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CigarBase | 27 | 220 | 99 |
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.util.MessageManager; | |
24 | ||
25 | import java.util.Vector; | |
26 | ||
27 | public abstract class CigarBase | |
28 | { | |
29 | /** | |
30 | * Base class for compact idiosyncratic representation of gaps and aligned | |
31 | * residues Regards to Tom Oldfield for his DynamicArray class. 17th July 2006 | |
32 | * Not thread safe. | |
33 | */ | |
34 | 173 | public CigarBase() |
35 | { | |
36 | // nothing to be done (probably) | |
37 | } | |
38 | ||
39 | protected int length = 0; | |
40 | ||
41 | protected int _inc_length = 10; // extension range for addition of new | |
42 | ||
43 | // operations | |
44 | ||
45 | protected char[] operation = null; | |
46 | ||
47 | protected int[] range = null; | |
48 | ||
49 | /** | |
50 | * Range of Hidden residues in seq (translated as deleted in seq) | |
51 | */ | |
52 | public static final char D = 'D'; | |
53 | ||
54 | /** | |
55 | * Range of insertions to seq | |
56 | */ | |
57 | public static final char I = 'I'; | |
58 | ||
59 | /** | |
60 | * Range of aligned residues | |
61 | */ | |
62 | public static final char M = 'M'; | |
63 | ||
64 | static protected final char _case_shift = 'a' - 'A'; | |
65 | ||
66 | /** | |
67 | * Ugly function to get edited sequence string, start and end symbol positions | |
68 | * and the deletion regions as an array of int pairs May return null for an | |
69 | * empty cigar string. May return null for deletion ranges if there are none. | |
70 | * | |
71 | * @param reference | |
72 | * - the symbol sequence to apply the cigar operations to (or null if | |
73 | * no sequence) | |
74 | * @param GapChar | |
75 | * - the symbol to use for Insert operations | |
76 | * @return Object[] { String, int[] {start, startcol, end, endcol}, int[][3] | |
77 | * {start, end, col} or null} the gapped sequence, first and last | |
78 | * residue index, and the deletion ranges on the reference sequence | |
79 | */ | |
80 | 208 | public Object[] getSequenceAndDeletions(String reference, char GapChar) |
81 | { | |
82 | 208 | int rlength = 0; |
83 | 208 | int[][] deletions = new int[length][]; |
84 | 208 | int[][] trunc_deletions = null; |
85 | 208 | StringBuffer sq = new StringBuffer(); |
86 | 208 | int cursor = 0, alcursor = 0, start = 0, startpos = 0, end = 0, |
87 | endpos = 0, delcount = -1; | |
88 | 208 | boolean consecutive_del = false; |
89 | 208 | if (length == 0) |
90 | { | |
91 | 0 | return null; |
92 | } | |
93 | 208 | if (reference != null) |
94 | { | |
95 | 208 | rlength = reference.length(); |
96 | } | |
97 | 208 | boolean modstart = true; |
98 | 1328 | for (int i = 0; i < length; i++) |
99 | { | |
100 | 1120 | switch (operation[i]) |
101 | { | |
102 | 106 | case D: |
103 | 106 | if (!consecutive_del) |
104 | { | |
105 | 106 | deletions[++delcount] = new int[] { cursor, 0, alcursor }; |
106 | } | |
107 | 106 | cursor += range[i]; |
108 | 106 | deletions[delcount][1] = cursor - 1; |
109 | 106 | consecutive_del = true; |
110 | 106 | break; |
111 | 410 | case I: |
112 | 410 | consecutive_del = false; |
113 | 1846 | for (int r = 0; r < range[i]; r++) |
114 | { | |
115 | 1436 | sq.append(GapChar); |
116 | 1436 | alcursor++; |
117 | } | |
118 | 410 | break; |
119 | 604 | case M: |
120 | 604 | consecutive_del = false; |
121 | 604 | if (modstart) |
122 | { | |
123 | 206 | start = cursor; |
124 | 206 | startpos = alcursor; |
125 | 206 | modstart = false; |
126 | } | |
127 | 604 | if (reference != null) |
128 | { | |
129 | 604 | int sbend = cursor + range[i]; |
130 | 604 | if (sbend > rlength) |
131 | { | |
132 | 0 | sq.append(reference.substring(cursor, rlength)); |
133 | 0 | while (sbend-- >= rlength) |
134 | { | |
135 | 0 | sq.append(GapChar); |
136 | } | |
137 | } | |
138 | else | |
139 | { | |
140 | 604 | sq.append(reference.substring(cursor, sbend)); |
141 | } | |
142 | } | |
143 | 604 | alcursor += range[i]; |
144 | 604 | cursor += range[i]; |
145 | 604 | end = cursor - 1; |
146 | 604 | endpos = alcursor; |
147 | 604 | break; |
148 | 0 | default: |
149 | 0 | throw new Error(MessageManager.formatMessage( |
150 | "error.unknown_seq_cigar_operation", new String[] | |
151 | { new StringBuffer(operation[i]).toString() })); | |
152 | } | |
153 | } | |
154 | 208 | if (++delcount > 0) |
155 | { | |
156 | 96 | trunc_deletions = new int[delcount][]; |
157 | 96 | System.arraycopy(deletions, 0, trunc_deletions, 0, delcount); |
158 | } | |
159 | 208 | deletions = null; |
160 | 208 | return new Object[] { ((reference != null) ? sq.toString() : null), |
161 | new int[] | |
162 | { start, startpos, end, endpos }, trunc_deletions }; | |
163 | } | |
164 | ||
165 | 101 | protected void compact_operations() |
166 | { | |
167 | 101 | int i = 1; |
168 | 101 | if (operation == null) |
169 | { | |
170 | 101 | return; |
171 | } | |
172 | 0 | char last = operation[0]; |
173 | 0 | while (i < length) |
174 | { | |
175 | 0 | if (last == operation[i]) |
176 | { | |
177 | 0 | range[i - 1] += range[i]; |
178 | 0 | int r = length - i; |
179 | 0 | if (r > 0) |
180 | { | |
181 | 0 | System.arraycopy(range, i + 1, range, i, r); |
182 | 0 | System.arraycopy(operation, i + 1, operation, i, r); |
183 | } | |
184 | 0 | length--; |
185 | } | |
186 | else | |
187 | { | |
188 | 0 | last = operation[i++]; |
189 | } | |
190 | } | |
191 | } | |
192 | ||
193 | /** | |
194 | * turn a cigar string into a series of operation range pairs | |
195 | * | |
196 | * @param cigarString | |
197 | * String | |
198 | * @return object[] {char[] operation, int[] range} | |
199 | * @throws java.lang.Exception | |
200 | * for improperly formated cigar strings or ones with unknown | |
201 | * operations | |
202 | */ | |
203 | 1 | public static Object[] parseCigarString(String cigarString) |
204 | throws Exception | |
205 | { | |
206 | 1 | int ops = 0; |
207 | 23 | for (int i = 0, l = cigarString.length(); i < l; i++) |
208 | { | |
209 | 22 | char c = cigarString.charAt(i); |
210 | 22 | if (c == M || c == (M - _case_shift) || c == I |
211 | || c == (I - _case_shift) || c == D || c == (D - _case_shift)) | |
212 | { | |
213 | 10 | ops++; |
214 | } | |
215 | } | |
216 | 1 | char[] operation = new char[ops]; |
217 | 1 | int[] range = new int[ops]; |
218 | 1 | int op = 0; |
219 | 1 | int i = 0, l = cigarString.length(); |
220 | 11 | while (i < l) |
221 | { | |
222 | 10 | char c; |
223 | 10 | int j = i; |
224 | 10 | do |
225 | { | |
226 | 22 | c = cigarString.charAt(j++); |
227 | 22 | } while (c >= '0' && c <= '9' && j < l); |
228 | 10 | if (j >= l && c >= '0' && c <= '9') |
229 | { | |
230 | 0 | throw new Exception(MessageManager |
231 | .getString("exception.unterminated_cigar_string")); | |
232 | } | |
233 | 10 | try |
234 | { | |
235 | 10 | String rangeint = cigarString.substring(i, j - 1); |
236 | 10 | range[op] = Integer.parseInt(rangeint); |
237 | 10 | i = j; |
238 | } catch (Exception e) | |
239 | { | |
240 | 0 | throw new Error(MessageManager |
241 | .getString("error.implementation_bug_parse_cigar_string")); | |
242 | } | |
243 | 10 | if (c >= 'a' && c <= 'z') |
244 | { | |
245 | 0 | c -= _case_shift; |
246 | } | |
247 | 10 | if ((c == M || c == I || c == D)) |
248 | { | |
249 | 10 | operation[op++] = c; |
250 | } | |
251 | else | |
252 | { | |
253 | 0 | throw new Exception(MessageManager.formatMessage( |
254 | "exception.unexpected_operation_cigar_string_pos", | |
255 | new String[] | |
256 | { new StringBuffer(c).toString(), | |
257 | Integer.valueOf(i).toString(), cigarString })); | |
258 | } | |
259 | } | |
260 | 1 | return new Object[] { operation, range }; |
261 | } | |
262 | ||
263 | /** | |
264 | * add an operation to cigar string | |
265 | * | |
266 | * @param op | |
267 | * char | |
268 | * @param range | |
269 | * int | |
270 | */ | |
271 | 1403 | public void addOperation(char op, int range) |
272 | { | |
273 | 1403 | if (op >= 'a' && op <= 'z') |
274 | { | |
275 | 0 | op -= _case_shift; |
276 | } | |
277 | 1403 | if (op != M && op != D && op != I) |
278 | { | |
279 | 0 | throw new Error(MessageManager.getString( |
280 | "error.implementation_error_invalid_operation_string")); | |
281 | } | |
282 | 1403 | if (range == 0) |
283 | { | |
284 | 0 | return; // No Operation to add. |
285 | } | |
286 | 1403 | if (range < 0) |
287 | { | |
288 | 0 | throw new Error( |
289 | MessageManager.getString("error.invalid_range_string")); | |
290 | } | |
291 | 1403 | int lngth = 0; |
292 | 1403 | if (operation == null) |
293 | { | |
294 | 272 | this.operation = new char[_inc_length]; |
295 | 272 | this.range = new int[_inc_length]; |
296 | } | |
297 | 1403 | if (length + 1 == operation.length) |
298 | { | |
299 | 23 | char[] ops = this.operation; |
300 | 23 | this.operation = new char[length + 1 + _inc_length]; |
301 | 23 | System.arraycopy(ops, 0, this.operation, 0, length); |
302 | 23 | ops = null; |
303 | 23 | int[] rng = this.range; |
304 | 23 | this.range = new int[length + 1 + _inc_length]; |
305 | 23 | System.arraycopy(rng, 0, this.range, 0, length); |
306 | 23 | rng = null; |
307 | } | |
308 | 1403 | if ((length > 0) && (operation[length - 1] == op)) |
309 | { | |
310 | 98 | length--; // modify existing operation. |
311 | } | |
312 | else | |
313 | { | |
314 | 1305 | this.range[length] = 0; // reset range |
315 | } | |
316 | 1403 | this.operation[length] = op; |
317 | 1403 | this.range[length++] += range; |
318 | } | |
319 | ||
320 | /** | |
321 | * semi-efficient insert an operation on the current cigar string set at | |
322 | * column pos (from 1) NOTE: Insertion operations simply extend width of cigar | |
323 | * result - affecting registration of alignment Deletion ops will shorten | |
324 | * length of result - and affect registration of alignment Match ops will also | |
325 | * affect length of result - affecting registration of alignment (ie | |
326 | * "10M".insert(4,I,3)->"4M3I3M") - (replace?) (ie | |
327 | * "10M".insert(4,D,3)->"4M3D3M") - (shortens alignment) (ie | |
328 | * "5I5M".insert(4,I,3)->"8I5M") - real insertion (ie | |
329 | * "5I5M".insert(4,D,3)->"4I2D3M") - shortens aligment - I's are removed, Ms | |
330 | * changed to Ds (ie "10M".insert(4,M,3)->"13M") - lengthens - Is changed to | |
331 | * M, Ds changed to M. (ie "5I5M".insert(4,M,3)->"4I8M") - effectively shifts | |
332 | * sequence left by 1 residue and extends it by 3 ( | |
333 | * "10D5M".insert(-1,M,3)->"3M7D5M") ( "10D5M".insert(0,M,3)->"7D8M") ( | |
334 | * "10D5M".insert(1,M,3)->"10D8M") ( "1M10D5M".insert(0,M,3)->"1M10D8M") ( | |
335 | * "1M10D5M".insert(1,M,3)->" | |
336 | * | |
337 | * if pos is beyond width - I operations are added before the operation | |
338 | * | |
339 | * @param pos | |
340 | * int -1, 0-length of visible region, or greater to append new ops | |
341 | * (with insertions in between) | |
342 | * @param op | |
343 | * char | |
344 | * @param range | |
345 | * int public void addOperationAt(int pos, char op, int range) { int | |
346 | * cursor = -1; // mark the position for the current operation being | |
347 | * edited. int o = 0; boolean last_d = false; // previous op was a | |
348 | * deletion. if (pos < -1) throw new Error("pos<-1 is not | |
349 | * supported."); while (o<length) { if (operation[o] != D) { if ( | |
350 | * (cursor + this.range[o]) < pos) { cursor += this.range[o]; o++; | |
351 | * last_d=false; } else { break; } } else { last_d=true; o++; } } if | |
352 | * (o==length) { // must insert more operations before pos if | |
353 | * (pos-cursor>0) addInsertion(pos-cursor); // then just add the new | |
354 | * operation. Regardless of what it is. addOperation(op, range); } | |
355 | * else { int diff = pos - cursor; | |
356 | * | |
357 | * int e_length = length-o; // new edit operation array length. // | |
358 | * diff<0 - can only happen before first insertion or match. - | |
359 | * affects op and all following // dif==0 - only when at first | |
360 | * position of existing op - // diff>0 - must preserve some existing | |
361 | * operations int[] e_range = new int[e_length]; | |
362 | * System.arraycopy(this.range, o, e_range, 0, e_length); char[] e_op | |
363 | * = new char[e_length]; System.arraycopy(this.operation, o, e_op, 0, | |
364 | * e_length); length = o; // can now use add_operation to extend | |
365 | * list. int e_o=0; // current operation being edited. switch (op) { | |
366 | * case M: switch (e_op[e_o]) { case M: if (last_d && diff <= 0) { // | |
367 | * reduce D's, if possible if (range<=this.range[o-1]) { this.range[o | |
368 | * - 1] -= range; } else { this.range[o-1]=0; } if | |
369 | * (this.range[o-1]==0) o--; // lose this op. } e_range[e_o] += | |
370 | * range; // just add more matched residues break; case I: // change | |
371 | * from insertion to match if (last_d && diff<=0) { // reduce D's, if | |
372 | * possible if (range<=this.range[o-1]) { this.range[o - 1] -= range; | |
373 | * } else { this.range[o-1]=0; } if (this.range[o-1]==0) o--; // lose | |
374 | * this op. } e_range[e_o] break; default: throw new Inp } | |
375 | * | |
376 | * break; case I: break; case D: } break; default: throw new | |
377 | * Error("Implementation Error: Unknown operation in addOperation!"); | |
378 | * } // finally, add remaining ops. while (e_o<e_length) { | |
379 | * addOperation(e_op[e_o], e_range[e_o]); e_o++; } } } | |
380 | */ | |
381 | /** | |
382 | * Mark residues from start to end (inclusive) as deleted from the alignment, | |
383 | * and removes any insertions. | |
384 | * | |
385 | * @param start | |
386 | * int | |
387 | * @param end | |
388 | * int | |
389 | * @return deleted int - number of symbols marked as deleted | |
390 | */ | |
391 | 101 | public int deleteRange(int start, int end) |
392 | { | |
393 | 101 | int deleted = 0; |
394 | 101 | if (length == 0) |
395 | { | |
396 | // nothing to do here | |
397 | 0 | return deleted; |
398 | } | |
399 | 101 | if (start < 0 || start > end) |
400 | { | |
401 | 0 | throw new Error(MessageManager.getString( |
402 | "error.implementation_error_delete_range_out_of_bounds")); | |
403 | } | |
404 | // find beginning | |
405 | 101 | int cursor = 0; // mark the position for the current operation being edited. |
406 | 101 | int rlength = 1 + end - start; // number of positions to delete |
407 | 101 | int oldlen = length; |
408 | 101 | int o = 0; |
409 | 101 | boolean editing = false; |
410 | 101 | char[] oldops = operation; |
411 | 101 | int[] oldrange = range; |
412 | 101 | length = 0; |
413 | 101 | operation = null; |
414 | 101 | range = null; |
415 | 101 | compact_operations(); |
416 | 655 | while (o < oldlen && cursor <= end && rlength > 0) |
417 | { | |
418 | 554 | if (oldops[o] == D) |
419 | { | |
420 | // absorbed into new deleted region. | |
421 | 70 | addDeleted(oldrange[o++]); |
422 | 70 | continue; |
423 | } | |
424 | ||
425 | 484 | int remain = oldrange[o]; // number of op characters left to edit |
426 | 484 | if (!editing) |
427 | { | |
428 | 430 | if ((cursor + remain) <= start) |
429 | { | |
430 | 329 | addOperation(oldops[o], oldrange[o]); |
431 | 329 | cursor += oldrange[o++]; |
432 | 329 | continue; // next operation |
433 | } | |
434 | 101 | editing = true; |
435 | // add operations before hidden region | |
436 | 101 | if (start - cursor > 0) |
437 | { | |
438 | 87 | addOperation(oldops[o], start - cursor); |
439 | 87 | remain -= start - cursor; |
440 | } | |
441 | } | |
442 | // start inserting new ops | |
443 | 155 | if (o < oldlen && editing && rlength > 0 && remain > 0) |
444 | { | |
445 | 155 | switch (oldops[o]) |
446 | { | |
447 | 106 | case M: |
448 | 106 | if (rlength > remain) |
449 | { | |
450 | 72 | addDeleted(remain); |
451 | 72 | deleted += remain; |
452 | } | |
453 | else | |
454 | { | |
455 | 34 | deleted += rlength; |
456 | 34 | addDeleted(rlength); |
457 | 34 | if (remain - rlength > 0) |
458 | { | |
459 | 14 | this.addOperation(M, remain - rlength); // add remaining back. |
460 | } | |
461 | 34 | rlength = 0; |
462 | 34 | remain = 0; |
463 | } | |
464 | 106 | break; |
465 | 49 | case I: |
466 | 49 | if (remain - rlength > 0) |
467 | { | |
468 | // only remove some gaps | |
469 | 13 | addInsertion(remain - rlength); |
470 | 13 | rlength = 0; |
471 | } | |
472 | 49 | break; |
473 | 0 | case D: |
474 | 0 | throw new Error( |
475 | MessageManager.getString("error.implementation_error")); // do | |
476 | // nothing; | |
477 | 0 | default: |
478 | 0 | throw new Error(MessageManager.formatMessage( |
479 | "error.implementation_error_unknown_operation", | |
480 | new String[] | |
481 | { new StringBuffer(oldops[o]).toString() })); | |
482 | } | |
483 | 155 | rlength -= remain; |
484 | 155 | remain = oldrange[++o]; // number of op characters left to edit |
485 | } | |
486 | } | |
487 | // add remaining | |
488 | 200 | while (o < oldlen) |
489 | { | |
490 | 99 | addOperation(oldops[o], oldrange[o++]); |
491 | } | |
492 | // if (cursor<(start+1)) { | |
493 | // ran out of ops - nothing to do here ? | |
494 | // addInsertion(start-cursor); | |
495 | // } | |
496 | 101 | return deleted; |
497 | } | |
498 | ||
499 | /** | |
500 | * Deleted regions mean that there will be discontinuous sequence numbering in | |
501 | * the sequence returned by getSeq(char). | |
502 | * | |
503 | * @return true if there deletions | |
504 | */ | |
505 | 1 | public boolean hasDeletedRegions() |
506 | { | |
507 | 9 | for (int i = 0; i < length; i++) |
508 | { | |
509 | 8 | if (operation[i] == D) |
510 | { | |
511 | 0 | return true; |
512 | } | |
513 | } | |
514 | 1 | return false; |
515 | } | |
516 | ||
517 | /** | |
518 | * enumerate the ranges on seq that are marked as deleted in this cigar | |
519 | * | |
520 | * @return int[] { vis_start, sym_start, length } | |
521 | */ | |
522 | 25 | public int[] getDeletedRegions() |
523 | { | |
524 | 25 | if (length == 0) |
525 | { | |
526 | 1 | return null; |
527 | } | |
528 | 24 | Vector dr = new Vector(); |
529 | 24 | int cursor = 0, vcursor = 0; |
530 | 68 | for (int i = 0; i < length; i++) |
531 | { | |
532 | 44 | switch (operation[i]) |
533 | { | |
534 | 28 | case M: |
535 | 28 | cursor += range[i]; |
536 | 28 | break; |
537 | 0 | case I: |
538 | 0 | vcursor += range[i]; |
539 | 0 | break; |
540 | 16 | case D: |
541 | 16 | dr.addElement(new int[] { vcursor, cursor, range[i] }); |
542 | 16 | cursor += range[i]; |
543 | } | |
544 | } | |
545 | 24 | if (dr.size() == 0) |
546 | { | |
547 | 14 | return null; |
548 | } | |
549 | 10 | int[] delregions = new int[dr.size() * 3]; |
550 | 26 | for (int i = 0, l = dr.size(); i < l; i++) |
551 | { | |
552 | 16 | int[] reg = (int[]) dr.elementAt(i); |
553 | 16 | delregions[i * 3] = reg[0]; |
554 | 16 | delregions[i * 3 + 1] = reg[1]; |
555 | 16 | delregions[i * 3 + 2] = reg[2]; |
556 | } | |
557 | 10 | return delregions; |
558 | } | |
559 | ||
560 | /** | |
561 | * sum of ranges in cigar string | |
562 | * | |
563 | * @return int number of residues hidden, matched, or gaps inserted into | |
564 | * sequence | |
565 | */ | |
566 | 1 | public int getFullWidth() |
567 | { | |
568 | 1 | int w = 0; |
569 | 1 | if (range != null) |
570 | { | |
571 | 9 | for (int i = 0; i < length; i++) |
572 | { | |
573 | 8 | w += range[i]; |
574 | } | |
575 | } | |
576 | 1 | return w; |
577 | } | |
578 | ||
579 | /** | |
580 | * Visible length of aligned sequence | |
581 | * | |
582 | * @return int length of including gaps and less hidden regions | |
583 | */ | |
584 | 37 | public int getWidth() |
585 | { | |
586 | 37 | int w = 0; |
587 | 37 | if (range != null) |
588 | { | |
589 | 165 | for (int i = 0; i < length; i++) |
590 | { | |
591 | 129 | if (operation[i] == M || operation[i] == I) |
592 | { | |
593 | 113 | w += range[i]; |
594 | } | |
595 | } | |
596 | } | |
597 | 37 | return w; |
598 | } | |
599 | ||
600 | /** | |
601 | * mark a range of inserted residues | |
602 | * | |
603 | * @param range | |
604 | * int | |
605 | */ | |
606 | 13 | public void addInsertion(int range) |
607 | { | |
608 | 13 | this.addOperation(I, range); |
609 | } | |
610 | ||
611 | /** | |
612 | * mark the next range residues as hidden (not aligned) or deleted | |
613 | * | |
614 | * @param range | |
615 | * int | |
616 | */ | |
617 | 176 | public void addDeleted(int range) |
618 | { | |
619 | 176 | this.addOperation(D, range); |
620 | } | |
621 | ||
622 | /** | |
623 | * Modifies operation list to delete columns from start to end (inclusive) | |
624 | * editing will remove insertion operations, and convert matches to deletions | |
625 | * | |
626 | * @param start | |
627 | * alignment column | |
628 | * @param end | |
629 | * alignment column | |
630 | * @return boolean true if residues were marked as deleted. public boolean | |
631 | * deleteRange(int start, int end) { boolean deleted = false; int op = | |
632 | * 0, prevop = -1, firstm = -1, lastm = -1, postop = -1; int width = | |
633 | * 0; // zero'th column if (length > 0) { // find operation bracketing | |
634 | * start of the range do { if (operation[op] != D) { width += | |
635 | * range[prevop = op]; } op++; } while (op < length && width < start); | |
636 | * } if (width < start) { // run off end - add more operations up to | |
637 | * deletion. addInsertion(start - width); } else { // edit existing | |
638 | * operations. op = prevop; width -= range[prevop]; int[] oldrange = | |
639 | * range; char[] oldops = operation; range = new int[oldrange.length]; | |
640 | * operation = new char[oldops.length]; if (op < length) { do { if | |
641 | * (operation[op] != D) { width += range[postop = op]; } op++; } while | |
642 | * (op < length && width <= end); } } if (deleted == true) { | |
643 | * addDeleted(end - start + 1); } return deleted; } | |
644 | */ | |
645 | /** | |
646 | * Return an ENSEMBL style cigar string where D may indicates excluded parts | |
647 | * of seq | |
648 | * | |
649 | * @return String of form ([0-9]+[IMD])+ | |
650 | */ | |
651 | 16 | public String getCigarstring() |
652 | { | |
653 | 16 | StringBuffer cigarString = new StringBuffer(); |
654 | 84 | for (int i = 0; i < length; i++) |
655 | { | |
656 | 68 | cigarString.append("" + range[i]); |
657 | 68 | cigarString.append(operation[i]); |
658 | } | |
659 | 16 | return cigarString.toString(); |
660 | } | |
661 | } |