Examples with TaxonSet beast.evolution.alignment.TaxonSet used on opensource projects

Example 16 with TaxonSet

use of beast.evolution.alignment.TaxonSet in project beast2 by CompEvol.

the class MRCAPriorInputEditor method getTaxonCandidates.

Set<Taxon> getTaxonCandidates(MRCAPrior prior) {
    Set<Taxon> candidates = new HashSet<>();
    Tree tree = prior.treeInput.get();
    String[] taxa = null;
    if (tree.m_taxonset.get() != null) {
        try {
            TaxonSet set = tree.m_taxonset.get();
            set.initAndValidate();
            taxa = set.asStringList().toArray(new String[0]);
        } catch (Exception e) {
            taxa = prior.treeInput.get().getTaxaNames();
        }
    } else {
        taxa = prior.treeInput.get().getTaxaNames();
    }
    for (String taxon : taxa) {
        candidates.add(doc.getTaxon(taxon));
    }
    return candidates;
}

Example 17 with TaxonSet

use of beast.evolution.alignment.TaxonSet in project beast2 by CompEvol.

the class MRCAPriorInputEditor method enableTipSampling.

// add TipDatesRandomWalker (if not present) and add to list of operators
private void enableTipSampling() {
    // First, create/find the operator
    TipDatesRandomWalker operator = null;
    MRCAPrior prior = (MRCAPrior) m_beastObject;
    TaxonSet taxonset = prior.taxonsetInput.get();
    taxonset.initAndValidate();
    // see if an old operator still hangs around -- happens when toggling the TipsOnly checkbox a few times
    for (BEASTInterface o : taxonset.getOutputs()) {
        if (o instanceof TipDatesRandomWalker) {
            operator = (TipDatesRandomWalker) o;
        }
    }
    if (operator == null) {
        operator = new TipDatesRandomWalker();
        operator.initByName("tree", prior.treeInput.get(), "taxonset", taxonset, "windowSize", 1.0, "weight", 1.0);
    }
    operator.setID("tipDatesSampler." + taxonset.getID());
    doc.mcmc.get().setInputValue("operator", operator);
}

Example 18 with TaxonSet

use of beast.evolution.alignment.TaxonSet in project bacter by tgvaughan.

the class TestBase method getTaxonSet.

public TaxonSet getTaxonSet(int nTaxa) {
    List<Taxon> taxonList = new ArrayList<>();
    for (int i = 0; i < nTaxa; i++) {
        try {
            taxonList.add(new Taxon("t" + i));
        } catch (Exception e) {
            System.out.println("Error creating test taxon.");
            System.exit(1);
        }
    }
    TaxonSet taxonSet = null;
    try {
        taxonSet = new TaxonSet(taxonList);
    } catch (Exception e) {
        System.out.println("Error creating test taxon set.");
        System.exit(1);
    }
    return taxonSet;
}

Example 19 with TaxonSet

use of beast.evolution.alignment.TaxonSet in project bacter by tgvaughan.

the class ACGLikelihoodTest method testLikelihoodCaching.

@Test
public void testLikelihoodCaching() throws Exception {
    ConstantPopulation popFunc = new ConstantPopulation();
    popFunc.initByName("popSize", new RealParameter("1.0"));
    Locus locus = new Locus("locus", 10000);
    TaxonSet taxonSet = getTaxonSet(10);
    ConversionGraph acg = new SimulatedACG();
    acg.initByName("rho", 5.0 / locus.getSiteCount(), "delta", 1000.0, "populationModel", popFunc, "locus", locus, "taxonset", taxonSet);
    State state = new State();
    state.initByName("stateNode", acg);
    state.initialise();
    System.out.println(acg);
    // Site model:
    JukesCantor jc = new JukesCantor();
    jc.initByName();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", new RealParameter("1"), "substModel", jc);
    // Simulate alignment:
    SimulatedAlignment alignment = new SimulatedAlignment();
    alignment.initByName("acg", acg, "siteModel", siteModel, "outputFileName", "simulated_alignment.nexus", "useNexus", true);
    // Calculate likelihood 1:
    ACGLikelihood argLikelihood = new ACGLikelihood();
    argLikelihood.initByName("locus", locus, "data", alignment, "tree", acg, "siteModel", siteModel);
    ACGLikelihoodSlow argLikelihoodSlow = new ACGLikelihoodSlow();
    argLikelihoodSlow.initByName("locus", locus, "data", alignment, "tree", acg, "siteModel", siteModel);
    double logP1 = argLikelihood.calculateLogP();
    double logP1prime = argLikelihoodSlow.calculateLogP();
    double relError = 2.0 * Math.abs(logP1 - logP1prime) / Math.abs(logP1 + logP1prime);
    System.out.format("logP=%g\nlogPprime=%g\nrelError=%g\n", logP1, logP1prime, relError);
    assertTrue(relError < 1e-13);
    // Add a single recombination event
    Node node1 = acg.getExternalNodes().get(0);
    Node node2 = node1.getParent();
    double height1 = 0.5 * (node1.getHeight() + node1.getParent().getHeight());
    double height2 = 0.5 * (node2.getHeight() + node2.getParent().getHeight());
    int startLocus = 500;
    int endLocus = 600;
    Conversion recomb1 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
    acg.addConversion(recomb1);
    double logP2 = argLikelihood.calculateLogP();
    double logP2prime = argLikelihoodSlow.calculateLogP();
    relError = 2.0 * Math.abs(logP2 - logP2prime) / Math.abs(logP2 + logP2prime);
    System.out.format("logP=%g\nlogPprime=%g\nrelError=%g\n", logP2, logP2prime, relError);
    assertTrue(relError < 1e-13);
    state.restore();
    double logP3 = argLikelihood.calculateLogP();
    double logP3prime = argLikelihoodSlow.calculateLogP();
    relError = 2.0 * Math.abs(logP3 - logP3prime) / Math.abs(logP3 + logP3prime);
    System.out.format("logP=%g\nlogPprime=%g\nrelError=%g\n", logP3, logP3prime, relError);
    assertTrue(relError < 1e-13);
}

Example 20 with TaxonSet

use of beast.evolution.alignment.TaxonSet in project bacter by tgvaughan.

the class SimulatedAlignmentTest method test.

@Test
public void test() throws Exception {
    // Randomizer.setSeed(26);
    Randomizer.setSeed(7);
    Locus locus = new Locus("locus", 100000);
    TaxonSet taxonSet = getTaxonSet(10);
    ConstantPopulation popFunc = new ConstantPopulation();
    popFunc.initByName("popSize", new RealParameter("1.0"));
    ConversionGraph acg = new SimulatedACG();
    acg.initByName("rho", 1.0 / 100000, "delta", 1000.0, "populationModel", popFunc, "locus", locus, "taxonset", taxonSet);
    System.out.println(acg);
    // Site model:
    JukesCantor jc = new JukesCantor();
    jc.initByName();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", new RealParameter("1.0"), "substModel", jc);
    // Simulate alignment:
    SimulatedAlignment alignment = new SimulatedAlignment();
    alignment.initByName("acg", acg, "siteModel", siteModel, "outputFileName", "simulated_alignment.nexus", "useNexus", true);
    for (Region region : acg.getRegions(locus)) System.out.println(new MarginalTree(acg, region));
    // (Should be enough info here for precise agreement)
    for (Region region : acg.getRegions(locus)) {
        Alignment margAlign = createMarginalAlignment(alignment, region);
        ClusterTree upgmaTree = new ClusterTree();
        upgmaTree.initByName("clusterType", "upgma", "taxa", margAlign);
        MarginalTree marginalTree = new MarginalTree(acg, region);
        // outfMarg.println(marginalTree.getRoot() + ";");
        // outfMarg.flush();
        // 
        // outfUPGMA.println(upgmaTree.getRoot() + ";");
        // outfUPGMA.flush();
        assertTrue(topologiesEquivalent(marginalTree.getRoot(), upgmaTree.getRoot()));
    }
// outfMarg.close();
// outfUPGMA.close();
}