1 package jalview.schemes;
3 import jalview.datamodel.AnnotatedCollectionI;
4 import jalview.datamodel.SequenceCollectionI;
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 sequence collection
26 public HmmerGlobalBackground(SequenceCollectionI ac)
28 super(ac.getHmmSequences());
29 String alphabetType = getHmm() == null
30 ? ResidueProperties.ALPHABET_AMINO
31 : getHmm().getAlphabetType();
33 ResidueProperties.backgroundFrequencies.get(alphabetType));
37 * Default constructor (required by ColourSchemes.loadColourSchemes)
39 public HmmerGlobalBackground()
44 public String getSchemeName()
46 return JalviewColourScheme.HMMERU.toString();
50 protected HmmerColourScheme newInstance(AnnotatedCollectionI ac)
52 return new HmmerGlobalBackground(ac);
56 float getMaxInformationScore()