Examples with ClusterTree beast.util.ClusterTree used on opensource projects

Example 1 with ClusterTree

use of beast.util.ClusterTree in project beast2 by CompEvol.

the class StateNodeInitialiserTest method testNewickTree.

@Test
public void testNewickTree() throws Exception {
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = new Tree();
    tree.initAndValidate();
    assertEquals(true, tree.getNodeCount() == 1);
    ClusterTree tree2 = new ClusterTree();
    tree2.initByName("initial", tree, "clusterType", "upgma", "taxa", data);
    assertEquals(true, tree.getNodeCount() > 1);
    assertEquals(11, tree.getNodeCount());
}

Example 2 with ClusterTree

use of beast.util.ClusterTree in project beast2 by CompEvol.

the class ClusterTreeTest method testUPGMA.

public void testUPGMA() throws Exception {
    Alignment alignment = BEASTTestCase.getAlignment();
    JukesCantor JC = new JukesCantor();
    JC.initAndValidate();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("substModel", JC);
    ClusterTree tree = new ClusterTree();
    tree.initByName("clusterType", "upgma", "taxa", alignment);
    String expectedNewick = "((((human:0.01903085702575253,(chimp:0.008560512208575313,bonobo:0.008560512208575313):0.010470344817177218):0.007962255880644985,gorilla:0.026993112906397516):0.019197419394211015,orangutan:0.04619053230060853):0.007214240662738673,siamang:0.053404772963347204):0.0";
    String actualNewick = tree.getRoot().toNewick();
    assertEquals(expectedNewick, actualNewick);
    // select 3 sequences
    List<Sequence> seqs = new ArrayList<Sequence>();
    seqs.addAll(alignment.sequenceInput.get());
    List<Sequence> newseqs = alignment.sequenceInput.get();
    newseqs.clear();
    newseqs.add(Sequence.getSequenceByTaxon("bonobo", seqs));
    newseqs.add(Sequence.getSequenceByTaxon("chimp", seqs));
    newseqs.add(Sequence.getSequenceByTaxon("human", seqs));
    alignment.initAndValidate();
    tree = new ClusterTree();
    tree.initByName("clusterType", "upgma", "taxa", alignment);
    expectedNewick = "((bonobo:0.008560512208575313,chimp:0.008560512208575313):0.010470344817177218,human:0.01903085702575253):0.0";
    System.err.println("Seqs:");
    for (Sequence s : seqs) {
        System.err.println(s.taxonInput.get());
    }
    System.err.println("Newseqs:");
    for (Sequence s : newseqs) {
        System.err.println(s.taxonInput.get());
    }
    actualNewick = tree.getRoot().toNewick();
    assertEquals(expectedNewick, actualNewick);
    // same sequences in different order
    newseqs.clear();
    newseqs.add(Sequence.getSequenceByTaxon("human", seqs));
    newseqs.add(Sequence.getSequenceByTaxon("chimp", seqs));
    newseqs.add(Sequence.getSequenceByTaxon("bonobo", seqs));
    alignment.initAndValidate();
    tree = new ClusterTree();
    tree.initByName("clusterType", "upgma", "taxa", alignment);
    actualNewick = tree.getRoot().toNewick();
    expectedNewick = "(human:0.01903085702575253,(chimp:0.008560512208575313,bonobo:0.008560512208575313):0.010470344817177218):0.0";
    assertEquals(expectedNewick, actualNewick);
}

Example 3 with ClusterTree

use of beast.util.ClusterTree 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 4 with ClusterTree

use of beast.util.ClusterTree 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 5 with ClusterTree

use of beast.util.ClusterTree in project bacter by tgvaughan.

the class ACGLikelihoodTest method testLikelihoodAmbiguities.

@Test
public void testLikelihoodAmbiguities() throws Exception {
    Locus locus = new Locus("locus", getAlignment());
    // ConversionGraph
    ConversionGraph acg = new ConversionGraph();
    ClusterTree tree = new ClusterTree();
    tree.initByName("clusterType", "upgma", "taxa", locus.getAlignment());
    acg.assignFrom(tree);
    acg.initByName("locus", locus);
    // Site model:
    JukesCantor jc = new JukesCantor();
    jc.initByName();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("substModel", jc);
    // Likelihood
    ACGLikelihood argLikelihood = new ACGLikelihood();
    argLikelihood.initByName("locus", locus, "tree", acg, "siteModel", siteModel, "useAmbiguities", true);
    ACGLikelihoodSlow argLikelihoodSlow = new ACGLikelihoodSlow();
    argLikelihoodSlow.initByName("locus", locus, "tree", acg, "siteModel", siteModel, "useAmbiguities", true);
    acg.setEverythingDirty(true);
    double logP = argLikelihood.calculateLogP();
    double logPtrue = argLikelihoodSlow.calculateLogP();
    double relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
    System.out.println("Test 1.  Truth: " + logPtrue + " Value: " + logP);
    assertTrue(relativeDiff < 1e-14);
    // 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 = 100;
    int endLocus = 200;
    Conversion recomb1 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
    acg.addConversion(recomb1);
    logP = argLikelihood.calculateLogP();
    logPtrue = argLikelihoodSlow.calculateLogP();
    relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
    assertTrue(relativeDiff < 1e-14);
    // Add another recombination event
    node1 = acg.getExternalNodes().get(0);
    node2 = acg.getNode(20);
    height1 = 0.75 * (node1.getHeight() + node1.getParent().getHeight());
    height2 = 0.5 * (node2.getHeight() + node2.getParent().getHeight());
    startLocus = 250;
    endLocus = 300;
    Conversion recomb2 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
    acg.addConversion(recomb2);
    logP = argLikelihood.calculateLogP();
    logPtrue = argLikelihoodSlow.calculateLogP();
    relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
    assertTrue(relativeDiff < 1e-14);
}