2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.datamodel;
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22 public abstract class CigarBase
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25 * Base class for compact idiosyncratic representation of gaps and aligned
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26 * residues Regards to Tom Oldfield for his DynamicArray class. 17th July 2006
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31 // nothing to be done (probably)
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34 protected int length = 0;
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36 protected int _inc_length = 10; // extension range for addition of new
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40 protected char[] operation = null;
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42 protected int[] range = null;
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45 * Range of Hidden residues in seq (translated as deleted in seq)
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47 public static final char D = 'D';
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50 * Range of insertions to seq
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52 public static final char I = 'I';
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55 * Range of aligned residues
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57 public static final char M = 'M';
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59 static protected final char _case_shift = 'a' - 'A';
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62 * Ugly function to get edited sequence string, start and end symbol positions
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63 * and the deletion regions as an array of int pairs May return null for an
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64 * empty cigar string. May return null for deletion ranges if there are none.
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67 * - the symbol sequence to apply the cigar operations to (or null if
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70 * - the symbol to use for Insert operations
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71 * @return Object[] { String, int[] {start, startcol, end, endcol}, int[][3]
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72 * {start, end, col} or null} the gapped sequence, first and last
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73 * residue index, and the deletion ranges on the reference sequence
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75 public Object[] getSequenceAndDeletions(String reference, char GapChar)
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78 int[][] deletions = new int[length][];
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79 int[][] trunc_deletions = null;
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80 StringBuffer sq = new StringBuffer();
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81 int cursor = 0, alcursor = 0, start = 0, startpos = 0, end = 0, endpos = 0, delcount = -1;
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82 boolean consecutive_del = false;
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87 if (reference != null)
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89 rlength = reference.length();
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91 boolean modstart = true;
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92 for (int i = 0; i < length; i++)
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94 switch (operation[i])
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97 if (!consecutive_del)
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99 deletions[++delcount] = new int[]
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100 { cursor, 0, alcursor };
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102 cursor += range[i];
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103 deletions[delcount][1] = cursor - 1;
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104 consecutive_del = true;
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107 consecutive_del = false;
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108 for (int r = 0; r < range[i]; r++)
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110 sq.append(GapChar);
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115 consecutive_del = false;
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119 startpos = alcursor;
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122 if (reference != null)
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124 int sbend = cursor + range[i];
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125 if (sbend > rlength)
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127 sq.append(reference.substring(cursor, rlength));
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128 while (sbend-- >= rlength)
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130 sq.append(GapChar);
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135 sq.append(reference.substring(cursor, sbend));
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138 alcursor += range[i];
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139 cursor += range[i];
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144 throw new Error("Unknown SeqCigar operation '" + operation[i] + "'");
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147 if (++delcount > 0)
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149 trunc_deletions = new int[delcount][];
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150 System.arraycopy(deletions, 0, trunc_deletions, 0, delcount);
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153 return new Object[]
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154 { ((reference != null) ? sq.toString() : null), new int[]
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155 { start, startpos, end, endpos }, trunc_deletions };
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158 protected void compact_operations()
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161 if (operation == null)
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165 char last = operation[0];
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168 if (last == operation[i])
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170 range[i - 1] += range[i];
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171 int r = length - i;
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174 System.arraycopy(range, i + 1, range, i, r);
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175 System.arraycopy(operation, i + 1, operation, i, r);
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181 last = operation[i++];
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187 * turn a cigar string into a series of operation range pairs
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189 * @param cigarString
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191 * @return object[] {char[] operation, int[] range}
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192 * @throws java.lang.Exception
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193 * for improperly formated cigar strings or ones with unknown
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196 public static Object[] parseCigarString(String cigarString)
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200 for (int i = 0, l = cigarString.length(); i < l; i++)
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202 char c = cigarString.charAt(i);
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203 if (c == M || c == (M - _case_shift) || c == I
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204 || c == (I - _case_shift) || c == D || c == (D - _case_shift))
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209 char[] operation = new char[ops];
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210 int[] range = new int[ops];
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212 int i = 0, l = cigarString.length();
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219 c = cigarString.charAt(j++);
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220 } while (c >= '0' && c <= '9' && j < l);
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221 if (j >= l && c >= '0' && c <= '9')
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223 throw new Exception("Unterminated cigar string.");
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227 String rangeint = cigarString.substring(i, j - 1);
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228 range[op] = Integer.parseInt(rangeint);
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230 } catch (Exception e)
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232 throw new Error("Implementation bug in parseCigarString");
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234 if (c >= 'a' && c <= 'z')
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238 if ((c == M || c == I || c == D))
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240 operation[op++] = c;
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244 throw new Exception("Unexpected operation '" + c
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245 + "' in cigar string (position " + i + " in '"
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246 + cigarString + "'");
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249 return new Object[]
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250 { operation, range };
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254 * add an operation to cigar string
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261 public void addOperation(char op, int range)
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263 if (op >= 'a' && op <= 'z')
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267 if (op != M && op != D && op != I)
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269 throw new Error("Implementation error. Invalid operation string.");
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274 "Invalid range string (must be non-zero positive number)");
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277 if (operation == null)
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279 this.operation = new char[_inc_length];
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280 this.range = new int[_inc_length];
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282 if (length + 1 == operation.length)
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284 char[] ops = this.operation;
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285 this.operation = new char[length + 1 + _inc_length];
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286 System.arraycopy(ops, 0, this.operation, 0, length);
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288 int[] rng = this.range;
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289 this.range = new int[length + 1 + _inc_length];
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290 System.arraycopy(rng, 0, this.range, 0, length);
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293 if ((length > 0) && (operation[length - 1] == op))
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295 length--; // modify existing operation.
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299 this.range[length] = 0; // reset range
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301 this.operation[length] = op;
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302 this.range[length++] += range;
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306 * semi-efficient insert an operation on the current cigar string set at
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307 * column pos (from 1) NOTE: Insertion operations simply extend width of cigar
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308 * result - affecting registration of alignment Deletion ops will shorten
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309 * length of result - and affect registration of alignment Match ops will also
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310 * affect length of result - affecting registration of alignment (ie
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311 * "10M".insert(4,I,3)->"4M3I3M") - (replace?) (ie
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312 * "10M".insert(4,D,3)->"4M3D3M") - (shortens alignment) (ie
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313 * "5I5M".insert(4,I,3)->"8I5M") - real insertion (ie
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314 * "5I5M".insert(4,D,3)->"4I2D3M") - shortens aligment - I's are removed, Ms
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315 * changed to Ds (ie "10M".insert(4,M,3)->"13M") - lengthens - Is changed to
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316 * M, Ds changed to M. (ie "5I5M".insert(4,M,3)->"4I8M") - effectively shifts
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317 * sequence left by 1 residue and extends it by 3 (
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318 * "10D5M".insert(-1,M,3)->"3M7D5M") ( "10D5M".insert(0,M,3)->"7D8M") (
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319 * "10D5M".insert(1,M,3)->"10D8M") ( "1M10D5M".insert(0,M,3)->"1M10D8M") (
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320 * "1M10D5M".insert(1,M,3)->"
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322 * if pos is beyond width - I operations are added before the operation
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325 * int -1, 0-length of visible region, or greater to append new ops
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326 * (with insertions in between)
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330 * int public void addOperationAt(int pos, char op, int range) { int
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331 * cursor = -1; // mark the position for the current operation being
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332 * edited. int o = 0; boolean last_d = false; // previous op was a
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333 * deletion. if (pos < -1) throw new
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334 * Error("pos<-1 is not supported."); while (o<length) { if
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335 * (operation[o] != D) { if ( (cursor + this.range[o]) < pos) {
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336 * cursor += this.range[o]; o++; last_d=false; } else { break; } }
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337 * else { last_d=true; o++; } } if (o==length) { // must insert more
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338 * operations before pos if (pos-cursor>0) addInsertion(pos-cursor);
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339 * // then just add the new operation. Regardless of what it is.
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340 * addOperation(op, range); } else { int diff = pos - cursor;
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342 * int e_length = length-o; // new edit operation array length. //
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343 * diff<0 - can only happen before first insertion or match. -
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344 * affects op and all following // dif==0 - only when at first
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345 * position of existing op - // diff>0 - must preserve some existing
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346 * operations int[] e_range = new int[e_length];
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347 * System.arraycopy(this.range, o, e_range, 0, e_length); char[] e_op
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348 * = new char[e_length]; System.arraycopy(this.operation, o, e_op, 0,
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349 * e_length); length = o; // can now use add_operation to extend
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350 * list. int e_o=0; // current operation being edited. switch (op) {
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351 * case M: switch (e_op[e_o]) { case M: if (last_d && diff <= 0) { //
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352 * reduce D's, if possible if (range<=this.range[o-1]) { this.range[o
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353 * - 1] -= range; } else { this.range[o-1]=0; } if
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354 * (this.range[o-1]==0) o--; // lose this op. } e_range[e_o] +=
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355 * range; // just add more matched residues break; case I: // change
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356 * from insertion to match if (last_d && diff<=0) { // reduce D's, if
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357 * possible if (range<=this.range[o-1]) { this.range[o - 1] -= range;
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358 * } else { this.range[o-1]=0; } if (this.range[o-1]==0) o--; // lose
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359 * this op. } e_range[e_o] break; default: throw new Inp }
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361 * break; case I: break; case D: } break; default: throw new
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362 * Error("Implementation Error: Unknown operation in addOperation!");
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363 * } // finally, add remaining ops. while (e_o<e_length) {
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364 * addOperation(e_op[e_o], e_range[e_o]); e_o++; } } }
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367 * Mark residues from start to end (inclusive) as deleted from the alignment,
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368 * and removes any insertions.
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374 * @return deleted int - number of symbols marked as deleted
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376 public int deleteRange(int start, int end)
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381 // nothing to do here
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384 if (start < 0 || start > end)
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387 "Implementation Error: deleteRange out of bounds: start must be non-negative and less than end.");
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390 int cursor = 0; // mark the position for the current operation being edited.
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391 int rlength = 1 + end - start; // number of positions to delete
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392 int oldlen = length;
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394 boolean editing = false;
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395 char[] oldops = operation;
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396 int[] oldrange = range;
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400 compact_operations();
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401 while (o < oldlen && cursor <= end && rlength > 0)
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403 if (oldops[o] == D)
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405 // absorbed into new deleted region.
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406 addDeleted(oldrange[o++]);
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410 int remain = oldrange[o]; // number of op characters left to edit
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413 if ((cursor + remain) <= start)
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415 addOperation(oldops[o], oldrange[o]);
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416 cursor += oldrange[o++];
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417 continue; // next operation
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420 // add operations before hidden region
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421 if (start - cursor > 0)
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423 addOperation(oldops[o], start - cursor);
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424 remain -= start - cursor;
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427 // start inserting new ops
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428 if (o < oldlen && editing && rlength > 0 && remain > 0)
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433 if (rlength > remain)
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435 addDeleted(remain);
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440 deleted += rlength;
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441 addDeleted(rlength);
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442 if (remain - rlength > 0)
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444 this.addOperation(M, remain - rlength); // add remaining back.
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451 if (remain - rlength > 0)
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453 // only remove some gaps
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454 addInsertion(remain - rlength);
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459 throw new Error("Implementation error."); // do nothing;
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461 throw new Error("Implementation Error! Unknown operation '"
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462 + oldops[o] + "'");
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465 remain = oldrange[++o]; // number of op characters left to edit
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471 addOperation(oldops[o], oldrange[o++]);
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473 // if (cursor<(start+1)) {
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474 // ran out of ops - nothing to do here ?
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475 // addInsertion(start-cursor);
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481 * Deleted regions mean that there will be discontinuous sequence numbering in
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482 * the sequence returned by getSeq(char).
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484 * @return true if there deletions
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486 public boolean hasDeletedRegions()
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488 for (int i = 0; i < length; i++)
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490 if (operation[i] == D)
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499 * enumerate the ranges on seq that are marked as deleted in this cigar
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501 * @return int[] { vis_start, sym_start, length }
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503 public int[] getDeletedRegions()
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509 Vector dr = new Vector();
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510 int cursor = 0, vcursor = 0;
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511 for (int i = 0; i < length; i++)
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513 switch (operation[i])
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516 cursor += range[i];
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518 vcursor += range[i];
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521 dr.addElement(new int[]
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522 { vcursor, cursor, range[i] });
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523 cursor += range[i];
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526 if (dr.size() == 0)
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530 int[] delregions = new int[dr.size() * 3];
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531 for (int i = 0, l = dr.size(); i < l; i++)
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533 int[] reg = (int[]) dr.elementAt(i);
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534 delregions[i * 3] = reg[0];
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535 delregions[i * 3 + 1] = reg[1];
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536 delregions[i * 3 + 2] = reg[2];
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542 * sum of ranges in cigar string
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544 * @return int number of residues hidden, matched, or gaps inserted into
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547 public int getFullWidth()
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552 for (int i = 0; i < length; i++)
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561 * Visible length of aligned sequence
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563 * @return int length of including gaps and less hidden regions
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565 public int getWidth()
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570 for (int i = 0; i < length; i++)
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572 if (operation[i] == M || operation[i] == I)
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582 * mark a range of inserted residues
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587 public void addInsertion(int range)
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589 this.addOperation(I, range);
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593 * mark the next range residues as hidden (not aligned) or deleted
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598 public void addDeleted(int range)
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600 this.addOperation(D, range);
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604 * Modifies operation list to delete columns from start to end (inclusive)
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605 * editing will remove insertion operations, and convert matches to deletions
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611 * @return boolean true if residues were marked as deleted. public boolean
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612 * deleteRange(int start, int end) { boolean deleted = false; int op =
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613 * 0, prevop = -1, firstm = -1, lastm = -1, postop = -1; int width =
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614 * 0; // zero'th column if (length > 0) { // find operation bracketing
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615 * start of the range do { if (operation[op] != D) { width +=
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616 * range[prevop = op]; } op++; } while (op < length && width < start);
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617 * } if (width < start) { // run off end - add more operations up to
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618 * deletion. addInsertion(start - width); } else { // edit existing
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619 * operations. op = prevop; width -= range[prevop]; int[] oldrange =
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620 * range; char[] oldops = operation; range = new int[oldrange.length];
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621 * operation = new char[oldops.length]; if (op < length) { do { if
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622 * (operation[op] != D) { width += range[postop = op]; } op++; } while
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623 * (op < length && width <= end); } } if (deleted == true) {
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624 * addDeleted(end - start + 1); } return deleted; }
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627 * Return an ENSEMBL style cigar string where D may indicates excluded parts
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630 * @return String of form ([0-9]+[IMD])+
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632 public String getCigarstring()
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634 StringBuffer cigarString = new StringBuffer();
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635 for (int i = 0; i < length; i++)
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637 cigarString.append("" + range[i]);
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638 cigarString.append(operation[i]);
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640 return cigarString.toString();
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