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Coverage Report

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

File HMMMatchScoreColourScheme.java

 

Coverage histogram

../../img/srcFileCovDistChart5.png
43% of files have more coverage

Code metrics

38
75
19
2
369
225
43
0.57
3.95
9.5
2.26

Classes

Class Line # Actions
HMMMatchScoreColourScheme 23 51 34
0.2234042622.3%
HMMMatchScoreColourScheme.MatchProbReader 32 24 9
1.0100%
 

Contributing tests

This file is covered by 195 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.io.BufferedReader;
12    import java.io.FileNotFoundException;
13    import java.io.FileReader;
14    import java.io.IOException;
15    import java.util.ArrayList;
16    import java.util.HashMap;
17    import java.util.List;
18    import java.util.Map;
19   
20   
21   
22   
 
23    public class HMMMatchScoreColourScheme extends ResidueColourScheme
24    {
25   
26    private Map<Character, Map<Integer, Map<String, Double>>> probabilities;
27   
28    private List<Integer> ranges;
29   
30    private static double binSize;
31   
 
32    public class MatchProbReader
33    {
34    private BufferedReader reader;
35   
 
36  1 toggle MatchProbReader() throws FileNotFoundException
37    {
38  1 reader = new BufferedReader(
39    new FileReader("resources/ProbabilityOfMatch"));
40    }
41   
42    /*
43    public Map<Character, Map<String, Double>> getProbabilities() throws IOException
44    {
45    Map<Character, Map<String, Double>> probabilities = new HashMap<>();
46   
47    String[] alphabet = reader.readLine().split("\\,");
48    for (int i = 1; i < alphabet.length - 1; i++)
49    {
50    probabilities.put(alphabet[i].replaceAll("\\ ", "").charAt(0),
51    new HashMap<>());
52    }
53   
54    String line = reader.readLine();
55    while(line != null)
56    {
57    String[] contents = line.split("\\,");
58   
59    for(int i = 1; i < contents.length; i++)
60    {
61    probabilities.get(alphabet[i].replaceAll("\\ ", "").charAt(0))
62    .put(contents[0], Double
63    .valueOf(contents[i].replaceAll("\\ ", "")));
64    }
65    line = reader.readLine();
66   
67    }
68    reader.close();
69    return probabilities;
70    }
71    */
72   
 
73  1 toggle public Map<Character, Map<Integer, Map<String, Double>>> getProbabilities()
74    throws IOException
75    {
76   
77  1 Map<Character, Map<Integer, Map<String, Double>>> probabilities = new HashMap<>();
78   
79  1 ranges = new ArrayList<>();
80  1 ranges.add(0);
81   
82  1 binSize = Double.valueOf((reader.readLine().replaceAll("\\ ", "")));
83  1 String line = reader.readLine();
84  1 char c = line.charAt(0);
85   
86  21 while (line != null)
87    {
88  20 line = reader.readLine();
89  140 while (line != null && line.split("\\,").length != 1)
90    {
91  120 String[] llrs = line.split("\\,");
92  120 String[] counts = reader.readLine().split("\\,");
93  120 int range = Integer.valueOf(llrs[0]);
94   
95  120 if (!ranges.contains(range))
96    {
97  6 ranges.add(range);
98    }
99  120 if (!probabilities.containsKey(c))
100    {
101  20 probabilities.put(c, new HashMap<>());
102    }
103  120 probabilities.get(c).put(range, new HashMap<>());
104   
105  3490 for (int i = 1; i < llrs.length; i++)
106    {
107  3370 probabilities.get(c).get(range).put(
108    llrs[i].replaceAll("\\ ", ""),
109    Double.valueOf(counts[i].replaceAll("\\ ", "")));
110    }
111   
112  120 line = reader.readLine();
113    }
114  20 if (line != null)
115    {
116  19 c = line.charAt(0);
117    }
118    }
119   
120  1 return probabilities;
121    }
122   
123    }
124   
125    private static final Color INSERTION_COLOUR = Color.white;
126   
127    /*
128    * the aligned HMM consensus sequence to use as reference for colouring
129    */
130    private SequenceI hmmSeq;
131   
132    private HiddenMarkovModel hmm;
133   
134    private Map<Character, Float> frequencies;
135   
136    /**
137    * Constructor given a list of Hidden Markov Model consensus sequences. The
138    * first sequence provides the HMM profile from which we can read the emission
139    * probabilities that determine the colour.
140    *
141    * @param hmmSeqs
142    * @throws IOException
143    */
 
144  1 toggle public HMMMatchScoreColourScheme(List<SequenceI> hmmSeqs)
145    {
146  1 hmmSeq = hmmSeqs.isEmpty() ? null : hmmSeqs.get(0);
147  1 hmm = hmmSeq == null ? null : hmmSeq.getHMM();
148   
149  1 try
150    {
151  1 MatchProbReader probabilityReader = new MatchProbReader();
152  1 probabilities = probabilityReader.getProbabilities();
153    } catch (IOException e)
154    {
155  0 System.out.println(e.getStackTrace());
156    }
157    }
158   
159    /**
160    * Default constructor (required by ColourSchemes.loadColourSchemes)
161    */
 
162  54 toggle public HMMMatchScoreColourScheme()
163    {
164    }
165   
 
166  0 toggle @Override
167    public Color findColour(char symbol, int column, SequenceI seq,
168    String consensusResidue, float pid)
169    {
170  0 if (seq == null)
171    {
172  0 return null;
173    }
174  0 return findColour(symbol, column, seq.gapMap().length);
175    }
176   
177    // TODO change documentation
178    /**
179    * Returns the colour at a particular symbol at a column in the alignment:
180    * <ul>
181    * <li>white for a gap</li>
182    * <li>red for an insertion</li>
183    * <li>orange for negative information content</li>
184    * <li>white to blue for increasing information content</li>
185    * </ul>
186    *
187    * @param symbol
188    * @param column
189    * @return
190    */
 
191  0 toggle private Color findColour(char symbol, int column, int length)
192    {
193  0 if (getHmm() == null || Comparison.isGap(symbol))
194    {
195  0 return Color.white;
196    }
197  0 if (Comparison.isGap(hmmSeq.getCharAt(column)))
198    {
199  0 return INSERTION_COLOUR;
200    }
201  0 if (Character.isLowerCase(symbol))
202    {
203  0 symbol = Character.toUpperCase(symbol);
204    }
205   
206  0 double prob = 0;
207  0 if (hmm.getBackgroundFrequencies().containsKey(symbol))
208    {
209  0 int lengthBin = getLengthBin(length);
210   
211  0 double llr = Math
212    .log(getHmm().getMatchEmissionProbability(column, symbol)
213    / hmm.getBackgroundFrequencies().get(symbol));
214   
215  0 if (!probabilities.containsKey(symbol)
216    || !probabilities.get(symbol).get(lengthBin)
217    .containsKey(format(llr)))
218    {
219  0 return new Color(140, 140, 140);
220    }
221   
222   
223  0 prob = probabilities.get(symbol).get(lengthBin).get(format(llr));
224    }
225    else
226    {
227  0 return new Color(140, 140, 140);
228    }
229   
230  0 Color colour = Color.ORANGE;
231  0 if (prob >= 0.5)
232    {
233   
234  0 colour = ColorUtils.getGraduatedColour((float) prob, 0.5f,
235    Color.WHITE, 1f,
236    Color.blue);
237    }
238    else
239    {
240  0 colour = ColorUtils.getGraduatedColour((float) prob, 0f, Color.red,
241    0.5f, Color.WHITE);
242    }
243   
244  0 return colour;
245    }
246   
 
247  0 toggle public static String format(Double d)
248    {
249  0 String formatArg = String.valueOf(binSize);
250   
251    // if bin size, need format "%.n" where n is number of decimal places
252  0 if (binSize < 1)
253    {
254  0 formatArg = "." + formatArg.split("\\.")[1].length();
255    }
256   
257  0 Double rounded = Math.round(d / binSize) * binSize;
258  0 String formatted = String.format("%" + formatArg + "f", rounded);
259   
260    // format sometimes returns a number rounded to 0 as -0
261    // this ensures output will always be 0
262  0 if (Double.valueOf(formatted) == 0)
263    {
264  0 formatted = "0";
265    }
266  0 return formatted;
267   
268    }
269   
270    /**
271    * Answers the maximum possible value of information score (log ratio), for use
272    * in scaling a graduated colour range
273    *
274    * @return
275    */
 
276  0 toggle protected float getMaxInformationScore()
277    {
278  0 return 0f;
279    }
280   
281    /**
282    * Answers a new colour scheme instance based on the HMM of the first sequence
283    * in ac that has an HMM
284    */
 
285  1 toggle @Override
286    public ColourSchemeI getInstance(AlignViewportI viewport,
287    AnnotatedCollectionI ac)
288    {
289  1 return newInstance(ac);
290    }
291   
292    /**
293    * Constructor given a sequence collection
294    *
295    * @param ac
296    */
 
297  1 toggle public HMMMatchScoreColourScheme(AnnotatedCollectionI ac)
298    {
299  1 this(ac.getHmmSequences());
300    }
301   
302    /**
303    * Answers a new instance of the colour scheme for the given HMM
304    *
305    * @param ac
306    * @return
307    */
 
308  1 toggle protected HMMMatchScoreColourScheme newInstance(AnnotatedCollectionI ac)
309    {
310  1 return new HMMMatchScoreColourScheme(ac);
311    }
312   
 
313  49 toggle @Override
314    public boolean isSimple()
315    {
316  49 return false;
317    }
318   
319    /**
320    * Answers true if the sequence collection has an HMM consensus sequence and
321    * that the first HMM sequence contains background frequencies, else false
322    */
 
323  497 toggle @Override
324    public boolean isApplicableTo(AnnotatedCollectionI ac)
325    {
326  497 return !ac.getHmmSequences().isEmpty() && ac.getHmmSequences().get(0)
327    .getHMM().getBackgroundFrequencies() != null;
328    }
329   
 
330  0 toggle protected Map<Character, Float> getFrequencies()
331    {
332  0 return frequencies;
333    }
334   
 
335  0 toggle protected void setFrequencies(Map<Character, Float> frequencies)
336    {
337  0 this.frequencies = frequencies;
338    }
339   
 
340  0 toggle protected HiddenMarkovModel getHmm()
341    {
342  0 return hmm;
343    }
344   
 
345  0 toggle protected SequenceI getHmmSequence()
346    {
347  0 return hmmSeq;
348    }
349   
 
350  618 toggle @Override
351    public String getSchemeName()
352    {
353  618 return JalviewColourScheme.HMMMatchScore.toString();
354    }
355   
 
356  0 toggle private int getLengthBin(int l)
357    {
358  0 for (int i = 1; i < ranges.size(); i++)
359    {
360  0 if (l >= ranges.get(i - 1) && l < ranges.get(i))
361    {
362  0 return ranges.get(i);
363    }
364    }
365  0 return -1;
366    }
367    }
368   
369   
  • 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.
  • OpenClover is free and open-source software.