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Coverage Report

  1. Project Clover database Wed Dec 3 2025 17:03:17 GMT
  2. Package jalview.schemes

File HmmerLocalBackground.java

 

Coverage histogram

../../img/srcFileCovDistChart10.png
0% of files have more coverage

Code metrics

2
18
6
1
96
59
7
0.39
3
6
1.17

Classes

Class Line # Actions
HmmerLocalBackground 18 18 7
1.0100%
 

Contributing tests

This file is covered by 195 tests. .

Source view

1    package jalview.schemes;
2   
3    import jalview.datamodel.AnnotatedCollectionI;
4    import jalview.datamodel.ResidueCount;
5    import jalview.datamodel.SequenceCollectionI;
6    import jalview.datamodel.SequenceI;
7   
8    import java.util.HashMap;
9    import java.util.List;
10    import java.util.Map;
11   
12    /**
13    * An HMM colour scheme that uses local (alignment or sub-group) background
14    * frequencies for residues
15    *
16    * @author tzvanaalten
17    */
 
18    public class HmmerLocalBackground extends HmmerColourScheme
19    {
20    float logTotalCount;
21   
22    /**
23    * Constructor given a sequence collection
24    *
25    * @param ac
26    */
 
27  2 toggle public HmmerLocalBackground(AnnotatedCollectionI ac)
28    {
29  2 super(ac.getHmmSequences());
30  2 countFrequencies(ac);
31    }
32   
33    /**
34    * Default constructor (required by ColourSchemes.loadColourSchemes)
35    */
 
36  54 toggle public HmmerLocalBackground()
37    {
38    }
39   
 
40  618 toggle @Override
41    public String getSchemeName()
42    {
43  618 return JalviewColourScheme.HMMERA.toString();
44    }
45   
46    /**
47    * Counts and stores the relative frequency of every residue in the alignment
48    * (apart from any HMM consensus sequences)
49    *
50    * @param sc
51    */
 
52  2 toggle public void countFrequencies(SequenceCollectionI sc)
53    {
54    // TODO or total counts in Consensus Profile (how do we get at it?)?
55  2 Map<Character, Float> freqs = new HashMap<>();
56   
57    /*
58    * count symbols, excluding any HMM consensus sequences
59    */
60  2 ResidueCount counts = new ResidueCount();
61  2 List<SequenceI> seqs = sc.getSequences();
62  2 for (SequenceI seq : seqs)
63    {
64  4 if (!seq.hasHMMProfile())
65    {
66  3 for (char c : seq.getSequence())
67    {
68  29 counts.add(c);
69    }
70    }
71    }
72  2 int total = counts.getTotalResidueCount(); // excludes gaps
73   
74  2 for (char symbol : counts.getSymbolCounts().symbols)
75    {
76  16 double freq = counts.getCount(symbol) / (double) total;
77  16 freqs.put(symbol, (float) freq);
78    }
79   
80  2 setFrequencies(freqs);
81   
82  2 logTotalCount = (float) Math.log(total);
83    }
84   
 
85  1 toggle @Override
86    float getMaxInformationScore()
87    {
88  1 return logTotalCount;
89    }
90   
 
91  1 toggle @Override
92    protected HmmerColourScheme newInstance(AnnotatedCollectionI ac)
93    {
94  1 return new HmmerLocalBackground(ac);
95    }
96    }
  • Report generated by OpenClover v 4.4.1 on Wed Dec 3 2025 17:13:21 GMT using coverage data from Wed Dec 3 2025 17:13:06 GMT.
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