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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.datamodel; | |
22 | ||
23 | import java.util.BitSet; | |
24 | import java.util.Iterator; | |
25 | import java.util.List; | |
26 | import java.util.Vector; | |
27 | ||
28 | import fr.orsay.lri.varna.models.rna.RNA; | |
29 | import jalview.datamodel.Sequence.DBModList; | |
30 | import jalview.datamodel.features.SequenceFeaturesI; | |
31 | import jalview.util.MapList; | |
32 | import jalview.ws.params.InvalidArgumentException; | |
33 | ||
34 | /** | |
35 | * Methods for manipulating a sequence, its metadata and related annotation in | |
36 | * an alignment or dataset. | |
37 | * | |
38 | * @author $author$ | |
39 | * @version $Revision$ | |
40 | */ | |
41 | public interface SequenceI extends ASequenceI, ContactMapHolderI | |
42 | { | |
43 | /** | |
44 | * Set the display name for the sequence | |
45 | * | |
46 | * @param name | |
47 | */ | |
48 | public void setName(String name); | |
49 | ||
50 | /** | |
51 | * Get the display name | |
52 | */ | |
53 | public String getName(); | |
54 | ||
55 | /** | |
56 | * Set start position of first non-gapped symbol in sequence | |
57 | * | |
58 | * @param start | |
59 | * new start position | |
60 | */ | |
61 | public void setStart(int start); | |
62 | ||
63 | /** | |
64 | * get start position of first non-gapped residue in sequence | |
65 | * | |
66 | * @return | |
67 | */ | |
68 | public int getStart(); | |
69 | ||
70 | /** | |
71 | * get the displayed id of the sequence | |
72 | * | |
73 | * @return true means the id will be returned in the form | |
74 | * DisplayName/Start-End | |
75 | */ | |
76 | public String getDisplayId(boolean jvsuffix); | |
77 | ||
78 | /** | |
79 | * set end position for last residue in sequence | |
80 | * | |
81 | * @param end | |
82 | */ | |
83 | public void setEnd(int end); | |
84 | ||
85 | /** | |
86 | * get end position for last residue in sequence getEnd()>getStart() unless | |
87 | * sequence only consists of gap characters | |
88 | * | |
89 | * @return | |
90 | */ | |
91 | public int getEnd(); | |
92 | ||
93 | /** | |
94 | * @return length of sequence including gaps | |
95 | * | |
96 | */ | |
97 | public int getLength(); | |
98 | ||
99 | /** | |
100 | * Replace the sequence with the given string | |
101 | * | |
102 | * @param sequence | |
103 | * new sequence string | |
104 | */ | |
105 | public void setSequence(String sequence); | |
106 | ||
107 | /** | |
108 | * @return sequence as string | |
109 | */ | |
110 | public String getSequenceAsString(); | |
111 | ||
112 | /** | |
113 | * get a range on the sequence as a string | |
114 | * | |
115 | * @param start | |
116 | * (inclusive) position relative to start of sequence including gaps | |
117 | * (from 0) | |
118 | * @param end | |
119 | * (exclusive) position relative to start of sequence including gaps | |
120 | * (from 0) | |
121 | * | |
122 | * @return String containing all gap and symbols in specified range | |
123 | */ | |
124 | public String getSequenceAsString(int start, int end); | |
125 | ||
126 | /** | |
127 | * Answers a copy of the sequence as a character array | |
128 | * | |
129 | * @return | |
130 | */ | |
131 | public char[] getSequence(); | |
132 | ||
133 | /** | |
134 | * get stretch of sequence characters in an array | |
135 | * | |
136 | * @param start | |
137 | * absolute index into getSequence() | |
138 | * @param end | |
139 | * exclusive index of last position in segment to be returned. | |
140 | * | |
141 | * @return char[max(0,end-start)]; | |
142 | */ | |
143 | public char[] getSequence(int start, int end); | |
144 | ||
145 | /** | |
146 | * create a new sequence object with a subsequence of this one but sharing the | |
147 | * same dataset sequence | |
148 | * | |
149 | * @param start | |
150 | * int index for start position (base 0, inclusive) | |
151 | * @param end | |
152 | * int index for end position (base 0, exclusive) | |
153 | * | |
154 | * @return SequenceI | |
155 | * @note implementations may use getSequence to get the sequence data | |
156 | */ | |
157 | public SequenceI getSubSequence(int start, int end); | |
158 | ||
159 | /** | |
160 | * get the i'th character in this sequence's local reference frame (ie from | |
161 | * 0-number of characters lying from start-end) | |
162 | * | |
163 | * @param i | |
164 | * index | |
165 | * @return character or ' ' | |
166 | */ | |
167 | public char getCharAt(int i); | |
168 | ||
169 | /** | |
170 | * DOCUMENT ME! | |
171 | * | |
172 | * @param desc | |
173 | * DOCUMENT ME! | |
174 | */ | |
175 | public void setDescription(String desc); | |
176 | ||
177 | /** | |
178 | * DOCUMENT ME! | |
179 | * | |
180 | * @return DOCUMENT ME! | |
181 | */ | |
182 | public String getDescription(); | |
183 | ||
184 | /** | |
185 | * Return the alignment column (from 1..) for a sequence position | |
186 | * | |
187 | * @param pos | |
188 | * lying from start to end | |
189 | * | |
190 | * @return aligned column for residue (0 if residue is upstream from | |
191 | * alignment, -1 if residue is downstream from alignment) note. | |
192 | * Sequence object returns sequence.getEnd() for positions upstream | |
193 | * currently. TODO: change sequence for | |
194 | * assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs | |
195 | * | |
196 | */ | |
197 | public int findIndex(int pos); | |
198 | ||
199 | /** | |
200 | * Returns the sequence position for an alignment (column) position. If at a | |
201 | * gap, returns the position of the next residue to the right. If beyond the | |
202 | * end of the sequence, returns 1 more than the last residue position. | |
203 | * | |
204 | * @param i | |
205 | * column index in alignment (from 0..<length) | |
206 | * | |
207 | * @return | |
208 | */ | |
209 | public int findPosition(int i); | |
210 | ||
211 | /** | |
212 | * Returns the sequence positions for first and last residues lying within the | |
213 | * given column positions [fromColum,toColumn] (where columns are numbered | |
214 | * from 1), or null if no residues are included in the range | |
215 | * | |
216 | * @param fromColum | |
217 | * - first column base 1 | |
218 | * @param toColumn | |
219 | * - last column, base 1 | |
220 | * @return | |
221 | */ | |
222 | public ContiguousI findPositions(int fromColum, int toColumn); | |
223 | ||
224 | /** | |
225 | * Returns an int array where indices correspond to each residue in the | |
226 | * sequence and the element value gives its position in the alignment | |
227 | * | |
228 | * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no | |
229 | * residues in SequenceI object | |
230 | */ | |
231 | public int[] gapMap(); | |
232 | ||
233 | /** | |
234 | * Build a bitset corresponding to sequence gaps | |
235 | * | |
236 | * @return a BitSet where set values correspond to gaps in the sequence | |
237 | */ | |
238 | public BitSet gapBitset(); | |
239 | ||
240 | /** | |
241 | * Returns an int array where indices correspond to each position in sequence | |
242 | * char array and the element value gives the result of findPosition for that | |
243 | * index in the sequence. | |
244 | * | |
245 | * @return int[SequenceI.getLength()] | |
246 | */ | |
247 | public int[] findPositionMap(); | |
248 | ||
249 | /** | |
250 | * Answers true if the sequence is composed of amino acid characters. Note | |
251 | * that implementations may use heuristic methods which are not guaranteed to | |
252 | * give the biologically 'right' answer. | |
253 | * | |
254 | * @return | |
255 | */ | |
256 | public boolean isProtein(); | |
257 | ||
258 | /** | |
259 | * Delete a range of aligned sequence columns, creating a new dataset sequence | |
260 | * if necessary and adjusting start and end positions accordingly. | |
261 | * | |
262 | * @param i | |
263 | * first column in range to delete (inclusive) | |
264 | * @param j | |
265 | * last column in range to delete (exclusive) | |
266 | */ | |
267 | public void deleteChars(int i, int j); | |
268 | ||
269 | /** | |
270 | * DOCUMENT ME! | |
271 | * | |
272 | * @param i | |
273 | * alignment column number | |
274 | * @param c | |
275 | * character to insert | |
276 | */ | |
277 | public void insertCharAt(int i, char c); | |
278 | ||
279 | /** | |
280 | * insert given character at alignment column position | |
281 | * | |
282 | * @param position | |
283 | * alignment column number | |
284 | * @param count | |
285 | * length of insert | |
286 | * @param ch | |
287 | * character to insert | |
288 | */ | |
289 | public void insertCharAt(int position, int count, char ch); | |
290 | ||
291 | /** | |
292 | * Answers a list of all sequence features associated with this sequence. The | |
293 | * list may be held by the sequence's dataset sequence if that is defined. | |
294 | * | |
295 | * @return | |
296 | */ | |
297 | public List<SequenceFeature> getSequenceFeatures(); | |
298 | ||
299 | /** | |
300 | * Answers the object holding features for the sequence | |
301 | * | |
302 | * @return | |
303 | */ | |
304 | SequenceFeaturesI getFeatures(); | |
305 | ||
306 | /** | |
307 | * Replaces the sequence features associated with this sequence with the given | |
308 | * features. If this sequence has a dataset sequence, then this method will | |
309 | * update the dataset sequence's features instead. | |
310 | * | |
311 | * @param features | |
312 | */ | |
313 | public void setSequenceFeatures(List<SequenceFeature> features); | |
314 | ||
315 | /** | |
316 | * DOCUMENT ME! | |
317 | * | |
318 | * @param id | |
319 | * DOCUMENT ME! | |
320 | */ | |
321 | public void setPDBId(Vector<PDBEntry> ids); | |
322 | ||
323 | /** | |
324 | * Returns a list | |
325 | * | |
326 | * @return DOCUMENT ME! | |
327 | */ | |
328 | public Vector<PDBEntry> getAllPDBEntries(); | |
329 | ||
330 | /** | |
331 | * Adds the entry to the *normalised* list of PDBIds. | |
332 | * | |
333 | * If a PDBEntry is passed with the same entry.getID() string as one already | |
334 | * in the list, or one is added that appears to be the same but has a chain ID | |
335 | * appended, then the existing PDBEntry will be updated with the new | |
336 | * attributes instead, unless the entries have distinct chain codes or | |
337 | * associated structure files. | |
338 | * | |
339 | * @param entry | |
340 | * @return true if the entry was added, false if updated | |
341 | */ | |
342 | public boolean addPDBId(PDBEntry entry); | |
343 | ||
344 | /** | |
345 | * update the list of PDBEntrys to include any DBRefEntrys citing structural | |
346 | * databases | |
347 | * | |
348 | * @return true if PDBEntry list was modified | |
349 | */ | |
350 | public boolean updatePDBIds(); | |
351 | ||
352 | public String getVamsasId(); | |
353 | ||
354 | public void setVamsasId(String id); | |
355 | ||
356 | /** | |
357 | * set the array of Database references for the sequence. | |
358 | * | |
359 | * BH 2019.02.04 changes param to DBModlist | |
360 | * | |
361 | * @param dbs | |
362 | * @deprecated - use is discouraged since side-effects may occur if DBRefEntry | |
363 | * set are not normalised. | |
364 | * @throws InvalidArgumentException | |
365 | * if the is not one created by Sequence itself | |
366 | */ | |
367 | @Deprecated | |
368 | public void setDBRefs(DBModList<DBRefEntry> dbs); | |
369 | ||
370 | public DBModList<DBRefEntry> getDBRefs(); | |
371 | ||
372 | /** | |
373 | * add the given entry to the list of DBRefs for this sequence, or replace a | |
374 | * similar one if entry contains a map object and the existing one doesnt. | |
375 | * | |
376 | * @param entry | |
377 | */ | |
378 | public void addDBRef(DBRefEntry entry); | |
379 | ||
380 | /** | |
381 | * Adds the given sequence feature and returns true, or returns false if it is | |
382 | * already present on the sequence, or if the feature type is null. | |
383 | * | |
384 | * @param sf | |
385 | * @return | |
386 | */ | |
387 | public boolean addSequenceFeature(SequenceFeature sf); | |
388 | ||
389 | public void deleteFeature(SequenceFeature sf); | |
390 | ||
391 | public void setDatasetSequence(SequenceI seq); | |
392 | ||
393 | public SequenceI getDatasetSequence(); | |
394 | ||
395 | /** | |
396 | * Returns a new array containing this sequence's annotations, or null. | |
397 | */ | |
398 | public AlignmentAnnotation[] getAnnotation(); | |
399 | ||
400 | /** | |
401 | * Returns true if this sequence has the given annotation (by object | |
402 | * identity). | |
403 | */ | |
404 | public boolean hasAnnotation(AlignmentAnnotation ann); | |
405 | ||
406 | /** | |
407 | * Add the given annotation, if not already added, and set its sequence ref to | |
408 | * be this sequence. Does nothing if this sequence's annotations already | |
409 | * include this annotation (by identical object reference). | |
410 | */ | |
411 | public void addAlignmentAnnotation(AlignmentAnnotation annotation); | |
412 | ||
413 | public void removeAlignmentAnnotation(AlignmentAnnotation annotation); | |
414 | ||
415 | /** | |
416 | * Derive a sequence (using this one's dataset or as the dataset) | |
417 | * | |
418 | * @return duplicate sequence and any annotation present with valid dataset | |
419 | * sequence | |
420 | */ | |
421 | public SequenceI deriveSequence(); | |
422 | ||
423 | /** | |
424 | * set the array of associated AlignmentAnnotation for this sequenceI | |
425 | * | |
426 | * @param revealed | |
427 | */ | |
428 | public void setAlignmentAnnotation(AlignmentAnnotation[] annotation); | |
429 | ||
430 | /** | |
431 | * Get one or more alignment annotations with a particular label. | |
432 | * | |
433 | * @param label | |
434 | * string which each returned annotation must have as a label. | |
435 | * @return null or array of annotations. | |
436 | */ | |
437 | public AlignmentAnnotation[] getAnnotation(String label); | |
438 | ||
439 | /** | |
440 | * Returns a (possibly empty) list of any annotations that match on given | |
441 | * calcId (source) and label (type). Null values do not match. | |
442 | * | |
443 | * @param calcId | |
444 | * @param label | |
445 | */ | |
446 | public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId, | |
447 | String label); | |
448 | ||
449 | /** | |
450 | * Returns a (possibly empty) list of any annotations that match on given | |
451 | * calcId (source), label (type) and description (observation instance). Null | |
452 | * values do not match. | |
453 | * | |
454 | * @param calcId | |
455 | * @param label | |
456 | * @param description | |
457 | */ | |
458 | public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId, | |
459 | String label, String description); | |
460 | ||
461 | /** | |
462 | * create a new dataset sequence (if necessary) for this sequence and sets | |
463 | * this sequence to refer to it. This call will move any features or | |
464 | * references on the sequence onto the dataset. It will also make a duplicate | |
465 | * of existing annotation rows for the dataset sequence, rather than relocate | |
466 | * them in order to preserve external references (since 2.8.2). | |
467 | * | |
468 | * @return dataset sequence for this sequence | |
469 | */ | |
470 | public SequenceI createDatasetSequence(); | |
471 | ||
472 | /** | |
473 | * Transfer any database references or annotation from entry under a sequence | |
474 | * mapping. <br/> | |
475 | * <strong>Note: DOES NOT transfer sequence associated alignment annotation | |
476 | * </strong><br/> | |
477 | * | |
478 | * @param entry | |
479 | * @param mp | |
480 | * null or mapping from entry's numbering to local start/end | |
481 | */ | |
482 | public void transferAnnotation(SequenceI entry, Mapping mp); | |
483 | ||
484 | /** | |
485 | * @return The RNA of the sequence in the alignment | |
486 | */ | |
487 | ||
488 | public RNA getRNA(); | |
489 | ||
490 | /** | |
491 | * @param rna | |
492 | * The RNA. | |
493 | */ | |
494 | public void setRNA(RNA rna); | |
495 | ||
496 | /** | |
497 | * | |
498 | * @return list of insertions (gap characters) in sequence | |
499 | */ | |
500 | public List<int[]> getInsertions(); | |
501 | ||
502 | /** | |
503 | * Given a pdbId String, return the equivalent PDBEntry if available in the | |
504 | * given sequence | |
505 | * | |
506 | * @param pdbId | |
507 | * @return | |
508 | */ | |
509 | public PDBEntry getPDBEntry(String pdbId); | |
510 | ||
511 | /** | |
512 | * Get all primary database/accessions for this sequence's data. These | |
513 | * DBRefEntry are expected to resolve to a valid record in the associated | |
514 | * external database, either directly or via a provided 1:1 Mapping. | |
515 | * | |
516 | * @return just the primary references (if any) for this sequence, or an empty | |
517 | * list | |
518 | */ | |
519 | public List<DBRefEntry> getPrimaryDBRefs(); | |
520 | ||
521 | /** | |
522 | * Returns a (possibly empty) list of sequence features that overlap the given | |
523 | * alignment column range, optionally restricted to one or more specified | |
524 | * feature types. If the range is all gaps, then features which enclose it are | |
525 | * included (but not contact features). | |
526 | * | |
527 | * @param fromCol | |
528 | * start column of range inclusive (1..) | |
529 | * @param toCol | |
530 | * end column of range inclusive (1..) | |
531 | * @param types | |
532 | * optional feature types to restrict results to | |
533 | * @return | |
534 | */ | |
535 | List<SequenceFeature> findFeatures(int fromCol, int toCol, | |
536 | String... types); | |
537 | ||
538 | /** | |
539 | * Method to call to indicate that the sequence (characters or alignment/gaps) | |
540 | * has been modified. Provided to allow any cursors on residue/column | |
541 | * positions to be invalidated. | |
542 | */ | |
543 | void sequenceChanged(); | |
544 | ||
545 | /** | |
546 | * | |
547 | * @return BitSet corresponding to index [0,length) where Comparison.isGap() | |
548 | * returns true. | |
549 | */ | |
550 | BitSet getInsertionsAsBits(); | |
551 | ||
552 | /** | |
553 | * Replaces every occurrence of c1 in the sequence with c2 and returns the | |
554 | * number of characters changed | |
555 | * | |
556 | * @param c1 | |
557 | * @param c2 | |
558 | */ | |
559 | public int replace(char c1, char c2); | |
560 | ||
561 | /** | |
562 | * Answers the GeneLociI, or null if not known | |
563 | * | |
564 | * @return | |
565 | */ | |
566 | GeneLociI getGeneLoci(); | |
567 | ||
568 | /** | |
569 | * Sets the mapping to gene loci for the sequence | |
570 | * | |
571 | * @param speciesId | |
572 | * @param assemblyId | |
573 | * @param chromosomeId | |
574 | * @param map | |
575 | */ | |
576 | void setGeneLoci(String speciesId, String assemblyId, String chromosomeId, | |
577 | MapList map); | |
578 | ||
579 | /** | |
580 | * Returns the sequence string constructed from the substrings of a sequence | |
581 | * defined by the int[] ranges provided by an iterator. E.g. the iterator | |
582 | * could iterate over all visible regions of the alignment | |
583 | * | |
584 | * @param it | |
585 | * the iterator to use | |
586 | * @return a String corresponding to the sequence | |
587 | */ | |
588 | public String getSequenceStringFromIterator(Iterator<int[]> it); | |
589 | ||
590 | /** | |
591 | * Locate the first position in this sequence which is not contained in an | |
592 | * iterator region. If no such position exists, return 0 | |
593 | * | |
594 | * @param it | |
595 | * iterator over regions | |
596 | * @return first residue not contained in regions | |
597 | */ | |
598 | public int firstResidueOutsideIterator(Iterator<int[]> it); | |
599 | ||
600 | public void addContactListFor(AlignmentAnnotation annotation, | |
601 | ContactMatrixI cm); | |
602 | ||
603 | } |