Clover icon

Coverage Report

  1. Project Clover database Wed Mar 4 2026 12:01:44 GMT
  2. Package jalview.analysis

File Conservation.java

 

Coverage histogram

../../img/srcFileCovDistChart10.png
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 197 tests. .

Source view

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  896 toggle public Conservation(String name, List<SequenceI> sequences, int start,
131    int end)
132    {
133  896 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  900 toggle public Conservation(String name, int threshold, List<SequenceI> sequences,
152    int start, int end)
153    {
154  900 this.name = name;
155  900 this.threshold = threshold;
156  900 this.start = start;
157  900 this.end = end;
158   
159  900 maxLength = end - start + 1; // default width includes bounds of
160    // calculation
161   
162  900 int s, sSize = sequences.size();
163  900 SequenceI[] sarray = new SequenceI[sSize];
164  900 this.sequences = sarray;
165  900 try
166    {
167  10143 for (s = 0; s < sSize; s++)
168    {
169  9243 sarray[s] = sequences.get(s);
170  9243 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  9169 toggle private void calcSeqNum(int i, ScoreMatrix sm)
192    {
193  9169 int sSize = sequences.length;
194   
195  9169 if ((i > -1) && (i < sSize))
196    {
197  9169 String sq = sequences[i].getSequenceAsString();
198   
199  9169 if (seqNums.size() <= i)
200    {
201  9169 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  9169 if (sq.hashCode() != seqNums.elementAt(i)[0])
209    {
210  9169 int j;
211  9169 int len;
212  9169 seqNumsChanged = true;
213  9169 len = sq.length();
214   
215  9169 if (maxLength < len)
216    {
217  0 maxLength = len;
218    }
219   
220  9169 int[] sqnum = new int[len + 1]; // better to always make a new array -
221    // sequence can change its length
222  9169 sqnum[0] = sq.hashCode();
223   
224  1492219 for (j = 1; j <= len; j++)
225    {
226    // sqnum[j] = ResidueProperties.aaIndex[sq.charAt(j - 1)];
227  1483053 char residue = sq.charAt(j - 1);
228  1483179 if (Comparison.isGap(residue))
229    {
230  291412 sqnum[j] = GAP_INDEX;
231    }
232    else
233    {
234  1191767 sqnum[j] = sm.getMatrixIndex(residue);
235  1191769 if (sqnum[j] == -1)
236    {
237  45 sqnum[j] = GAP_INDEX;
238    }
239    }
240    }
241   
242  9169 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  896 toggle public void calculate()
261    {
262  896 int height = sequences.length;
263   
264  896 total = new Map[maxLength];
265   
266  122808 for (int column = start; column <= end; column++)
267    {
268  121912 ResidueCount values = countResidues(column);
269   
270    /*
271    * percentage count at or below which we ignore residues
272    */
273  121907 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  121906 SortedMap<String, Integer> resultHash = new TreeMap<>();
282  121908 SymbolCounts symbolCounts = values.getSymbolCounts();
283  121913 char[] symbols = symbolCounts.symbols;
284  121912 int[] counts = symbolCounts.values;
285  389442 for (int j = 0; j < symbols.length; j++)
286    {
287  267513 char c = symbols[j];
288  267511 if (counts[j] > thresh)
289    {
290  267497 recordConservation(resultHash, String.valueOf(c));
291    }
292    }
293  121921 if (values.getGapCount() > thresh)
294    {
295  65596 recordConservation(resultHash, "-");
296    }
297   
298  121915 if (total.length > 0)
299    {
300  121914 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  333045 toggle protected static void recordConservation(Map<String, Integer> resultMap,
315    String res)
316    {
317  333052 res = res.toUpperCase(Locale.ROOT);
318  333068 for (Entry<String, Map<String, Integer>> property : ResidueProperties.propHash
319    .entrySet())
320    {
321  3327219 String propertyName = property.getKey();
322  3327914 Integer residuePropertyValue = property.getValue().get(res);
323   
324  3330136 if (!resultMap.containsKey(propertyName))
325    {
326    /*
327    * first time we've seen this residue - note whether it has this property
328    */
329  1219083 if (residuePropertyValue != null)
330    {
331  1218596 resultMap.put(propertyName, residuePropertyValue);
332    }
333    else
334    {
335    /*
336    * unrecognised residue - use default value for property
337    */
338  330 resultMap.put(propertyName, property.getValue().get("-"));
339    }
340    }
341    else
342    {
343  2110777 Integer currentResult = resultMap.get(propertyName);
344  2111751 if (currentResult.intValue() != -1
345    && !currentResult.equals(residuePropertyValue))
346    {
347    /*
348    * property is unconserved - residues seen both with and without it
349    */
350  609633 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  121912 toggle protected ResidueCount countResidues(int column)
363    {
364  121912 ResidueCount values = new ResidueCount(false);
365   
366  1637437 for (int row = 0; row < sequences.length; row++)
367    {
368  1515497 if (sequences[row].getLength() > column)
369    {
370  1489220 char c = sequences[row].getCharAt(column);
371  1489134 if (canonicaliseAa)
372    {
373  1489153 int index = ResidueProperties.aaIndex[c];
374  1489671 c = index > 20 ? '-' : ResidueProperties.aa[index].charAt(0);
375    }
376    else
377    {
378  0 c = toUpperCase(c);
379    }
380  1489706 if (Comparison.isGap(c))
381    {
382  292650 values.addGap();
383    }
384    else
385    {
386  1197065 values.add(c);
387    }
388    }
389    else
390    {
391  26299 values.addGap();
392    }
393    }
394  121908 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  121909 toggle public int[] countConservationAndGaps(int column)
403    {
404  121909 int gapCount = 0;
405  121909 boolean fullyConserved = true;
406  121909 int iSize = sequences.length;
407   
408  121910 if (iSize == 0)
409    {
410  0 return new int[] { 0, 0 };
411    }
412   
413  121910 char lastRes = '0';
414  1638222 for (int i = 0; i < iSize; i++)
415    {
416  1516255 if (column >= sequences[i].getLength())
417    {
418  26299 gapCount++;
419  26299 continue;
420    }
421   
422  1489957 char c = sequences[i].getCharAt(column); // gaps do not have upper/lower
423    // case
424   
425  1490159 if (Comparison.isGap((c)))
426    {
427  292640 gapCount++;
428    }
429    else
430    {
431  1197519 c = toUpperCase(c);
432  1197625 if (lastRes == '0')
433    {
434  117547 lastRes = c;
435    }
436  1197940 if (c != lastRes)
437    {
438  367740 fullyConserved = false;
439    }
440    }
441    }
442   
443  121908 int[] r = new int[] { fullyConserved ? 1 : 0, gapCount };
444  121903 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  1197523 toggle char toUpperCase(char c)
455    {
456  1197528 if ('a' <= c && c <= 'z')
457    {
458  5053 c -= TOUPPERCASE;
459    }
460  1197527 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  894 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  894 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  984 for (int i = 0; i < start; i++)
483    {
484  90 consString.append('-');
485    }
486  894 consSymbs = new String[end - start + 1];
487  122799 for (int i = start; i <= end; i++)
488    {
489  121905 int[] gapcons = countConservationAndGaps(i);
490  121899 boolean fullyConserved = gapcons[0] == 1;
491  121899 int totGaps = gapcons[1];
492  121899 float pgaps = (totGaps * 100f) / sequences.length;
493   
494  121903 if (maxPercentageGaps > pgaps)
495    {
496  89264 Map<String, Integer> resultHash = total[i - start];
497  89264 int count = 0;
498  89264 StringBuilder positives = new StringBuilder(64);
499  89272 StringBuilder negatives = new StringBuilder(32);
500  89271 for (String type : resultHash.keySet())
501    {
502  892520 int result = resultHash.get(type).intValue();
503  892626 if (result == -1)
504    {
505    /*
506    * not conserved (present or absent)
507    */
508  376449 continue;
509    }
510  516181 count++;
511  516223 if (result == 1)
512    {
513    /*
514    * positively conserved property (all residues have it)
515    */
516  158424 positives.append(positives.length() == 0 ? "" : " ");
517  158422 positives.append(type);
518    }
519  516237 if (result == 0 && !positiveOnly)
520    {
521    /*
522    * absense of property is conserved (all residues lack it)
523    */
524  357816 negatives.append(negatives.length() == 0 ? "" : " ");
525  357818 negatives.append("!").append(type);
526    }
527    }
528  89274 if (negatives.length() > 0)
529    {
530  56065 positives.append(" ").append(negatives);
531    }
532  89270 consSymbs[i - start] = positives.toString();
533   
534  89272 if (count < 10)
535    {
536  55692 consString.append(count); // Conserved props!=Identity
537    }
538    else
539    {
540  33580 consString.append(fullyConserved ? "*" : "+");
541    }
542    }
543    else
544    {
545  32639 consString.append('-');
546    }
547    }
548   
549  894 consSequence = new Sequence(name, consString.toString(), start, end);
550    }
551   
552    /**
553    *
554    *
555    * @return Conservation sequence
556    */
 
557  913 toggle public SequenceI getConsSequence()
558    {
559  913 return consSequence;
560    }
561   
562    // From Alignment.java in jalview118
 
563  882 toggle public void findQuality()
564    {
565  882 findQuality(0, maxLength - 1, ScoreModels.getInstance().getBlosum62());
566    }
567   
568    /**
569    * DOCUMENT ME!
570    *
571    * @param sm
572    */
 
573  882 toggle private void percentIdentity(ScoreMatrix sm)
574    {
575  882 seqNums = new Vector<>();
576  882 int i = 0, iSize = sequences.length;
577    // Do we need to calculate this again?
578  10051 for (i = 0; i < iSize; i++)
579    {
580  9169 calcSeqNum(i, sm);
581    }
582   
583  882 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  882 cons2 = new int[maxLength][24];
588  882 cons2GapCounts = new int[maxLength];
589   
590  882 int j = 0;
591   
592  10051 while (j < sequences.length)
593    {
594  9169 int[] sqnum = seqNums.elementAt(j);
595   
596  1492945 for (i = 1; i < sqnum.length; i++)
597    {
598  1483776 int index = sqnum[i];
599  1483776 if (index == GAP_INDEX)
600    {
601  291477 cons2GapCounts[i - 1]++;
602    }
603    else
604    {
605  1192299 cons2[i - 1][index]++;
606    }
607    }
608   
609    // TODO should this start from sqnum.length?
610  35423 for (i = sqnum.length - 1; i < maxLength; i++)
611    {
612  26254 cons2GapCounts[i]++;
613    }
614  9169 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  882 toggle protected void findQuality(int startCol, int endCol,
628    ScoreMatrix scoreMatrix)
629    {
630  882 quality = new Vector<>();
631   
632  882 double max = -Double.MAX_VALUE;
633  882 float[][] scores = scoreMatrix.getMatrix();
634   
635  882 percentIdentity(scoreMatrix);
636   
637  882 int size = seqNums.size();
638  882 int[] lengths = new int[size];
639   
640  10051 for (int l = 0; l < size; l++)
641    {
642  9169 lengths[l] = seqNums.elementAt(l).length - 1;
643    }
644   
645  882 final int symbolCount = scoreMatrix.getSize();
646   
647  121924 for (int j = startCol; j <= endCol; j++)
648    {
649  121043 double bigtot = 0;
650   
651    // First Xr = depends on column only
652  121043 double[] x = new double[symbolCount];
653   
654  3020003 for (int ii = 0; ii < symbolCount; ii++)
655    {
656  2899141 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  69359339 for (int i2 = 0; i2 < symbolCount - 1; i2++)
664    {
665  66527272 x[ii] += (((double) cons2[j][i2] * scores[ii][i2]) + 4D);
666    }
667  2904054 x[ii] += 4D + cons2GapCounts[j] * scoreMatrix.getMinimumScore();
668   
669  2898937 x[ii] /= size;
670    }
671   
672    // Now calculate D for each position and sum
673  1629557 for (int k = 0; k < size; k++)
674    {
675  1508276 double tot = 0;
676  1508287 double[] xx = new double[symbolCount];
677    // sequence character index, or implied gap if sequence too short
678  1507824 int seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1]
679    : GAP_INDEX;
680   
681  35929715 for (int i = 0; i < symbolCount - 1; i++)
682    {
683  34423773 double sr = 4D;
684  34503660 if (seqNum == GAP_INDEX)
685    {
686  7301856 sr += scoreMatrix.getMinimumScore();
687    }
688    else
689    {
690  27207649 sr += scores[i][seqNum];
691    }
692   
693  34448417 xx[i] = x[i] - sr;
694   
695  34431918 tot += (xx[i] * xx[i]);
696    }
697   
698  1508489 bigtot += Math.sqrt(tot);
699    }
700   
701  121034 max = Math.max(max, bigtot);
702   
703  121037 quality.addElement(Double.valueOf(bigtot));
704    }
705   
706  882 double newmax = -Double.MAX_VALUE;
707   
708  121928 for (int j = startCol; j <= endCol; j++)
709    {
710  121046 double tmp = quality.elementAt(j).doubleValue();
711    // tmp = ((max - tmp) * (size - cons2[j][23])) / size;
712  121046 tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size;
713   
714    // jalview.bin.Console.outPrintln(tmp+ " " + j);
715  121046 quality.setElementAt(Double.valueOf(tmp), j);
716   
717  121046 if (tmp > newmax)
718    {
719  2359 newmax = tmp;
720    }
721    }
722   
723  882 qualityMinimum = 0D;
724  882 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  882 toggle public void completeAnnotations(AlignmentAnnotation conservation,
742    AlignmentAnnotation quality2, int istart, int alWidth)
743    {
744  882 SequenceI cons = getConsSequence();
745   
746    /*
747    * colour scale for Conservation and Quality;
748    */
749  882 float minR = 0.3f;
750  882 float minG = 0.0f;
751  882 float minB = 0f;
752  882 float maxR = 1.0f - minR;
753  882 float maxG = 0.9f - minG;
754  882 float maxB = 0f - minB;
755   
756  882 float min = 0f;
757  882 float max = 11f;
758  882 float qmin = 0f;
759  882 float qmax = 0f;
760  882 if (conservation!=null)
761    {
762  880 conservation.setNoOfSequencesIncluded(sequences.length);
763    }
764  882 if (quality2!=null)
765    {
766  882 quality2.setNoOfSequencesIncluded(sequences.length);
767    }
768   
769  882 if (conservation != null && conservation.annotations != null
770    && conservation.annotations.length != alWidth)
771    {
772  401 conservation.annotations = new Annotation[alWidth];
773    }
774   
775  882 if (quality2 != null)
776    {
777  882 quality2.graphMax = (float) qualityMaximum;
778  882 if (quality2.annotations != null
779    && quality2.annotations.length != alWidth)
780    {
781  402 quality2.annotations = new Annotation[alWidth];
782    }
783  882 qmin = (float) qualityMinimum;
784  882 qmax = (float) qualityMaximum;
785    }
786   
787  121293 for (int i = istart; i < alWidth; i++)
788    {
789  120410 float value = 0;
790   
791  120410 char c = cons.getCharAt(i);
792   
793  120409 if (Character.isDigit(c))
794    {
795  55020 value = c - '0';
796    }
797  65390 else if (c == '*')
798    {
799  33057 value = 11;
800    }
801  32333 else if (c == '+')
802    {
803  85 value = 10;
804    }
805   
806  120388 if (conservation != null)
807    {
808  120073 float vprop = value - min;
809  120074 vprop /= max;
810  120072 int consp = i - start;
811  120086 String conssym = (value > 0 && consp > -1
812    && consp < consSymbs.length) ? consSymbs[consp] : "";
813  120073 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  120408 if (quality2 != null)
820    {
821  120407 value = quality.elementAt(i).floatValue();
822  120406 float vprop = value - qmin;
823  120403 vprop /= qmax;
824  120404 String description = FORMAT_3DP.form(value);
825  120417 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  885 toggle public static Conservation calculateConservation(String name,
852    List<SequenceI> seqs, int start, int end, boolean positiveOnly,
853    int maxPercentGaps, boolean calcQuality)
854    {
855  885 Conservation cons = new Conservation(name, seqs, start, end);
856  885 cons.calculate();
857  885 cons.verdict(positiveOnly, maxPercentGaps);
858   
859  885 if (calcQuality)
860    {
861  882 cons.findQuality();
862    }
863   
864  885 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 Wed Mar 4 2026 12:10:17 GMT using coverage data from Wed Mar 4 2026 12:10:06 GMT.
  • OpenClover is free and open-source software.