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SeqCigar | 31 | 189 | 91 |
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 jalview.analysis.AlignSeq; | |
24 | import jalview.analysis.SeqsetUtils; | |
25 | import jalview.util.MessageManager; | |
26 | import jalview.util.ShiftList; | |
27 | ||
28 | import java.util.Enumeration; | |
29 | import java.util.Hashtable; | |
30 | ||
31 | public class SeqCigar extends CigarSimple | |
32 | { | |
33 | /** | |
34 | * start(inclusive) and end(exclusive) of subsequence on refseq | |
35 | */ | |
36 | private int start, end; | |
37 | ||
38 | private SequenceI refseq = null; | |
39 | ||
40 | private Hashtable seqProps; | |
41 | ||
42 | /** | |
43 | * Reference dataset sequence for the cigar string | |
44 | * | |
45 | * @return SequenceI | |
46 | */ | |
47 | 104 | public SequenceI getRefSeq() |
48 | { | |
49 | 104 | return refseq; |
50 | } | |
51 | ||
52 | /** | |
53 | * | |
54 | * @return int start index of cigar ops on refSeq | |
55 | */ | |
56 | 0 | public int getStart() |
57 | { | |
58 | 0 | return start; |
59 | } | |
60 | ||
61 | /** | |
62 | * | |
63 | * @return int end index (exclusive) of cigar ops on refSeq | |
64 | */ | |
65 | 0 | public int getEnd() |
66 | { | |
67 | 0 | return end; |
68 | } | |
69 | ||
70 | /** | |
71 | * | |
72 | * @param column | |
73 | * @return position in sequence for column (or -1 if no match state exists) | |
74 | */ | |
75 | 133 | public int findPosition(int column) |
76 | { | |
77 | 133 | int w = 0, ew, p = refseq.findPosition(start); |
78 | 133 | if (column < 0) |
79 | { | |
80 | 0 | return -1; |
81 | } | |
82 | 133 | if (range != null) |
83 | { | |
84 | 215 | for (int i = 0; i < length; i++) |
85 | { | |
86 | 215 | if (operation[i] == M || operation[i] == D) |
87 | { | |
88 | 163 | p += range[i]; |
89 | } | |
90 | 215 | if (operation[i] == M || operation[i] == I) |
91 | { | |
92 | 215 | ew = w + range[i]; |
93 | 215 | if (column < ew) |
94 | { | |
95 | 133 | if (operation[i] == I) |
96 | { | |
97 | 22 | return -1; |
98 | } | |
99 | 111 | return p - (ew - column); |
100 | } | |
101 | 82 | w = ew; |
102 | } | |
103 | } | |
104 | } | |
105 | 0 | return -1; |
106 | } | |
107 | ||
108 | /** | |
109 | * Returns sequence as a string with cigar operations applied to it | |
110 | * | |
111 | * @return String | |
112 | */ | |
113 | 26 | @Override |
114 | public String getSequenceString(char GapChar) | |
115 | { | |
116 | 26 | return (length == 0) ? "" |
117 | : (String) getSequenceAndDeletions( | |
118 | refseq.getSequenceAsString(start, end), GapChar)[0]; | |
119 | } | |
120 | ||
121 | /** | |
122 | * recreates a gapped and edited version of RefSeq or null for an empty cigar | |
123 | * string | |
124 | * | |
125 | * @return SequenceI | |
126 | */ | |
127 | 172 | public SequenceI getSeq(char GapChar) |
128 | { | |
129 | 172 | Sequence seq; |
130 | 172 | if (refseq == null || length == 0) |
131 | { | |
132 | 0 | return null; |
133 | } | |
134 | 172 | Object[] edit_result = getSequenceAndDeletions( |
135 | refseq.getSequenceAsString(start, end), GapChar); | |
136 | 172 | if (edit_result == null) |
137 | { | |
138 | 0 | throw new Error(MessageManager.getString( |
139 | "error.implementation_error_unexpected_null_from_get_sequence_and_deletions")); | |
140 | } | |
141 | 172 | int bounds[] = (int[]) edit_result[1]; |
142 | 172 | seq = new Sequence(refseq.getName(), (String) edit_result[0], |
143 | refseq.getStart() + start + bounds[0], refseq.getStart() + start | |
144 | 172 | + ((bounds[2] == 0) ? -1 : bounds[2])); |
145 | 172 | seq.setDescription(refseq.getDescription()); |
146 | 172 | int sstart = seq.getStart(), send = seq.getEnd(); |
147 | // seq.checkValidRange(); probably not needed | |
148 | // recover local properties if present | |
149 | 172 | if (seqProps != null) |
150 | { | |
151 | // this recovers dataset sequence reference as well as local features, | |
152 | // names, start/end settings. | |
153 | 172 | SeqsetUtils.SeqCharacterUnhash(seq, seqProps); |
154 | } | |
155 | // ensure dataset sequence is up to date from local reference | |
156 | 172 | seq.setDatasetSequence(refseq); |
157 | 172 | seq.setStart(sstart); |
158 | 172 | seq.setEnd(send); |
159 | 172 | return seq; |
160 | } | |
161 | ||
162 | /* | |
163 | * We don't allow this - refseq is given at construction time only public void | |
164 | * setSeq(SequenceI seq) { this.seq = seq; } | |
165 | */ | |
166 | /** | |
167 | * internal constructor - sets seq to a gapless sequence derived from seq and | |
168 | * prepends any 'D' operations needed to get to the first residue of seq. | |
169 | * | |
170 | * @param seq | |
171 | * SequenceI | |
172 | * @param initialDeletion | |
173 | * true to mark initial dataset sequence residues as deleted in | |
174 | * subsequence | |
175 | * @param _s | |
176 | * index of first position in seq | |
177 | * @param _e | |
178 | * index after last position in (possibly gapped) seq | |
179 | * @return true if gaps are present in seq | |
180 | */ | |
181 | 136 | private boolean _setSeq(SequenceI seq, boolean initialDeletion, int _s, |
182 | int _e) | |
183 | { | |
184 | 136 | boolean hasgaps = false; |
185 | 136 | if (seq == null) |
186 | { | |
187 | 0 | throw new Error(MessageManager |
188 | .getString("error.implementation_error_set_seq_null")); | |
189 | } | |
190 | 136 | if (_s < 0) |
191 | { | |
192 | 0 | throw new Error(MessageManager |
193 | .formatMessage("error.implementation_error_s", new String[] | |
194 | { Integer.valueOf(_s).toString() })); | |
195 | } | |
196 | 136 | String seq_string = seq.getSequenceAsString(); |
197 | 136 | if (_e == 0 || _e < _s || _e > seq_string.length()) |
198 | { | |
199 | 10 | _e = seq_string.length(); |
200 | } | |
201 | // resolve start and end positions relative to ungapped reference sequence | |
202 | 136 | start = seq.findPosition(_s) - seq.getStart(); |
203 | 136 | end = seq.findPosition(_e) - seq.getStart(); |
204 | 136 | int l_ungapped = end - start; |
205 | // Find correct sequence to reference and correct start and end - if | |
206 | // necessary | |
207 | 136 | SequenceI ds = seq.getDatasetSequence(); |
208 | 136 | if (ds == null) |
209 | { | |
210 | // make a new dataset sequence | |
211 | 17 | String ungapped = AlignSeq.extractGaps( |
212 | jalview.util.Comparison.GapChars, new String(seq_string)); | |
213 | 17 | l_ungapped = ungapped.length(); |
214 | // check that we haven't just duplicated an ungapped sequence. | |
215 | 17 | if (l_ungapped == seq.getLength()) |
216 | { | |
217 | 16 | ds = seq; |
218 | } | |
219 | else | |
220 | { | |
221 | 1 | ds = new Sequence(seq.getName(), ungapped, seq.getStart(), |
222 | seq.getStart() + ungapped.length() - 1); | |
223 | // JBPNote: this would be consistent but may not be useful | |
224 | // seq.setDatasetSequence(ds); | |
225 | } | |
226 | } | |
227 | // add in offset between seq and the dataset sequence | |
228 | 136 | if (ds.getStart() < seq.getStart()) |
229 | { | |
230 | 14 | int offset = seq.getStart() - ds.getStart(); |
231 | 14 | if (initialDeletion) |
232 | { | |
233 | // absolute cigar string | |
234 | 0 | addDeleted(_s + offset); |
235 | 0 | start = 0; |
236 | 0 | end += offset; |
237 | } | |
238 | else | |
239 | { | |
240 | // normal behaviour - just mark start and end subsequence | |
241 | 14 | start += offset; |
242 | 14 | end += offset; |
243 | ||
244 | } | |
245 | ||
246 | } | |
247 | ||
248 | // any gaps to process ? | |
249 | 136 | if (l_ungapped != (_e - _s)) |
250 | { | |
251 | 106 | hasgaps = true; |
252 | } | |
253 | ||
254 | 136 | refseq = ds; |
255 | // copy over local properties for the sequence instance of the refseq | |
256 | 136 | seqProps = SeqsetUtils.SeqCharacterHash(seq); |
257 | // Check offsets | |
258 | 136 | if (end > ds.getLength()) |
259 | { | |
260 | 0 | throw new Error(MessageManager |
261 | .getString("error.implementation_error_seqcigar_possible")); | |
262 | // end = ds.getLength(); | |
263 | } | |
264 | ||
265 | 136 | return hasgaps; |
266 | } | |
267 | ||
268 | /** | |
269 | * directly initialise a cigar object with a sequence of range, operation | |
270 | * pairs and a sequence to apply it to. operation and range should be relative | |
271 | * to the seq.getStart()'th residue of the dataset seq resolved from seq. | |
272 | * | |
273 | * @param seq | |
274 | * SequenceI | |
275 | * @param operation | |
276 | * char[] | |
277 | * @param range | |
278 | * int[] | |
279 | */ | |
280 | 1 | public SeqCigar(SequenceI seq, char operation[], int range[]) |
281 | { | |
282 | 1 | super(); |
283 | 1 | if (seq == null) |
284 | { | |
285 | 0 | throw new Error( |
286 | MessageManager.getString("error.implmentation_bug_seq_null")); | |
287 | } | |
288 | 1 | if (operation.length != range.length) |
289 | { | |
290 | 0 | throw new Error(MessageManager.getString( |
291 | "error.implementation_bug_cigar_operation_list_range_list")); | |
292 | } | |
293 | ||
294 | 1 | if (operation != null) |
295 | { | |
296 | 1 | this.operation = new char[operation.length + _inc_length]; |
297 | 1 | this.range = new int[operation.length + _inc_length]; |
298 | ||
299 | 1 | if (_setSeq(seq, false, 0, 0)) |
300 | { | |
301 | 0 | throw new Error(MessageManager.getString( |
302 | "error.not_yet_implemented_cigar_object_from_cigar_string")); | |
303 | } | |
304 | 11 | for (int i = this.length, j = 0; j < operation.length; i++, j++) |
305 | { | |
306 | 10 | char op = operation[j]; |
307 | 10 | if (op != M && op != I && op != D) |
308 | { | |
309 | 0 | throw new Error(MessageManager.formatMessage( |
310 | "error.implementation_bug_cigar_operation", new String[] | |
311 | { Integer.valueOf(j).toString(), | |
312 | Integer.valueOf(op).toString(), | |
313 | Integer.valueOf(M).toString(), | |
314 | Integer.valueOf(I).toString(), | |
315 | Integer.valueOf(D).toString() })); | |
316 | } | |
317 | 10 | this.operation[i] = op; |
318 | 10 | this.range[i] = range[j]; |
319 | } | |
320 | 1 | this.length += operation.length; |
321 | } | |
322 | else | |
323 | { | |
324 | 0 | this.operation = null; |
325 | 0 | this.range = null; |
326 | 0 | this.length = 0; |
327 | 0 | if (_setSeq(seq, false, 0, 0)) |
328 | { | |
329 | 0 | throw new Error(MessageManager.getString( |
330 | "error.not_yet_implemented_cigar_object_from_cigar_string")); | |
331 | } | |
332 | } | |
333 | } | |
334 | ||
335 | /** | |
336 | * add range matched residues to cigar string | |
337 | * | |
338 | * @param range | |
339 | * int | |
340 | */ | |
341 | 0 | public void addMatch(int range) |
342 | { | |
343 | 0 | this.addOperation(M, range); |
344 | } | |
345 | ||
346 | /** | |
347 | * Adds insertion and match operations based on seq to the cigar up to the | |
348 | * endpos column of seq. | |
349 | * | |
350 | * @param cigar | |
351 | * CigarBase | |
352 | * @param seq | |
353 | * SequenceI | |
354 | * @param startpos | |
355 | * int | |
356 | * @param endpos | |
357 | * int | |
358 | * @param initialDeletions | |
359 | * if true then initial deletions will be added from start of seq to | |
360 | * startpos | |
361 | */ | |
362 | 135 | protected static void addSequenceOps(CigarBase cigar, SequenceI seq, |
363 | int startpos, int endpos, boolean initialDeletions) | |
364 | { | |
365 | 135 | char op = '\0'; |
366 | 135 | int range = 0; |
367 | 135 | int p = 0, res = seq.getLength(); |
368 | ||
369 | 135 | if (!initialDeletions) |
370 | { | |
371 | 135 | p = startpos; |
372 | } | |
373 | ||
374 | 13220 | while (p <= endpos) |
375 | { | |
376 | 13085 | boolean isGap = (p < res) |
377 | ? jalview.util.Comparison.isGap(seq.getCharAt(p)) | |
378 | : true; | |
379 | 13085 | if ((startpos <= p) && (p <= endpos)) |
380 | { | |
381 | 13085 | if (isGap) |
382 | { | |
383 | 1076 | if (range > 0 && op != I) |
384 | { | |
385 | 243 | cigar.addOperation(op, range); |
386 | 243 | range = 0; |
387 | } | |
388 | 1076 | op = I; |
389 | 1076 | range++; |
390 | } | |
391 | else | |
392 | { | |
393 | 12009 | if (range > 0 && op != M) |
394 | { | |
395 | 223 | cigar.addOperation(op, range); |
396 | 223 | range = 0; |
397 | } | |
398 | 12009 | op = M; |
399 | 12009 | range++; |
400 | } | |
401 | } | |
402 | else | |
403 | { | |
404 | 0 | if (!isGap) |
405 | { | |
406 | 0 | if (range > 0 && op != D) |
407 | { | |
408 | 0 | cigar.addOperation(op, range); |
409 | 0 | range = 0; |
410 | } | |
411 | 0 | op = D; |
412 | 0 | range++; |
413 | } | |
414 | else | |
415 | { | |
416 | // do nothing - insertions are not made in flanking regions | |
417 | } | |
418 | } | |
419 | 13085 | p++; |
420 | } | |
421 | 135 | if (range > 0) |
422 | { | |
423 | 135 | cigar.addOperation(op, range); |
424 | } | |
425 | } | |
426 | ||
427 | /** | |
428 | * create a cigar string for given sequence | |
429 | * | |
430 | * @param seq | |
431 | * SequenceI | |
432 | */ | |
433 | 9 | public SeqCigar(SequenceI seq) |
434 | { | |
435 | 9 | super(); |
436 | 9 | if (seq == null) |
437 | { | |
438 | 0 | throw new Error(MessageManager |
439 | .getString("error.implementation_error_for_new_cigar")); | |
440 | } | |
441 | 9 | _setSeq(seq, false, 0, 0); |
442 | // there is still work to do | |
443 | 9 | addSequenceOps(this, seq, 0, seq.getLength() - 1, false); |
444 | } | |
445 | ||
446 | /** | |
447 | * Create Cigar from a range of gaps and residues on a sequence object | |
448 | * | |
449 | * @param seq | |
450 | * SequenceI | |
451 | * @param start | |
452 | * int - first column in range | |
453 | * @param end | |
454 | * int - last column in range | |
455 | */ | |
456 | 126 | public SeqCigar(SequenceI seq, int start, int end) |
457 | { | |
458 | 126 | super(); |
459 | 126 | if (seq == null) |
460 | { | |
461 | 0 | throw new Error(MessageManager |
462 | .getString("error.implementation_error_for_new_cigar")); | |
463 | } | |
464 | 126 | _setSeq(seq, false, start, end + 1); |
465 | // there is still work to do | |
466 | 126 | addSequenceOps(this, seq, start, end, false); |
467 | } | |
468 | ||
469 | /** | |
470 | * Create a cigar object from a cigar string like '[<I|D|M><range>]+' Will | |
471 | * fail if the given seq already contains gaps (JBPNote: future implementation | |
472 | * will fix) | |
473 | * | |
474 | * @param seq | |
475 | * SequenceI object resolvable to a dataset sequence | |
476 | * @param cigarString | |
477 | * String | |
478 | * @return Cigar | |
479 | */ | |
480 | 1 | public static SeqCigar parseCigar(SequenceI seq, String cigarString) |
481 | throws Exception | |
482 | { | |
483 | 1 | Object[] opsandrange = parseCigarString(cigarString); |
484 | 1 | return new SeqCigar(seq, (char[]) opsandrange[0], |
485 | (int[]) opsandrange[1]); | |
486 | } | |
487 | ||
488 | /** | |
489 | * create an alignment from the given array of cigar sequences and gap | |
490 | * character, and marking the given segments as visible in the given | |
491 | * hiddenColumns. | |
492 | * | |
493 | * @param alseqs | |
494 | * @param gapCharacter | |
495 | * @param hidden | |
496 | * - hiddenColumns where hidden regions are marked | |
497 | * @param segments | |
498 | * - visible regions of alignment | |
499 | * @return SequenceI[] | |
500 | */ | |
501 | 5 | public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs, |
502 | char gapCharacter, HiddenColumns hidden, int[] segments) | |
503 | { | |
504 | 5 | SequenceI[] seqs = new SequenceI[alseqs.length]; |
505 | 5 | StringBuffer[] g_seqs = new StringBuffer[alseqs.length]; |
506 | 5 | String[] alseqs_string = new String[alseqs.length]; |
507 | 5 | Object[] gs_regions = new Object[alseqs.length]; |
508 | 15 | for (int i = 0; i < alseqs.length; i++) |
509 | { | |
510 | 10 | alseqs_string[i] = alseqs[i].getRefSeq() |
511 | .getSequenceAsString(alseqs[i].start, alseqs[i].end); | |
512 | 10 | gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i], |
513 | gapCharacter); // gapped sequence, {start, start col, end. | |
514 | // endcol}, hidden regions {{start, end, col}}) | |
515 | 10 | if (gs_regions[i] == null) |
516 | { | |
517 | 0 | throw new Error(MessageManager.formatMessage( |
518 | "error.implementation_error_cigar_seq_no_operations", | |
519 | new String[] | |
520 | { Integer.valueOf(i).toString() })); | |
521 | } | |
522 | 10 | g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the |
523 | // visible | |
524 | // gapped | |
525 | // sequence | |
526 | } | |
527 | // Now account for insertions. (well - deletions) | |
528 | // this is complicated because we must keep track of shifted positions in | |
529 | // each sequence | |
530 | 5 | ShiftList shifts = new ShiftList(); |
531 | 15 | for (int i = 0; i < alseqs.length; i++) |
532 | { | |
533 | 10 | Object[] gs_region = ((Object[]) ((Object[]) gs_regions[i])[2]); |
534 | 10 | if (gs_region != null) |
535 | ||
536 | { | |
537 | 2 | for (int hr = 0; hr < gs_region.length; hr++) |
538 | { | |
539 | 1 | int[] region = (int[]) gs_region[hr]; |
540 | 1 | char[] insert = new char[region[1] - region[0] + 1]; |
541 | 7 | for (int s = 0; s < insert.length; s++) |
542 | { | |
543 | 6 | insert[s] = gapCharacter; |
544 | } | |
545 | 1 | int inspos = shifts.shift(region[2]); // resolve insertion position in |
546 | // current alignment frame of | |
547 | // reference | |
548 | 4 | for (int s = 0; s < alseqs.length; s++) |
549 | { | |
550 | 3 | if (s != i) |
551 | { | |
552 | 2 | if (g_seqs[s].length() <= inspos) |
553 | { | |
554 | // prefix insertion with more gaps. | |
555 | 0 | for (int l = inspos - g_seqs[s].length(); l > 0; l--) |
556 | { | |
557 | 0 | g_seqs[s].append(gapCharacter); // to debug - use a diffferent |
558 | // gap character here | |
559 | } | |
560 | } | |
561 | 2 | g_seqs[s].insert(inspos, insert); |
562 | } | |
563 | else | |
564 | { | |
565 | 1 | g_seqs[s].insert(inspos, |
566 | alseqs_string[i].substring(region[0], region[1] + 1)); | |
567 | } | |
568 | } | |
569 | 1 | shifts.addShift(region[2], insert.length); // update shift in |
570 | // alignment frame of | |
571 | // reference | |
572 | 1 | if (segments == null) |
573 | { | |
574 | // add a hidden column for this deletion | |
575 | 1 | hidden.hideColumns(inspos, inspos + insert.length - 1); |
576 | } | |
577 | } | |
578 | } | |
579 | } | |
580 | 15 | for (int i = 0; i < alseqs.length; i++) |
581 | { | |
582 | 10 | int[] bounds = ((int[]) ((Object[]) gs_regions[i])[1]); |
583 | 10 | SequenceI ref = alseqs[i].getRefSeq(); |
584 | 10 | seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(), |
585 | ref.getStart() + alseqs[i].start + bounds[0], | |
586 | ref.getStart() + alseqs[i].start | |
587 | 10 | + (bounds[2] == 0 ? -1 : bounds[2])); |
588 | 10 | seqs[i].setDatasetSequence(ref); |
589 | 10 | seqs[i].setDescription(ref.getDescription()); |
590 | } | |
591 | 5 | if (segments != null) |
592 | { | |
593 | 4 | for (int i = 0; i < segments.length; i += 3) |
594 | { | |
595 | // int start=shifts.shift(segments[i]-1)+1; | |
596 | // int end=shifts.shift(segments[i]+segments[i+1]-1)-1; | |
597 | 2 | hidden.hideColumns(segments[i + 1], |
598 | segments[i + 1] + segments[i + 2] - 1); | |
599 | } | |
600 | } | |
601 | 5 | return seqs; |
602 | } | |
603 | ||
604 | /** | |
605 | * references to entities that this sequence cigar is associated with. | |
606 | */ | |
607 | private Hashtable selGroups = null; | |
608 | ||
609 | 33 | public void setGroupMembership(Object group) |
610 | { | |
611 | 33 | if (selGroups == null) |
612 | { | |
613 | 33 | selGroups = new Hashtable(); |
614 | } | |
615 | 33 | selGroups.put(group, new int[0]); |
616 | } | |
617 | ||
618 | /** | |
619 | * Test for and if present remove association to group. | |
620 | * | |
621 | * @param group | |
622 | * @return true if group was associated and it was removed | |
623 | */ | |
624 | 0 | public boolean removeGroupMembership(Object group) |
625 | { | |
626 | 0 | if (selGroups != null && selGroups.containsKey(group)) |
627 | { | |
628 | 0 | selGroups.remove(group); |
629 | 0 | return true; |
630 | } | |
631 | 0 | return false; |
632 | } | |
633 | ||
634 | /** | |
635 | * forget all associations for this sequence. | |
636 | */ | |
637 | 0 | public void clearMemberships() |
638 | { | |
639 | 0 | if (selGroups != null) |
640 | { | |
641 | 0 | selGroups.clear(); |
642 | } | |
643 | 0 | selGroups = null; |
644 | } | |
645 | ||
646 | /** | |
647 | * | |
648 | * @return null or array of all associated entities | |
649 | */ | |
650 | 0 | public Object[] getAllMemberships() |
651 | { | |
652 | 0 | if (selGroups == null) |
653 | { | |
654 | 0 | return null; |
655 | } | |
656 | 0 | Object[] mmbs = new Object[selGroups.size()]; |
657 | 0 | Enumeration en = selGroups.keys(); |
658 | 0 | for (int i = 0; en.hasMoreElements(); i++) |
659 | { | |
660 | 0 | mmbs[i] = en.nextElement(); |
661 | } | |
662 | 0 | return mmbs; |
663 | } | |
664 | ||
665 | /** | |
666 | * Test for group membership | |
667 | * | |
668 | * @param sgr | |
669 | * - a selection group or some other object that may be associated | |
670 | * with seqCigar | |
671 | * @return true if sgr is associated with this seqCigar | |
672 | */ | |
673 | 363 | public boolean isMemberOf(Object sgr) |
674 | { | |
675 | 363 | return (selGroups != null) && selGroups.get(sgr) != null; |
676 | } | |
677 | } |