Examples with SitePatterns dr.evolution.alignment.SitePatterns used on opensource projects

Example 11 with SitePatterns

use of dr.evolution.alignment.SitePatterns in project beast-mcmc by beast-dev.

the class AscertainmentCorrectedLikelihoodTest method testMissingPatterns.

public void testMissingPatterns() {
    SitePatterns patterns = new SitePatterns(alignment, null, 10, -1, 1, true);
    System.out.println("Using " + patterns.getPatternCount() + " patterns");
    double total = computeSumOfPatterns(patterns);
    System.out.println("Total of 10 missing (uncorrected) probabilities = " + total);
    assertEquals("uncorrected", 0.78287044, total, tolerance);
}

Example 12 with SitePatterns

use of dr.evolution.alignment.SitePatterns in project beast-mcmc by beast-dev.

the class AscertainmentCorrectedLikelihoodTest method testAllPatterns.

public void testAllPatterns() {
    SitePatterns patterns = new SitePatterns(alignment, null, 0, -1, 1, true);
    System.out.println("Using " + patterns.getPatternCount() + " patterns");
    double total = computeSumOfPatterns(patterns);
    System.out.println("Total of all (uncorrected) probabilities = " + total);
    assertEquals("uncorrected", 1.0, total, tolerance);
}

Example 13 with SitePatterns

use of dr.evolution.alignment.SitePatterns in project beast-mcmc by beast-dev.

the class LikelihoodTest method testLikelihoodJC69.

public void testLikelihoodJC69() {
    System.out.println("\nTest Likelihood using JC69:");
    // Sub model
    Parameter freqs = new Parameter.Default(new double[] { 0.25, 0.25, 0.25, 0.25 });
    Parameter kappa = new Parameter.Default(HKYParser.KAPPA, 1.0, 0, 100);
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    HKY hky = new HKY(kappa, f);
    //siteModel
    GammaSiteModel siteModel = new GammaSiteModel(hky);
    Parameter mu = new Parameter.Default(GammaSiteModelParser.MUTATION_RATE, 1.0, 0, Double.POSITIVE_INFINITY);
    siteModel.setMutationRateParameter(mu);
    //treeLikelihood
    SitePatterns patterns = new SitePatterns(alignment, null, 0, -1, 1, true);
    TreeLikelihood treeLikelihood = new TreeLikelihood(patterns, treeModel, siteModel, null, null, false, false, true, false, false);
    assertEquals("treeLikelihoodJC69", format.format(-1992.20564), format.format(treeLikelihood.getLogLikelihood()));
}

Example 14 with SitePatterns

use of dr.evolution.alignment.SitePatterns in project beast-mcmc by beast-dev.

the class SlidingPatternsOperator method doOperation.

public double doOperation() {
    // Select boundary to update, 0 => btw partition 0 and 1,  1 => btw partition 1 and 2, etc.
    int whichBoundary = MathUtils.nextInt(breakPoints.getDimension());
    int cBreakPt = (int) breakPoints.getParameterValue(whichBoundary);
    SitePatterns left = partitions.get(whichBoundary);
    SitePatterns right = partitions.get(whichBoundary + 1);
    int min = left.getFrom();
    int max = right.getTo();
    int pBreakPt = min;
    while (pBreakPt <= min || pBreakPt >= max) {
        // cBreakPt + [windowSize-1, windowSize+1] (and not 0)
        if (MathUtils.nextBoolean())
            pBreakPt = cBreakPt + MathUtils.nextInt(windowSize) + 1;
        else
            pBreakPt = cBreakPt - MathUtils.nextInt(windowSize) - 1;
    }
    return 0;
}

Example 15 with SitePatterns

use of dr.evolution.alignment.SitePatterns in project beast-mcmc by beast-dev.

the class PatternListGenerator method writePatternList.

/**
     * Write a single pattern list
     *
     * @param partition the partition to write a pattern list for
     * @param offset    offset by
     * @param every     skip every
     * @param writer    the writer
     */
private void writePatternList(final PartitionData partition, int offset, int every, final String codonPrefix, final boolean unique, final boolean strip, final XMLWriter writer) {
    Alignment alignment = partition.getAlignment();
    int from = partition.getFromSite();
    int to = partition.getToSite();
    int partEvery = partition.getEvery();
    if (partEvery > 1 && every > 1)
        throw new IllegalArgumentException();
    if (from < 1)
        from = 1;
    every = Math.max(partEvery, every);
    from += offset;
    // this object is created solely to calculate the number of patterns in the alignment
    SitePatterns patterns = new SitePatterns(alignment, null, from - 1, to - 1, every, strip, unique);
    writer.writeComment("The " + (unique ? "unique " : "") + "patterns from " + from + " to " + (to > 0 ? to : "end") + ((every > 1) ? " every " + every : ""), "npatterns=" + patterns.getPatternCount());
    List<Attribute> attributes = new ArrayList<Attribute>();
    // no 11 of 112 codon, which uses mergePatterns id instead
    if (codonPrefix != null) {
        attributes.add(new Attribute.Default<String>(XMLParser.ID, partition.getPrefix() + codonPrefix + SitePatternsParser.PATTERNS));
    }
    attributes.add(new Attribute.Default<String>("from", "" + from));
    if (to >= 0)
        attributes.add(new Attribute.Default<String>("to", "" + to));
    if (every > 1) {
        attributes.add(new Attribute.Default<String>("every", "" + every));
    }
    if (!unique) {
        attributes.add(new Attribute.Default<Boolean>(SitePatternsParser.UNIQUE, false));
    }
    if (strip) {
        // default true
        attributes.add(new Attribute.Default<Boolean>(SitePatternsParser.STRIP, false));
    }
    // generate <patterns>
    writer.writeOpenTag(SitePatternsParser.PATTERNS, attributes);
    writer.writeIDref(AlignmentParser.ALIGNMENT, alignment.getId());
    writer.writeCloseTag(SitePatternsParser.PATTERNS);
}