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

Example 11 with TreeParser

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

the class MRCAPriorTest method testMRCATimePrior.

@Test
public void testMRCATimePrior() throws Exception {
    Alignment data = BEASTTestCase.getAlignment();
    TreeParser tree = new TreeParser();
    tree.initByName("taxa", data, "newick", "((human:0.024003,(chimp:0.010772,bonobo:0.010772):0.013231):0.012035," + "(gorilla:0.024003,(orangutan:0.010772,siamang:0.010772):0.013231):0.012035);", "IsLabelledNewick", true);
    Taxon human = new Taxon();
    human.setID("human");
    Taxon bonobo = new Taxon();
    bonobo.setID("bonobo");
    Taxon chimp = new Taxon();
    chimp.setID("chimp");
    Taxon gorilla = new Taxon();
    gorilla.setID("gorilla");
    Taxon orangutan = new Taxon();
    orangutan.setID("orangutan");
    Taxon siamang = new Taxon();
    siamang.setID("siamang");
    MRCAPrior prior = new MRCAPrior();
    TaxonSet set = new TaxonSet();
    set.initByName("taxon", human, "taxon", bonobo, "taxon", chimp);
    Exponential exp = new Exponential();
    /* get distribution for set (human, bonobo, chimp) */
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true, "distr", exp);
    double logP = prior.calculateLogP();
    assertEquals(-0.024003, logP, BEASTTestCase.PRECISION);
    /* get distribution for set (human, chimp), do not require the set to by monophyletic */
    set = new TaxonSet();
    set.initByName("taxon", human, "taxon", chimp);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", false);
    logP = prior.calculateLogP();
    assertEquals(-0.024003, logP, BEASTTestCase.PRECISION);
    /* get distribution for set (human, chimp), DO require the set to by monophyletic */
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true);
    logP = prior.calculateLogP();
    assertEquals(Double.NEGATIVE_INFINITY, logP, 0);
    /* get distribution for set (human, gorilla) = root, not monophyletic */
    set = new TaxonSet();
    set.initByName("taxon", human, "taxon", gorilla);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", false);
    logP = prior.calculateLogP();
    assertEquals(-0.024003 - 0.012035, logP, BEASTTestCase.PRECISION);
}

Example 12 with TreeParser

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

the class MRCAPriorTest method testSingleMonophyleticConstraint.

@Test
public void testSingleMonophyleticConstraint() throws Exception {
    Alignment data = BEASTTestCase.getAlignment();
    TreeParser tree = new TreeParser();
    tree.initByName("taxa", data, "newick", "((human:0.024003,(chimp:0.010772,bonobo:0.010772):0.013231):0.012035," + "(gorilla:0.024003,(orangutan:0.010772,siamang:0.010772):0.013231):0.012035);", "IsLabelledNewick", true);
    Taxon human = new Taxon();
    human.setID("human");
    Taxon bonobo = new Taxon();
    bonobo.setID("bonobo");
    Taxon chimp = new Taxon();
    chimp.setID("chimp");
    Taxon gorilla = new Taxon();
    gorilla.setID("gorilla");
    Taxon orangutan = new Taxon();
    orangutan.setID("orangutan");
    Taxon siamang = new Taxon();
    siamang.setID("siamang");
    MRCAPrior prior = new MRCAPrior();
    /* check (human, bonobo, chimp) is monophyletic **/
    TaxonSet set = new TaxonSet();
    set.initByName("taxon", human, "taxon", bonobo, "taxon", chimp);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true);
    double logP = prior.calculateLogP();
    assertEquals(logP, 0, 0);
    /* check (gorilla, siamang) is NOT monophyletic **/
    set = new TaxonSet();
    set.initByName("taxon", gorilla, "taxon", siamang);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true);
    logP = prior.calculateLogP();
    assertEquals(logP, Double.NEGATIVE_INFINITY, 0);
    /* check (gorilla, orangutan, siamang) is monophyletic **/
    set = new TaxonSet();
    set.initByName("taxon", gorilla, "taxon", orangutan, "taxon", siamang);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true);
    logP = prior.calculateLogP();
    assertEquals(logP, 0, 0);
    /* check (human, gorilla) is NOT monophyletic **/
    set = new TaxonSet();
    set.initByName("taxon", human, "taxon", gorilla);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true);
    logP = prior.calculateLogP();
    assertEquals(logP, Double.NEGATIVE_INFINITY, 0);
    set.setID("test");
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    PrintStream ps = new PrintStream(baos);
    prior.init(ps);
    String log = new String(baos.toByteArray(), StandardCharsets.UTF_8);
    assertEquals(log, "mrcatime(test)\t");
    baos = new ByteArrayOutputStream();
    ps = new PrintStream(baos);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true, "useOriginate", true);
    prior.init(ps);
    log = new String(baos.toByteArray(), StandardCharsets.UTF_8);
    assertEquals(log, "mrcatime(test.originate)\t");
}

Example 13 with TreeParser

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

the class TreeParserTest method testBinarization.

@Test
public void testBinarization() throws Exception {
    String newick = "((A:1.0,B:1.0,C:1.0):1.0,(D:1.0,E:1.0,F:1.0,G:1.0):1.0):0.0;";
    String binaryNewick = "((A:1.0,(B:1.0,C:1.0):0.0):1.0,(D:1.0,(E:1.0,(F:1.0,G:1.0):0.0):0.0):1.0):0.0;";
    boolean isLabeled = true;
    TreeParser treeParser = new TreeParser(newick, false, false, isLabeled, 1);
    Assert.assertEquals(binaryNewick.split(";")[0], treeParser.getRoot().toNewick());
}

Example 14 with TreeParser

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

the class TreeParserTest method testSomeInternalNodesLabelled.

@Test
public void testSomeInternalNodesLabelled() {
    String newick = "((A:1.0,B:1.0)E:1.0,(C:1.0,D:1.0):1.0):0.0;";
    try {
        boolean isLabeled = true;
        TreeParser treeParser = new TreeParser(newick, false, false, isLabeled, 1);
        Assert.assertEquals(newick.split(";")[0], treeParser.getRoot().toNewick());
    } catch (Exception e) {
        // To change body of catch statement use File | Settings | File Templates.  \
        e.printStackTrace();
        Assert.assertTrue("Exception!", false);
    }
}

Example 15 with TreeParser

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

the class TreeParserTest method testOnlyLeafLabels.

@Test
public void testOnlyLeafLabels() throws Exception {
    String newick = "((A:1.0,B:1.0):1.0,(C:1.0,D:1.0):1.0):0.0;";
    boolean isLabeled = true;
    TreeParser treeParser = new TreeParser(newick, false, false, isLabeled, 1);
    System.out.println("adfgad");
    Assert.assertEquals(newick.split(";")[0], treeParser.getRoot().toNewick());
}