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

Example 1 with TreeParser

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

the class YuleModelTest method testYule.

@Test
public void testYule() throws Exception {
    YuleModel bdssm = new YuleModel();
    Tree tree1 = new TreeParser("((A:1.0,B:1.0):1.0,C:2.0);", false);
    bdssm.setInputValue("tree", tree1);
    bdssm.setInputValue("birthDiffRate", new RealParameter("10."));
    bdssm.setInputValue("originHeight", new RealParameter("10."));
    bdssm.initAndValidate();
    double logP1 = bdssm.calculateTreeLogLikelihood(tree1);
    Tree tree = new TreeParser("((A:1.0,B:1.0):2.0,C:3.0);", false);
    bdssm.setInputValue("tree", tree);
    bdssm.setInputValue("birthDiffRate", new RealParameter("10."));
    bdssm.setInputValue("originHeight", new RealParameter("10."));
    bdssm.initAndValidate();
    double logP2 = bdssm.calculateTreeLogLikelihood(tree);
    assertEquals(logP1 - logP2, 10.0);
}

Example 2 with TreeParser

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

the class Tree method fromXML.

/**
 * reconstruct tree from XML fragment in the form of a DOM node *
 */
@Override
public void fromXML(final org.w3c.dom.Node node) {
    final String newick = node.getTextContent();
    final TreeParser parser = new TreeParser();
    try {
        parser.thresholdInput.setValue(1e-10, parser);
    } catch (Exception e1) {
        e1.printStackTrace();
    }
    try {
        parser.offsetInput.setValue(0, parser);
        setRoot(parser.parseNewick(newick));
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    initArrays();
}

Example 3 with TreeParser

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

the class StateNodeInitialiserTest method testClusterTree.

@Test
public void testClusterTree() throws Exception {
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = new Tree();
    tree.initAndValidate();
    assertEquals(true, tree.getNodeCount() == 1);
    TreeParser tree2 = new TreeParser();
    tree2.initByName("initial", tree, "taxa", data, "newick", "((((human:0.024003,(chimp:0.010772,bonobo:0.010772):0.013231):0.012035,gorilla:0.036038):0.033087000000000005,orangutan:0.069125):0.030456999999999998,siamang:0.099582);", "IsLabelledNewick", true);
    assertEquals(true, tree.getNodeCount() > 1);
    assertEquals(11, tree.getNodeCount());
}

Example 4 with TreeParser

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

the class NodeTest method testBinarySortedNewickTest.

@Test
public void testBinarySortedNewickTest() {
    String newick = "((D:5.0,C:4.0):6.0,(A:1.0,B:2.0):3.0):0.0;";
    TreeParser treeParser = new TreeParser();
    treeParser.initByName("IsLabelledNewick", true, "newick", newick, "adjustTipHeights", false);
    String sortedNewick = treeParser.getRoot().toSortedNewick(new int[1], false);
    String goal = "((1:1.0,2:2.0):3.0,(3:4.0,4:5.0):6.0):0.0";
    assertEquals(goal.split(";")[0], sortedNewick);
}

Example 5 with TreeParser

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

the class UncertainAlignmentTest method getTreeA.

public static Tree getTreeA(Alignment data) throws Exception {
    TreeParser tree = new TreeParser();
    tree.initByName("taxa", data, "newick", "((seq1:1,seq2:1):1,seq3:2);", "IsLabelledNewick", true);
    return tree;
}