package jalview.schemes; import jalview.datamodel.AnnotatedCollectionI; import jalview.datamodel.HiddenMarkovModel; import jalview.datamodel.ResidueCount; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceI; import jalview.util.ColorUtils; import jalview.util.Comparison; import java.awt.Color; import java.util.HashMap; import java.util.List; import java.util.Map; /** * A colour scheme based on a selected Hidden Markov Model. The colour is * * where information content is the log ratio * *
 *   log(profile match emission probability / residue background probability>
 * 
* * using the alignment's background frequencies for residues. * * @author tzvanaalten * */ public class HMMERAlignmentColourScheme extends ResidueColourScheme { /* * the ratio, for each symbol, of its frequency to total symbol count */ Map frequency = new HashMap<>(); float logTotalCount; HiddenMarkovModel hmm; /** * Constructor given a Hidden Markov Model * * @param sg * * @param markov */ public HMMERAlignmentColourScheme(AnnotatedCollectionI sg, HiddenMarkovModel markov) { hmm = markov; countFrequencies(sg); } /** * Default constructor (required by ColourSchemes.loadColourSchemes) */ public HMMERAlignmentColourScheme() { } @Override public Color findColour(char symbol, int position, SequenceI seq, String consensusResidue, float pid) { return findColour(symbol, position); } /** * Returns the colour at a particular symbol at a column in the alignment: * * * @param symbol * @param column * @return */ private Color findColour(char symbol, int column) { if (hmm == null || Comparison.isGap(symbol)) { return Color.white; } if (Character.isLowerCase(symbol)) { symbol = Character.toUpperCase(symbol); } double prob = hmm.getMatchEmissionProbability(column, symbol); Double freq = frequency.get(symbol); if (freq == null) { return Color.white; } if (prob == 0) { return new Color(230, 0, 0); } double value = Math.log(prob / freq.doubleValue()); Color colour = null; if (value > 0) { colour = ColorUtils.getGraduatedColour((float) value, 0, Color.WHITE, logTotalCount, Color.blue); } else if (value < 0) { return Color.ORANGE; } return colour; } @Override public void alignmentChanged(AnnotatedCollectionI collection, Map hiddenReps) { /* * ? no need to do anything if alignment is adjusted * since findColour() handles everything */ } @Override public ColourSchemeI getInstance(AnnotatedCollectionI sg, Map hiddenRepSequences) { List hmms = sg.getHMMConsensusSequences(); HiddenMarkovModel model = hmms.isEmpty() ? null : hmms.get(0).getHMM(); return new HMMERAlignmentColourScheme(sg, model); } @Override public boolean isApplicableTo(AnnotatedCollectionI ac) { return !ac.getHMMConsensusSequences().isEmpty(); } @Override public String getSchemeName() { return JalviewColourScheme.HMMERA.toString(); } @Override public boolean isSimple() { return false; } /** * Counts and stores the relatively frequency of every residue in the * alignment * * @param sg */ public void countFrequencies(AnnotatedCollectionI sg) { ResidueCount counts = new ResidueCount(sg.getSequences()); int total = counts.getTotalCount(); // excludes gaps for (char symbol : counts.getSymbolCounts().symbols) { double freq = counts.getCount(symbol) / (double) total; frequency.put(symbol, freq); } logTotalCount = (float) Math.log(total); } }