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  1. Project Clover database Thu Jun 4 2026 14:16:38 BST
  2. Package jalview.analysis

File Conservation.java

 

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0% of files have more coverage

Code metrics

144
254
16
1
887
539
101
0.4
15.88
16
6.31

Classes

Class Line # Actions
Conservation 48 254 101
0.954106395.4%
 

Contributing tests

This file is covered by 190 tests. .

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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.analysis;
22   
23    import java.util.Locale;
24   
25    import jalview.analysis.scoremodels.ScoreMatrix;
26    import jalview.analysis.scoremodels.ScoreModels;
27    import jalview.datamodel.AlignmentAnnotation;
28    import jalview.datamodel.Annotation;
29    import jalview.datamodel.ResidueCount;
30    import jalview.datamodel.ResidueCount.SymbolCounts;
31    import jalview.datamodel.Sequence;
32    import jalview.datamodel.SequenceI;
33    import jalview.schemes.ResidueProperties;
34    import jalview.util.Comparison;
35    import jalview.util.Format;
36   
37    import java.awt.Color;
38    import java.util.List;
39    import java.util.Map;
40    import java.util.Map.Entry;
41    import java.util.SortedMap;
42    import java.util.TreeMap;
43    import java.util.Vector;
44   
45    /**
46    * Calculates conservation values for a given set of sequences
47    */
 
48    public class Conservation
49    {
50    /*
51    * need to have a minimum of 3% of sequences with a residue
52    * for it to be included in the conservation calculation
53    */
54    private static final int THRESHOLD_PERCENT = 3;
55   
56    private static final int TOUPPERCASE = 'a' - 'A';
57   
58    private static final int GAP_INDEX = -1;
59   
60    private static final Format FORMAT_3DP = new Format("%2.5f");
61   
62    SequenceI[] sequences;
63   
64    int start;
65   
66    int end;
67   
68    /*
69    * a list whose i'th element is an array whose first entry is the checksum
70    * of the i'th sequence, followed by residues encoded to score matrix index
71    */
72    Vector<int[]> seqNums;
73   
74    int maxLength = 0; // used by quality calcs
75   
76    boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
77   
78    /*
79    * a map per column with {property, conservation} where conservation value is
80    * 1 (property is conserved), 0 (absence of property is conserved) or -1
81    * (property is not conserved i.e. column has residues with and without it)
82    */
83    Map<String, Integer>[] total;
84   
85    /*
86    * if true then conservation calculation will map all symbols to canonical aa
87    * numbering rather than consider conservation of that symbol
88    */
89    boolean canonicaliseAa = true;
90   
91    private Vector<Double> quality;
92   
93    private double qualityMinimum;
94   
95    private double qualityMaximum;
96   
97    private Sequence consSequence;
98   
99    /*
100    * percentage of residues in a column to qualify for counting conservation
101    */
102    private int threshold;
103   
104    private String name = "";
105   
106    /*
107    * an array, for each column, of counts of symbols (by score matrix index)
108    */
109    private int[][] cons2;
110   
111    /*
112    * gap counts for each column
113    */
114    private int[] cons2GapCounts;
115   
116    private String[] consSymbs;
117   
118    /**
119    * Constructor using default threshold of 3%
120    *
121    * @param name
122    * Name of conservation
123    * @param sequences
124    * sequences to be used in calculation
125    * @param start
126    * start residue position
127    * @param end
128    * end residue position
129    */
 
130  909 toggle public Conservation(String name, List<SequenceI> sequences, int start,
131    int end)
132    {
133  909 this(name, THRESHOLD_PERCENT, sequences, start, end);
134    }
135   
136    /**
137    * Constructor
138    *
139    * @param name
140    * Name of conservation
141    * @param threshold
142    * percentage of sequences at or below which property conservation is
143    * ignored
144    * @param sequences
145    * sequences to be used in calculation
146    * @param start
147    * start column position
148    * @param end
149    * end column position
150    */
 
151  913 toggle public Conservation(String name, int threshold, List<SequenceI> sequences,
152    int start, int end)
153    {
154  913 this.name = name;
155  913 this.threshold = threshold;
156  913 this.start = start;
157  913 this.end = end;
158   
159  913 maxLength = end - start + 1; // default width includes bounds of
160    // calculation
161   
162  913 int s, sSize = sequences.size();
163  913 SequenceI[] sarray = new SequenceI[sSize];
164  913 this.sequences = sarray;
165  913 try
166    {
167  10184 for (s = 0; s < sSize; s++)
168    {
169  9271 sarray[s] = sequences.get(s);
170  9276 if (sarray[s].getLength() > maxLength)
171    {
172  6 maxLength = sarray[s].getLength();
173    }
174    }
175    } catch (ArrayIndexOutOfBoundsException ex)
176    {
177    // bail - another thread has modified the sequence array, so the current
178    // calculation is probably invalid.
179  0 this.sequences = new SequenceI[0];
180  0 maxLength = 0;
181    }
182    }
183   
184    /**
185    * Translate sequence i into score matrix indices and store it in the i'th
186    * position of the seqNums array.
187    *
188    * @param i
189    * @param sm
190    */
 
191  9210 toggle private void calcSeqNum(int i, ScoreMatrix sm)
192    {
193  9210 int sSize = sequences.length;
194   
195  9210 if ((i > -1) && (i < sSize))
196    {
197  9210 String sq = sequences[i].getSequenceAsString();
198   
199  9210 if (seqNums.size() <= i)
200    {
201  9210 seqNums.addElement(new int[sq.length() + 1]);
202    }
203   
204    /*
205    * the first entry in the array is the sequence's hashcode,
206    * following entries are matrix indices of sequence characters
207    */
208  9210 if (sq.hashCode() != seqNums.elementAt(i)[0])
209    {
210  9210 int j;
211  9210 int len;
212  9210 seqNumsChanged = true;
213  9210 len = sq.length();
214   
215  9210 if (maxLength < len)
216    {
217  0 maxLength = len;
218    }
219   
220  9210 int[] sqnum = new int[len + 1]; // better to always make a new array -
221    // sequence can change its length
222  9210 sqnum[0] = sq.hashCode();
223   
224  1482979 for (j = 1; j <= len; j++)
225    {
226    // sqnum[j] = ResidueProperties.aaIndex[sq.charAt(j - 1)];
227  1473773 char residue = sq.charAt(j - 1);
228  1473885 if (Comparison.isGap(residue))
229    {
230  290176 sqnum[j] = GAP_INDEX;
231    }
232    else
233    {
234  1183709 sqnum[j] = sm.getMatrixIndex(residue);
235  1183709 if (sqnum[j] == -1)
236    {
237  54 sqnum[j] = GAP_INDEX;
238    }
239    }
240    }
241   
242  9210 seqNums.setElementAt(sqnum, i);
243    }
244    else
245    {
246  0 jalview.bin.Console.outPrintln("SEQUENCE HAS BEEN DELETED!!!");
247    }
248    }
249    else
250    {
251    // JBPNote INFO level debug
252  0 jalview.bin.Console.errPrintln(
253    "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
254    }
255    }
256   
257    /**
258    * Calculates the conservation values for given set of sequences
259    */
 
260  908 toggle public void calculate()
261    {
262  908 int height = sequences.length;
263   
264  908 total = new Map[maxLength];
265   
266  122088 for (int column = start; column <= end; column++)
267    {
268  121178 ResidueCount values = countResidues(column);
269   
270    /*
271    * percentage count at or below which we ignore residues
272    */
273  121169 int thresh = (threshold * height) / 100;
274   
275    /*
276    * check observed residues in column and record whether each
277    * physico-chemical property is conserved (+1), absence conserved (0),
278    * or not conserved (-1)
279    * Using TreeMap means properties are displayed in alphabetical order
280    */
281  121169 SortedMap<String, Integer> resultHash = new TreeMap<>();
282  121170 SymbolCounts symbolCounts = values.getSymbolCounts();
283  121182 char[] symbols = symbolCounts.symbols;
284  121182 int[] counts = symbolCounts.values;
285  382320 for (int j = 0; j < symbols.length; j++)
286    {
287  261132 char c = symbols[j];
288  261114 if (counts[j] > thresh)
289    {
290  261105 recordConservation(resultHash, String.valueOf(c));
291    }
292    }
293  121176 if (values.getGapCount() > thresh)
294    {
295  64851 recordConservation(resultHash, "-");
296    }
297   
298  121179 if (total.length > 0)
299    {
300  121176 total[column - start] = resultHash;
301    }
302    }
303    }
304   
305    /**
306    * Updates the conservation results for an observed residue
307    *
308    * @param resultMap
309    * a map of {property, conservation} where conservation value is +1
310    * (all residues have the property), 0 (no residue has the property)
311    * or -1 (some do, some don't)
312    * @param res
313    */
 
314  325922 toggle protected static void recordConservation(Map<String, Integer> resultMap,
315    String res)
316    {
317  325924 res = res.toUpperCase(Locale.ROOT);
318  325934 for (Entry<String, Map<String, Integer>> property : ResidueProperties.propHash
319    .entrySet())
320    {
321  3256870 String propertyName = property.getKey();
322  3257356 Integer residuePropertyValue = property.getValue().get(res);
323   
324  3259030 if (!resultMap.containsKey(propertyName))
325    {
326    /*
327    * first time we've seen this residue - note whether it has this property
328    */
329  1211726 if (residuePropertyValue != null)
330    {
331  1211400 resultMap.put(propertyName, residuePropertyValue);
332    }
333    else
334    {
335    /*
336    * unrecognised residue - use default value for property
337    */
338  340 resultMap.put(propertyName, property.getValue().get("-"));
339    }
340    }
341    else
342    {
343  2048052 Integer currentResult = resultMap.get(propertyName);
344  2047990 if (currentResult.intValue() != -1
345    && !currentResult.equals(residuePropertyValue))
346    {
347    /*
348    * property is unconserved - residues seen both with and without it
349    */
350  599762 resultMap.put(propertyName, Integer.valueOf(-1));
351    }
352    }
353    }
354    }
355   
356    /**
357    * Counts residues (upper-cased) and gaps in the given column
358    *
359    * @param column
360    * @return
361    */
 
362  121176 toggle protected ResidueCount countResidues(int column)
363    {
364  121176 ResidueCount values = new ResidueCount(false);
365   
366  1618151 for (int row = 0; row < sequences.length; row++)
367    {
368  1496843 if (sequences[row].getLength() > column)
369    {
370  1480513 char c = sequences[row].getCharAt(column);
371  1480428 if (canonicaliseAa)
372    {
373  1480449 int index = ResidueProperties.aaIndex[c];
374  1480807 c = index > 20 ? '-' : ResidueProperties.aa[index].charAt(0);
375    }
376    else
377    {
378  0 c = toUpperCase(c);
379    }
380  1480826 if (Comparison.isGap(c))
381    {
382  291418 values.addGap();
383    }
384    else
385    {
386  1189427 values.add(c);
387    }
388    }
389    else
390    {
391  16377 values.addGap();
392    }
393    }
394  121171 return values;
395    }
396   
397    /**
398    * Counts conservation and gaps for a column of the alignment
399    *
400    * @return { 1 if fully conserved, else 0, gap count }
401    */
 
402  121163 toggle public int[] countConservationAndGaps(int column)
403    {
404  121163 int gapCount = 0;
405  121163 boolean fullyConserved = true;
406  121164 int iSize = sequences.length;
407   
408  121164 if (iSize == 0)
409    {
410  0 return new int[] { 0, 0 };
411    }
412   
413  121164 char lastRes = '0';
414  1617837 for (int i = 0; i < iSize; i++)
415    {
416  1496597 if (column >= sequences[i].getLength())
417    {
418  16377 gapCount++;
419  16377 continue;
420    }
421   
422  1480220 char c = sequences[i].getCharAt(column); // gaps do not have upper/lower
423    // case
424   
425  1480518 if (Comparison.isGap((c)))
426    {
427  291338 gapCount++;
428    }
429    else
430    {
431  1189187 c = toUpperCase(c);
432  1189392 if (lastRes == '0')
433    {
434  116980 lastRes = c;
435    }
436  1189743 if (c != lastRes)
437    {
438  360937 fullyConserved = false;
439    }
440    }
441    }
442   
443  121169 int[] r = new int[] { fullyConserved ? 1 : 0, gapCount };
444  121162 return r;
445    }
446   
447    /**
448    * Returns the upper-cased character if between 'a' and 'z', else the
449    * unchanged value
450    *
451    * @param c
452    * @return
453    */
 
454  1189194 toggle char toUpperCase(char c)
455    {
456  1189233 if ('a' <= c && c <= 'z')
457    {
458  4779 c -= TOUPPERCASE;
459    }
460  1189266 return c;
461    }
462   
463    /**
464    * Calculates the conservation sequence
465    *
466    * @param positiveOnly
467    * if true, calculate positive conservation; else calculate both
468    * positive and negative conservation
469    * @param maxPercentageGaps
470    * the percentage of gaps in a column, at or above which no
471    * conservation is asserted
472    */
 
473  907 toggle public void verdict(boolean positiveOnly, float maxPercentageGaps)
474    {
475    // TODO call this at the end of calculate(), should not be a public method
476   
477  907 StringBuilder consString = new StringBuilder(end);
478   
479    // NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
480    // EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
481    // DOES NOT EXIST IN JALVIEW 2.1.2
482  997 for (int i = 0; i < start; i++)
483    {
484  90 consString.append('-');
485    }
486  907 consSymbs = new String[end - start + 1];
487  122066 for (int i = start; i <= end; i++)
488    {
489  121160 int[] gapcons = countConservationAndGaps(i);
490  121161 boolean fullyConserved = gapcons[0] == 1;
491  121162 int totGaps = gapcons[1];
492  121162 float pgaps = (totGaps * 100f) / sequences.length;
493   
494  121166 if (maxPercentageGaps > pgaps)
495    {
496  89092 Map<String, Integer> resultHash = total[i - start];
497  89092 int count = 0;
498  89092 StringBuilder positives = new StringBuilder(64);
499  89094 StringBuilder negatives = new StringBuilder(32);
500  89098 for (String type : resultHash.keySet())
501    {
502  890753 int result = resultHash.get(type).intValue();
503  890956 if (result == -1)
504    {
505    /*
506    * not conserved (present or absent)
507    */
508  370145 continue;
509    }
510  520827 count++;
511  520827 if (result == 1)
512    {
513    /*
514    * positively conserved property (all residues have it)
515    */
516  159792 positives.append(positives.length() == 0 ? "" : " ");
517  159788 positives.append(type);
518    }
519  520826 if (result == 0 && !positiveOnly)
520    {
521    /*
522    * absense of property is conserved (all residues lack it)
523    */
524  361039 negatives.append(negatives.length() == 0 ? "" : " ");
525  361041 negatives.append("!").append(type);
526    }
527    }
528  89100 if (negatives.length() > 0)
529    {
530  56156 positives.append(" ").append(negatives);
531    }
532  89094 consSymbs[i - start] = positives.toString();
533   
534  89096 if (count < 10)
535    {
536  54931 consString.append(count); // Conserved props!=Identity
537    }
538    else
539    {
540  34165 consString.append(fullyConserved ? "*" : "+");
541    }
542    }
543    else
544    {
545  32074 consString.append('-');
546    }
547    }
548   
549  907 consSequence = new Sequence(name, consString.toString(), start, end);
550    }
551   
552    /**
553    *
554    *
555    * @return Conservation sequence
556    */
 
557  925 toggle public SequenceI getConsSequence()
558    {
559  925 return consSequence;
560    }
561   
562    // From Alignment.java in jalview118
 
563  895 toggle public void findQuality()
564    {
565  895 findQuality(0, maxLength - 1, ScoreModels.getInstance().getBlosum62());
566    }
567   
568    /**
569    * DOCUMENT ME!
570    *
571    * @param sm
572    */
 
573  895 toggle private void percentIdentity(ScoreMatrix sm)
574    {
575  895 seqNums = new Vector<>();
576  895 int i = 0, iSize = sequences.length;
577    // Do we need to calculate this again?
578  10105 for (i = 0; i < iSize; i++)
579    {
580  9210 calcSeqNum(i, sm);
581    }
582   
583  895 if ((cons2 == null) || seqNumsChanged)
584    {
585    // FIXME remove magic number 24 without changing calc
586    // sm.getSize() returns 25 so doesn't quite do it...
587  895 cons2 = new int[maxLength][24];
588  895 cons2GapCounts = new int[maxLength];
589   
590  895 int j = 0;
591   
592  10105 while (j < sequences.length)
593    {
594  9210 int[] sqnum = seqNums.elementAt(j);
595   
596  1483646 for (i = 1; i < sqnum.length; i++)
597    {
598  1474436 int index = sqnum[i];
599  1474436 if (index == GAP_INDEX)
600    {
601  290241 cons2GapCounts[i - 1]++;
602    }
603    else
604    {
605  1184195 cons2[i - 1][index]++;
606    }
607    }
608   
609    // TODO should this start from sqnum.length?
610  25542 for (i = sqnum.length - 1; i < maxLength; i++)
611    {
612  16332 cons2GapCounts[i]++;
613    }
614  9210 j++;
615    }
616    }
617    }
618   
619    /**
620    * Calculates the quality of the set of sequences over the given inclusive
621    * column range, using the specified substitution score matrix
622    *
623    * @param startCol
624    * @param endCol
625    * @param scoreMatrix
626    */
 
627  895 toggle protected void findQuality(int startCol, int endCol,
628    ScoreMatrix scoreMatrix)
629    {
630  895 quality = new Vector<>();
631   
632  895 double max = -Double.MAX_VALUE;
633  895 float[][] scores = scoreMatrix.getMatrix();
634   
635  895 percentIdentity(scoreMatrix);
636   
637  895 int size = seqNums.size();
638  895 int[] lengths = new int[size];
639   
640  10105 for (int l = 0; l < size; l++)
641    {
642  9210 lengths[l] = seqNums.elementAt(l).length - 1;
643    }
644   
645  895 final int symbolCount = scoreMatrix.getSize();
646   
647  121201 for (int j = startCol; j <= endCol; j++)
648    {
649  120307 double bigtot = 0;
650   
651    // First Xr = depends on column only
652  120307 double[] x = new double[symbolCount];
653   
654  3001279 for (int ii = 0; ii < symbolCount; ii++)
655    {
656  2878962 x[ii] = 0;
657   
658    /*
659    * todo JAL-728 currently assuming last symbol in matrix is * for gap
660    * (which we ignore as counted separately); true for BLOSUM62 but may
661    * not be once alternative matrices are supported
662    */
663  68963678 for (int i2 = 0; i2 < symbolCount - 1; i2++)
664    {
665  66116666 x[ii] += (((double) cons2[j][i2] * scores[ii][i2]) + 4D);
666    }
667  2886413 x[ii] += 4D + cons2GapCounts[j] * scoreMatrix.getMinimumScore();
668   
669  2881420 x[ii] /= size;
670    }
671   
672    // Now calculate D for each position and sum
673  1610604 for (int k = 0; k < size; k++)
674    {
675  1490310 double tot = 0;
676  1490314 double[] xx = new double[symbolCount];
677    // sequence character index, or implied gap if sequence too short
678  1489794 int seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1]
679    : GAP_INDEX;
680   
681  35626248 for (int i = 0; i < symbolCount - 1; i++)
682    {
683  34137158 double sr = 4D;
684  34197270 if (seqNum == GAP_INDEX)
685    {
686  7046100 sr += scoreMatrix.getMinimumScore();
687    }
688    else
689    {
690  27155551 sr += scores[i][seqNum];
691    }
692   
693  34174542 xx[i] = x[i] - sr;
694   
695  34155409 tot += (xx[i] * xx[i]);
696    }
697   
698  1490556 bigtot += Math.sqrt(tot);
699    }
700   
701  120306 max = Math.max(max, bigtot);
702   
703  120306 quality.addElement(Double.valueOf(bigtot));
704    }
705   
706  895 double newmax = -Double.MAX_VALUE;
707   
708  121203 for (int j = startCol; j <= endCol; j++)
709    {
710  120308 double tmp = quality.elementAt(j).doubleValue();
711    // tmp = ((max - tmp) * (size - cons2[j][23])) / size;
712  120308 tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size;
713   
714    // jalview.bin.Console.outPrintln(tmp+ " " + j);
715  120308 quality.setElementAt(Double.valueOf(tmp), j);
716   
717  120308 if (tmp > newmax)
718    {
719  2358 newmax = tmp;
720    }
721    }
722   
723  895 qualityMinimum = 0D;
724  895 qualityMaximum = newmax;
725    }
726   
727    /**
728    * Complete the given consensus and quuality annotation rows. Note: currently
729    * this method will reallocate the given annotation row if it is different to
730    * the calculated width, otherwise will leave its length unchanged.
731    *
732    * @param conservation
733    * conservation annotation row
734    * @param quality2
735    * (optional - may be null)
736    * @param istart
737    * first column for conservation
738    * @param alWidth
739    * extent of conservation
740    */
 
741  895 toggle public void completeAnnotations(AlignmentAnnotation conservation,
742    AlignmentAnnotation quality2, int istart, int alWidth)
743    {
744  895 SequenceI cons = getConsSequence();
745   
746    /*
747    * colour scale for Conservation and Quality;
748    */
749  895 float minR = 0.3f;
750  895 float minG = 0.0f;
751  895 float minB = 0f;
752  895 float maxR = 1.0f - minR;
753  895 float maxG = 0.9f - minG;
754  895 float maxB = 0f - minB;
755   
756  895 float min = 0f;
757  895 float max = 11f;
758  895 float qmin = 0f;
759  895 float qmax = 0f;
760  895 if (conservation!=null)
761    {
762  893 conservation.setNoOfSequencesIncluded(sequences.length);
763    }
764  895 if (quality2!=null)
765    {
766  895 quality2.setNoOfSequencesIncluded(sequences.length);
767    }
768   
769  895 if (conservation != null && conservation.annotations != null
770    && conservation.annotations.length != alWidth)
771    {
772  399 conservation.annotations = new Annotation[alWidth];
773    }
774   
775  895 if (quality2 != null)
776    {
777  895 quality2.graphMax = (float) qualityMaximum;
778  895 if (quality2.annotations != null
779    && quality2.annotations.length != alWidth)
780    {
781  400 quality2.annotations = new Annotation[alWidth];
782    }
783  895 qmin = (float) qualityMinimum;
784  895 qmax = (float) qualityMaximum;
785    }
786   
787  120731 for (int i = istart; i < alWidth; i++)
788    {
789  119838 float value = 0;
790   
791  119838 char c = cons.getCharAt(i);
792   
793  119838 if (Character.isDigit(c))
794    {
795  54358 value = c - '0';
796    }
797  65479 else if (c == '*')
798    {
799  33675 value = 11;
800    }
801  31803 else if (c == '+')
802    {
803  87 value = 10;
804    }
805   
806  119831 if (conservation != null)
807    {
808  119515 float vprop = value - min;
809  119514 vprop /= max;
810  119513 int consp = i - start;
811  119515 String conssym = (value > 0 && consp > -1
812    && consp < consSymbs.length) ? consSymbs[consp] : "";
813  119514 conservation.annotations[i] = new Annotation(String.valueOf(c),
814    conssym, ' ', value, new Color(minR + (maxR * vprop),
815    minG + (maxG * vprop), minB + (maxB * vprop)));
816    }
817   
818    // Quality calc
819  119837 if (quality2 != null)
820    {
821  119837 value = quality.elementAt(i).floatValue();
822  119838 float vprop = value - qmin;
823  119837 vprop /= qmax;
824  119836 String description = FORMAT_3DP.form(value);
825  119837 quality2.annotations[i] = new Annotation(" ", description, ' ',
826    value, new Color(minR + (maxR * vprop),
827    minG + (maxG * vprop), minB + (maxB * vprop)));
828    }
829    }
830    }
831   
832    /**
833    * construct and call the calculation methods on a new Conservation object
834    *
835    * @param name
836    * - name of conservation
837    * @param seqs
838    * @param start
839    * first column in calculation window
840    * @param end
841    * last column in calculation window
842    * @param positiveOnly
843    * calculate positive (true) or positive and negative (false)
844    * conservation
845    * @param maxPercentGaps
846    * percentage of gaps tolerated in column
847    * @param calcQuality
848    * flag indicating if alignment quality should be calculated
849    * @return Conservation object ready for use in visualization
850    */
 
851  898 toggle public static Conservation calculateConservation(String name,
852    List<SequenceI> seqs, int start, int end, boolean positiveOnly,
853    int maxPercentGaps, boolean calcQuality)
854    {
855  898 Conservation cons = new Conservation(name, seqs, start, end);
856  898 cons.calculate();
857  898 cons.verdict(positiveOnly, maxPercentGaps);
858   
859  898 if (calcQuality)
860    {
861  895 cons.findQuality();
862    }
863   
864  898 return cons;
865    }
866   
867    /**
868    * Returns the computed tooltip (annotation description) for a given column.
869    * The tip is empty if the conservation score is zero, otherwise holds the
870    * conserved properties (and, optionally, properties whose absence is
871    * conserved).
872    *
873    * @param column
874    * @return
875    */
 
876  7 toggle String getTooltip(int column)
877    {
878  7 SequenceI cons = getConsSequence();
879  7 char val = column < cons.getLength() ? cons.getCharAt(column) : '-';
880  7 boolean hasConservation = val != '-' && val != '0';
881  7 int consp = column - start;
882  7 String tip = (hasConservation && consp > -1 && consp < consSymbs.length)
883    ? consSymbs[consp]
884    : "";
885  7 return tip;
886    }
887    }
  • Report generated by OpenClover v 4.4.1 on Thu Jun 4 2026 14:25:22 BST using coverage data from Thu Jun 4 2026 14:25:10 BST.
  • OpenClover is free and open-source software.