Examples with Node beast.evolution.tree.Node used on opensource projects

Example 36 with Node

use of beast.evolution.tree.Node in project MultiTypeTree by tgvaughan.

the class NodeRetype method proposal.

@Override
public double proposal() {
    double logHR = 0.0;
    // Select node:
    Node node = mtTree.getNode(mtTree.getLeafNodeCount() + Randomizer.nextInt(mtTree.getInternalNodeCount()));
    // Record probability of current types along attached branches:
    if (!node.isRoot())
        logHR += getBranchTypeProb(node);
    logHR += getBranchTypeProb(node.getLeft()) + getBranchTypeProb(node.getRight());
    // Select new node type:
    ((MultiTypeNode) node).setNodeType(Randomizer.nextInt(migModel.getNTypes()));
    // Retype attached branches:
    try {
        if (!node.isRoot())
            logHR -= retypeBranch(node);
        logHR -= retypeBranch(node.getLeft()) + retypeBranch(node.getRight());
    } catch (NoValidPathException e) {
        return Double.NEGATIVE_INFINITY;
    }
    return logHR;
}

Example 37 with Node

use of beast.evolution.tree.Node in project bacter by tgvaughan.

the class SerializationDeserializationTest method testXML.

@Test
public void testXML() throws Exception {
    Alignment alignment = getAlignment();
    alignment.setID("alignment");
    Locus locus = new Locus("locus", alignment.getSiteCount());
    // ConversionGraph
    ConversionGraph acg = new ConversionGraph();
    ClusterTree tree = new ClusterTree();
    tree.initByName("clusterType", "upgma", "taxa", alignment);
    acg.assignFrom(tree);
    acg.initByName("locus", locus);
    // Add recombination event 1
    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 = 100;
    int endLocus = 200;
    Conversion recomb1 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
    acg.addConversion(recomb1);
    // Add recombination event 2
    node1 = acg.getExternalNodes().get(0);
    node2 = acg.getRoot();
    height1 = 0.5 * (node1.getHeight() + node1.getParent().getHeight());
    height2 = node2.getHeight() + 1.0;
    startLocus = 300;
    endLocus = 400;
    Conversion recomb2 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
    acg.addConversion(recomb2);
    // Write ARG out to XML string
    String xmlStr = acg.toXML();
    // Build DOM from XML string
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    Document doc = factory.newDocumentBuilder().parse(new ByteArrayInputStream(xmlStr.getBytes()));
    doc.normalize();
    NodeList nodes = doc.getElementsByTagName("*");
    org.w3c.dom.Node docNode = nodes.item(0);
    // Read ARG back in from DOM
    ConversionGraph argNew = new ConversionGraph();
    argNew.assignFrom(tree);
    argNew.initByName("locus", locus);
    argNew.fromXML(docNode);
    // Check that new ARG matches old
    Conversion newRecomb1 = argNew.getConversions(locus).get(0);
    assertEquals(newRecomb1.getNode1().getNr(), recomb1.getNode1().getNr());
    assertEquals(newRecomb1.getNode2().getNr(), recomb1.getNode2().getNr());
    assertEquals(newRecomb1.getHeight1(), recomb1.getHeight1(), 1e-15);
    assertEquals(newRecomb1.getHeight2(), recomb1.getHeight2(), 1e-15);
    assertEquals(newRecomb1.getStartSite(), recomb1.getStartSite());
    assertEquals(newRecomb1.getEndSite(), recomb1.getEndSite());
    Conversion newRecomb2 = argNew.getConversions(locus).get(1);
    assertEquals(newRecomb2.getNode1().getNr(), recomb2.getNode1().getNr());
    assertEquals(newRecomb2.getNode2().getNr(), recomb2.getNode2().getNr());
    assertEquals(newRecomb2.getHeight1(), recomb2.getHeight1(), 1e-15);
    assertEquals(newRecomb2.getHeight2(), recomb2.getHeight2(), 1e-15);
    assertEquals(newRecomb2.getStartSite(), recomb2.getStartSite());
    assertEquals(newRecomb2.getEndSite(), recomb2.getEndSite());
// Note that there are minor differences in the tree due to
// rounding errors.  Is this normal!?
}

Example 38 with Node

use of beast.evolution.tree.Node in project bacter by tgvaughan.

the class SerializationDeserializationTest method testString.

@Test
public void testString() throws Exception {
    Alignment alignment = getAlignment();
    alignment.setID("alignment");
    Locus locus = new Locus("locus", alignment.getSiteCount());
    // ConversionGraph
    ConversionGraph acg = new ConversionGraph();
    ClusterTree tree = new ClusterTree();
    tree.initByName("clusterType", "upgma", "taxa", alignment);
    acg.assignFrom(tree);
    acg.initByName("locus", locus);
    // Add recombination event 1
    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 = 100;
    int endLocus = 200;
    Conversion conv1 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
    acg.addConversion(conv1);
    // Add recombination event 2
    node1 = acg.getExternalNodes().get(0);
    node2 = acg.getRoot();
    height1 = 0.5 * (node1.getHeight() + node1.getParent().getHeight());
    height2 = node2.getHeight() + 1.0;
    startLocus = 300;
    endLocus = 400;
    Conversion conv2 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
    acg.addConversion(conv2);
    // Write ACG out to string
    String argString = acg.toStringOld();
    // Read ACG back in from string
    ConversionGraph argNew = new ConversionGraph();
    argNew.initByName("locus", locus, "fromString", argString);
    // Check that new ACG matches old
    Conversion newConv1 = argNew.getConversions(locus).get(0);
    assertEquals(newConv1.getNode1().getNr(), conv1.getNode1().getNr());
    assertEquals(newConv1.getNode2().getNr(), conv1.getNode2().getNr());
    assertEquals(newConv1.getHeight1(), conv1.getHeight1(), 1e-15);
    assertEquals(newConv1.getHeight2(), conv1.getHeight2(), 1e-15);
    assertEquals(newConv1.getStartSite(), conv1.getStartSite());
    assertEquals(newConv1.getEndSite(), conv1.getEndSite());
    Conversion newConv2 = argNew.getConversions(locus).get(1);
    assertEquals(newConv2.getNode1().getNr(), conv2.getNode1().getNr());
    assertEquals(newConv2.getNode2().getNr(), conv2.getNode2().getNr());
    assertEquals(newConv2.getHeight1(), conv2.getHeight1(), 1e-15);
    assertEquals(newConv2.getHeight2(), conv2.getHeight2(), 1e-15);
    assertEquals(newConv2.getStartSite(), conv2.getStartSite());
    assertEquals(newConv2.getEndSite(), conv2.getEndSite());
// Note that there are minor differences in the tree due to
// rounding errors.  Is this normal!?
}

Example 39 with Node

use of beast.evolution.tree.Node in project bacter by tgvaughan.

the class TestBase method getCladeHeights.

/**
 * Retrieve clades and heights of clade MRCAs from tree.
 *
 * @param root
 * @return Map from clades to corresponding MRCA heights.
 */
private Map<Clade, Double> getCladeHeights(Node root) {
    Map<Clade, Double> cladeHeights = new HashMap<>();
    cladeHeights.put(new Clade(root), root.getHeight());
    for (Node node : root.getAllChildNodesAndSelf()) if (!node.isLeaf())
        cladeHeights.put(new Clade(node), node.getHeight());
    return cladeHeights;
}

Example 40 with Node

use of beast.evolution.tree.Node 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);
}