1 package jalview.schemes;
3 import jalview.datamodel.AnnotatedCollectionI;
4 import jalview.datamodel.HiddenMarkovModel;
7 * An HMM colour scheme that uses global ('Uniprot') background frequencies for
12 public class HmmerGlobalBackground extends HmmerColourScheme
15 * The highest possible log ratio is when match emission probability in
16 * the HMM model is 1, and background (for W) is 0.0109 giving
17 * log(1/0.0109) = log(91.743) = 4.519
19 private static final float MAX_LOG_RATIO = 4.519f;
22 * Constructor given a Hidden Markov Model
26 public HmmerGlobalBackground(HiddenMarkovModel markov)
29 setFrequencies(ResidueProperties.backgroundFrequencies
30 .get(getHmm().getAlphabetType()));
34 * Default constructor (required by ColourSchemes.loadColourSchemes)
36 public HmmerGlobalBackground()
41 public String getSchemeName()
43 return JalviewColourScheme.HMMERU.toString();
47 protected HmmerColourScheme newInstance(AnnotatedCollectionI ac,
48 HiddenMarkovModel model)
50 return new HmmerGlobalBackground(model);
54 float getMaxInformationScore()