1 package jalview.schemes;
3 import jalview.datamodel.AnnotatedCollectionI;
4 import jalview.datamodel.HiddenMarkovModel;
5 import jalview.datamodel.SequenceCollectionI;
6 import jalview.datamodel.SequenceI;
7 import jalview.util.ColorUtils;
8 import jalview.util.Comparison;
10 import java.awt.Color;
11 import java.util.List;
14 public class HMMERColourScheme extends ResidueColourScheme
17 AnnotatedCollectionI alignment;
19 HiddenMarkovModel hmm;
21 boolean peptideSpecific;
23 boolean nucleotideSpecific;
25 public HMMERColourScheme(HiddenMarkovModel markov)
29 public HMMERColourScheme()
36 public Color findColour(char symbol, int position, SequenceI seq,
37 String consensusResidue, float pid)
43 return findColour(symbol, position);
47 * Returns the colour at a particular symbol at a column in the alignment.
51 * @return Red for an insertion, white for a gap, orange for a negative
52 * information content, white to blue for increasing information
55 private Color findColour(char symbol, int position)
58 if (Comparison.isGap(symbol))
62 if (Character.isLowerCase(symbol))
64 symbol = Character.toUpperCase(symbol);
67 prob = hmm.getMatchEmissionProbability(position, symbol);
69 String alpha = hmm.getAlphabetType();
70 if (!ResidueProperties.backgroundFrequencies.get(alpha).containsKey(symbol))
76 freq = ResidueProperties.backgroundFrequencies.get(alpha).get(symbol);
80 return new Color(230, 0, 0);
82 Double value = Math.log(prob / freq);
87 colour = ColorUtils.getGraduatedColour(value.floatValue(), 0,
88 Color.WHITE, 4.52f, Color.blue);
105 public void alignmentChanged(AnnotatedCollectionI collection,
106 Map<SequenceI, SequenceCollectionI> hiddenReps)
108 List<SequenceI> seqs = collection.getSequences();
109 for (SequenceI seq : seqs)
111 if (seq.isHMMConsensusSequence())
123 public ColourSchemeI getInstance(AnnotatedCollectionI sg,
124 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
126 HiddenMarkovModel markov = null;
127 List<SequenceI> seqs = sg.getSequences();
128 for (SequenceI seq : seqs)
130 if (seq.getHMM() != null)
132 markov = seq.getHMM();
136 HMMERColourScheme colour = new HMMERColourScheme(markov);
142 public boolean isApplicableTo(AnnotatedCollectionI ac)
149 public String getSchemeName()
152 return JalviewColourScheme.HMMER.name();
156 public boolean isSimple()