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.analysis;
23 import java.awt.Color;
26 import jalview.datamodel.*;
29 * Calculates conservation values for a given set of sequences
34 public class Conservation
36 SequenceI[] sequences;
42 Vector seqNums; // vector of int vectors where first is sequence checksum
44 int maxLength = 0; // used by quality calcs
46 boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
50 boolean canonicaliseAa = true; // if true then conservation calculation will
52 // map all symbols to canonical aa numbering
53 // rather than consider conservation of that
56 /** Stores calculated quality values */
57 public Vector quality;
59 /** Stores maximum and minimum values of quality values */
60 public Double[] qualityRange = new Double[2];
62 String consString = "";
64 Sequence consSequence;
75 * Creates a new Conservation object.
78 * Name of conservation
80 * hash of properties for each symbol
82 * to count the residues in residueHash(). commonly used value is 3
84 * sequences to be used in calculation
86 * start residue position
88 * end residue position
90 public Conservation(String name, Hashtable propHash, int threshold,
91 List<SequenceI> sequences, int start, int end)
94 this.propHash = propHash;
95 this.threshold = threshold;
99 maxLength = end - start + 1; // default width includes bounds of
102 int s, sSize = sequences.size();
103 SequenceI[] sarray = new SequenceI[sSize];
104 this.sequences = sarray;
107 for (s = 0; s < sSize; s++)
109 sarray[s] = (SequenceI) sequences.get(s);
110 if (sarray[s].getLength() > maxLength)
112 maxLength = sarray[s].getLength();
115 } catch (ArrayIndexOutOfBoundsException ex)
117 // bail - another thread has modified the sequence array, so the current
118 // calculation is probably invalid.
119 this.sequences = new SequenceI[0];
125 * Translate sequence i into a numerical representation and store it in the
126 * i'th position of the seqNums array.
130 private void calcSeqNum(int i)
132 String sq = null; // for dumb jbuilder not-inited exception warning
135 int sSize = sequences.length;
137 if ((i > -1) && (i < sSize))
139 sq = sequences[i].getSequenceAsString();
141 if (seqNums.size() <= i)
143 seqNums.addElement(new int[sq.length() + 1]);
146 if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0])
150 seqNumsChanged = true;
158 sqnum = new int[len + 1]; // better to always make a new array -
159 // sequence can change its length
160 sqnum[0] = sq.hashCode();
162 for (j = 1; j <= len; j++)
164 sqnum[j] = jalview.schemes.ResidueProperties.aaIndex[sq
168 seqNums.setElementAt(sqnum, i);
172 System.out.println("SEQUENCE HAS BEEN DELETED!!!");
177 // JBPNote INFO level debug
179 .println("ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
184 * Calculates the conservation values for given set of sequences
186 public void calculate()
188 Hashtable resultHash, ht;
189 int thresh, j, jSize = sequences.length;
190 int[] values; // Replaces residueHash
191 String type, res = null;
193 Enumeration enumeration2;
195 total = new Hashtable[maxLength];
197 for (int i = start; i <= end; i++)
199 values = new int[255];
201 for (j = 0; j < jSize; j++)
203 if (sequences[j].getLength() > i)
205 c = sequences[j].getCharAt(i);
208 { // lookup the base aa code symbol
209 c = (char) jalview.schemes.ResidueProperties.aaIndex[sequences[j]
217 // recover canonical aa symbol
218 c = jalview.schemes.ResidueProperties.aa[c].charAt(0);
223 // original behaviour - operate on ascii symbols directly
224 // No need to check if its a '-'
225 if (c == '.' || c == ' ')
230 if (!canonicaliseAa && 'a' <= c && c <= 'z')
232 c -= (32); // 32 = 'a' - 'A'
243 // What is the count threshold to count the residues in residueHash()
244 thresh = (threshold * (jSize)) / 100;
246 // loop over all the found residues
247 resultHash = new Hashtable();
248 for (char v = '-'; v < 'Z'; v++)
251 if (values[v] > thresh)
253 res = String.valueOf(v);
255 // Now loop over the properties
256 enumeration2 = propHash.keys();
258 while (enumeration2.hasMoreElements())
260 type = (String) enumeration2.nextElement();
261 ht = (Hashtable) propHash.get(type);
263 // Have we ticked this before?
264 if (!resultHash.containsKey(type))
266 if (ht.containsKey(res))
268 resultHash.put(type, ht.get(res));
272 resultHash.put(type, ht.get("-"));
275 else if (((Integer) resultHash.get(type)).equals((Integer) ht
278 resultHash.put(type, new Integer(-1));
284 if (total.length > 0)
286 total[i - start] = resultHash;
291 /*****************************************************************************
292 * count conservation for the j'th column of the alignment
294 * @return { gap count, conserved residue count}
296 public int[] countConsNGaps(int j)
301 int[] r = new int[2];
303 int i, iSize = sequences.length;
306 for (i = 0; i < iSize; i++)
308 if (j >= sequences[i].getLength())
314 c = sequences[i].getCharAt(j); // gaps do not have upper/lower case
316 if (jalview.util.Comparison.isGap((c)))
336 r[0] = (nres == cons) ? 1 : 0;
343 * Calculates the conservation sequence
346 * if true, poitiveve conservation; false calculates negative
348 * @param percentageGaps
349 * commonly used value is 25
351 public void verdict(boolean consflag, float percentageGaps)
353 StringBuffer consString = new StringBuffer();
359 Hashtable resultHash;
360 Enumeration enumeration;
362 // NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
363 // EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
364 // DOES NOT EXIST IN JALVIEW 2.1.2
365 for (int i = 0; i < start; i++)
367 consString.append('-');
370 for (int i = start; i <= end; i++)
372 gapcons = countConsNGaps(i);
373 totGaps = gapcons[1];
374 pgaps = ((float) totGaps * 100) / (float) sequences.length;
376 if (percentageGaps > pgaps)
378 resultHash = total[i - start];
380 // Now find the verdict
382 enumeration = resultHash.keys();
384 while (enumeration.hasMoreElements())
386 type = (String) enumeration.nextElement();
387 result = (Integer) resultHash.get(type);
389 // Do we want to count +ve conservation or +ve and -ve cons.?
392 if (result.intValue() == 1)
399 if (result.intValue() != -1)
408 consString.append(count); // Conserved props!=Identity
412 consString.append((gapcons[0] == 1) ? "*" : "+");
417 consString.append('-');
421 consSequence = new Sequence(name, consString.toString(), start, end);
427 * @return Conservation sequence
429 public Sequence getConsSequence()
434 // From Alignment.java in jalview118
435 public void findQuality()
437 findQuality(0, maxLength - 1);
443 private void percentIdentity2()
445 seqNums = new Vector();
447 int i = 0, iSize = sequences.length;
448 // Do we need to calculate this again?
449 for (i = 0; i < iSize; i++)
454 if ((cons2 == null) || seqNumsChanged)
456 cons2 = new int[maxLength][24];
458 // Initialize the array
459 for (int j = 0; j < 24; j++)
461 for (i = 0; i < maxLength; i++)
470 while (j < sequences.length)
472 sqnum = (int[]) seqNums.elementAt(j);
474 for (i = 1; i < sqnum.length; i++)
476 cons2[i - 1][sqnum[i]]++;
479 for (i = sqnum.length - 1; i < maxLength; i++)
481 cons2[i][23]++; // gap count
490 * for (int i=start; i <= end; i++) { int max = -1000; int maxi = -1; int
493 * for (int j=0;j<24;j++) { if (cons2[i][j] > max) { max = cons2[i][j];
494 * maxi = i; maxj = j; } } }
500 * Calculates the quality of the set of sequences
507 public void findQuality(int start, int end)
509 quality = new Vector();
512 int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
514 // Loop over columns // JBPNote Profiling info
515 // long ts = System.currentTimeMillis();
516 // long te = System.currentTimeMillis();
519 int size = seqNums.size();
520 int[] lengths = new int[size];
521 double tot, bigtot, sr, tmp;
523 int l, j, i, ii, i2, k, seqNum;
525 for (l = 0; l < size; l++)
527 lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;
530 for (j = start; j <= end; j++)
534 // First Xr = depends on column only
537 for (ii = 0; ii < 24; ii++)
541 for (i2 = 0; i2 < 24; i2++)
543 x[ii] += (((double) cons2[j][i2] * BLOSUM62[ii][i2]) + 4);
549 // Now calculate D for each position and sum
550 for (k = 0; k < size; k++)
554 seqNum = (j < lengths[k]) ? ((int[]) seqNums.elementAt(k))[j + 1]
555 : 23; // Sequence, or gap at the end
557 // This is a loop over r
558 for (i = 0; i < 23; i++)
562 sr = (double) BLOSUM62[i][seqNum] + 4;
564 // Calculate X with another loop over residues
565 // System.out.println("Xi " + i + " " + x[i] + " " + sr);
568 tot += (xx[i] * xx[i]);
571 bigtot += Math.sqrt(tot);
574 // This is the quality for one column
580 // bigtot = bigtot * (size-cons2[j][23])/size;
581 quality.addElement(new Double(bigtot));
583 // Need to normalize by gaps
586 double newmax = -10000;
588 for (j = start; j <= end; j++)
590 tmp = ((Double) quality.elementAt(j)).doubleValue();
591 tmp = ((max - tmp) * (size - cons2[j][23])) / size;
593 // System.out.println(tmp+ " " + j);
594 quality.setElementAt(new Double(tmp), j);
602 // System.out.println("Quality " + s);
603 qualityRange[0] = new Double(0);
604 qualityRange[1] = new Double(newmax);
608 * complete the given consensus and quuality annotation rows. Note: currently
609 * this method will enlarge the given annotation row if it is too small,
610 * otherwise will leave its length unchanged.
612 * @param conservation
613 * conservation annotation row
615 * (optional - may be null)
617 * first column for conservation
619 * extent of conservation
621 public void completeAnnotations(AlignmentAnnotation conservation,
622 AlignmentAnnotation quality2, int istart, int alWidth)
624 char[] sequence = getConsSequence().getSequence();
636 maxB = 0f - minB; // scalable range for colouring both Conservation and
646 if (conservation.annotations != null
647 && conservation.annotations.length < alWidth)
649 conservation.annotations = new Annotation[alWidth];
652 if (quality2 != null)
654 quality2.graphMax = qualityRange[1].floatValue();
655 if (quality2.annotations != null
656 && quality2.annotations.length < alWidth)
658 quality2.annotations = new Annotation[alWidth];
660 qmin = qualityRange[0].floatValue();
661 qmax = qualityRange[1].floatValue();
664 for (int i = 0; i < alWidth; i++)
670 if (Character.isDigit(c))
672 value = (int) (c - '0');
683 float vprop = value - min;
685 conservation.annotations[i] = new Annotation(String.valueOf(c),
686 String.valueOf(value), ' ', value, new Color(minR
687 + (maxR * vprop), minG + (maxG * vprop), minB
691 if (quality2 != null)
693 value = ((Double) quality.elementAt(i)).floatValue();
694 vprop = value - qmin;
696 quality2.annotations[i] = new Annotation(" ",
697 String.valueOf(value), ' ', value, new Color(minR
698 + (maxR * vprop), minG + (maxG * vprop), minB
705 * construct and call the calculation methods on a new Conservation object
708 * - name of conservation
710 * - hash table of properties for each amino acid (normally
711 * ResidueProperties.propHash)
713 * - minimum number of conserved residues needed to indicate
714 * conservation (typically 3)
717 * first column in calculation window
719 * last column in calculation window
721 * positive (true) or negative (false) conservation
722 * @param consPercGaps
723 * percentage of gaps tolerated in column
725 * flag indicating if alignment quality should be calculated
726 * @return Conservation object ready for use in visualization
728 public static Conservation calculateConservation(String name,
729 Hashtable consHash, int threshold, List<SequenceI> seqs,
730 int start, int end, boolean posOrNeg, int consPercGaps,
733 Conservation cons = new Conservation(name, consHash, threshold, seqs,
735 return calculateConservation(cons, posOrNeg, consPercGaps, calcQuality);
740 * positive (true) or negative (false) conservation
741 * @param consPercGaps
742 * percentage of gaps tolerated in column
744 * flag indicating if alignment quality should be calculated
745 * @return Conservation object ready for use in visualization
747 public static Conservation calculateConservation(Conservation cons,
748 boolean b, int consPercGaps, boolean calcQuality)
751 cons.verdict(b, consPercGaps);