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Coverage Report

  1. Project Clover database Thu Dec 4 2025 14:43:25 GMT
  2. Package jalview.schemes

File HmmerColourScheme.java

 

Coverage histogram

../../img/srcFileCovDistChart9.png
13% of files have more coverage

Code metrics

14
27
11
1
197
100
19
0.7
2.45
11
1.73

Classes

Class Line # Actions
HmmerColourScheme 35 27 19
0.8846153688.5%
 

Contributing tests

This file is covered by 196 tests. .

Source view

1    package jalview.schemes;
2   
3    import jalview.api.AlignViewportI;
4    import jalview.datamodel.AnnotatedCollectionI;
5    import jalview.datamodel.HiddenMarkovModel;
6    import jalview.datamodel.SequenceI;
7    import jalview.util.ColorUtils;
8    import jalview.util.Comparison;
9   
10    import java.awt.Color;
11    import java.util.List;
12    import java.util.Map;
13   
14    /**
15    * Base class for colour schemes based on a selected Hidden Markov Model. The
16    * colour is with reference to an HMM consensus sequence and HMM profile
17    * <ul>
18    * <li>white for a gap</li>
19    * <li>red for an insertion (position is gapped in the HMM consensus)</li>
20    * <li>orange for negative information content</li>
21    * <li>white to blue for increasing information content</li>
22    * </ul>
23    * where information content is the log ratio
24    *
25    * <pre>
26    * log(profile match emission probability / residue background probability)
27    * </pre>
28    *
29    * Sub-class implementations use either global ('Uniprot') or local
30    * ('alignment') background frequencies.
31    *
32    * @author tzvanaalten
33    * @author gmcarstairs
34    */
 
35    public abstract class HmmerColourScheme extends ResidueColourScheme
36    {
37    private static final Color INSERTION_COLOUR = new Color(230, 0, 0); // reddish
38   
39    /*
40    * the aligned HMM consensus sequence to use as reference for colouring
41    */
42    private SequenceI hmmSeq;
43   
44    private HiddenMarkovModel hmm;
45   
46    private Map<Character, Float> frequencies;
47   
48    /**
49    * Constructor given a list of Hidden Markov Model consensus sequences. The
50    * first sequence provides the HMM profile from which we can read the emission
51    * probabilities that determine the colour.
52    *
53    * @param hmmSeqs
54    */
 
55  4 toggle public HmmerColourScheme(List<SequenceI> hmmSeqs)
56    {
57  4 hmmSeq = hmmSeqs.isEmpty() ? null : hmmSeqs.get(0);
58  4 hmm = hmmSeq == null ? null : hmmSeq.getHMM();
59    }
60   
61    /**
62    * Default constructor (required by ColourSchemes.loadColourSchemes)
63    */
 
64  108 toggle public HmmerColourScheme()
65    {
66    }
67   
 
68  15 toggle @Override
69    public Color findColour(char symbol, int column, SequenceI seq,
70    String consensusResidue, float pid)
71    {
72  15 return findColour(symbol, column);
73    }
74   
75    /**
76    * Returns the colour at a particular symbol at a column in the alignment:
77    * <ul>
78    * <li>white for a gap</li>
79    * <li>red for an insertion</li>
80    * <li>orange for negative information content</li>
81    * <li>white to blue for increasing information content</li>
82    * </ul>
83    *
84    * @param symbol
85    * @param column
86    * @return
87    */
 
88  15 toggle private Color findColour(char symbol, int column)
89    {
90  15 if (getHmm() == null || Comparison.isGap(symbol))
91    {
92  6 return Color.white;
93    }
94  9 if (Comparison.isGap(hmmSeq.getCharAt(column)))
95    {
96  1 return INSERTION_COLOUR;
97    }
98  8 if (Character.isLowerCase(symbol))
99    {
100  0 symbol = Character.toUpperCase(symbol);
101    }
102   
103  8 final double prob = getHmm().getMatchEmissionProbability(column,
104    symbol);
105   
106  8 Float freq = 0f;
107   
108  8 if (!frequencies.containsKey(symbol))
109    {
110  2 return Color.WHITE;
111    }
112    else
113    {
114  6 freq = frequencies.get(symbol);
115    }
116   
117    /*
118    * Orange if match emission probability is less than background probability
119    */
120  6 double infoRatio = prob / freq.floatValue();
121  6 Color colour = Color.ORANGE;
122  6 if (infoRatio >= 1)
123    {
124    /*
125    * log-scale graduated shade of blue if prob is greater than background
126    */
127  3 float infoLog = (float) Math.log(infoRatio);
128  3 colour = ColorUtils.getGraduatedColour(infoLog, 0, Color.WHITE,
129    getMaxInformationScore(), Color.blue);
130    }
131   
132  6 return colour;
133    }
134   
135    /**
136    * Answers the maximum possible value of information score (log ratio), for
137    * use in scaling a graduated colour range
138    *
139    * @return
140    */
141    abstract float getMaxInformationScore();
142   
143    /**
144    * Answers a new colour scheme instance based on the HMM of the first sequence
145    * in ac that has an HMM
146    */
 
147  1 toggle @Override
148    public ColourSchemeI getInstance(AlignViewportI viewport,
149    AnnotatedCollectionI ac)
150    {
151  1 return newInstance(ac);
152    }
153   
154    /**
155    * Answers a new instance of the colour scheme for the given HMM
156    *
157    * @param ac
158    * @return
159    */
160    protected abstract HmmerColourScheme newInstance(AnnotatedCollectionI ac);
161   
 
162  98 toggle @Override
163    public boolean isSimple()
164    {
165  98 return false;
166    }
167   
168    /**
169    * Answers true if the sequence collection has an HMM consensus sequence, else
170    * false
171    */
 
172  994 toggle @Override
173    public boolean isApplicableTo(AnnotatedCollectionI ac)
174    {
175  994 return !ac.getHmmSequences().isEmpty();
176    }
177   
 
178  0 toggle protected Map<Character, Float> getFrequencies()
179    {
180  0 return frequencies;
181    }
182   
 
183  4 toggle protected void setFrequencies(Map<Character, Float> frequencies)
184    {
185  4 this.frequencies = frequencies;
186    }
187   
 
188  26 toggle protected HiddenMarkovModel getHmm()
189    {
190  26 return hmm;
191    }
192   
 
193  0 toggle protected SequenceI getHmmSequence()
194    {
195  0 return hmmSeq;
196    }
197    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 14:53:28 GMT using coverage data from Thu Dec 4 2025 14:53:14 GMT.
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