |
1119 | + " is not a dataset sequence."); | |
1120 | } | |
1121 | // we recurse to add all forward references to dataset sequences via | |
1122 | // DBRefs/etc | |
1123 | 6 | toProcess.add(dbr.getMap().getTo()); |
1124 | } | |
1125 | } | |
1126 | } | |
1127 | } | |
1128 | } | |
1129 | ||
1130 | /** | |
1131 | * Creates a new dataset for this alignment. Can only be done once - if | |
1132 | * dataset is not null this will not be performed. | |
1133 | */ | |
1134 | 577 | public void createDatasetAlignment() |
1135 | { | |
1136 | 577 | if (dataset != null) |
1137 | { | |
1138 | 0 | return; |
1139 | } | |
1140 | // try to avoid using SequenceI.equals at this stage, it will be expensive | |
1141 | 577 | Set<SequenceI> seqs = new LinkedIdentityHashSet<>(); |
1142 | ||
1143 | 4568 | for (int i = 0; i < getHeight(); i++) |
1144 | { | |
1145 | 3991 | SequenceI currentSeq = getSequenceAt(i); |
1146 | 3991 | resolveAndAddDatasetSeq(currentSeq, seqs, true); |
1147 | } | |
1148 | ||
1149 | // verify all mappings are in dataset | |
1150 | 577 | for (AlignedCodonFrame cf : codonFrameList) |
1151 | { | |
1152 | 3 | for (SequenceToSequenceMapping ssm : cf.getMappings()) |
1153 | { | |
1154 | 1 | if (!seqs.contains(ssm.getFromSeq())) |
1155 | { | |
1156 | 0 | resolveAndAddDatasetSeq(ssm.getFromSeq(), seqs, false); |
1157 | } | |
1158 | 1 | if (!seqs.contains(ssm.getMapping().getTo())) |
1159 | { | |
1160 | 0 | resolveAndAddDatasetSeq(ssm.getMapping().getTo(), seqs, false); |
1161 | } | |
1162 | } | |
1163 | } | |
1164 | // finally construct dataset | |
1165 | 577 | dataset = new Alignment(seqs.toArray(new SequenceI[seqs.size()])); |
1166 | // move mappings to the dataset alignment | |
1167 | 577 | dataset.codonFrameList = this.codonFrameList; |
1168 | 577 | this.codonFrameList = null; |
1169 | } | |
1170 | ||
1171 | /** | |
1172 | * reference count for number of alignments referencing this one. | |
1173 | */ | |
1174 | int alignmentRefs = 0; | |
1175 | ||
1176 | /** | |
1177 | * increase reference count to this alignment. | |
1178 | */ | |
1179 | 642 | private void addAlignmentRef() |
1180 | { | |
1181 | 642 | alignmentRefs++; |
1182 | } | |
1183 | ||
1184 | 2894 | @Override |
1185 | public Alignment getDataset() | |
1186 | { | |
1187 | 2894 | return dataset; |
1188 | } | |
1189 | ||
1190 | 522 | @Override |
1191 | public boolean padGaps() | |
1192 | { | |
1193 | 522 | boolean modified = false; |
1194 | ||
1195 | // Remove excess gaps from the end of alignment | |
1196 | 522 | int maxLength = -1; |
1197 | ||
1198 | 522 | SequenceI current; |
1199 | 522 | int nseq = sequences.size(); |
1200 | 4234 | for (int i = 0; i < nseq; i++) |
1201 | { | |
1202 | 3712 | current = getSequenceAt(i); |
1203 | 9658 | for (int j = current.getLength(); j > maxLength; j--) |
1204 | { | |
1205 | 6669 | if (j > maxLength |
1206 | && !jalview.util.Comparison.isGap(current.getCharAt(j))) | |
1207 | { | |
1208 | 723 | maxLength = j; |
1209 | 723 | break; |
1210 | } | |
1211 | } | |
1212 | } | |
1213 | ||
1214 | 522 | maxLength++; |
1215 | ||
1216 | 522 | int cLength; |
1217 | 4234 | for (int i = 0; i < nseq; i++) |
1218 | { | |
1219 | 3712 | current = getSequenceAt(i); |
1220 | 3712 | cLength = current.getLength(); |
1221 | ||
1222 | 3712 | if (cLength < maxLength) |
1223 | { | |
1224 | 76 | current.insertCharAt(cLength, maxLength - cLength, gapCharacter); |
1225 | 76 | modified = true; |
1226 | } | |
1227 | 3636 | else if (current.getLength() > maxLength) |
1228 | { | |
1229 | 2 | current.deleteChars(maxLength, current.getLength()); |
1230 | } | |
1231 | } | |
1232 | 522 | return modified; |
1233 | } | |
1234 | ||
1235 | /** | |
1236 | * Justify the sequences to the left or right by deleting and inserting gaps | |
1237 | * before the initial residue or after the terminal residue | |
1238 | * | |
1239 | * @param right | |
1240 | * true if alignment padded to right, false to justify to left | |
1241 | * @return true if alignment was changed | |
1242 | */ | |
1243 | 0 | @Override |
1244 | public boolean justify(boolean right) | |
1245 | { | |
1246 | 0 | boolean modified = false; |
1247 | ||
1248 | // Remove excess gaps from the end of alignment | |
1249 | 0 | int maxLength = -1; |
1250 | 0 | int ends[] = new int[sequences.size() * 2]; |
1251 | 0 | SequenceI current; |
1252 | 0 | for (int i = 0; i < sequences.size(); i++) |
1253 | { | |
1254 | 0 | current = getSequenceAt(i); |
1255 | // This should really be a sequence method | |
1256 | 0 | ends[i * 2] = current.findIndex(current.getStart()); |
1257 | 0 | ends[i * 2 + 1] = current |
1258 | .findIndex(current.getStart() + current.getLength()); | |
1259 | 0 | boolean hitres = false; |
1260 | 0 | for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++) |
1261 | { | |
1262 | 0 | if (!jalview.util.Comparison.isGap(current.getCharAt(j))) |
1263 | { | |
1264 | 0 | if (!hitres) |
1265 | { | |
1266 | 0 | ends[i * 2] = j; |
1267 | 0 | hitres = true; |
1268 | } | |
1269 | else | |
1270 | { | |
1271 | 0 | ends[i * 2 + 1] = j; |
1272 | 0 | if (j - ends[i * 2] > maxLength) |
1273 | { | |
1274 | 0 | maxLength = j - ends[i * 2]; |
1275 | } | |
1276 | } | |
1277 | } | |
1278 | } | |
1279 | } | |
1280 | ||
1281 | 0 | maxLength++; |
1282 | // now edit the flanking gaps to justify to either left or right | |
1283 | 0 | int cLength, extent, diff; |
1284 | 0 | for (int i = 0; i < sequences.size(); i++) |
1285 | { | |
1286 | 0 | current = getSequenceAt(i); |
1287 | ||
1288 | 0 | cLength = 1 + ends[i * 2 + 1] - ends[i * 2]; |
1289 | 0 | diff = maxLength - cLength; // number of gaps to indent |
1290 | 0 | extent = current.getLength(); |
1291 | 0 | if (right) |
1292 | { | |
1293 | // right justify | |
1294 | 0 | if (extent > ends[i * 2 + 1]) |
1295 | { | |
1296 | 0 | current.deleteChars(ends[i * 2 + 1] + 1, extent); |
1297 | 0 | modified = true; |
1298 | } | |
1299 | 0 | if (ends[i * 2] > diff) |
1300 | { | |
1301 | 0 | current.deleteChars(0, ends[i * 2] - diff); |
1302 | 0 | modified = true; |
1303 | } | |
1304 | else | |
1305 | { | |
1306 | 0 | if (ends[i * 2] < diff) |
1307 | { | |
1308 | 0 | current.insertCharAt(0, diff - ends[i * 2], gapCharacter); |
1309 | 0 | modified = true; |
1310 | } | |
1311 | } | |
1312 | } | |
1313 | else | |
1314 | { | |
1315 | // left justify | |
1316 | 0 | if (ends[i * 2] > 0) |
1317 | { | |
1318 | 0 | current.deleteChars(0, ends[i * 2]); |
1319 | 0 | modified = true; |
1320 | 0 | ends[i * 2 + 1] -= ends[i * 2]; |
1321 | 0 | extent -= ends[i * 2]; |
1322 | } | |
1323 | 0 | if (extent > maxLength) |
1324 | { | |
1325 | 0 | current.deleteChars(maxLength + 1, extent); |
1326 | 0 | modified = true; |
1327 | } | |
1328 | else | |
1329 | { | |
1330 | 0 | if (extent < maxLength) |
1331 | { | |
1332 | 0 | current.insertCharAt(extent, maxLength - extent, gapCharacter); |
1333 | 0 | modified = true; |
1334 | } | |
1335 | } | |
1336 | } | |
1337 | } | |
1338 | 0 | return modified; |
1339 | } | |
1340 | ||
1341 | 18947 | @Override |
1342 | public HiddenSequences getHiddenSequences() | |
1343 | { | |
1344 | 18947 | return hiddenSequences; |
1345 | } | |
1346 | ||
1347 | 28098 | @Override |
1348 | public HiddenColumns getHiddenColumns() | |
1349 | { | |
1350 | 28098 | return hiddenCols; |
1351 | } | |
1352 | ||
1353 | 0 | @Override |
1354 | public CigarArray getCompactAlignment() | |
1355 | { | |
1356 | 0 | synchronized (sequences) |
1357 | { | |
1358 | 0 | SeqCigar alseqs[] = new SeqCigar[sequences.size()]; |
1359 | 0 | int i = 0; |
1360 | 0 | for (SequenceI seq : sequences) |
1361 | { | |
1362 | 0 | alseqs[i++] = new SeqCigar(seq); |
1363 | } | |
1364 | 0 | CigarArray cal = new CigarArray(alseqs); |
1365 | 0 | cal.addOperation(CigarArray.M, getWidth()); |
1366 | 0 | return cal; |
1367 | } | |
1368 | } | |
1369 | ||
1370 | 143 | @Override |
1371 | public void setProperty(Object key, Object value) | |
1372 | { | |
1373 | 143 | if (alignmentProperties == null) |
1374 | { | |
1375 | 15 | alignmentProperties = new Hashtable(); |
1376 | } | |
1377 | ||
1378 | 143 | alignmentProperties.put(key, value); |
1379 | } | |
1380 | ||
1381 | 0 | @Override |
1382 | public Object getProperty(Object key) | |
1383 | { | |
1384 | 0 | if (alignmentProperties != null) |
1385 | { | |
1386 | 0 | return alignmentProperties.get(key); |
1387 | } | |
1388 | else | |
1389 | { | |
1390 | 0 | return null; |
1391 | } | |
1392 | } | |
1393 | ||
1394 | 361 | @Override |
1395 | public Hashtable getProperties() | |
1396 | { | |
1397 | 361 | return alignmentProperties; |
1398 | } | |
1399 | ||
1400 | /** | |
1401 | * Adds the given mapping to the stored set. Note this may be held on the | |
1402 | * dataset alignment. | |
1403 | */ | |
1404 | 81 | @Override |
1405 | public void addCodonFrame(AlignedCodonFrame codons) | |
1406 | { | |
1407 | 81 | List<AlignedCodonFrame> acfs = getCodonFrames(); |
1408 | 81 | if (codons != null && acfs != null && !acfs.contains(codons)) |
1409 | { | |
1410 | 78 | acfs.add(codons); |
1411 | } | |
1412 | } | |
1413 | ||
1414 | /* | |
1415 | * (non-Javadoc) | |
1416 | * | |
1417 | * @see | |
1418 | * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI) | |
1419 | */ | |
1420 | 53 | @Override |
1421 | public List<AlignedCodonFrame> getCodonFrame(SequenceI seq) | |
1422 | { | |
1423 | 53 | if (seq == null) |
1424 | { | |
1425 | 0 | return null; |
1426 | } | |
1427 | 53 | List<AlignedCodonFrame> cframes = new ArrayList<>(); |
1428 | 53 | for (AlignedCodonFrame acf : getCodonFrames()) |
1429 | { | |
1430 | 105 | if (acf.involvesSequence(seq)) |
1431 | { | |
1432 | 46 | cframes.add(acf); |
1433 | } | |
1434 | } | |
1435 | 53 | return cframes; |
1436 | } | |
1437 | ||
1438 | /** | |
1439 | * Sets the codon frame mappings (replacing any existing mappings). Note the | |
1440 | * mappings are set on the dataset alignment instead if there is one. | |
1441 | * | |
1442 | * @see jalview.datamodel.AlignmentI#setCodonFrames() | |
1443 | */ | |
1444 | 52 | @Override |
1445 | public void setCodonFrames(List<AlignedCodonFrame> acfs) | |
1446 | { | |
1447 | 52 | if (dataset != null) |
1448 | { | |
1449 | 24 | dataset.setCodonFrames(acfs); |
1450 | } | |
1451 | else | |
1452 | { | |
1453 | 28 | this.codonFrameList = acfs; |
1454 | } | |
1455 | } | |
1456 | ||
1457 | /** | |
1458 | * Returns the set of codon frame mappings. Any changes to the returned set | |
1459 | * will affect the alignment. The mappings are held on (and read from) the | |
1460 | * dataset alignment if there is one. | |
1461 | * | |
1462 | * @see jalview.datamodel.AlignmentI#getCodonFrames() | |
1463 | */ | |
1464 | 6481 | @Override |
1465 | public List<AlignedCodonFrame> getCodonFrames() | |
1466 | { | |
1467 | // TODO: Fix this method to fix failing AlignedCodonFrame tests | |
1468 | // this behaviour is currently incorrect. method should return codon frames | |
1469 | // for just the alignment, | |
1470 | // selected from dataset | |
1471 | 6481 | return dataset != null ? dataset.getCodonFrames() : codonFrameList; |
1472 | } | |
1473 | ||
1474 | /** | |
1475 | * Removes the given mapping from the stored set. Note that the mappings are | |
1476 | * held on the dataset alignment if there is one. | |
1477 | */ | |
1478 | 0 | @Override |
1479 | public boolean removeCodonFrame(AlignedCodonFrame codons) | |
1480 | { | |
1481 | 0 | List<AlignedCodonFrame> acfs = getCodonFrames(); |
1482 | 0 | if (codons == null || acfs == null) |
1483 | { | |
1484 | 0 | return false; |
1485 | } | |
1486 | 0 | return acfs.remove(codons); |
1487 | } | |
1488 | ||
1489 | 1 | @Override |
1490 | public void append(AlignmentI toappend) | |
1491 | { | |
1492 | // TODO JAL-1270 needs test coverage | |
1493 | // currently tested for use in jalview.gui.SequenceFetcher | |
1494 | 1 | char oldc = toappend.getGapCharacter(); |
1495 | 1 | boolean samegap = oldc == getGapCharacter(); |
1496 | 1 | boolean hashidden = toappend.getHiddenSequences() != null |
1497 | && toappend.getHiddenSequences().hiddenSequences != null; | |
1498 | // get all sequences including any hidden ones | |
1499 | 1 | List<SequenceI> sqs = (hashidden) |
1500 | ? toappend.getHiddenSequences().getFullAlignment() | |
1501 | .getSequences() | |
1502 | : toappend.getSequences(); | |
1503 | 1 | if (sqs != null) |
1504 | { | |
1505 | // avoid self append deadlock by | |
1506 | 1 | List<SequenceI> toappendsq = new ArrayList<>(); |
1507 | 1 | synchronized (sqs) |
1508 | { | |
1509 | 1 | for (SequenceI addedsq : sqs) |
1510 | { | |
1511 | 1 | if (!samegap) |
1512 | { | |
1513 | 1 | addedsq.replace(oldc, gapCharacter); |
1514 | } | |
1515 | 1 | toappendsq.add(addedsq); |
1516 | } | |
1517 | } | |
1518 | 1 | for (SequenceI addedsq : toappendsq) |
1519 | { | |
1520 | 1 | addSequence(addedsq); |
1521 | } | |
1522 | } | |
1523 | 1 | AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation(); |
1524 | 1 | for (int a = 0; alan != null && a < alan.length; a++) |
1525 | { | |
1526 | 0 | addAnnotation(alan[a]); |
1527 | } | |
1528 | ||
1529 | // use add method | |
1530 | 1 | getCodonFrames().addAll(toappend.getCodonFrames()); |
1531 | ||
1532 | 1 | List<SequenceGroup> sg = toappend.getGroups(); |
1533 | 1 | if (sg != null) |
1534 | { | |
1535 | 1 | for (SequenceGroup _sg : sg) |
1536 | { | |
1537 | 0 | addGroup(_sg); |
1538 | } | |
1539 | } | |
1540 | 1 | if (toappend.getHiddenSequences() != null) |
1541 | { | |
1542 | 1 | HiddenSequences hs = toappend.getHiddenSequences(); |
1543 | 1 | if (hiddenSequences == null) |
1544 | { | |
1545 | 0 | hiddenSequences = new HiddenSequences(this); |
1546 | } | |
1547 | 1 | if (hs.hiddenSequences != null) |
1548 | { | |
1549 | 0 | for (int s = 0; s < hs.hiddenSequences.length; s++) |
1550 | { | |
1551 | // hide the newly appended sequence in the alignment | |
1552 | 0 | if (hs.hiddenSequences[s] != null) |
1553 | { | |
1554 | 0 | hiddenSequences.hideSequence(hs.hiddenSequences[s]); |
1555 | } | |
1556 | } | |
1557 | } | |
1558 | } | |
1559 | 1 | if (toappend.getProperties() != null) |
1560 | { | |
1561 | // we really can't do very much here - just try to concatenate strings | |
1562 | // where property collisions occur. | |
1563 | 0 | Enumeration key = toappend.getProperties().keys(); |
1564 | 0 | while (key.hasMoreElements()) |
1565 | { | |
1566 | 0 | Object k = key.nextElement(); |
1567 | 0 | Object ourval = this.getProperty(k); |
1568 | 0 | Object toapprop = toappend.getProperty(k); |
1569 | 0 | if (ourval != null) |
1570 | { | |
1571 | 0 | if (ourval.getClass().equals(toapprop.getClass()) |
1572 | && !ourval.equals(toapprop)) | |
1573 | { | |
1574 | 0 | if (ourval instanceof String) |
1575 | { | |
1576 | // append strings | |
1577 | 0 | this.setProperty(k, |
1578 | ((String) ourval) + "; " + ((String) toapprop)); | |
1579 | } | |
1580 | else | |
1581 | { | |
1582 | 0 | if (ourval instanceof Vector) |
1583 | { | |
1584 | // append vectors | |
1585 | 0 | Enumeration theirv = ((Vector) toapprop).elements(); |
1586 | 0 | while (theirv.hasMoreElements()) |
1587 | { | |
1588 | 0 | ((Vector) ourval).addElement(theirv); |
1589 | } | |
1590 | } | |
1591 | } | |
1592 | } | |
1593 | } | |
1594 | else | |
1595 | { | |
1596 | // just add new property directly | |
1597 | 0 | setProperty(k, toapprop); |
1598 | } | |
1599 | ||
1600 | } | |
1601 | } | |
1602 | } | |
1603 | ||
1604 | 19 | @Override |
1605 | public AlignmentAnnotation findOrCreateAnnotation(String name, | |
1606 | String calcId, boolean autoCalc, SequenceI seqRef, | |
1607 | SequenceGroup groupRef) | |
1608 | { | |
1609 | 18 | if (annotations != null) |
1610 | { | |
1611 | 18 | for (AlignmentAnnotation annot : getAlignmentAnnotation()) |
1612 | { | |
1613 | 192 | if (annot.autoCalculated == autoCalc && (name.equals(annot.label)) |
1614 | && (calcId == null || annot.getCalcId().equals(calcId)) | |
1615 | && annot.sequenceRef == seqRef | |
1616 | && annot.groupRef == groupRef) | |
1617 | { | |
1618 | 0 | return annot; |
1619 | } | |
1620 | } | |
1621 | } | |
1622 | 19 | AlignmentAnnotation annot = new AlignmentAnnotation(name, name, |
1623 | new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH); | |
1624 | 18 | annot.hasText = false; |
1625 | 18 | if (calcId != null) |
1626 | { | |
1627 | 17 | annot.setCalcId(new String(calcId)); |
1628 | } | |
1629 | 18 | annot.autoCalculated = autoCalc; |
1630 | 19 | if (seqRef != null) |
1631 | { | |
1632 | 16 | annot.setSequenceRef(seqRef); |
1633 | } | |
1634 | 19 | annot.groupRef = groupRef; |
1635 | 18 | addAnnotation(annot); |
1636 | ||
1637 | 19 | return annot; |
1638 | } | |
1639 | ||
1640 | 498 | @Override |
1641 | public Iterable<AlignmentAnnotation> findAnnotation(String calcId) | |
1642 | { | |
1643 | 498 | AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation(); |
1644 | 498 | if (alignmentAnnotation != null) |
1645 | { | |
1646 | 489 | return AlignmentAnnotation.findAnnotation( |
1647 | Arrays.asList(getAlignmentAnnotation()), calcId); | |
1648 | } | |
1649 | 9 | return Arrays.asList(new AlignmentAnnotation[] {}); |
1650 | } | |
1651 | ||
1652 | 166 | @Override |
1653 | public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq, | |
1654 | String calcId, String label) | |
1655 | { | |
1656 | 166 | return annotations == null ? null |
1657 | : AlignmentAnnotation.findAnnotations( | |
1658 | Arrays.asList(getAlignmentAnnotation()), seq, calcId, | |
1659 | label); | |
1660 | } | |
1661 | ||
1662 | 0 | @Override |
1663 | public void moveSelectedSequencesByOne(SequenceGroup sg, | |
1664 | Map<SequenceI, SequenceCollectionI> map, boolean up) | |
1665 | { | |
1666 | 0 | synchronized (sequences) |
1667 | { | |
1668 | 0 | if (up) |
1669 | { | |
1670 | ||
1671 | 0 | for (int i = 1, iSize = sequences.size(); i < iSize; i++) |
1672 | { | |
1673 | 0 | SequenceI seq = sequences.get(i); |
1674 | 0 | if (!sg.getSequences(map).contains(seq)) |
1675 | { | |
1676 | 0 | continue; |
1677 | } | |
1678 | ||
1679 | 0 | SequenceI temp = sequences.get(i - 1); |
1680 | 0 | if (sg.getSequences(null).contains(temp)) |
1681 | { | |
1682 | 0 | continue; |
1683 | } | |
1684 | ||
1685 | 0 | sequences.set(i, temp); |
1686 | 0 | sequences.set(i - 1, seq); |
1687 | } | |
1688 | } | |
1689 | else | |
1690 | { | |
1691 | 0 | for (int i = sequences.size() - 2; i > -1; i--) |
1692 | { | |
1693 | 0 | SequenceI seq = sequences.get(i); |
1694 | 0 | if (!sg.getSequences(map).contains(seq)) |
1695 | { | |
1696 | 0 | continue; |
1697 | } | |
1698 | ||
1699 | 0 | SequenceI temp = sequences.get(i + 1); |
1700 | 0 | if (sg.getSequences(map).contains(temp)) |
1701 | { | |
1702 | 0 | continue; |
1703 | } | |
1704 | ||
1705 | 0 | sequences.set(i, temp); |
1706 | 0 | sequences.set(i + 1, seq); |
1707 | } | |
1708 | } | |
1709 | ||
1710 | } | |
1711 | } | |
1712 | ||
1713 | 0 | @Override |
1714 | public void validateAnnotation(AlignmentAnnotation alignmentAnnotation) | |
1715 | { | |
1716 | 0 | alignmentAnnotation.validateRangeAndDisplay(); |
1717 | 0 | if (isNucleotide() && alignmentAnnotation.isValidStruc()) |
1718 | { | |
1719 | 0 | hasRNAStructure = true; |
1720 | } | |
1721 | } | |
1722 | ||
1723 | private SequenceI seqrep = null; | |
1724 | ||
1725 | /** | |
1726 | * | |
1727 | * @return the representative sequence for this group | |
1728 | */ | |
1729 | 20941 | @Override |
1730 | public SequenceI getSeqrep() | |
1731 | { | |
1732 | 20941 | return seqrep; |
1733 | } | |
1734 | ||
1735 | /** | |
1736 | * set the representative sequence for this group. Note - this affects the | |
1737 | * interpretation of the Hidereps attribute. | |
1738 | * | |
1739 | * @param seqrep | |
1740 | * the seqrep to set (null means no sequence representative) | |
1741 | */ | |
1742 | 200 | @Override |
1743 | public void setSeqrep(SequenceI seqrep) | |
1744 | { | |
1745 | 200 | this.seqrep = seqrep; |
1746 | } | |
1747 | ||
1748 | /** | |
1749 | * | |
1750 | * @return true if group has a sequence representative | |
1751 | */ | |
1752 | 26934 | @Override |
1753 | public boolean hasSeqrep() | |
1754 | { | |
1755 | 26934 | return seqrep != null; |
1756 | } | |
1757 | ||
1758 | 31 | @Override |
1759 | public int getEndRes() | |
1760 | { | |
1761 | 31 | return getWidth() - 1; |
1762 | } | |
1763 | ||
1764 | 31 | @Override |
1765 | public int getStartRes() | |
1766 | { | |
1767 | 31 | return 0; |
1768 | } | |
1769 | ||
1770 | /* | |
1771 | * In the case of AlignmentI - returns the dataset for the alignment, if set | |
1772 | * (non-Javadoc) | |
1773 | * | |
1774 | * @see jalview.datamodel.AnnotatedCollectionI#getContext() | |
1775 | */ | |
1776 | 476 | @Override |
1777 | public AnnotatedCollectionI getContext() | |
1778 | { | |
1779 | 476 | return dataset; |
1780 | } | |
1781 | ||
1782 | /** | |
1783 | * Align this alignment like the given (mapped) one. | |
1784 | */ | |
1785 | 4 | @Override |
1786 | public int alignAs(AlignmentI al) | |
1787 | { | |
1788 | /* | |
1789 | * Currently retains unmapped gaps (in introns), regaps mapped regions | |
1790 | * (exons) | |
1791 | */ | |
1792 | 4 | return alignAs(al, false, true); |
1793 | } | |
1794 | ||
1795 | /** | |
1796 | * Align this alignment 'the same as' the given one. Mapped sequences only are | |
1797 | * realigned. If both of the same type (nucleotide/protein) then align both | |
1798 | * identically. If this is nucleotide and the other is protein, make 3 gaps | |
1799 | * for each gap in the protein sequences. If this is protein and the other is | |
1800 | * nucleotide, insert a gap for each 3 gaps (or part thereof) between | |
1801 | * nucleotide bases. If this is protein and the other is nucleotide, gaps | |
1802 | * protein to match the relative ordering of codons in the nucleotide. | |
1803 | * | |
1804 | * Parameters control whether gaps in exon (mapped) and intron (unmapped) | |
1805 | * regions are preserved. Gaps that connect introns to exons are treated | |
1806 | * conservatively, i.e. only preserved if both intron and exon gaps are | |
1807 | * preserved. TODO: check caveats below where the implementation fails | |
1808 | * | |
1809 | * @param al | |
1810 | * - must have same dataset, and sequences in al must have equivalent | |
1811 | * dataset sequence and start/end bounds under given mapping | |
1812 | * @param preserveMappedGaps | |
1813 | * if true, gaps within and between mapped codons are preserved | |
1814 | * @param preserveUnmappedGaps | |
1815 | * if true, gaps within and between unmapped codons are preserved | |
1816 | */ | |
1817 | // @Override | |
1818 | 10 | public int alignAs(AlignmentI al, boolean preserveMappedGaps, |
1819 | boolean preserveUnmappedGaps) | |
1820 | { | |
1821 | // TODO should this method signature be the one in the interface? | |
1822 | // JBPComment - yes - neither flag is used, so should be deleted. | |
1823 | 10 | boolean thisIsNucleotide = this.isNucleotide(); |
1824 | 10 | boolean thatIsProtein = !al.isNucleotide(); |
1825 | 10 | if (!thatIsProtein && !thisIsNucleotide) |
1826 | { | |
1827 | 3 | return AlignmentUtils.alignProteinAsDna(this, al); |
1828 | } | |
1829 | 7 | else if (thatIsProtein && thisIsNucleotide) |
1830 | { | |
1831 | 4 | return AlignmentUtils.alignCdsAsProtein(this, al); |
1832 | } | |
1833 | 3 | return AlignmentUtils.alignAs(this, al); |
1834 | } | |
1835 | ||
1836 | /** | |
1837 | * Returns the alignment in Fasta format. Behaviour of this method is not | |
1838 | * guaranteed between versions. | |
1839 | */ | |
1840 | 3 | @Override |
1841 | public String toString() | |
1842 | { | |
1843 | 3 | return new FastaFile().print(getSequencesArray(), true); |
1844 | } | |
1845 | ||
1846 | /** | |
1847 | * Returns the set of distinct sequence names. No ordering is guaranteed. | |
1848 | */ | |
1849 | 44 | @Override |
1850 | public Set<String> getSequenceNames() | |
1851 | { | |
1852 | 44 | Set<String> names = new HashSet<>(); |
1853 | 44 | for (SequenceI seq : getSequences()) |
1854 | { | |
1855 | 420 | names.add(seq.getName()); |
1856 | } | |
1857 | 44 | return names; |
1858 | } | |
1859 | ||
1860 | 316 | @Override |
1861 | public boolean hasValidSequence() | |
1862 | { | |
1863 | 316 | boolean hasValidSeq = false; |
1864 | 316 | for (SequenceI seq : getSequences()) |
1865 | { | |
1866 | 316 | if ((seq.getEnd() - seq.getStart()) > 0) |
1867 | { | |
1868 | 316 | hasValidSeq = true; |
1869 | 316 | break; |
1870 | } | |
1871 | } | |
1872 | 316 | return hasValidSeq; |
1873 | } | |
1874 | ||
1875 | /** | |
1876 | * Update any mappings to 'virtual' sequences to compatible real ones, if | |
1877 | * present in the added sequences. Returns a count of mappings updated. | |
1878 | * | |
1879 | * @param seqs | |
1880 | * @return | |
1881 | */ | |
1882 | 21 | @Override |
1883 | public int realiseMappings(List<SequenceI> seqs) | |
1884 | { | |
1885 | 21 | int count = 0; |
1886 | 21 | for (SequenceI seq : seqs) |
1887 | { | |
1888 | 58 | for (AlignedCodonFrame mapping : getCodonFrames()) |
1889 | { | |
1890 | 0 | count += mapping.realiseWith(seq); |
1891 | } | |
1892 | } | |
1893 | 21 | return count; |
1894 | } | |
1895 | ||
1896 | /** | |
1897 | * Returns the first AlignedCodonFrame that has a mapping between the given | |
1898 | * dataset sequences | |
1899 | * | |
1900 | * @param mapFrom | |
1901 | * @param mapTo | |
1902 | * @return | |
1903 | */ | |
1904 | 38 | @Override |
1905 | public AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo) | |
1906 | { | |
1907 | 38 | for (AlignedCodonFrame acf : getCodonFrames()) |
1908 | { | |
1909 | 13 | if (acf.getAaForDnaSeq(mapFrom) == mapTo) |
1910 | { | |
1911 | 12 | return acf; |
1912 | } | |
1913 | } | |
1914 | 26 | return null; |
1915 | } | |
1916 | ||
1917 | 42 | @Override |
1918 | public boolean setHiddenColumns(HiddenColumns cols) | |
1919 | { | |
1920 | 42 | boolean changed = cols == null ? hiddenCols != null |
1921 | : !cols.equals(hiddenCols); | |
1922 | 42 | hiddenCols = cols; |
1923 | 42 | return changed; |
1924 | } | |
1925 | ||
1926 | 0 | @Override |
1927 | public void setupJPredAlignment() | |
1928 | { | |
1929 | 0 | SequenceI repseq = getSequenceAt(0); |
1930 | 0 | setSeqrep(repseq); |
1931 | 0 | HiddenColumns cs = new HiddenColumns(); |
1932 | 0 | cs.hideList(repseq.getInsertions()); |
1933 | 0 | setHiddenColumns(cs); |
1934 | } | |
1935 | ||
1936 | 2 | @Override |
1937 | public HiddenColumns propagateInsertions(SequenceI profileseq, | |
1938 | AlignmentView input) | |
1939 | { | |
1940 | 2 | int profsqpos = 0; |
1941 | ||
1942 | 2 | char gc = getGapCharacter(); |
1943 | 2 | Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc); |
1944 | 2 | HiddenColumns nview = (HiddenColumns) alandhidden[1]; |
1945 | 2 | SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos]; |
1946 | 2 | return propagateInsertions(profileseq, origseq, nview); |
1947 | } | |
1948 | ||
1949 | /** | |
1950 | * | |
1951 | * @param profileseq | |
1952 | * sequence in al which corresponds to origseq | |
1953 | * @param al | |
1954 | * alignment which is to have gaps inserted into it | |
1955 | * @param origseq | |
1956 | * sequence corresponding to profileseq which defines gap map for | |
1957 | * modifying al | |
1958 | */ | |
1959 | 2 | private HiddenColumns propagateInsertions(SequenceI profileseq, |
1960 | SequenceI origseq, HiddenColumns hc) | |
1961 | { | |
1962 | // take the set of hidden columns, and the set of gaps in origseq, | |
1963 | // and remove all the hidden gaps from hiddenColumns | |
1964 | ||
1965 | // first get the gaps as a Bitset | |
1966 | // then calculate hidden ^ not(gap) | |
1967 | 2 | BitSet gaps = origseq.gapBitset(); |
1968 | 2 | hc.andNot(gaps); |
1969 | ||
1970 | // for each sequence in the alignment, except the profile sequence, | |
1971 | // insert gaps corresponding to each hidden region but where each hidden | |
1972 | // column region is shifted backwards by the number of preceding visible | |
1973 | // gaps update hidden columns at the same time | |
1974 | 2 | HiddenColumns newhidden = new HiddenColumns(); |
1975 | ||
1976 | 2 | int numGapsBefore = 0; |
1977 | 2 | int gapPosition = 0; |
1978 | 2 | Iterator<int[]> it = hc.iterator(); |
1979 | 4 | while (it.hasNext()) |
1980 | { | |
1981 | 2 | int[] region = it.next(); |
1982 | ||
1983 | // get region coordinates accounting for gaps | |
1984 | // we can rely on gaps not being *in* hidden regions because we already | |
1985 | // removed those | |
1986 | 26 | while (gapPosition < region[0]) |
1987 | { | |
1988 | 24 | gapPosition++; |
1989 | 24 | if (gaps.get(gapPosition)) |
1990 | { | |
1991 | 8 | numGapsBefore++; |
1992 | } | |
1993 | } | |
1994 | ||
1995 | 2 | int left = region[0] - numGapsBefore; |
1996 | 2 | int right = region[1] - numGapsBefore; |
1997 | ||
1998 | 2 | newhidden.hideColumns(left, right); |
1999 | 2 | padGaps(left, right, profileseq); |
2000 | } | |
2001 | 2 | return newhidden; |
2002 | } | |
2003 | ||
2004 | /** | |
2005 | * Pad gaps in all sequences in alignment except profileseq | |
2006 | * | |
2007 | * @param left | |
2008 | * position of first gap to insert | |
2009 | * @param right | |
2010 | * position of last gap to insert | |
2011 | * @param profileseq | |
2012 | * sequence not to pad | |
2013 | */ | |
2014 | 2 | private void padGaps(int left, int right, SequenceI profileseq) |
2015 | { | |
2016 | 2 | char gc = getGapCharacter(); |
2017 | ||
2018 | // make a string with number of gaps = length of hidden region | |
2019 | 2 | StringBuilder sb = new StringBuilder(); |
2020 | 7 | for (int g = 0; g < right - left + 1; g++) |
2021 | { | |
2022 | 5 | sb.append(gc); |
2023 | } | |
2024 | ||
2025 | // loop over the sequences and pad with gaps where required | |
2026 | 22 | for (int s = 0, ns = getHeight(); s < ns; s++) |
2027 | { | |
2028 | 20 | SequenceI sqobj = getSequenceAt(s); |
2029 | 20 | if ((sqobj != profileseq) && (sqobj.getLength() >= left)) |
2030 | { | |
2031 | 15 | String sq = sqobj.getSequenceAsString(); |
2032 | 15 | sqobj.setSequence( |
2033 | sq.substring(0, left) + sb.toString() + sq.substring(left)); | |
2034 | } | |
2035 | } | |
2036 | } | |
2037 | ||
2038 | //// | |
2039 | //// Contact Matrix Holder Boilerplate | |
2040 | //// | |
2041 | ContactMapHolder cmholder = new ContactMapHolder(); | |
2042 | ||
2043 | 21 | @Override |
2044 | public Collection<ContactMatrixI> getContactMaps() | |
2045 | { | |
2046 | 21 | return cmholder.getContactMaps(); |
2047 | } | |
2048 | ||
2049 | 140 | @Override |
2050 | public ContactMatrixI getContactMatrixFor(AlignmentAnnotation _aa) | |
2051 | { | |
2052 | 140 | ContactMatrixI cm = cmholder.getContactMatrixFor(_aa); |
2053 | 140 | if (cm == null && _aa.groupRef != null) |
2054 | { | |
2055 | 0 | cm = _aa.groupRef.getContactMatrixFor(_aa); |
2056 | } | |
2057 | 140 | if (cm == null && _aa.sequenceRef != null) |
2058 | { | |
2059 | 140 | cm = _aa.sequenceRef.getContactMatrixFor(_aa); |
2060 | 140 | if (cm == null && _aa.sequenceRef.getDatasetSequence() != null) |
2061 | { | |
2062 | // TODO fix up this logic and unify with getContactListFor | |
2063 | 0 | cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa); |
2064 | } | |
2065 | } | |
2066 | 140 | return cm; |
2067 | } | |
2068 | ||
2069 | 3556 | @Override |
2070 | public ContactListI getContactListFor(AlignmentAnnotation _aa, int column) | |
2071 | { | |
2072 | 3556 | if (_aa.annotations == null || column >= _aa.annotations.length |
2073 | || column < 0) | |
2074 | { | |
2075 | 1 | return null; |
2076 | } | |
2077 | 3555 | ContactListI cl = cmholder.getContactListFor(_aa, column); |
2078 | 3555 | if (cl == null && _aa.groupRef != null) |
2079 | { | |
2080 | 0 | cl = _aa.groupRef.getContactListFor(_aa, column); |
2081 | } | |
2082 | 3555 | if (cl == null && _aa.sequenceRef != null) |
2083 | { | |
2084 | 3555 | if (_aa.annotations[column] != null) |
2085 | { | |
2086 | // sequence associated | |
2087 | 3555 | cl = _aa.sequenceRef.getContactListFor(_aa, column); |
2088 | 3555 | if (cl == null && _aa.sequenceRef.getDatasetSequence() != null) |
2089 | { | |
2090 | 0 | int spos = _aa.sequenceRef.findPosition(column); |
2091 | 0 | if (spos >= _aa.sequenceRef.getStart() |
2092 | && spos <= 1 + _aa.sequenceRef.getEnd()) | |
2093 | { | |
2094 | 0 | cl = _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa, |
2095 | spos - _aa.sequenceRef.getStart()); | |
2096 | } | |
2097 | } | |
2098 | } | |
2099 | } | |
2100 | 3555 | return cl; |
2101 | } | |
2102 | ||
2103 | 0 | @Override |
2104 | public AlignmentAnnotation addContactList(ContactMatrixI cm) | |
2105 | { | |
2106 | 0 | AlignmentAnnotation aa = cmholder.addContactList(cm); |
2107 | ||
2108 | 0 | Annotation _aa[] = new Annotation[getWidth()]; |
2109 | 0 | for (int i = 0; i < _aa.length; _aa[i++] = new Annotation(0.0f)) |
2110 | { | |
2111 | 0 | ; |
2112 | } | |
2113 | 0 | aa.annotations = _aa; |
2114 | 0 | addAnnotation(aa); |
2115 | 0 | return aa; |
2116 | } | |
2117 | ||
2118 | 0 | @Override |
2119 | public void addContactListFor(AlignmentAnnotation annotation, | |
2120 | ContactMatrixI cm) | |
2121 | { | |
2122 | 0 | cmholder.addContactListFor(annotation, cm); |
2123 | ||
2124 | } | |
2125 | ||
2126 | } |