2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.datamodel;
25 public abstract class CigarBase
28 * Base class for compact idiosyncratic representation of gaps and aligned
29 * residues Regards to Tom Oldfield for his DynamicArray class. 17th July 2006
34 // nothing to be done (probably)
37 protected int length = 0;
39 protected int _inc_length = 10; // extension range for addition of new
43 protected char[] operation = null;
45 protected int[] range = null;
48 * Range of Hidden residues in seq (translated as deleted in seq)
50 public static final char D = 'D';
53 * Range of insertions to seq
55 public static final char I = 'I';
58 * Range of aligned residues
60 public static final char M = 'M';
62 static protected final char _case_shift = 'a' - 'A';
65 * Ugly function to get edited sequence string, start and end symbol positions
66 * and the deletion regions as an array of int pairs May return null for an
67 * empty cigar string. May return null for deletion ranges if there are none.
70 * - the symbol sequence to apply the cigar operations to (or null if
73 * - the symbol to use for Insert operations
74 * @return Object[] { String, int[] {start, startcol, end, endcol}, int[][3]
75 * {start, end, col} or null} the gapped sequence, first and last
76 * residue index, and the deletion ranges on the reference sequence
78 public Object[] getSequenceAndDeletions(String reference, char GapChar)
81 int[][] deletions = new int[length][];
82 int[][] trunc_deletions = null;
83 StringBuffer sq = new StringBuffer();
84 int cursor = 0, alcursor = 0, start = 0, startpos = 0, end = 0, endpos = 0, delcount = -1;
85 boolean consecutive_del = false;
90 if (reference != null)
92 rlength = reference.length();
94 boolean modstart = true;
95 for (int i = 0; i < length; i++)
100 if (!consecutive_del)
102 deletions[++delcount] = new int[]
103 { cursor, 0, alcursor };
106 deletions[delcount][1] = cursor - 1;
107 consecutive_del = true;
110 consecutive_del = false;
111 for (int r = 0; r < range[i]; r++)
118 consecutive_del = false;
125 if (reference != null)
127 int sbend = cursor + range[i];
130 sq.append(reference.substring(cursor, rlength));
131 while (sbend-- >= rlength)
138 sq.append(reference.substring(cursor, sbend));
141 alcursor += range[i];
147 throw new Error("Unknown SeqCigar operation '" + operation[i] + "'");
152 trunc_deletions = new int[delcount][];
153 System.arraycopy(deletions, 0, trunc_deletions, 0, delcount);
157 { ((reference != null) ? sq.toString() : null), new int[]
158 { start, startpos, end, endpos }, trunc_deletions };
161 protected void compact_operations()
164 if (operation == null)
168 char last = operation[0];
171 if (last == operation[i])
173 range[i - 1] += range[i];
177 System.arraycopy(range, i + 1, range, i, r);
178 System.arraycopy(operation, i + 1, operation, i, r);
184 last = operation[i++];
190 * turn a cigar string into a series of operation range pairs
194 * @return object[] {char[] operation, int[] range}
195 * @throws java.lang.Exception
196 * for improperly formated cigar strings or ones with unknown
199 public static Object[] parseCigarString(String cigarString)
203 for (int i = 0, l = cigarString.length(); i < l; i++)
205 char c = cigarString.charAt(i);
206 if (c == M || c == (M - _case_shift) || c == I
207 || c == (I - _case_shift) || c == D || c == (D - _case_shift))
212 char[] operation = new char[ops];
213 int[] range = new int[ops];
215 int i = 0, l = cigarString.length();
222 c = cigarString.charAt(j++);
223 } while (c >= '0' && c <= '9' && j < l);
224 if (j >= l && c >= '0' && c <= '9')
226 throw new Exception("Unterminated cigar string.");
230 String rangeint = cigarString.substring(i, j - 1);
231 range[op] = Integer.parseInt(rangeint);
233 } catch (Exception e)
235 throw new Error("Implementation bug in parseCigarString");
237 if (c >= 'a' && c <= 'z')
241 if ((c == M || c == I || c == D))
247 throw new Exception("Unexpected operation '" + c
248 + "' in cigar string (position " + i + " in '"
249 + cigarString + "'");
253 { operation, range };
257 * add an operation to cigar string
264 public void addOperation(char op, int range)
266 if (op >= 'a' && op <= 'z')
270 if (op != M && op != D && op != I)
272 throw new Error("Implementation error. Invalid operation string.");
276 return; // No Operation to add.
281 "Invalid range string (must be zero or positive number)");
284 if (operation == null)
286 this.operation = new char[_inc_length];
287 this.range = new int[_inc_length];
289 if (length + 1 == operation.length)
291 char[] ops = this.operation;
292 this.operation = new char[length + 1 + _inc_length];
293 System.arraycopy(ops, 0, this.operation, 0, length);
295 int[] rng = this.range;
296 this.range = new int[length + 1 + _inc_length];
297 System.arraycopy(rng, 0, this.range, 0, length);
300 if ((length > 0) && (operation[length - 1] == op))
302 length--; // modify existing operation.
306 this.range[length] = 0; // reset range
308 this.operation[length] = op;
309 this.range[length++] += range;
313 * semi-efficient insert an operation on the current cigar string set at
314 * column pos (from 1) NOTE: Insertion operations simply extend width of cigar
315 * result - affecting registration of alignment Deletion ops will shorten
316 * length of result - and affect registration of alignment Match ops will also
317 * affect length of result - affecting registration of alignment (ie
318 * "10M".insert(4,I,3)->"4M3I3M") - (replace?) (ie
319 * "10M".insert(4,D,3)->"4M3D3M") - (shortens alignment) (ie
320 * "5I5M".insert(4,I,3)->"8I5M") - real insertion (ie
321 * "5I5M".insert(4,D,3)->"4I2D3M") - shortens aligment - I's are removed, Ms
322 * changed to Ds (ie "10M".insert(4,M,3)->"13M") - lengthens - Is changed to
323 * M, Ds changed to M. (ie "5I5M".insert(4,M,3)->"4I8M") - effectively shifts
324 * sequence left by 1 residue and extends it by 3 (
325 * "10D5M".insert(-1,M,3)->"3M7D5M") ( "10D5M".insert(0,M,3)->"7D8M") (
326 * "10D5M".insert(1,M,3)->"10D8M") ( "1M10D5M".insert(0,M,3)->"1M10D8M") (
327 * "1M10D5M".insert(1,M,3)->"
329 * if pos is beyond width - I operations are added before the operation
332 * int -1, 0-length of visible region, or greater to append new ops
333 * (with insertions in between)
337 * int public void addOperationAt(int pos, char op, int range) { int
338 * cursor = -1; // mark the position for the current operation being
339 * edited. int o = 0; boolean last_d = false; // previous op was a
340 * deletion. if (pos < -1) throw new
341 * Error("pos<-1 is not supported."); while (o<length) { if
342 * (operation[o] != D) { if ( (cursor + this.range[o]) < pos) {
343 * cursor += this.range[o]; o++; last_d=false; } else { break; } }
344 * else { last_d=true; o++; } } if (o==length) { // must insert more
345 * operations before pos if (pos-cursor>0) addInsertion(pos-cursor);
346 * // then just add the new operation. Regardless of what it is.
347 * addOperation(op, range); } else { int diff = pos - cursor;
349 * int e_length = length-o; // new edit operation array length. //
350 * diff<0 - can only happen before first insertion or match. -
351 * affects op and all following // dif==0 - only when at first
352 * position of existing op - // diff>0 - must preserve some existing
353 * operations int[] e_range = new int[e_length];
354 * System.arraycopy(this.range, o, e_range, 0, e_length); char[] e_op
355 * = new char[e_length]; System.arraycopy(this.operation, o, e_op, 0,
356 * e_length); length = o; // can now use add_operation to extend
357 * list. int e_o=0; // current operation being edited. switch (op) {
358 * case M: switch (e_op[e_o]) { case M: if (last_d && diff <= 0) { //
359 * reduce D's, if possible if (range<=this.range[o-1]) { this.range[o
360 * - 1] -= range; } else { this.range[o-1]=0; } if
361 * (this.range[o-1]==0) o--; // lose this op. } e_range[e_o] +=
362 * range; // just add more matched residues break; case I: // change
363 * from insertion to match if (last_d && diff<=0) { // reduce D's, if
364 * possible if (range<=this.range[o-1]) { this.range[o - 1] -= range;
365 * } else { this.range[o-1]=0; } if (this.range[o-1]==0) o--; // lose
366 * this op. } e_range[e_o] break; default: throw new Inp }
368 * break; case I: break; case D: } break; default: throw new
369 * Error("Implementation Error: Unknown operation in addOperation!");
370 * } // finally, add remaining ops. while (e_o<e_length) {
371 * addOperation(e_op[e_o], e_range[e_o]); e_o++; } } }
374 * Mark residues from start to end (inclusive) as deleted from the alignment,
375 * and removes any insertions.
381 * @return deleted int - number of symbols marked as deleted
383 public int deleteRange(int start, int end)
388 // nothing to do here
391 if (start < 0 || start > end)
394 "Implementation Error: deleteRange out of bounds: start must be non-negative and less than end.");
397 int cursor = 0; // mark the position for the current operation being edited.
398 int rlength = 1 + end - start; // number of positions to delete
401 boolean editing = false;
402 char[] oldops = operation;
403 int[] oldrange = range;
407 compact_operations();
408 while (o < oldlen && cursor <= end && rlength > 0)
412 // absorbed into new deleted region.
413 addDeleted(oldrange[o++]);
417 int remain = oldrange[o]; // number of op characters left to edit
420 if ((cursor + remain) <= start)
422 addOperation(oldops[o], oldrange[o]);
423 cursor += oldrange[o++];
424 continue; // next operation
427 // add operations before hidden region
428 if (start - cursor > 0)
430 addOperation(oldops[o], start - cursor);
431 remain -= start - cursor;
434 // start inserting new ops
435 if (o < oldlen && editing && rlength > 0 && remain > 0)
440 if (rlength > remain)
449 if (remain - rlength > 0)
451 this.addOperation(M, remain - rlength); // add remaining back.
458 if (remain - rlength > 0)
460 // only remove some gaps
461 addInsertion(remain - rlength);
466 throw new Error("Implementation error."); // do nothing;
468 throw new Error("Implementation Error! Unknown operation '"
472 remain = oldrange[++o]; // number of op characters left to edit
478 addOperation(oldops[o], oldrange[o++]);
480 // if (cursor<(start+1)) {
481 // ran out of ops - nothing to do here ?
482 // addInsertion(start-cursor);
488 * Deleted regions mean that there will be discontinuous sequence numbering in
489 * the sequence returned by getSeq(char).
491 * @return true if there deletions
493 public boolean hasDeletedRegions()
495 for (int i = 0; i < length; i++)
497 if (operation[i] == D)
506 * enumerate the ranges on seq that are marked as deleted in this cigar
508 * @return int[] { vis_start, sym_start, length }
510 public int[] getDeletedRegions()
516 Vector dr = new Vector();
517 int cursor = 0, vcursor = 0;
518 for (int i = 0; i < length; i++)
520 switch (operation[i])
528 dr.addElement(new int[]
529 { vcursor, cursor, range[i] });
537 int[] delregions = new int[dr.size() * 3];
538 for (int i = 0, l = dr.size(); i < l; i++)
540 int[] reg = (int[]) dr.elementAt(i);
541 delregions[i * 3] = reg[0];
542 delregions[i * 3 + 1] = reg[1];
543 delregions[i * 3 + 2] = reg[2];
549 * sum of ranges in cigar string
551 * @return int number of residues hidden, matched, or gaps inserted into
554 public int getFullWidth()
559 for (int i = 0; i < length; i++)
568 * Visible length of aligned sequence
570 * @return int length of including gaps and less hidden regions
572 public int getWidth()
577 for (int i = 0; i < length; i++)
579 if (operation[i] == M || operation[i] == I)
589 * mark a range of inserted residues
594 public void addInsertion(int range)
596 this.addOperation(I, range);
600 * mark the next range residues as hidden (not aligned) or deleted
605 public void addDeleted(int range)
607 this.addOperation(D, range);
611 * Modifies operation list to delete columns from start to end (inclusive)
612 * editing will remove insertion operations, and convert matches to deletions
618 * @return boolean true if residues were marked as deleted. public boolean
619 * deleteRange(int start, int end) { boolean deleted = false; int op =
620 * 0, prevop = -1, firstm = -1, lastm = -1, postop = -1; int width =
621 * 0; // zero'th column if (length > 0) { // find operation bracketing
622 * start of the range do { if (operation[op] != D) { width +=
623 * range[prevop = op]; } op++; } while (op < length && width < start);
624 * } if (width < start) { // run off end - add more operations up to
625 * deletion. addInsertion(start - width); } else { // edit existing
626 * operations. op = prevop; width -= range[prevop]; int[] oldrange =
627 * range; char[] oldops = operation; range = new int[oldrange.length];
628 * operation = new char[oldops.length]; if (op < length) { do { if
629 * (operation[op] != D) { width += range[postop = op]; } op++; } while
630 * (op < length && width <= end); } } if (deleted == true) {
631 * addDeleted(end - start + 1); } return deleted; }
634 * Return an ENSEMBL style cigar string where D may indicates excluded parts
637 * @return String of form ([0-9]+[IMD])+
639 public String getCigarstring()
641 StringBuffer cigarString = new StringBuffer();
642 for (int i = 0; i < length; i++)
644 cigarString.append("" + range[i]);
645 cigarString.append(operation[i]);
647 return cigarString.toString();